# Physics

## New submissions

[ total of 146 entries: 1-146 ]
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### New submissions for Tue, 19 Sep 17

[1]
Title: Fibre-optic metadevice for all-optical signal modulation based on coherent absorption
Subjects: Optics (physics.optics)

Recently, coherent control of the optical response of thin films of matter in standing waves has attracted considerable attention, ranging from applications in excitation-selective spectroscopy and nonlinear optics to demonstrations of all-optical image processing. Here we show that integration of metamaterial and optical fibre technologies allows the use of coherently controlled absorption in a fully fiberized and packaged switching metadevice. With this metadevice, that controls light with light in a nanoscale plasmonic metamaterial film on an optical fibre tip, we provide proof-of-principle demonstrations of logical functions XOR, NOT and AND that are performed within a coherent fully fiberized network at wavelengths between 1530 nm and 1565 nm. The metadevice performance has been tested with optical signals equivalent to a bitrate of up to 40 Gbit/s and sub-milliwatt power levels. Since coherent absorption can operate at the single photon level and also with 100 THz bandwidth, we argue that the demonstrated all-optical switch concept has potential applications in coherent and quantum information networks.

[2]
Title: Instrumentation and its Interaction with the Secondary Beam for the Fermilab Muon Campus
Authors: D. Stratakis, B. Drendel (Fermilab) M.J. Syphers (Fermilab and Northern Illinois U.)
Subjects: Accelerator Physics (physics.acc-ph); Instrumentation and Detectors (physics.ins-det)

The Fermilab Muon Campus will host the Muon g-2 experiment - a world class experiment dedicated to the search for signals of new physics. Strict demands are placed on beam diagnostics in order to ensure delivery of high quality beams to the storage ring with minimal losses. In this study, we briefly describe the available secondary beam diagnostics for the Fermilab Muon Campus. Then, with the aid of numerical simulations we detail their interaction with the secondary beam. Finally, we compare our results against theoretical findings.

[3]
Title: Student ownership of projects in an upper-division optics laboratory course: A multiple case study of successful experiences
Comments: 22 pages, 3 tables, submitted to Phys. Rev. PER
Subjects: Physics Education (physics.ed-ph)

We investigate students' sense of ownership of multiweek final projects in an upper-division optics lab course. Using a multiple case study approach, we describe three student projects in detail. Within-case analyses focused on identifying key issues in each project, and constructing chronological descriptions of those events. Cross-case analysis focused on identifying emergent themes with respect to five dimensions of project ownership: student agency, instructor mentorship, peer collaboration, interest and value, and affective responses. Our within- and cross-case analyses yielded three major findings. First, coupling division of labor with collective brainstorming can help balance student agency, instructor mentorship, and peer collaboration. Second, students' interest in the project and perceptions of its value can increase over time; initial student interest in the project topic is not a necessary condition for student ownership of the project. Third, student ownership is characterized by a wide range of emotions that fluctuate as students alternate between extended periods of struggle and moments of success while working on their projects. These findings not only extend the literature on student ownership into a new educational domain---namely, upper-division physics labs---they also have concrete implications for the design of experimental physics projects in courses for which student ownership is a desired learning outcome. We describe the course and projects in sufficient detail that others can adapt our results to their particular contexts.

[4]
Title: Transport Regimes Spanning Magnetization-Coupling Phase Space
Subjects: Plasma Physics (physics.plasm-ph)

The manner in which transport properties vary over the entire parameter-space of coupling and magnetization strength is explored for the first time. Four regimes are identified based on the relative size of the gyroradius compared to other fundamental length scales: the collision mean free path, Debye length, distance of closest approach and interparticle spacing. Molecular dynamics simulations of self-diffusion and temperature anisotropy relaxation spanning the parameter space are found to agree well with the predicted boundaries. Comparison with existing theories reveals regimes where they succeed, where they fail, and where no theory has yet been developed.

[5]
Title: Cholesterol-dependent, nanoscale dynamics of single-molecule trajectories dictate the ensemble anomalous diffusion of cell-surface acetylcholine receptors
Comments: 21 pages, 6 figures, 4 tables
Subjects: Biological Physics (physics.bio-ph)

Single molecule superresolution microscopy was used to follow the translational diffusion of a key neurotransmitter receptor protein, the nicotinic acetylcholine receptor. Individual trajectories and ensemble averages were obtained from single particle tracking of receptors labeled with a monovalent ligand, fluorescent bungarotoxin or a monoclonal antibody. Bayesian inference analysis of the mean square displacements yielded the relative probabilities of the highly heterogeneous mobile populations, a combination of Brownian, anomalous subdiffusive and constrained motions, the proportions of which were differentially modified by cholesterol levels. At the ensemble level, trajectories exhibited weak ergodicity breaking, dominated by anomalous subdiffusion. When the trajectories were separated into subpopulations according to their diffusivity, most of them were found to be ergodic, suggesting that ergodicity breaking stemmed from their heterogeneous nature. The distribution of the trajectories turning angles, markedly anticorrelated in the subdiffusive tracks, appeared to conform to the obstructed diffusion model, characteristically observed in the presence of obstacles. At the single track level, walks were transiently interrupted by intervals of confinement in small ellipsoidal nanodomains with major semi-axis less than 60 nm. In conclusion, a combination of non ergodic and ergodic anomalous mobilities, modulated by cholesterol, coexists with Brownian diffusion. The signature motional behavior at the single-trajectory level, i.e. the nanoscale heterogeneity, underlies the heterogeneous anomalous dynamics at the ensemble level in the complex plasma membrane environment.

[6]
Title: Non-Adiabatic Contributions to Bragg Regime Dynamics in the Atomic Kapitza-Dirac Effect
Authors: Dylan Manna
Comments: 10 pages, 15 figures, 9 citations
Subjects: Atomic Physics (physics.atom-ph)

The primary mechanism of the atomic Kapitza-Dirac effect is a multi-photon process in which the electronic state is virtually excited while the direct product state is altered as the velocity of the atom undergoes spatial quantization. The Bragg resonance is a virtual multi-photon stimulated Raman scattering in which couterpropagating photons act as pump and probe imparting transverse velocity to the atom through recoil while the energy in the field is lowered such that the energy of the system is conserved. The bulk of the literature for the past three decades has presumed that the energy-nonconserving intermediate states which are described by non-adiabatic contributions could be neglected once the perturbative effects of next-order off-resonant states were included. This paper demonstrates the necessity of including higher-order non-adiabatic contributions of energy-nonconserving momentum states in calculating the final populations of Bragg resonances as a function of field strength. As the field strength is increased, the Pendell\"{o}sung frequency varies while generally decreasing dramatically, requiring a greater number of intermediate states to calculate. This paper demonstrates that $n\propto\sqrt{\beta/\delta}$ states must be included to precisely calculate the populations of diffracted atoms as a function of field strength in better agreement with experiment.

[7]
Title: Review of Jean Bricmont's book "Making Sense of Quantum Mechanics"
Comments: 14 pages, to appear in Journal of Statistical Physics
Subjects: History and Philosophy of Physics (physics.hist-ph); Quantum Physics (quant-ph)

This is an invited review of Jean Bricmont's book "Making Sense of Quantum Mechanics."

[8]
Title: Final State Resolved Quantum Predissociation Dynamics of SO2(C1B2) and Its Isotopomers via a Crossing with a Singlet Repulsive State
Journal-ref: J. Phys. Chem. A 2017, 121, 4930-4938
Subjects: Chemical Physics (physics.chem-ph)

The fragmentation dynamics of predissociative SO2(C1B2) is investigated on an accurate adiabatic potential energy surface (PES) determined from high level ab initio data. This singlet PES features non-C2v equilibrium geometries for SO2, which are separated from the SO + O dissociation limit by a barrier resulting from a conical intersection with a repulsive singlet state. The ro-vibrational state distribution of the SO fragment is determined quantum mechanically for many predissociative states of several sulfur isotopomers of SO2. Significant rotational and vibrational excitations are found in the SO fragment. It is shown that these fragment internal state distributions are strongly dependent on the predissociative vibronic states, and the excitation typically increases with the photon energy.

[9]
Title: A third-order discrete unified gas kinetic scheme for continuum and rarefied flows: low-speed isothermal case
Subjects: Fluid Dynamics (physics.flu-dyn)

An efficient third-order discrete unified gas kinetic scheme (DUGKS) with efficiency is presented in this work for simulating continuum and rarefied flows. By employing two-stage time-stepping scheme and the high-order DUGKS flux reconstruction strategy, third-order of accuracy in both time and space can be achieved in the present method. It is also analytically proven that the second-order DUGKS is a special case of the present method. Compared with the high-order lattice Boltzmann equation {LBE} based methods, the present method is capable to deal with the rarefied flows by adopting the Newton-Cotes quadrature to approximate the integrals of moments. Instead of being constrained by the second-order (or lower-order) of accuracy in time splitting scheme as in the conventional high-order Runge-Kutta (RK) based kinetic methods, the present method solves the original BE, which overcomes the limitation in time accuracy. Typical benchmark tests are carried out for comprehensive evaluation of the present method. It is observed in the tests that the present method is advantageous over the original DUGKS in accuracy and capturing delicate flow structures. Moreover, the efficiency of the present third-order method is also shown in simulating rarefied flows.

[10]
Title: High-speed XYZ-nanopositioner for scanning ion conductance microscopy
Journal-ref: Applied Physics Letters (Vol.111, Issue 11)(2017)
Subjects: Instrumentation and Detectors (physics.ins-det); Applied Physics (physics.app-ph)

We describe a tip-scan-type high-speed XYZ-nanopositioner designed for scanning ion conductance microscopy (SICM), with a special care being devoted to the way of nanopipette holding. The nanopipette probe is mounted in the center of a hollow piezoactuator, both ends of which are attached to identical diaphragm flexures, for Z-positioning. This design minimizes the generation of undesirable mechanical vibrations. Mechanical amplification is used to increase the XY-travel range of the nanopositioner. The first resonance frequencies of the nanopositioner are measured as $\sim$100 kHz and $\sim$2.3 kHz for the Z- and XY-displacements, respectively. The travel ranges are $\sim$6 $\mu$m and $\sim$34 $\mu$m for Z and XY, respectively. When this nanopositioner is used for hopping mode imaging of SICM with a $\sim$10-nm radius tip, the vertical tip velocity can be increased to 400 nm/ms; hence, the one-pixel acquisition time can be minimized to $\sim$1 ms.

[11]
Title: Inter-pulse intervals of external anal sphincter surface EMG signals recorded from colorectal cancer patients
Subjects: Medical Physics (physics.med-ph)

Intervals between electrical pulses generated by the electrical activity produced by the motor units of an external anal sphincter were studied at four time intervals during multimodal rectal cancer treatment. Probability distribution function of such intervals does not exhibit significant differences for all considered time intervals. It is found that the probability distribution rescaled with an average interval time can be described by means of the stretched exponential function with the threshold dependent scale and shape parameters. Interval trains possess rather strong correlations as their shuffled counterparts show exponential Poisson like probability distribution. Finally the clustering effects were not found as the conditional probability distributions can also be described by the exponential function.

[12]
Title: Teaching Computation in Introductory Physics using Complex Problems
Subjects: Physics Education (physics.ed-ph)

Computation is a central aspect of modern science and engineering work, and yet, computational instruction has yet to fully pervade university STEM curricula. In physics, we have begun to integrate computation into our courses in a variety of ways. Here, we discuss a method for integrating computation into calculus-based mechanics where the lecture and laboratory for the course are decoupled. At Michigan State University, we have developed a "lecture" course, called "Projects and Practices in Physics", where science and engineering students solve complex problems in groups of four using analytical and computational techniques. In this paper, we provide details on the computational instruction, activities, and assessment used to teach these introductory students how to model motion using VPython.

[13]
Title: Probability of Induced Emission in Atoms
Authors: K.V. Ivanyan
Subjects: Atomic Physics (physics.atom-ph)

Expression for the probability of induced emission of high-order harmonics is obtained in the region where the multiphoton approximation is applicable to the description of the ionization of an atom. The dependence of this probability on the main parameters of the pump wave and the atomic medium is established. Criteria for observing emission are formulated with the consideration of phase locking. The possibility of amplifying a UV probe wave aimed through the region where the atoms interact with the pump wave is considered.

[14]
Title: Fluorescent Silicon Clusters and Nanoparticles
Comments: 5 figures, chapter in "Silicon Nanomaterials Sourcebook", editor Klaus D. Sattler, CRC Press, August 2017
Subjects: Atomic and Molecular Clusters (physics.atm-clus)

The fluorescence of silicon clusters is reviewed. Atomic clusters of silicon have been at the focus of research for several decades because of the relevance of size effects for material properties, the importance of silicon in electronics and the potential applications in bio-medicine. To date numerous examples of nanostructured forms of fluorescent silicon have been reported. This article introduces the principles and underlying concepts relevant for fluorescence of nanostructured silicon such as excitation, energy relaxation, radiative and non-radiative decay pathways and surface passivation. Experimental methods for the production of silicon clusters are presented. The geometric and electronic properties are reviewed and the implications for the ability to emit fluorescence are discussed. Free and pure silicon clusters produced in molecular beams appear to have properties that are unfavourable for light emission. However, when passivated or embedded in a suitable host, they may emit fluorescence. The current available data show that both quantum confinement and localised transitions, often at the surface, are responsible for fluorescence. By building silicon clusters atom by atom, and by embedding them in shells atom by atom, new insights into the microscopic origins of fluorescence from nanoscale silicon can be expected.

[15]
Title: Editorial (a preface to a Special Issue of journal Applied Sciences on "Guided-Wave Optics")
Authors: Boris A. Malomed
Subjects: Optics (physics.optics); Pattern Formation and Solitons (nlin.PS)

This is a preface introducing a Special Issue on the topic of "Guided-Wave Optics" published by Applied Sciences. The Special Issue is a collection of 20 original and review articles dealing with various fundamental and applied aspects of the topic.

[16]
Subjects: Optics (physics.optics)

The realization of geometric phase optical device operating over a broad spectral range is usually confronted with intrinsic limitations depending of the physical process at play. Here we propose to use chiral nematic liquid crystal slabs with helical ordering that varies in three dimensions. Namely, gradient-pitch cholesterics endowed with in-plane space-variant angular positioning of the supramolecular helix. By doing so, we show that the recently introduced Bragg-Berry mirrors [Opt. Lett. {\bf 41}, 3972-3975 (2016)] can be endowed with ultra-broadband spectral range. Experimental demonstration is made in the case of ultra-broadband optical vortex generation in the visible domain. These results offer practical solution to the polychromatic management of the orbital angular momentum of light combining the circular Bragg reflection of chiral media with the Berry phase.

[17]
Title: Accurate Anisotropic Gaussian Type Orbital Basis Sets for Atoms in Strong Magnetic Fields
Subjects: Computational Physics (physics.comp-ph); Chemical Physics (physics.chem-ph)

In high magnetic field calculations, anisotropic Gaussian type orbital (AGTO) basis functions are capable of reconciling the competing demands of the spherically symmetric Coulombic interaction and cylindrical magnetic ($B$ field) confinement. However, the best available {\it a priori} procedure for composing highly accurate AGTO sets for atoms in a strong $B$ field [Phys.\ Rev. A {\bf 90}, 022504 (2014)] yields very large basis sets. Their size is problematical for use in any calculation with unfavorable computational cost scaling. Here we provide an alternative constructive procedure. It is based upon analysis of the underlying physics of atoms in $B$ fields that allows identification of several principles for the construction of AGTO basis sets. Aided by numerical optimization and parameter fitting, followed by fine tuning of fitting parameters, we devise formulae for generating accurate AGTO basis sets in an arbitrary $B$ field. For the hydrogen iso-electronic sequence, a set depends on $B$ field strength, nuclear charge, and upon orbital quantum numbers. For multi-electron systems, the basis set formulae also include adjustment to account for orbital occupations. Tests of the new basis sets for atoms H through C ($1 \le Z \le 6$), and ions Li$^+$, Be$^+$, and B$^+$, in a wide $B$ field range ($0 \le B \le 2000$ a.u.), show an accuracy better than a few $\mu$H for single-electron systems, and a few hundredths to a few mHs for multi-electron atoms. The relative errors are similar for different atoms and ions in a large $B$ field range, from a few to a couple of tens of millionths, thereby confirming rather uniform accuracy across the nuclear charge $Z$ and $B$ field strength values. Residual basis set errors are two to three orders of magnitude smaller than the electronic correlation energies in muti-electron atoms ...

[18]
Title: Modified-Bloch Equation Based on Fractal Derivative for Analyzing PFG Anomalous Diffusion
Authors: Guoxing Lin
Subjects: Chemical Physics (physics.chem-ph); Statistical Mechanics (cond-mat.stat-mech)

A modified-Bloch equation based on the fractal derivative is proposed to analyze pulsed field gradient (PFG) anomalous diffusion. Anomalous diffusion exists in many systems such as in polymer or biological systems. PFG anomalous diffusion could be analyzed based on the fractal derivative or the fractional derivative. Compared to the fractional derivative, the fractal derivative is simpler, and it is faster in numerical evaluations. In this paper, the fractal derivative is employed to build the modified-Bloch equation that is a fundamental method to describe the spin magnetization evolution affected by fractional diffusion, Larmor precession, and relaxation. An equivalent form of the fractal derivative is proposed to convert the fractional diffusion equation, which can then be combined with the precession and relaxation equations to get the modified-Bloch equation. This modified-Bloch equation yields a general PFG signal attenuation expression that includes the finite gradient pulse width (FGPW) effect, namely, the signal attenuation during field gradient pulse. The FGPW effect needs to be considered in most clinical MRI applications, and including FGPW effect allows the detecting of slower diffusion that is often encountered in polymer systems. Additionally, the spin-spin relaxation effect can be analyzed, which provides a broad view of the dynamic process in materials. The modified-Bloch equation based on the fractal derivative could provide a fundamental theoretical model for PFG anomalous diffusion.

[19]
Title: Two electrostatic gyrokinetic models derived by two different perturbative methods
Authors: Shuangxi Zhang
Subjects: Plasma Physics (physics.plasm-ph)

This paper presents two different electrostatic gyrokinetic models derived through two different perturbative methods. One of the two models is just the conventional electrostatic gyrokinetic model, the derivation of which is repeated using the Lie transform perturbative method. One term is rectified in the derivation of the conventional model. To derive the other model, we use a new method, which is based on the covariant transform formula of the differential 1-form. The new method doesn't split the coordinate transform into the guiding-center transform and the gyrocenter transform. It carries out the coordinate transform up to the order equaling that of the amplitude of the perturbative wave. Compared with the conventional model, the finite Larmor radius terms are completely removed from the orbit equations of the new one, making it simpler for the numerical application.

[20]
Title: On the Application of Optimal Control Theory to Climate Engineering
Comments: 28 pages, 8 figures, 5 tables
Subjects: Atmospheric and Oceanic Physics (physics.ao-ph)

The new method is considered for identifying the perfect (optimal) scenario of climate engineering operations based on the optimal control theory. The application of this approach is demonstrated using zero-dimensional energy-balance climate model. The global average surface temperature represents the state variable and the reflective power of aerosols injected into the stratosphere is designated as the control variable. Maximum principle is used to find the best possible control and the associated climate system trajectory for a specific objective function (performance measure). Discussed illustrative results were analytically and numerically calculated using the four greenhouse gas concentration scenarios based on the Representative Concentration Pathways.

[21]
Title: Orbital angular momentum beam instabilities in engineered nonlinear colloidal media
Subjects: Optics (physics.optics)

In this letter, we experimentally demonstrate the evolution of the optical vortex beams of different topological charges propagating in engineered nano-colloidal suspension of negative polarizability with saturable nonlinearities. Due to the high power of the incident beam, the modulation instability leads to an exponential growth of weak perturbations and thus splits the original vortex beam into a necklace beam consisting of several bright spots. The number of observed bright spots is intrinsically determined by the topological charge of the incident beam and agrees well with the predictions of our linear stability analysis and numerical simulations. Besides contributing to the fundamental science of light-matter interactions in engineered soft-matter media, this work opens new opportunities for dynamic optical manipulation and transmission of light through scattering media as well as formation of complex optical patterns and light filamentation in naturally existing colloids such as fog and clouds.

[22]
Title: Effect of texture randomization on the slip and interfacial robustness in turbulent flows over superhydrophobic surfaces
Authors: Jongmin Seo, Ali Mani
Subjects: Fluid Dynamics (physics.flu-dyn)

Superhydrophobic surfaces demonstrate promising potential for skin friction reduction in naval and hydrodynamic applications. Recent developments of superhydrophobic surfaces aiming for scalable applications use random distribution of roughness, such as spray coating and etched process. However, most of previous analyses of the interaction between flows and superhydrophobic surfaces studied periodic geometries that are economically feasible only in lab-scale experiments. We conduct direct numerical simulations of turbulent flows over randomly patterned interfaces considering a range of texture widths $w^+\approx 4-26$, and solid fractions $\phi_s=11\%$ to $25\%$. Slip and no-slip boundary conditions are implemented in a pattern, modeling the presence of gas-liquid interfaces and solid elements. Our results indicate that slip of randomly distributed textures under turbulent flows are about $30\%$ less than those of surfaces with aligned features of the same size. In the small texture size limit $w^+\approx 4$, the slip length of the randomly distributed textures in turbulent flows is well described by a previously introduced Stokes flow solution of randomly distributed shear-free holes. By comparing DNS results for patterned slip and no-slip boundary against the corresponding homogenized slip length boundary conditions, we show that turbulent flows over randomly distributed posts can be represented by an isotropic slip length in streamwise and spanwise direction. The average pressure fluctuation on gas pocket is similar to that of the aligned features with the same texture size and gas fraction, but the maximum interface deformation at the leading edge of the roughness element is about twice larger when the textures are randomly distributed.

[23]
Title: Virtual Molecular Dynamics
Comments: 60 pages, 42 figures, 3 tables
Subjects: Chemical Physics (physics.chem-ph); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to the more coherent behavior of collective modes such as density profiles. The notion of virtual molecular dynamics is introduced here based on temporal coarse-graining via Pade approximants and the Ito formula for stochastic processes. It is demonstrated that this framework leads to significant efficiency over traditional molecular dynamics and avoids the need to introduce coarse-grained variables and phenomenological equations for their evolution. In this framework, an all-atom trajectory is represented by a Markov chain of virtual atomic states at a discrete sequence of timesteps, transitions between which are determined by an integration of conventional molecular dynamics with Pade approximants and a microstate energy annealing methodology. The latter is achieved by a conventional and an MD NVE energy minimization schemes. This multiscale framework is demonstrated for a pertussis toxin subunit undergoing a structural transition, a T=1 capsid-like structure of HPV16 L1 protein, and two coalescing argon droplets.

[24]
Title: Neo-logistic model
Subjects: Biological Physics (physics.bio-ph)

We propose the neo-logistic model which can describe the bacteria growth data precisely. The model is not derived by modifying the logistic model formally, but by incorporating the synthesis of inducible enzymes into the logistic model indirectly, and so the parameters of the neo-logistic model are physically clear. It is relieved that our model can approximate the bacteria growth better than other models. We also try to predict the saturated number of bacteria in the stationary phase from the initial data and find that the neo-logistic model can predict the order of the number much more accurately than others.

[25]
Title: A reversible numerical integrator of the isokinetic equations of motion
Authors: Dimitri Laikov
Comments: submitted to the Journal of Chemical Physics
Subjects: Chemical Physics (physics.chem-ph); Computational Physics (physics.comp-ph)

An explicit second-order numerical method to integrate the isokinetic equations of motion is derived by fitting circular arcs through every three consecutive points of the discretized trajectory, which is reversible and robust, and allows a good control of the variable step length. Its performance is tested by computing the thermodynamic properties of simple pair-potential models, and its chemical application is shown for the global search for stable structures, using canonical sampling and energy minimization, of hydrogen-bonded molecular clusters.

[26]
Title: Correlation between photoemissive and morphological properties of KBr thin film photocathodes
Subjects: Instrumentation and Detectors (physics.ins-det)

In the present work, the morphological properties of KBr photocathodes are correlated with their photoemissive behaviour using a combination of analyzing techniques including SEM, TEM and AFM. From morphological studies, it is observed that KBr films have granular characteristics with varied average grain size and grain density. Structure and orientation of individual grains have been investigated by selected area electron diffraction technique and found to be the crystalline in nature with a face centered cubic structure. It is evident from the AFM analysis that the root mean square roughness and maximum area peak height have been decreased with the deposition of more KBr layers. The photoemission studies reveal that the resultant photocurrent is enhanced with increasing film thickness and it is directly related to the surface area coverage and grain density.

[27]
Title: Mapping temporal-network percolation to weighted, static event graphs
Subjects: Physics and Society (physics.soc-ph); Social and Information Networks (cs.SI); Data Analysis, Statistics and Probability (physics.data-an)

Many processes of spreading and diffusion take place on temporal networks, and their outcomes are influenced by correlations in the times of contact. These correlations have a particularly strong influence on processes where the spreading agent has a limited lifetime at nodes: disease spreading (recovery time), diffusion of rumors (lifetime of information), and passenger routing (maximum acceptable time between transfers). Here, we introduce weighted event graphs as a powerful and fast framework for studying connectivity determined by time-respecting paths where the allowed waiting times between contacts have an upper limit. We study percolation on the weighted event graphs and in the underlying temporal networks, with simulated and real-world networks. We show that this type of temporal-network percolation is analogous to directed percolation, and that it can be characterized by multiple order parameters.

[28]
Title: A monolithic ALE Newton-Krylov solver with Multigrid-Richardson-Schwarz preconditioning for incompressible Fluid Structure Interaction
Subjects: Computational Physics (physics.comp-ph); Numerical Analysis (math.NA)

In this paper we study a monolithic Newton-Krylov solver with exact Jacobian for the solution of incompressible FSI problems. A main focus of this work is on the use of geometric multigrid preconditioners with modified Richardson smoothers preconditioned by an additive Schwarz algorithm. The definition of the subdomains in the Schwarz smoother is driven by the natural splitting between fluid and solid. The monolithic approach guarantees the automatic satisfaction of the stress balance and the kinematic conditions across the fluid-solid interface. The enforcement of the incompressibility conditions both for the fluid and for the solid parts is taken care of by using inf-sup stable finite element pairs without stabilization terms. A suitable Arbitrary Lagrangian Eulerian (ALE) operator is chosen in order to avoid mesh entanglement while solving for large displacements of the moving fluid domain. Numerical results of two and three-dimensional benchmark tests with Newtonian fluids and nonlinear hyperelastic solids show a robust performance of our fully incompressible solver especially for the more challenging direct-to-steady-state problems.

[29]
Title: Verification of nonlinear particle simulation of radio frequency waves in tokamak
Journal-ref: Physics. Plasmas. 22, (2015) 102515
Subjects: Plasma Physics (physics.plasm-ph)

Nonlinear simulation model for radio frequency (RF) waves in fusion plasmas has been developed and verified using fully kinetic ion and drift kinetic electron. Ion cyclotron motion in the toroidal geometry is implemented using Boris push in the Boozer coordinates. Linear dispersion relation and nonlinear particle trapping are verified for the lower hybrid (LH) wave and ion Bernstein wave (IBW). Parametric decay instability is observed where a large amplitude pump wave decays into an IBW sideband and an ion cyclotron quasimode (ICQM). The ICQM induces an ion perpendicular heating with a heating rate proportional to the pump wave intensity.

[30]
Title: Kinetic Band Gap Analysis of Plasma Photonic Crystals
Subjects: Plasma Physics (physics.plasm-ph); Optics (physics.optics)

The dispersion relation of plasma and plasma-dielectric photonic multilayer structures is approached in terms of a one-dimensional Particle-in-Cell simulation. It is first shown that the dispersion relation of a homogeneous plasma slab is well described by the cold-plasma model even at low pressures of 1 Pa. The study is extended to the simulation of plasma photonic crystals with a variety of configurations, based on the work of Hojo and Mase [J. Plasma Fusion Res. {\bf 80}, 89 (2004)]. Considering a 1D plasma photonic crystal made from alternating layers of dielectric and homogeneous plasma it is shown that the assumption of a cold-plasma description is well justified also in this case. Moreover in this work the results are reformatted and analyzed in a band diagram representation, in particular based on the lattice constant $a$. Based on these considerations a scaling invariant representation is presented, specifying a slightly modified set of selective parameters. The study is completed with an exemplary comparison of three plasma-dielectric photonic crystal configurations and their corresponding band diagrams.

[31]
Title: Modeling Smooth Backgrounds and Generic Localized Signals with Gaussian Processes
Subjects: Data Analysis, Statistics and Probability (physics.data-an); High Energy Physics - Experiment (hep-ex); High Energy Physics - Phenomenology (hep-ph)

We describe a procedure for constructing a model of a smooth data spectrum using Gaussian processes rather than the historical parametric description. This approach considers a fuller space of possible functions, is robust at increasing luminosity, and allows us to incorporate our understanding of the underlying physics. We demonstrate the application of this approach to modeling the background to searches for dijet resonances at the Large Hadron Collider and describe how the approach can be used in the search for generic localized signals.

[32]
Title: Experimental techniques and performance of $Λ$-hypernuclear spectroscopy with the $(e,e^{\prime}K^{+})$ reaction
Subjects: Instrumentation and Detectors (physics.ins-det); Nuclear Experiment (nucl-ex)

The missing-mass spectroscopy of $\Lambda$ hypernuclei via the $(e,e^{\prime}K^{+})$ reaction has been developed through experiments at JLab Halls A and C in the last two decades. For the latest experiment, E05-115 in Hall C, we developed a new spectrometer system consisting of the HKS and HES; resulting in the best energy resolution ($E_{\Lambda} \simeq0.5$-MeV FWHM) and $B_{\Lambda}$ accuracy ($B_{\Lambda}\leq0.2$ MeV) in $\Lambda$-hypernuclear reaction spectroscopy. This paper describes the characteristics of the $(e,e^{\prime}K^{+})$ reaction compared to other reactions and experimental methods. In addition, the experimental apparatus, some of the important analyses such as the semi-automated calibration of absolute energy scale, and the performance achieved in E05-115 are presented.

[33]
Title: Representation of Reynolds Stress Perturbations with Application in Machine-Learning-Assisted Turbulence Modeling
Subjects: Fluid Dynamics (physics.flu-dyn)

Numerical simulations based on Reynolds-Averaged Navier--Stokes (RANS) equations are widely used in engineering design and analysis involving turbulent flows. However, RANS simulations are known to be unreliable in many flows of engineering relevance, which is largely caused by model-form uncertainties associated with the Reynolds stresses. Recently, a machine-learning approach has been proposed to assist RANS modeling by building a functional mapping from mean flow features to discrepancies in RANS modeled Reynolds stresses as compared to high-fidelity data. However, it remains a challenge to represent discrepancies in the Reynolds stress eigenvectors in machine learning due to the requirements of spatial smoothness, frame-independence, and realizability. In this work, we propose three schemes for representing perturbations to the eigenvectors of RANS modeled Reynolds stresses: (1) discrepancy-based Euler angles, (2) direct-rotation-based Euler angles, and (3) unit quaternions. We compare these metrics by performing a priori and a posteriori tests on two canonical flows: fully developed turbulent flows in a square duct and massively separated flows over periodic hills. The results demonstrate that the direct-rotation-based Euler angles representation lacks spatial smoothness while the discrepancy-based Euler angles representation lacks frame-independence, making them unsuitable for being used in machine-learning-assisted turbulence modeling. In contrast, the representation based on unit quaternion satisfies all the requirements stated above, and thus it is an ideal choice in representing the perturbations associated with the eigenvectors of Reynolds stress tensors. This finding has clear importance for uncertainty quantification and machine learning in turbulence modeling and for data-driven computational mechanics in general.

[34]
Title: 3D tomography of cells in micro-channels
Journal-ref: Appl. Phys. Lett. 111, 103701 (2017)
Subjects: Fluid Dynamics (physics.flu-dyn); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Optics (physics.optics); Cell Behavior (q-bio.CB)

We combine confocal imaging, microfluidics and image analysis to record 3D-images of cells in flow. This enables us to recover the full 3D representation of several hundred living cells per minute. Whereas 3D confocal imaging has thus far been limited to steady specimen, we overcome this restriction and present a method to access the 3D shape of moving objects. The key of our principle is a tilted arrangement of the micro-channel with respect to the focal plane of the microscope. This forces cells to traverse the focal plane in an inclined manner. As a consequence, individual layers of passing cells are recorded which can then be assembled to obtain the volumetric representation. The full 3D information allows for a detailed comparisons with theoretical and numerical predictions unfeasible with e.g.\ 2D imaging. Our technique is exemplified by studying flowing red blood cells in a micro-channel reflecting the conditions prevailing in the microvasculature. We observe two very different types of shapes: croissants' and slippers'. Additionally, we perform 3D numerical simulations of our experiment to confirm the observations. Since 3D confocal imaging of cells in flow has not yet been realized, we see high potential in the field of flow cytometry where cell classification thus far mostly relies on 1D scattering and fluorescence signals.

[35]
Title: Adsorption of the astatine species on gold surface: a relativistic density functional theory study
Subjects: Chemical Physics (physics.chem-ph)

We report on first-principle based studies of the adsorption interaction of astatine species on a gold surface. These studies are aimed primarily at the support and interpretation of gas chromatographic experiments with Superheavy Elements, tennessine (Ts, $Z=117$) as the heavier homologue of At and possibly nihonium (Nh, $Z=113$) as its pseudo-homologue. The adsorption energies of elemental astatine or the corresponding monohydroxide on a stable gold (111) surface are estimated using gold clusters with up to 69 atoms in order to simulate the adsorption site. To simulate the electronic structure of $\rm At-Au_n$ and $\rm AtOH-Au_n$ complexes, we combine accurate shape-consistent relativistic pseudopotentials and non-collinear two-component relativistic density functional theory. The predicted adsorption energies for At and AtOH on gold are $\rm 130 \pm 10$ kJ/mol and $\rm 90 \pm 10$ kJ/mol, respectively.

[36]
Title: Response to 'Burden of proof: A comprehensive review of the feasibility of 100% renewable-electricity systems'
Subjects: Physics and Society (physics.soc-ph)

A recent article 'Burden of proof: A comprehensive review of the feasibility of 100% renewable-electricity systems' claims that many studies of 100% renewable electricity systems do not demonstrate sufficient technical feasibility, according to the authors' criteria. Here we analyse the authors' methodology and find it problematic. The feasibility criteria chosen by the authors are important, but are also easily addressed at low cost, while not affecting the main conclusions of the reviewed studies and certainly not affecting their technical feasibility. A more thorough review reveals that all of the issues have already been addressed in the engineering and modelling literature. Nuclear power, as advocated by some of the authors, faces other, genuine feasibility problems, such as the finiteness of uranium resources and a reliance on unproven technologies in the medium- to long-term. Energy systems based on renewables, on the other hand, are not only feasible, but already economically viable and getting cheaper every day.

[37]
Title: Structural invariants in street networks: modeling and practical implications
Comments: 52 pages. Main manuscript and Supporting Information in the same document
Subjects: Physics and Society (physics.soc-ph)

We study structural properties of street networks from 97 of the most populous cities worldwide at scales significantly larger than previous studies. We find that the distribution of betweenness centrality (BC), a global structural metric based on network flow, is invariant in all studied street networks, despite the obvious structural differences between them. We also find that the BC distribution is robust to major alterations in the network, including significant changes to its topology and edge weight structure, indicating that the only relevant factors shaping the distribution are the number of nodes in a network, the number of edges, and the constraint of planarity. Through a combination of simulations of random planar graph models and analytical calculations on Cayley trees, this remarkable invariance is demonstrated to be a consequence of a bimodal regime consisting of an underlying tree structure for high betweenness nodes, and a low betweenness regime arising from the presence of loops providing local path alternatives. Furthermore, the high betweenness nodes display a non-trivial spatial dependence, with increasing spatial correlation as a function of the number of roads, leading them to cluster around the barycenter for cities with high density of streets. As the BC is a static predictor of traffic flow, this invariance has important implications for urban planning; indeed, as long as planarity is conserved, bottlenecks will persist and the effect of planned interventions to alleviate congestion will be limited primarily to load redistribution, a feature confirmed by analyzing 200 years of data for central Paris.

[38]
Title: Molecular Mechanism of Transition from Catch-Bond to Slip-Bond in Fibrin
Subjects: Biological Physics (physics.bio-ph)

The lifetimes of non-covalent A:a knob-hole bonds in fibrin probed with the optical trap-based force-clamp first increases ("catch bonds") and then decreases ("slip bonds") with increasing tensile force. Molecular modeling of "catch-to-slip" transition using the atomic structure of the A:a complex reveals that the movable flap serves as tension-dependent molecular switch. Flap dissociation from the regulatory B-domain in $\gamma$-nodule and translocation from the periphery to knob A' triggers the hole a' closure and interface remodeling, which results in the increased binding affinity and prolonged bond lifetimes. Fluctuating bottleneck theory is developed to understand the "catch-to-slip" transition in terms of the interface stiffness $\kappa =$ 15.7 pN nm $^{-1}$, interface size fluctuations 0.7-2.7 nm, knob A' escape rate constant $k_0 =$ 0.11 nm$^2$ s$^{-1}$, and transition distance for dissociation $\sigma_y =$ 0.25 nm. Strengthening of the A:a knob-hole bonds under small tension might favor formation and reinforcement of nascent fibrin clots under hydrodynamic shear.

[39]
Title: Maxwell-Hydrodynamic Model for Simulating Nonlinear Terahertz Generation from Plasmonic Metasurfaces
Comments: 8 pages, 7 figures, IEEE Journal on Multiscale and Multiphysics Computational Techniques, 2017
Subjects: Optics (physics.optics); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Numerical Analysis (math.NA); Computational Physics (physics.comp-ph)

The interaction between the electromagnetic field and plasmonic nanostructures leads to both the strong linear response and inherent nonlinear behavior. In this paper, a time-domain hydrodynamic model for describing the motion of electrons in plasmonic nanostructures is presented, in which both surface and bulk contributions of nonlinearity are considered. A coupled Maxwell-hydrodynamic system capturing full-wave physics and free electron dynamics is numerically solved with the parallel finite-difference time-domain (FDTD) method. The validation of the proposed method is presented to simulate linear and nonlinear responses from a plasmonic metasurface. The linear response is compared with the Drude dispersion model and the nonlinear terahertz emission from a difference-frequency generation process is validated with theoretical analyses. The proposed scheme is fundamentally important to design nonlinear plasmonic nanodevices, especially for efficient and broadband THz emitters.

[40]
Title: Decoding the spectroscopic features and timescales of aqueous proton defects
Comments: 8 page manuscript (6 figures) with 8 page supplementary information (9 figures)
Subjects: Chemical Physics (physics.chem-ph)

Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton defects in the water hydrogen bond network and the mechanisms for their interconversion remains a formidable challenge. Here, we use simulations treating the quantum nature of both the electrons and nuclei to show how the experimentally observed spectroscopic features and relaxation timescales can be elucidated using a physically transparent coordinate that encodes the overall asymmetry of the solvation environment of the proton defect. We demonstrate that this coordinate can be used both to discriminate the extremities of the features observed in the linear vibrational spectrum and to explain the molecular motions that give rise to the interconversion timescales observed in recent nonlinear experiments. This analysis provides a unified condensed-phase picture of proton structure and dynamics that, at its extrema, encompasses proton sharing and spectroscopic features resembling the limiting Eigen [H$_{3}$O(H$_{2}$O)$_{3}$]$^{+}$ and Zundel [H(H$_{2}$O)$_{2}$]$^{+}$ gas-phase structures, while also describing the rich variety of interconverting environments in the liquid phase.

[41]
Title: Generation, amplification, frequency conversion and reversal of propagation of THz photons in nonlinear hyperbolic metamaterial
Subjects: Optics (physics.optics)

The metamaterial is proposed which supports a mixture of three or more normal and backward electromagnetic modes with equal co-directed phase velocities and mutually contra-directed energy fluxes. This enables extraordinary three-wave mixing, greatly enhanced optical parametric amplification and frequency-changing generation of entangled photons in the reflection direction. Proof-of-principle numerical simulation of such processes is presented based on the particular example of the wave-guided THz waves contra-propagating in the metamaterial made of carbon nanotubes.

[42]
Title: Entrenched time delays versus accelerating opinion dynamics: are advanced democracies inherently unstable?
Authors: Claudius Gros
Comments: European Physical Journal B (in press)
Subjects: Physics and Society (physics.soc-ph); Adaptation and Self-Organizing Systems (nlin.AO)

Modern societies face the challenge that the time scale of opinion formation is continuously accelerating in contrast to the time scale of political decision making. With the latter remaining of the order of the election cycle we examine here the case that the political state of a society is determined by the continuously evolving values of the electorate. Given this assumption we show that the time lags inherent in the election cycle will inevitable lead to political instabilities for advanced democracies characterized both by an accelerating pace of opinion dynamics and by high sensibilities (political correctness) to deviations from mainstream values. Our result is based on the observation that dynamical systems become generically unstable whenever time delays become comparable to the time it takes to adapt to the steady state. The time needed to recover from external shocks grows in addition dramatically close to the transition. Our estimates for the order of magnitude of the involved time scales indicate that socio-political instabilities may develop once the aggregate time scale for the evolution of the political values of the electorate falls below 7-15 months.

[43]
Title: Topological Hyperbolic and Dirac Plasmons
Authors: Nahid Talebi
Subjects: Optics (physics.optics)

In this chapter, criteria for existence of propagating optical modes which are transversely bound at the interface of two materials are studied. In particular, quite general cases are considered, where the materials involved are assumed to be anisotropic, but also demonstrating magneto-electric effects. Moreover, surface states of two-dimensional materials like topological insulators and graphene are also modeled via consideration of a conductivity sheet existing at the interface. A characteristic equation for obtaining the propagation constant of generalized interface modes is presented. Furthermore, optical modes sustained by a thin film of anisotropic materials with magneto-electric effect and topological surface states are also investigated. It is shown that interface modes supported by such a system are hybrid in nature, and can be further decomposed into the well-known classes of transverse magnetic and electric modes, only at the absence of magneto-electric effect. Although the formulations driven here are mathematically abstract, they can be used to investigate polaritons in van der Waal materials, hyperbolic materials, and topological insulators.

[44]
Title: On-chip electro-mechanical routing of single photons from an embedded quantum emitter
Subjects: Applied Physics (physics.app-ph); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Optics (physics.optics); Quantum Physics (quant-ph)

The electro-mechanical control of an on-chip GaAs optical router operating at the single-photon level is demonstrated. The routing of single photons is achieved by electro-mechanical tuning of the splitting ratio of an optical beam splitter in the form of a nanobeam waveguide directional coupler (DC). One of the two waveguides forming the DC is located at the free end of a cantilever, which can be displaced vertically downwards by applying an actuation voltage, $V_{act}$, between the cantilever and the substrate. The resulting out-of-plane separation between the waveguides is used to control the splitting ratio of the DC. In the absence of $V_{act}$, photons emitted by an InGaAs self-assembled quantum dot embedded within the fixed arm of the device are split $83$:$17$ between the co-planar through and drop ports of the DC respectively. As $V_{act}$ is applied the drop port displaces downwards by over $400$ nm causing the splitting ratio to approach $100$:$0$. The single-photon nature of the collected emission is verified with autocorrelation measurements. The proposed system is compact, easy to fabricate and scalable with applications in on-chip photon routing as well as in-situ fine tuning of photonic elements.

[45]
Title: 2D microscopic and macroscopic simulation of water and porous material interaction
Subjects: Fluid Dynamics (physics.flu-dyn)

In various areas of science, technology, environment protection, construction, it is very important to study processes of porous materials interaction with different substances in different aggregation states. From the point of view of ecology and environmental protection it is particularly actual to investigate processes of porous materials interaction with water in liquid and gaseous phases. Since one mole of water contains $6,022140857\cdot 10^{23}$ molecules of $\mathtt{H_2O}$, macroscopic approaches considering the water vapor as continuum media in the framework of classical aerodynamics are mainly used to describe properties, for example properties of water vapor in the pore. In this paper we construct and use for simulation the macroscopic two-dimensional diffusion model describing the behavior of water vapor inside the isolated pore. Together with the macroscopic model it is proposed microscopic model of the behavior of water vapor inside the isolated pores. This microscopic model is built within the molecular dynamics approach. In the microscopic model a description of each water molecule motion is based on Newton classical mechanics considering interactions with other molecules and pore walls. Time evolution of water vapor - pore system is explored. Depending on the external to the pore conditions the system evolves to various states of equilibrium, characterized by different values of the macroscopic characteristics such as temperature, density, pressure. Comparisons of results of molecular dynamic simulations with the results of calculations based on the macroscopic diffusion model and experimental data allow to conclude that the combination of macroscopic and microscopic approach could produce more adequate and more accurate description of processes of water vapor interaction with porous materials.

[46]
Title: Applying the Spacecraft with a Solar Sail to Form the Climate on a Mars Base
Subjects: Space Physics (physics.space-ph)

This article is devoted to research the application of the spacecraft with a solar sail to support the certain climatic conditions in an area of the Mars surface. Authors propose principles of functioning of the spacecraft, intended to create a light and thermal light spot in a predetermined area of the Martian surface. The mathematical motion model in such condition of the solar sail's orientation is considered and used for motion simulation session. Moreover, the analysis of this motion is performed. Thus, were obtained parameters of the stationary orbit of the spacecraft with a solar sail and were given recommendations for further applying spacecrafts to reflect the sunlight on a planet's surface.

[47]
Title: Power Supply Options for a Naval Railgun
Comments: Submitted to IEEE Transactions on Plasma Physics
Subjects: Plasma Physics (physics.plasm-ph); Applied Physics (physics.app-ph); Instrumentation and Detectors (physics.ins-det)

Large railguns require powerful power supply units. At the French-German Research Institute of Saint-Louis (ISL) most experimental railguns are driven by power supply units based on capacitors. Recent investigations at ISL explore the possibility to use coil based systems to increase the energy density of the power supply. In this study an electrical circuit simulation is used to investigate the difference for railgun operation in between a capacitor and a coil based power supply with respect to current amplitude behavior and projectile velocity. For this a scenario of a 25 MJ muzzle energy railgun is simulated with two different power supply options, replacing capacitors by coils and using a range of circuit resistances. The resistance determines to a large part the losses of the system and defines therefore the efficiency of the launch and the size of the power supply. The interpretation of the results of the performed simulations leads to the conclusion that the capacitor based system "naturally" pro- duces a favorable current pulse trace with respect to launching a mechanical delicate payload. Further simulations show that the disadvantage of the inductor based supply can be mitigated by increasing the power supply unit subdivision into smaller units.

[48]
Title: Interaction between electrostatic collisionless shocks generates strong magnetic fields
Subjects: Plasma Physics (physics.plasm-ph)

The head-on collision between electrostatic shocks is studied via multi-dimensional Particle-In-Cell simulations. It is found that the shock velocities drop significantly and a strong magnetic field is generated after the interaction. This transverse magnetic field is due to the Weibel instability caused by pressure anisotropies due to longitudinal electron heating while the shocks approach each other. Finally, it is shown that this phenomenon can be explored in the laboratory with current laser facilities within a significant parameter range.

[49]
Title: A novel solution for remote sensing of air quality: From satellite reflectance to ground PM2.5
Subjects: Atmospheric and Oceanic Physics (physics.ao-ph)

With a large spatiotemporal coverage, the satellite-derived aerosol optical depth (AOD) has been widely used to estimate ground-level PM2.5 concentrations (AOD-PM modeling). However, the retrieval errors exit in the AOD products, and they will be accumulated in PM2.5 estimation. To avoid the intermediate error/process, a novel solution to estimate PM2.5 directly from satellite top-of-atmosphere (TOA) reflectance (denoted as Ref-PM modeling) is proposed. Using multiple linear regression, neural networks, and deep learning to establish the specific relationship between PM2.5, satellite reflectance, and other predictors, the Ref-PM modeling is validated with data from Wuhan Metropolitan Area in 2016. Furthermore, the geographical correlation is incorporated into deep belief network (Geoi-DBN) to better estimate PM2.5 concentrations. The results show that the performance of Ref-PM modeling (cross-validation R2=0.64 for DBN) has a competitive advantage than that of conventional AOD-PM modeling (cross-validation R2=0.46 for DBN). Moreover, the out-of-sample cross-validation R2 and RMSE for Geoi-DBN in Ref-PM modeling are 0.87 and 9.89 ug/m3, respectively. On this basis, the daily distributions of PM2.5 with a resolution of 0.01 degree are mapped, and they have similar spatial patterns with ground station measurements. These results demonstrate that the proposed Ref-PM modeling is effective for estimating ground-level PM2.5 concentrations from satellite reflectance. This study will significantly promote the application of satellite remote sensing in environmental monitoring.

[50]
Title: Interference between two resonant transitions with distinct initial and final states connected by radiative decay
Subjects: Atomic Physics (physics.atom-ph)

The resonant line shape from driving a transition between two states, $|\rm{a}\rangle$ and $|\rm{b}\rangle$, can be distorted due to a quantum-mechanical interference effect involving a resonance between two different states, $|\rm{c}\rangle$ and $|\rm{d}\rangle$, if $|\rm{c}\rangle$ has a decay path to $|\rm{a}\rangle$ and $|\rm{d}\rangle$ has a decay path to $|\rm{b}\rangle$. This interference can cause a shift of the measured resonance, despite the fact that the two resonances do not have a common initial or final state. As an example, we demonstrate that such a shift affects measurements of the atomic hydrogen 2S$_{1/2}$-to-2P$_{1/2}$ Lamb-shift transition due to 3S-to-3P transitions if the 3S$_{1/2}$ state has some initial population.

[51]
Title: Modulation of Solar Wind Energy Flux Input on Global Tropical Cyclone Activity
Subjects: Space Physics (physics.space-ph); Atmospheric and Oceanic Physics (physics.ao-ph)

Studies on Sun-climate connection have been carried out for several decades, and almost all of them focused on the effects of solar total irradiation energy. As the second major terrestrial energy source from outer space, the solar wind energy flux exhibits more significant long-term variations. However, its link to the global climate change is rarely concerned and remain a mystery. As a fundamental and important aspect of the Earth's weather and climate system, tropical cyclone activity has been causing more and more attentions. Here we investigate the possible modulation of the total energy flux input from the solar wind into the Earth's magnetosphere on the global tropical cyclone activity during 1963--2012. From a global perspective, the accumulated cyclone energy increases gradually since 1963 and start to decrease after 1994. Compare to the previously frequently used parameters, e,g., the sunspot number, the total solar irradiation, the solar F10.7 irradiation, the tropical sea surface temperature, and the south oscillation index, the total solar wind energy flux input exhibits a better correlation with the global tropical cyclone activity. Furthermore, the tropical cyclones seem to be more intense with higher geomagnetic activities. A plausible modulation mechanism is thus proposed to link the terrestrial weather phenomenon to the seemly-unrelated solar wind energy input.

[52]
Title: Fast Desktop-Scale Extrusion Additive Manufacturing
Subjects: Applied Physics (physics.app-ph)

Significant improvements to the production rate of additive manufacturing (AM) technologies are essential to their cost-effectiveness and competitiveness with traditional processing routes. Moreover, much faster AM processes, in combination with the geometric versatility of AM, will enable entirely new workflows for product design and customization. We present the design and validation of a desktop-scale extrusion AM system that achieves far greater build rate than benchmarked commercial systems. This system, which we call FastFFF, is motivated by our recent analysis of the rate-limiting mechanisms to conventional fused filament fabrication (FFF) technology. The FastFFF system mutually overcomes these limits, using a nut-feed extruder, laser-heated polymer liquefier, and servo-driven parallel gantry system to achieve high extrusion force, rapid filament heating, and fast gantry motion, respectively. The extrusion and heating mechanisms are contained in a compact printhead that receives a threaded filament and augments conduction heat transfer with a fiber-coupled diode laser. The prototype system achieves a volumetric build rate of 127 cm3/hr, which is 7-fold greater than commercial desktop FFF systems, at comparable resolution; the maximum extrusion rate of the printhead is ~14-fold greater (282 cm3/hr). The performance limits of the printhead and motion systems are characterized, and the tradeoffs between build rate and resolution are assessed and discussed. The combination of high-speed motion and high deposition rate achieved by the FastFFF technology also poses challenges and opportunities for toolpath optimization and real-time deposition control. High-speed desktop printing raises the possibility of new use cases and business models for AM, where handheld parts are built in minutes rather than hours.

[53]
Title: Rapid Design of Wide-Area Heterogeneous Electromagnetic Metasurfaces beyond the Unit-Cell Approximation
Subjects: Applied Physics (physics.app-ph); Optics (physics.optics)

We propose a novel numerical approach for the optimal design of wide-area heterogeneous electromagnetic metasurfaces beyond the conventionally used unit-cell approximation. The proposed method exploits the combination of Rigorous Coupled Wave Analysis (RCWA) and global optimization techniques (two evolutionary algorithms namely the Genetic Algorithm (GA) and a modified form of the Artificial Bee Colony (ABC with memetic search phase method) are considered). As a specific example, we consider the design of beam deflectors using all-dielectric nanoantennae for operation in the visible wavelength region; beam deflectors can serve as building blocks for other more complicated devices like metalenses. Compared to previous reports using local optimization approaches our approach improves device efficiency; transmission efficiency is especially improved for wide deflection angle beam deflectors. The ABC method with memetic search phase is also an improvement over the more commonly used GA as it reaches similar efficiency levels with upto 35% reduction in computation time. The method described here is of interest for the rapid design of a wide variety of electromagnetic metasurfaces irrespective of their operational wavelength.

[54]
Title: LED receiver impedance and its effects on LED-LED visible light communications
Comments: 9 pages, 9 figures, submitted to Optics Express
Subjects: Applied Physics (physics.app-ph)

This paper experimentally demonstrates that the AC impedance spectrum of the LED as a photodetector heavily depends on the received optical power, which may cause the impedance mismatch between the LED and the post trans-impedance amplifier. The optical power dependent impedance of the LED is well fitted by a modified dispersive carrier transport model for inorganic semiconductors. The bandwidth of the LED-LED visible light communication link is further shown to decrease with the optical power received by the LED. This leads to a trade-off between link bandwidth and SNR, and consequently affects the choice of the proper dada modulation scheme.

[55]
Title: Financial Analysis of a Grid-connected Photovoltaic System in South Florida
Comments: 6 Pages, IEEE PVSC 2017 Conference, Washington D.C
Subjects: Physics and Society (physics.soc-ph)

In this paper the performance and financial analysis of a grid-connected photovoltaic system installed at Florida Atlantic University (FAU) is evaluated. The power plant has the capacity of 14.8 kW and has been under operation since August 2014. This solar PV system is composed of two 7.4 kW sub-arrays, one fixed and one with single axis tracking. First, an overview of the system followed by local weather characteristics in Boca Raton, Florida is presented. In addition, monthly averaged daily solar radiation in Boca Raton as well as system AC are calculated utilizing the PVwatts simulation calculator. Inputs such as module and inverter specifications are applied to the System Advisor Model (SAM) to design and optimize the system. Finally, the estimated local load demand as well as simulation results are extracted and analyzed.

[56]
Title: Analysis of the design of a resonant miniature optical gyroscope based on integrated optics technologies
Authors: Gilles Feugnet (1), Alexia Ravaille (1,2,3), Sylvain Schwartz (1), Fabien Bretenaker (3) ((1) TRT, (2) TAV, (3) LAC)
Subjects: Applied Physics (physics.app-ph)

We present a simple analysis of the design of a miniature resonant optical gyroscope. By combining the requirements on the angular random walk and the bias stability, we end up with simple expressions of the minimum diameter of the ring waveguide cavity and the maximum power that should be used to probe it. Using state-of-the-art performances of photonic integrated circuit technology in terms of propagation losses and mode size, we show that tactical grade gyroscope performances can be achieved with a diameter of a few cm provided the detrimental influence of Kerr effect is mitigated, using for instance an active control of the unbalance in the intensities. We further extend the analysis to medium performance gyroscope and give some hints on the efforts to be made to potentially demonstrate a miniature resonant optical gyroscope with this level of performance.

[57]
Title: Capacitive Deionization -- defining a class of desalination technologies
Subjects: Applied Physics (physics.app-ph)

Over the past decade, capacitive deionization (CDI) has realized a surge in attention in the field of water desalination and can now be considered as an important technology class, along with reverse osmosis and electrodialysis. While many of the recently developed technologies no longer use a mechanism that follows the strict definition of the term "capacitive", these methods nevertheless share many common elements that encourage treating them with similar metrics and analyses. Specifically, they all involve electrically driven removal of ions from a feed stream, storage in an electrode (i.e., ion electrosorption) and release, in charge/discharge cycles. Grouping all these methods in the technology class of CDI makes it possible to treat evolving new technologies in standardized terms and compare them to other technologies in the same class.

[58]
Title: Wang tiling aided statistical determination of the Representative Volume Element size of random heterogeneous materials
Authors: Martin Doškář (1), Jan Zeman (1 and 2), Daniela Jarušková (1), Jan Novák (1) ((1) Faculty of Civil Engineering, Czech Technical University in Prague, (2) Institute of Information Theory and Automation, Academy of Sciences of the Czech Republic)
Subjects: Applied Physics (physics.app-ph)

Wang tile based representation of a heterogeneous material facilitates fast synthesis of non-periodic microstructure realizations. In this paper, we apply the tiling approach in numerical homogenization to determine the Representative Volume Element size related to the user-defined significance level and the discrepancy between bounds on the apparent properties. First, the tiling concept is employed to efficiently generate arbitrarily large, statistically consistent realizations of investigated microstructures. Second, benefiting from the regular structure inherent to the tiling concept, the Partition theorem, and statistical sampling, we construct confidence intervals of the apparent properties related to the size of a microstructure specimen. Based on the interval width and the upper and lower bounds on the apparent properties, we adaptively generate additional microstructure realizations in order to arrive at an RVE satisfying the prescribed tolerance. The methodology is illustrated with the homogenization of thermo-mechanical properties of three two-dimensional microstructure models: a microstructure with mono-disperse elliptic inclusions, foam, and sandstone.

[59]
Title: Lattice Wigner equation
Subjects: Computational Physics (physics.comp-ph)

We present a numerical scheme to solve the Wigner equation, based on a lattice discretization of momentum space. The moments of the Wigner function are recovered exactly, up to the desired order given by the number of discrete momenta retained in the discretisation, which also determines the accuracy of the method. The Wigner equation is equipped with an additional collision operator, designed in such a way as to ensure numerical stability without affecting the evolution of the relevant moments of the Wigner function. The lattice Wigner scheme is validated for the case of quantum harmonic and anharmonic potentials, showing good agreement with theoretical results. It is further applied to the study of the transport properties of one and two dimensional open quantum systems with potential barriers. Finally, the computational viability of the scheme for the case of three- dimensional open systems is also illustrated.

[60]
Title: Line shape analysis of the K$β$ transition in muonic hydrogen
Subjects: Atomic Physics (physics.atom-ph); Nuclear Experiment (nucl-ex)

The K$\beta$ transition in muonic hydrogen was measured with a high-resolution crystal spectrometer. The spectrum is shown to be sensitive to the ground-state hyperfine splitting, the corresponding triplet-to-singlet ratio, and the kinetic energy distribution in the $3p$ state. The hyperfine splitting and triplet-to-singlet ratio are found to be consistent with the values expected from theoretical and experimental investigations and, therefore, were fixed accordingly in order to reduce the uncertainties in the further reconstruction of the kinetic energy distribution. The presence of high-energetic components was established and quantified in both a phenomenological, i.e. cascade-model-free fit, and in a direct deconvolution of the Doppler broadening based on the Bayesian approach.

[61]
Title: Analytic quantum-interference conditions in Coulomb corrected photoelectron holography
Comments: 28 pages, 10 figures. The figures have been simplified in order to comply with the arXiV size requirements
Subjects: Atomic Physics (physics.atom-ph)

We provide approximate analytic expressions for above-threshold ionization (ATI) transition probabilities and photoelectron angular distributions (PADs). These analytic expressions are more general than those existing in the literature and include the residual binding potential in the electron continuum propagation. They successfully reproduce the ATI side lobes and specific holographic structures such as the near-threshold fan-shaped pattern and the spider-like structure that extends up to relatively high photoelectron energies. We compare such expressions with the Coulomb quantum orbit strong-field approximation (CQSFA) and the full solution of the time-dependent Schr\"odinger equation for different driving-field frequencies and intensities, and provide an in-depth analysis of the physical mechanisms behind specific holographic structures. Our results shed additional light on what aspects of the CQSFA must be prioritized in order to obtain the key holographic features, and highlight the importance of forward scattered trajectories. Furthermore, we find that the holographic patterns change considerably for different field parameters, even if the Keldysh parameter is kept roughly the same.

[62]
Title: The MCUCN simulation code for ultracold neutron physics
Authors: G. Zsigmond
Subjects: Instrumentation and Detectors (physics.ins-det); Nuclear Experiment (nucl-ex)

Ultracold neutrons (UCN) have very low kinetic energies 0-300 neV, thereby can be stored in specific material or magnetic confinements for many hundreds of seconds. This makes them a very useful tool in probing fundamental symmetries of nature (for instance charge-parity violation by neutron electric dipole moment experiments) and contributing important parameters for the Big Bang nucleosynthesis (neutron lifetime measurements). Improved precision experiments are in construction at new and planned UCN sources around the world. MC simulations play an important role in the optimization of such systems with a large number of parameters, but also in the estimation of systematic effects, in benchmarking of analysis codes, or as part of the analysis. The MCUCN code written at PSI has been extensively used for the optimization of the UCN source optics and in the optimization and analysis of (test) experiments within the nEDM project based at PSI. In this paper we present the main features of MCUCN and interesting benchmark and application examples.

[63]
Title: Radiative heat transfer between spatially nonlocally responding dielectric objects
Subjects: Optics (physics.optics); Quantum Physics (quant-ph)

We calculate numerically the heat transfer rate between a spatially dispersive sphere and a half-space. By utilising Huygens' principle and the extinction theorem, we derive the necessary reflection coefficients at the sphere and the plate without the need to resort to additional boundary conditions. We find for small distances $d\sim 1$nm a significant modification of the spectral heat transfer rate due to spatial dispersion. As a consequence, the spurious divergencies that occur in spatially local approach are absent.

[64]
Title: Saturation of energetic-particle-driven geodesic acoustic modes due to wave-particle nonlinearity
Subjects: Plasma Physics (physics.plasm-ph)

The nonlinear dynamics of energetic-particle (EP) driven geodesic acoustic modes (EGAM) is investigated here. A numerical analysis with the global gyrokinetic particle-in-cell code ORB5 is performed, and the results are interpreted with the analytical theory, in close comparison with the theory of the beam-plasma instability. Only axisymmetric modes are considered, with a nonlinear dynamics determined by wave-particle interaction. Quadratic scalings of the saturated electric field with respect to the linear growth rate are found for the case of interest. The EP bounce frequency is calculated as a function of the EGAM frequency, and shown not to depend on the value of the bulk temperature. Near the saturation, we observe a transition from adiabatic to non-adiabatic dynamics, i.e., the frequency chirping rate becomes comparable to the resonant EP bounce frequency. The numerical analysis is performed here with electrostatic simulations with circular flux surfaces, and kinetic effects of the electrons are neglected.

[65]
Title: A motility-induced phase transition drives Myxococcus xanthus aggregation
Subjects: Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

A hallmark of living systems is their ability to generate complex spatial patterns at the molecular, cellular, and multicellular levels. Many such systems rely on coupled biochemical and genetic signaling mechanisms that can produce large-scale organization. Long-range order and patterning can also emerge, however, through purely mechanical interactions. Here, we study the starvation-induced aggregation of gliding Myxococcus xanthus bacteria and show that these cells phase separate by tuning their motility over time. By experimentally varying the density and speed of gliding cells, tracking individual cells in large populations, and comparing to simulations of a model of reversing Active Brownian Particles (ABPs), we show that cell aggregation can be understood with a single phase diagram in terms of density and a dimensionless inverse rotational Peclet number that characterizes cell motility. We further track changes in motility of the wild-type during starvation and show that a reduction of the reversal frequency and an increase in gliding speed change the rotational Peclet number to drive aggregation. Thus, M. xanthus evolved to take advantage of an active-matter phase transition that can be controlled through changes in motility at the individual cell level without complex feedback and chemical communication between cells.

[66]
Title: Analysis of High Frequency Impedance Measurement Techniques for Power Line Network Sensing
Comments: A version of this article has been accepted for publication on IEEE Sensors Journal, Special Issue on "Smart Sensors for Smart Grids and Smart Cities"
Subjects: Physics and Society (physics.soc-ph)

A major aspect in power line distribution networks is the constant monitoring of the network properties. With the advent of the smart grid concept, distributed monitoring has started complementing the information of the central stations. In this context, power line communications modems deployed throughout the network provide a tool to monitor high frequency components of the signals traveling through a power line network. We propose therefore to use them not only as communication devices but also as network sensors. Besides classical voltage measurements, these sensors can be designed to monitor high frequency impedances, which provide useful information about the power line network, as for instance status of the topology, cable degradation and occurrence of faults. In this article, we provide a technical analysis of different voltage and impedance measurement techniques that can be integrated into power line modems. We assess the accuracy of the techniques under analysis in the presence of network noise and we discuss the statistical characteristics of the measurement noise. We finally compare the performances of the examined techniques when applied to the fault detection problem in distribution networks, in order to establish which technique gives more accurate results.

### Cross-lists for Tue, 19 Sep 17

[67]  arXiv:1709.05354 (cross-list from hep-ph) [pdf, other]
Title: Resonant absorption of bosonic dark matter in molecules
Subjects: High Energy Physics - Phenomenology (hep-ph); High Energy Physics - Theory (hep-th); Atomic Physics (physics.atom-ph); Optics (physics.optics)

We propose a new class of bosonic dark matter (DM) detectors based on resonant absorption onto a gas of small polyatomic molecules. Bosonic DM acts on the molecules as a narrow-band perturbation, like an intense but weakly coupled laser. The excited molecules emit the absorbed energy into fluorescence photons that are picked up by sensitive photodetectors with low dark count rates. This setup is sensitive to any DM candidate that couples to electrons, photons, and nuclei, and may improve on current searches by several orders of magnitude in coupling for DM masses between 0.2 eV and 20 eV. This type of detector has excellent intrinsic energy resolution, along with several control variables---pressure, temperature, external electromagnetic fields, molecular species/isotopes---that allow for powerful background rejection methods as well as precision studies of a potential DM signal. The proposed experiment does not require usage of novel exotic materials or futuristic technologies, relying instead on the well-established field of molecular spectroscopy, and on recent advances in single-photon detection. Cooperative radiation effects, which arise due to the large spatial coherence of the nonrelativistic DM field in certain detector geometries, can tightly focus the DM-induced fluorescence photons in a direction that depends on the DM's velocity, possibly permitting a detailed reconstruction of the full 3D velocity distribution in our Galactic neighborhood, as well as further background rejection.

[68]  arXiv:1709.05370 (cross-list from quant-ph) [pdf]
Title: Ultrahigh-Quality Magneto-Optical Resonances of Electromagnetically Induced Absorption in a Buffer-Gas-Filled Vapor Cell
Subjects: Quantum Physics (quant-ph); Atomic Physics (physics.atom-ph)

A new configuration for observation of magneto-optical subnatural-linewidth resonances of electromagnetically induced absorption (EIA) in alkali vapor has been verified experimentally. The configuration includes using two counter-propagating pump and probe light waves with mutually orthogonal linear polarizations, exciting an open optical transition of an alkali atom in the presence of a buffer gas. The main advantage of the novel observation scheme consists in the possibility of obtaining simultaneously high-contrast and quite narrow nonlinear signals. Here a 2.5-cm long rubidium-87 vapor cell filled with Ar buffer gas is used, and the excited optical transition is the F$_g$=2 $\to$ F$_e$=1 of the D$_1$ line. The signals registered reach a contrast of 57.7% with a FWHM of 7.2 mG. The contrast with respect to a wide Doppler pedestal well exceeds 100%. To our knowledge, to date this is the best result for EIA resonances in terms of contrast-to-width ratio. In general, the results demonstrate that the new magneto-optical scheme has very good prospects for various applications in quantum metrology, nonlinear optics and photonics.

[69]  arXiv:1709.05428 (cross-list from astro-ph.HE) [pdf, other]
Title: Pressure-anisotropy-induced nonlinearities in the kinetic magnetorotational instability
Comments: Submitted to Journal of Plasma Physics
Subjects: High Energy Astrophysical Phenomena (astro-ph.HE); Plasma Physics (physics.plasm-ph)

In collisionless and weakly collisional plasmas, such as hot accretion flows onto compact objects, the magnetorotational instability (MRI) can differ significantly from the standard (collisional) MRI. In particular, pressure anisotropy with respect to the local magnetic-field direction can both change the linear MRI dispersion relation and cause nonlinear modifications to the mode structure and growth rate, even when the field and flow perturbations are very small. This work studies these pressure-anisotropy-induced nonlinearities in the weakly nonlinear regime, before the MRI saturates into strong turbulence. Our goal is to better understand how the saturation of the MRI in a low collisionality plasma might differ from that in the collisional regime. We focus on two key effects: (i) the direct impact of self-induced pressure-anisotropy nonlinearities on the evolution of an MRI mode, and (ii) the influence of pressure anisotropy on the "parasitic instabilities" that are suspected to cause the mode to break up into turbulence. Our main conclusions are: (i) The mirror instability regulates the pressure anisotropy in such a way that the linear MRI in a collisionless plasma is an approximate non-linear solution once the mode amplitude becomes larger than the background field (just as in MHD). This implies that differences between the collisionless and collisional MRI become unimportant at large amplitudes. (ii) The break up of large amplitude MRI modes into turbulence via parasitic instabilities is similar in collisionless and collisional plasmas. Together, these conclusions suggest that the route to magnetorotational turbulence in a collisionless plasma may well be similar to that in a collisional plasma, as suggested by recent kinetic simulations. As a supplement to these findings, we offer guidance for the design of future kinetic simulations of magnetorotational turbulence.

[70]  arXiv:1709.05456 (cross-list from cond-mat.stat-mech) [pdf, other]
Title: Detection of Transition Times from Single-particle-tracking Trajectories
Subjects: Statistical Mechanics (cond-mat.stat-mech); Data Analysis, Statistics and Probability (physics.data-an)

In heterogeneous environments, the diffusivity is not constant but changes with time. It is important to detect changes in the diffusivity from single-particle-tracking trajectories in experiments. Here, we devise a novel method for detecting the transition times of the diffusivity from trajectory data. A key idea of this method is the introduction of a characteristic time scale of the diffusive states, which is obtained by a fluctuation analysis of the time-averaged mean square displacements. We test our method in silico by using the Langevin equation with a fluctuating diffusivity. We show that our method can successfully detect the transition times of diffusive states and obtain the diffusion coefficient as a function of time. This method will provide a quantitative description of the fluctuating diffusivity in heterogeneous environments and can be applied to time series with transitions of states.

[71]  arXiv:1709.05461 (cross-list from cond-mat.soft) [pdf, ps, other]
Title: Inertial Effects on the Stress Generation of Active Fluids
Subjects: Soft Condensed Matter (cond-mat.soft); Fluid Dynamics (physics.flu-dyn)

Suspensions of self-propelled bodies generate a unique mechanical stress owing to their motility that impacts their large-scale collective behavior. For microswimmers suspended in a fluid with negligible particle inertia, we have shown that the virial swim stress' is a useful quantity to understand the rheology and nonequilibrium behaviors of active soft matter systems. For larger self-propelled organisms like fish, it is unclear how particle inertia impacts their stress generation and collective movement. Here, we analyze the effects of finite particle inertia on the mechanical pressure (or stress) generated by a suspension of self-propelled bodies. We find that swimmers of all scales generate a unique swim stress' and Reynolds stress' that impacts their collective motion. We discover that particle inertia plays a similar role as confinement in overdamped active Brownian systems, where the reduced run length of the swimmers decreases the swim stress and affects the phase behavior. Although the swim and Reynolds stresses vary individually with the magnitude of particle inertia, the sum of the two contributions is independent of particle inertia. This points to an important concept when computing stresses in computer simulations of nonequilibrium systems---the Reynolds and the virial stresses must both be calculated to obtain the overall stress generated by a system.

[72]  arXiv:1709.05462 (cross-list from cond-mat.quant-gas) [pdf, other]
Title: Quantum Scattering in an Optical Collider for Ultracold Atoms
Comments: Proceedings of ICPEAC XXX, to appear in J. Phys. Conf. Ser
Subjects: Quantum Gases (cond-mat.quant-gas); Atomic Physics (physics.atom-ph)

We report on experiments investigating the collisional properties of atoms at ultralow collision energies using an all-optical atom collider. By using a pair of optical tweezers, we can manipulate two ultracold atom clouds and collide them together at energies up to three orders of magnitude larger than their thermal energy. Our experiments measure the scattering of $\rm ^{87}Rb$, $\rm ^{40}K$, and $\rm ^{40}K$-$\rm ^{87}Rb$ collisions. The versatility of our collider allows us to probe both shape resonances and Feshbach resonances in any partial wave. As examples, we present experiments demonstrating p-wave scattering with indistinguishable fermions, inelastic scattering at non-zero energies near a homonuclear Feshbach resonance, and partial wave interference in heteronuclear collisions.

[73]  arXiv:1709.05494 (cross-list from cond-mat.mes-hall) [pdf, other]
Title: A Theory of a Self-Assembling Electrovariable Smart Mirror
Subjects: Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Applied Physics (physics.app-ph)

A theory describing the forces governing the self-assembly of nanoparticles at the solid-liquid interface is developed. In the process, new theoretical results are derived to describe the effect that the field penetration of a point-like particle, into an electrode, has on the image potential energy, and pair interaction energy profiles at the electrode-electrolyte interface. The application of the theory is demonstrated for gold and ITO electrode systems, promising materials for novel colour-tuneable electrovariable smart mirrors and mirror-window devices respectively. Model estimates suggest that electrovariability is attainable in both systems and will act as a guide for future experiments. Lastly, the generalisability of the theory towards electrovariable, nanoplasmonic systems suggests that it may contribute towards the design of intelligent metamaterials with programmable properties.

[74]  arXiv:1709.05503 (cross-list from nlin.PS) [pdf, other]
Title: Delay dynamics of neuromorphic optoelectronic nanoscale resonators: Perspectives and applications
Comments: 26 pages, 18 figures, Accepted in Chaos special issue on Time-delay Dynamics
Subjects: Pattern Formation and Solitons (nlin.PS); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Optics (physics.optics)

With the recent exponential growth of applications using artificial intelligence (AI), the development of efficient and ultrafast brain-like (neuromorphic) systems is crucial for future information and communication technologies. While the implementation of AI systems using computer algorithms of neural networks is emerging rapidly, scientists are just taking the very first steps in the development of the hardware elements of an artificial brain, specifically neuromorphic microchips. In this review article, we present the current state of neuromorphic photonic circuits based on solid-state optoelectronic oscillators formed by nanoscale double barrier quantum well resonant tunneling diodes. We address, both experimentally and theoretically, the key dynamic properties of recently developed artificial solid-state neuron microchips with delayed perturbations and describe their role in the study of neural activity and regenerative memory. This review covers our recent research work on excitable and delay dynamic characteristics of both single and autaptic (delayed) artificial neurons including all-or-none response, spike-based data encoding, storage, signal regeneration and signal healing. Furthermore, the neural responses of these neuromorphic microchips display all the signatures of extended spatio-temporal localized structures (LSs) of light, which are reviewed here in detail. By taking advantage of the dissipative nature of LSs, we demonstrate potential applications in optical data reconfiguration and clock and timing at high-speeds and with short transients. The results reviewed in this article are a key enabler for the development of high-performance optoelectronic devices in future high-speed brain-inspired optical memories and neuromorphic computing.

[75]  arXiv:1709.05531 (cross-list from quant-ph) [pdf, other]
Title: Information Geometry of Quantum Resources
Authors: Davide Girolami
Comments: Contribution to Conference IGAIA IV, submitted to Springer Proceedings in Mathematics & Statistics
Subjects: Quantum Physics (quant-ph); Data Analysis, Statistics and Probability (physics.data-an)

I review recent works showing that information geometry is a useful framework to characterize quantum coherence and entanglement. Quantum systems exhibit peculiar properties which cannot be justified by classical physics, e.g. quantum coherence and quantum correlations. Once confined to thought experiments, they are nowadays created and manipulated by exerting an exquisite experimental control of atoms, molecules and photons. It is important to identify and quantify such quantum features, as they are deemed to be key resources to achieve supraclassical performances in computation and communication protocols. The information geometry viewpoint elucidates the advantage provided by quantum superpositions in phase estimation. Also, it enables to link measures of coherence and entanglement to observables, which can be evaluated in a laboratory by a limited number of measurements.

[76]  arXiv:1709.05561 (cross-list from cond-mat.stat-mech) [pdf, other]
Title: Exact combinatorial approach to finite coagulating systems
Subjects: Statistical Mechanics (cond-mat.stat-mech); Chemical Physics (physics.chem-ph)

The paper outlines an exact combinatorial approach to finite coagulating systems. In this approach, cluster sizes and time are discrete, and the binary aggregation alone governs the time evolution of the systems. By considering the growth histories of all possible clusters, the exact expression is derived for the probability of a coagulating system with an arbitrary kernel being found in a given cluster configuration when monodisperse initial conditions are applied. Then, this probability is used to calculate the time-dependent distribution for the number of clusters of a given size, the average number of such clusters and that average's standard deviation. The correctness of our general expressions is proved based on the (analytical and numerical) results obtained for systems with the constant kernel. In addition, the results obtained are compared with the results arising from the solutions to the mean-field Smoluchowski coagulation equation, indicating its weak points. The paper closes with a brief discussion on the extensibility to other systems of the approach presented herein, emphasizing the issue of arbitrary initial conditions.

[77]  arXiv:1709.05564 (cross-list from astro-ph.EP) [pdf, other]
Title: Catalog of fine-structured electron velocity distribution functions $-$ Part 1: Antiparallel magnetic-field reconnection (Geospace Environmental Modeling case)
Comments: 17 pages, 11 figures, published
Journal-ref: Ann. Geophys., 35, 1051-1067, 2017
Subjects: Earth and Planetary Astrophysics (astro-ph.EP); Solar and Stellar Astrophysics (astro-ph.SR); Plasma Physics (physics.plasm-ph); Space Physics (physics.space-ph)

To understand the essential physics needed to reproduce magnetic reconnection events in 2.5-D particle-in-cell (PIC) simulations, we revisit the Geospace Environmental Modeling (GEM) setup. We set up a 2-D Harris current sheet (that also specifies the initial conditions) to evolve the reconnection of antiparallel magnetic fields. In contrast to the GEM setup, we use a much smaller initial perturbation to trigger the reconnection and evolve it more self-consistently. From PIC simulation data with high-quality particle statistics we study a symmetric reconnection site, including separatrix layers, as well as the inflow and the outflow regions. The velocity distribution functions (VDFs) of electrons have a fine structure and vary strongly depending on their location within the reconnection setup. The goal is to start cataloging multidimensional fine-structured electron velocity distributions showing different reconnection processes in the Earth's magnetotail under various conditions. This will enable a direct comparison with observations from, e.g., the NASA Magnetospheric MultiScale (MMS) mission, to identify reconnection-related events. We find regions with strong non-gyrotropy also near the separatrix layer and provide a refined criterion to identify an electron diffusion region in the magnetotail. The good statistical significance of this work for relatively small analysis areas reveals the gradual changes within the fine structure of electron VDFs depending on their sampling site.

[78]  arXiv:1709.05571 (cross-list from quant-ph) [pdf, other]
Title: Experimental Verification of Position-Dependent Angular-Momentum Selection Rules for Absorption of Twisted Light by a Bound Electron
Subjects: Quantum Physics (quant-ph); Atomic Physics (physics.atom-ph); Optics (physics.optics)

We analyze the multipole excitation of atoms with twisted light, i.e., by a vortex light field that carries orbital angular momentum. A single trapped $^{40}$Ca$^+$ ion serves as a localized and positioned probe of the exciting field. We drive the $S_{1/2} \to D_{5/2}$ transition and observe the relative strengths of different transitions, depending on the ion's transversal position with respect to the center of the vortex light field. On the other hand, transition amplitudes are calculated for a twisted light field in form of a Bessel beam, a Bessel-Gauss and a Gauss-Laguerre mode. Analyzing experimental obtained transition amplitudes we find agreement with the theoretical predictions at a level of better than 3\%. Finally, we propose measurement schemes with two-ion crystals to enhance the sensing accuracy of vortex modes in future experiments.

[79]  arXiv:1709.05594 (cross-list from q-fin.GN) [pdf, other]
Title: GDP growth rates as confined Lévy flights
Subjects: General Finance (q-fin.GN); Physics and Society (physics.soc-ph)

A new model that combines economic growth rate fluctuations at the microscopic and macroscopic level is presented. At the microscopic level, firms are growing at different rates while also being exposed to idiosyncratic shocks at the firm and sector level. We describe such fluctuations as independent L\'evy-stable fluctuations, varying over multiple orders of magnitude. These fluctuations are aggregated and measured at the macroscopic level in averaged economic output quantities such as GDP. A fundamental question is thereby to what extend individual firm size fluctuations can have a noticeable impact on the overall economy. We argue that this question can be answered by considering the L\'evy fluctuations as embedded in a steep confining potential well, ensuring nonlinear mean-reversal behavior, without having to rely on microscopic details of the system. The steepness of the potential well directly controls the extend towards which idiosyncratic shocks to firms and sectors are damped at the level of the economy. Additionally, the theory naturally accounts for business cycles, represented in terms of a bimodal economic output distribution, and thus connects two so far unrelated fields in economics. By analyzing 200 years of US GDP growth rates, we find that the model is in good agreement with the data.

[80]  arXiv:1709.05619 (cross-list from stat.AP) [pdf]
Title: An adsorbed gas estimation model for shale gas reservoirs via statistical learning
Journal-ref: Applied Energy, 2017, 197: 327-341
Subjects: Applications (stat.AP); Geophysics (physics.geo-ph)

Shale gas plays an important role in reducing pollution and adjusting the structure of world energy. Gas content estimation is particularly significant in shale gas resource evaluation. There exist various estimation methods, such as first principle methods and empirical models. However, resource evaluation presents many challenges, especially the insufficient accuracy of existing models and the high cost resulting from time-consuming adsorption experiments. In this research, a low-cost and high-accuracy model based on geological parameters is constructed through statistical learning methods to estimate adsorbed shale gas content

[81]  arXiv:1709.05634 (cross-list from cs.SI) [pdf, other]
Title: Label propagation for clustering
Authors: Lovro Šubelj
Comments: 27 pages, 13 figures, 2 tables, chapter in "Advances in Network Clustering and Blockmodeling" edited by P. Doreian, V. Batagelj & A. Ferligoj (Wiley, New York, 2018)
Subjects: Social and Information Networks (cs.SI); Data Analysis, Statistics and Probability (physics.data-an); Physics and Society (physics.soc-ph)

Label propagation is a heuristic method initially proposed for community detection in networks, while the method can be adopted also for other types of network clustering and partitioning. Among all the approaches and techniques described in this book, label propagation is neither the most accurate nor the most robust method. It is, however, without doubt one of the simplest and fastest clustering methods. Label propagation can be implemented with a few lines of programming code and applied to networks with hundreds of millions of nodes and edges on a standard computer, which is true only for a handful of other methods in the literature.
In this chapter, we present the basic framework of label propagation, review different advances and extensions of the original method, and highlight its equivalences with other approaches. We show how label propagation can be used effectively for large-scale community detection, graph partitioning, identification of structurally equivalent nodes and other network structures. We conclude the chapter with a summary of the label propagation methods and suggestions for future research.

[82]  arXiv:1709.05639 (cross-list from cond-mat.soft) [pdf, ps, other]
Title: Twist-stretch profiles of DNA chains
Authors: Marco Zoli
Journal-ref: Journal of Physics: Condensed Matter v.29 225101 (2017)
Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)

Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are applied to generate a large ensemble of possible configurations for the base pairs of the sequence. The model also accounts for the bending and twisting fluctuations between adjacent base pairs along the molecules stack. Simulating a broad range of twisting conformation, we compute the helix structural parameters by averaging over the ensemble of base pairs configurations. The method selects, for any applied force, the average twist angle which minimizes the molecule's free energy. It is found that the chains generally over-twist under an applied stretching and the over-twisting is physically associated to the contraction of the average helix diameter, i.e. to the damping of the base pair fluctuations. Instead, assuming that the maximum amplitude of the bending fluctuations may decrease against the external load, the DNA molecule first over-twists for weak applied forces and then untwists above a characteristic force value. Our results are discussed in relation to available experimental information albeit for kilo-base long molecules.

[83]  arXiv:1709.05777 (cross-list from quant-ph) [pdf, ps, other]
Title: Hidden Variable Theory of a Single World from Many-Worlds Quantum Mechanics
Authors: Don Weingarten
Subjects: Quantum Physics (quant-ph); History and Philosophy of Physics (physics.hist-ph)

We propose a method for finding an initial state vector which by ordinary Hamiltonian time evolution follows a single branch of many-worlds quantum mechanics. The resulting deterministic system appears to exhibit random behavior as a result of the successive emergence over time of information present in the initial state but not previously observed.

[84]  arXiv:1709.05798 (cross-list from quant-ph) [pdf, ps, other]
Title: Second-order coherence properties of amplified spontaneous emission from a high-power tapered superluminescent diode
Journal-ref: Laser Physics Letters, 14, 086201 (2017)
Subjects: Quantum Physics (quant-ph); Optics (physics.optics)

We study the degree of second-order coherence of the emission of a high-power multi-quantum well superluminescent diode with a lateral tapered amplifier section with and without feedback. When operated in an external cavity, the degree of second-order coherence changed from the almost thermal case of g$^{(2)}$(0)$\approx$1.9 towards the mostly coherent case of g$^{(2)}$(0)$\approx$1.2 when the injection current at the tapered section was increased. We found good agreement with semi-classical laser theory near and below threshold while above laser threshold a slightly higher g$^{(2)}$(0) was observed. As a free running device, the superluminescent diode yielded more than 400 mW of optical output power with good spatial beam quality of $M^2_{slow} < 1.6$. In this case, the DSOC dropped only slightly from 1.9 at low powers to 1.6 at the maximum output power. To our knowledge, this is the first investigation of a high-power tapered superluminescent diode concerning the degree of second-order coherence. Such a device might be useful for real-world applications probing the second order coherence function, such as ghost imaging.

[85]  arXiv:1709.05811 (cross-list from astro-ph.HE) [pdf, other]
Title: Dissipation in Relativistic Pair-plasma Reconnection: Revisited
Authors: Seiji Zenitani
Subjects: High Energy Astrophysical Phenomena (astro-ph.HE); Plasma Physics (physics.plasm-ph); Space Physics (physics.space-ph)

Basic properties of relativistic magnetic reconnection in electron-positron pair plasmas are investigated by using a particle-in-cell (PIC) simulation. We first revisit a problem by Hesse & Zenitani (2007), who examined the kinetic Ohm's law across the X line. We formulate a relativistic Ohm's law by decomposing the stress-energy tensor. Then, the role of the new term, called the heat-flow inertial term, is examined in the PIC simulation data. We further evaluate the energy balance in the reconnection system. These analyses demonstrate physically transparent ways to diagnose relativistic kinetic data.

[86]  arXiv:1709.05858 (cross-list from astro-ph.SR) [pdf, other]
Title: Optimal Energy Growth in Current Sheets
Subjects: Solar and Stellar Astrophysics (astro-ph.SR); Fluid Dynamics (physics.flu-dyn); Plasma Physics (physics.plasm-ph)

In this paper, we investigate the possibility of transient growth in the linear perturbation of current sheets. The resistive magnetohydrodynamic (MHD) operator for a background field consisting of a current sheet is non-normal, meaning that associated eigenvalues and eigenmodes can be very sensitive to perturbation. In a linear stability analysis of a tearing current sheet, we show that modes that are damped as $t\rightarrow\infty$ can produce transient energy growth, contributing faster growth rates and higher energy attainment (within a fixed finite time) than the unstable tearing mode found from normal-mode analysis. We determine the transient growth for tearing-stable and tearing-unstable regimes and discuss the consequences of our results for processes in the solar atmosphere, such as flares and coronal heating. Our results have significant potential impact on how fast current sheets can be disrupted. In particular, transient energy growth due to (asymptotically) damped modes may lead to accelerated current sheet thinning and, hence, a faster onset of the plasmoid instability, compared to the rate determined by the tearing mode alone.

[87]  arXiv:1709.05887 (cross-list from quant-ph) [pdf, ps, other]
Title: Unidirectional Reflection and Invisibility in Nonlinear Media with an Incoherent Nonlinearity
Comments: 11 pages, 2 figures, 1 table
Subjects: Quantum Physics (quant-ph); Optics (physics.optics)

We give explicit criteria for the reflectionlessness, transparency, and invisibility of a finite-range potential in the presence of an incoherent (intensity-dependent) nonlinearity that is confined to the range of the potential. This allows us to conduct a systematic study of the effects of such a nonlinearity on a locally periodic class of finite-range potentials that display perturbative unidirectional invisibility. We use our general results to examine the effects of a weak Kerr nonlinearity on the behavior of these potentials and show that the presence of nonlinearity destroys the unidirectional invisibility of these potentials. If the strength of the Kerr nonlinearity is so weak that the first-order perturbation theory is reliable, the presence of nonlinearity does not affect the unidirectional reflectionlessness and transmission reciprocity of the potential. We show that the expected violation of the latter is a second order perturbative effect.

[88]  arXiv:1709.05920 (cross-list from cond-mat.mes-hall) [pdf]
Title: Observation of topological valley transport of sound in sonic crystals
Journal-ref: Nat. Phys., 13, 369 (2017)
Subjects: Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Applied Physics (physics.app-ph)

Valley pseudospin, labeling quantum states of energy extrema in momentum space, is attracting tremendous attention1-13 because of its potential in constructing new carrier of information. Compared with the non-topological bulk valley transport realized soon after predictions1-5, the topological valley transport in domain walls6-13 is extremely challenging owing to the inter-valley scattering inevitably induced by atomic scale imperfectness, until the recent electronic signature observed in bilayer graphene12,13. Here we report the first experimental observation of topological valley transport of sound in sonic crystals. The macroscopic nature of sonic crystals permits the flexible and accurate design of domain walls. In addition to a direct visualization of the valley-selective edge modes through spatial scanning of sound field, reflection immunity is observed in sharply curved interfaces. The topologically protected interface transport of sound, strikingly different from that in traditional sound waveguides14,15, may serve as the basis of designing devices with unconventional functions.

[89]  arXiv:1709.05929 (cross-list from cs.CV) [pdf]
Title: Institutionally Distributed Deep Learning Networks
Subjects: Computer Vision and Pattern Recognition (cs.CV); Learning (cs.LG); Medical Physics (physics.med-ph)

Deep learning has become a promising approach for automated medical diagnoses. When medical data samples are limited, collaboration among multiple institutions is necessary to achieve high algorithm performance. However, sharing patient data often has limitations due to technical, legal, or ethical concerns. In such cases, sharing a deep learning model is a more attractive alternative. The best method of performing such a task is unclear, however. In this study, we simulate the dissemination of learning deep learning network models across four institutions using various heuristics and compare the results with a deep learning model trained on centrally hosted patient data. The heuristics investigated include ensembling single institution models, single weight transfer, and cyclical weight transfer. We evaluated these approaches for image classification in three independent image collections (retinal fundus photos, mammography, and ImageNet). We find that cyclical weight transfer resulted in a performance (testing accuracy = 77.3%) that was closest to that of centrally hosted patient data (testing accuracy = 78.7%). We also found that there is an improvement in the performance of cyclical weight transfer heuristic with high frequency of weight transfer.

[90]  arXiv:1709.05930 (cross-list from cond-mat.mtrl-sci) [pdf, other]
Title: Room temperature ferromagnetism in transparent and conducting Mn-doped $SnO_{2}$ thin films
Comments: 17 pages, 15 figures, 4 Tables, 108 References. arXiv admin note: text overlap with arXiv:1512.06119, arXiv:1612.05150
Subjects: Materials Science (cond-mat.mtrl-sci); Applied Physics (physics.app-ph)

The magnetization as a function of magnetic field showed hysteretic behavior at room temperature. According to the temperature dependence of the magnetization, the Curie temperature $(T_{C})$ is higher than 350 K. Ferromagnetic Mn-doped tin oxide thin films exhibited low electrical resistivity and high optical transmittance in the visible region (400-800 nm). The coexistence of ferromagnetism, high visible transparency and high electrical conductivity in the Mn-doped $SnO_{2}$ films is expected to be a desirable trait for spintronics devices.

[91]  arXiv:1709.05953 (cross-list from quant-ph) [pdf, ps, other]
Title: Vacuum Friction
Comments: 8 pages, 2 figures. Published in Journal of Modern Optics on 14 September 2017
Subjects: Quantum Physics (quant-ph); Atomic Physics (physics.atom-ph); Optics (physics.optics)

We know that in empty space there is no preferred state of rest. This is true both in special relativity but also in Newtonian mechanics with its associated Galilean relativity. It comes as something of a surprise, therefore, to discover the existence a friction force associated with spontaneous emission. he resolution of this paradox relies on a central idea from special relativity even though our derivation of it is non-relativistic. We examine the possibility that the physics underlying this effect might be explored in an ion trap, via the observation of a superposition of different mass states.

[92]  arXiv:1709.05999 (cross-list from cond-mat.mtrl-sci) [pdf]
Title: Cleavage Tendency of Anisotropic Two Dimensional Materials: ReX2 (X=S, Se) and WTe2
Subjects: Materials Science (cond-mat.mtrl-sci); Applied Physics (physics.app-ph)

With unique distorted 1T structure and the associated in-plane anisotropic properties, mono- and few-layer ReX2 (X=S, Se) have recently attracted particular interest. Based on experiment and first-principles calculations, we investigate the fracture behavior of ReX2. We find that the cleaved edges of ReX2 flakes usually form an angle of ~120{\deg} or ~60{\deg}. In order to understand such phenomenon, we perform comprehensive investigations on the uniaxial tensile stress-strain relation of monolayer and multi-layer ReX2 sheets. Our numerical calculation shows that the particular cleaved edges of ReX2 flakes are caused by unique anisotropic ultimate tensile strengths and critical strains. We also calculate the stress-strain relation of WTe2, which explains why their cleaved edges are not corresponding to the principle axes. Our proposed mechanism about the fracture angle has also been supported by the calculated cleavage energies and surface energies for different edge surfaces.

[93]  arXiv:1709.06001 (cross-list from cs.OH) [pdf, ps, other]
Title: From Logic to Biology via Physics: a survey
Comments: accepted for publication in Logical Methods in Computer Science
Subjects: Other Computer Science (cs.OH); Physics and Society (physics.soc-ph)

This short text summarizes the work in biology proposed in our book, Perspectives on Organisms, where we analyse the unity proper to organisms by looking at it from different viewpoints. We discuss the theoretical roles of biological time, complexity, theoretical symmetries, singularities and critical transitions. We explicitly borrow from the conclusions in some key chapters and introduce them by a reflection on "incompleteness", also proposed in the book. We consider that incompleteness is a fundamental notion to understand the way in which we construct knowledge. Then we will introduce an approach to biological dynamics where randomness is central to the theoretical determination: randomness does not oppose biological stability but contributes to it by variability, adaptation, and diversity. Then, evolutionary and ontogenetic trajectories are continual changes of coherence structures involving symmetry changes within an ever-changing global stability.

[94]  arXiv:1709.06005 (cross-list from cs.GR) [pdf, other]
Title: TikZ-network manual
Authors: Jürgen Hackl
Subjects: Graphics (cs.GR); Physics and Society (physics.soc-ph)

TikZ-network is an open source software project for visualizing graphs and networks in LaTeX. It aims to provide a simple and easy tool to create, visualize and modify complex networks. The packaged is based on the PGF/TikZ languages for producing vector graphics from a geometric/algebraic description. Particular focus is made on the software usability and interoperability with other tools. Simple networks can be directly created within LaTeX, while more complex networks can be imported from external sources (e.g. igraph, networkx, QGIS, ...). Additionally, tikz-network supports visualization of multilayer networks in two and three dimensions. The software is available at: https://github.com/hackl/tikz-network.

[95]  arXiv:1709.06028 (cross-list from cond-mat.soft) [pdf, other]
Title: A hexatic smectic phase with algebraically decaying bond-orientational order
Comments: Submitted to Phys. Rev. Letters
Subjects: Soft Condensed Matter (cond-mat.soft); Materials Science (cond-mat.mtrl-sci); Computational Physics (physics.comp-ph)

The hexatic phase predicted by the theories of two-dimensional melting is characterised by the power law decay of the orientational correlations whereas the in-layer bond orientational order in all the hexatic smectic phases observed so far was found to be long-range. We report a hexatic smectic phase where the in-layer bond orientational correlations decay as $\propto r^{-1/4}$, in quantitative agreement with the hexatic ordering predicted by the theory for two dimensions. The phase was formed in a molecular dynamics simulation of a one-component system of particles interacting via a spherically symmetric potential. This is the first observation of the theoretically predicted two-dimensional hexatic order in a three-dimensional system.

[96]  arXiv:1709.06045 (cross-list from cond-mat.stat-mech) [pdf, other]
Title: Thermodynamically Consistent Coarse Graining of Biocatalysts beyond Michaelis--Menten
Subjects: Statistical Mechanics (cond-mat.stat-mech); Chemical Physics (physics.chem-ph); Molecular Networks (q-bio.MN)

Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Moreover, we identify the conditions under which a relation between fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux--force relation.

[97]  arXiv:1709.06065 (cross-list from cond-mat.mtrl-sci) [pdf]
Title: Discovery of ideal Weyl points with helicoid surface states
Subjects: Materials Science (cond-mat.mtrl-sci); Applied Physics (physics.app-ph); Optics (physics.optics)

Weyl points, serving as monopoles in the momentum space and laying the foundation of topological gapless phases, have recently been experimentally demonstrated in various physical systems. However, none of the observed Weyl degeneracies are ideal: they either offset in energy or coexist with trivial dispersions at other momenta. The lack of an ideal Weyl system sets a serious limit to the further development of Weyl physics and potential applications. Here, by constructing a photonic metamaterial, we experimentally observe an ideal Weyl system, whose nodal frequencies are pinned by symmetries to exactly the same value. Benefitting from the ideal Weyl nodes, we are able to map out the complete evolution of the helicoid surface states spinning around the projections of each Weyl nodes. Our discovery provides an ideal photonic platform for Weyl systems and novel topological devices.

### Replacements for Tue, 19 Sep 17

[98]  arXiv:1305.5693 (replaced) [pdf, other]
Title: Observationally driven 3D MHD model of the solar corona above an active region
Authors: Ph.-A. Bourdin (1 and 2), S. Bingert (1), H. Peter (1) ((1) Max-Planck-Institut für Sonnensystemforschung, (2) Institut für Astrophysik, Universität Göttingen)
Comments: 6 pages, 3 figures, published
Journal-ref: A&A, 555, A123 (2013)
Subjects: Solar and Stellar Astrophysics (astro-ph.SR); Plasma Physics (physics.plasm-ph)
[99]  arXiv:1507.03573 (replaced) [pdf, other]
Title: Coronal energy input and dissipation in a solar active region 3D MHD model
Authors: Philippe-A. Bourdin (1 and 2), Sven Bingert (3), Hardi Peter (2) ((1) Space Research Institute, Austrian Academy of Sciences, Graz/Austria, (2) Max Planck Institute for Solar System Research, Göttingen/Germany, (3) Gesellschaft für wissenschaftliche Datenverarbeitung, Göttingen/Germany)
Comments: 8 pages, 8 figures, published
Journal-ref: A&A 580, A72 (2015)
Subjects: Solar and Stellar Astrophysics (astro-ph.SR); Plasma Physics (physics.plasm-ph); Space Physics (physics.space-ph)
[100]  arXiv:1510.05898 (replaced) [pdf, other]
Title: A solid state source of photon triplets based on quantum dot molecules
Journal-ref: Nature Communications 8 15716 (2017)
Subjects: Quantum Physics (quant-ph); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Optics (physics.optics)
[101]  arXiv:1512.04346 (replaced) [pdf, other]
Title: Neutron spectroscopy with the Spherical Proportional Counter
Subjects: Instrumentation and Detectors (physics.ins-det)
[102]  arXiv:1512.08347 (replaced) [pdf]
Title: Communicating with sentences: A multi-word naming game model
Comments: 19 pagesa, 11 figures, Physica A (2017)
Subjects: Computation and Language (cs.CL); Physics and Society (physics.soc-ph)
[103]  arXiv:1602.07302 (replaced) [pdf, ps, other]
Title: GPView: a program for wave function analysis and visualization
Authors: Tian Shi, Ping Wang
Subjects: Chemical Physics (physics.chem-ph)
[104]  arXiv:1603.05276 (replaced) [pdf, other]
Title: Scaling laws of coronal loops compared to a 3D MHD model of an Active Region
Authors: Philippe-A. Bourdin (1 and 2), Sven Bingert (3), Hardi Peter (2) ((1) Space Research Institute, Austrian Academy of Sciences, Graz/Austria, (2) Max Planck Institute for Solar System Research, Göttingen/Germany, (3) Gesellschaft für wissenschaftliche Datenverarbeitung, Göttingen/Germany)
Comments: 8 pages, 9 figures, published
Journal-ref: A&A 589, A86 (2016)
Subjects: Solar and Stellar Astrophysics (astro-ph.SR); Plasma Physics (physics.plasm-ph); Space Physics (physics.space-ph)
[105]  arXiv:1603.06112 (replaced) [pdf, ps, other]
Title: Quantum Superpositions and the Representation of Physical Reality Beyond Measurement Outcomes and Mathematical Structures
Subjects: Quantum Physics (quant-ph); History and Philosophy of Physics (physics.hist-ph)
[106]  arXiv:1606.02146 (replaced) [pdf, other]
Title: Low energy recoil detection with a spherical proportional counter
Comments: 16 pages, 16 figures, preprint
Subjects: Instrumentation and Detectors (physics.ins-det); High Energy Physics - Experiment (hep-ex)
[107]  arXiv:1608.03976 (replaced) [pdf]
Title: Geometric phase mediated topological transport of sound
Subjects: Classical Physics (physics.class-ph); Optics (physics.optics)
[108]  arXiv:1609.03324 (replaced) [pdf, other]
Title: Generation of Spatially Embedded Random Networks to Model Complex Transportation Networks
Comments: 7 pages, 4 figures, 2 tables
Journal-ref: In 14th International Probabilistic Workshop (pp. 217-230). Springer International Publishing (2017)
Subjects: Physics and Society (physics.soc-ph)
[109]  arXiv:1609.07231 (replaced) [pdf, other]
Title: Confining rigid balls by mimicking quadrupole ion trapping
Subjects: Classical Physics (physics.class-ph)
[110]  arXiv:1609.07981 (replaced) [pdf]
Title: The excitation energy spectrum for a system with electron pairs tunneling in a two-leg ladder has a doping depended gap
Comments: 7 pages, in the last version has added one paragraph on page three related to two mental pictures helpful for visualizing the bonding process between the electrons
Subjects: General Physics (physics.gen-ph)
[111]  arXiv:1611.05795 (replaced) [pdf, other]
Title: A Fast Stable Discretization of the Constant-Convection-Diffusion-Reaction Equations of Kinetic Capillary Electrophoresis (KCE)
Comments: Accepted for publication. (Contains 18 pages with 3 figures.)
Subjects: Computational Physics (physics.comp-ph)
[112]  arXiv:1611.07989 (replaced) [pdf, other]
Title: The effects of stochasticity at the single-cell level and cell size control on the population growth
Authors: Jie Lin, Ariel Amir
Subjects: Populations and Evolution (q-bio.PE); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph)
[113]  arXiv:1701.00520 (replaced) [pdf, ps, other]
Title: Anomalous electron states
Authors: Boris I. Ivlev
Subjects: General Physics (physics.gen-ph)
[114]  arXiv:1701.00534 (replaced) [pdf, ps, other]
Title: The Theoretical Proof for GLHUA EM Invisible Double Layer Cloak By Using GL No Scattering Modeling and Inversion
Comments: 16 pages and 144 formulas in this paper, this paper is theoretical proof of paper arXiv:1612.02857. It is academical publication for open review. Please colleagues send comments and question to Jianhua Li by email glhua@glgeo.com, or give coments in arXiv. If some colleague refer our paper, please cite it as reference
Subjects: Classical Physics (physics.class-ph); Mathematical Physics (math-ph); Optics (physics.optics)
[115]  arXiv:1701.07750 (replaced) [pdf, other]
Title: Skyrmion Gas Manipulation for Probabilistic Computing
Subjects: Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Disordered Systems and Neural Networks (cond-mat.dis-nn); Computational Physics (physics.comp-ph)
[116]  arXiv:1702.05076 (replaced) [pdf, other]
Title: Bridging ultra-high-Q devices and photonic circuits
Comments: (1) Added Fig.4 to show high-coherence Brillouin lasing using the integrated resonator; (2) Added system illustrations (Fig. 1a); (3) Changed title of paper to reflect demonstrations of both low-repetition-rate soliton mode locking and Brillouin laser using the integrated resonator; (4) Fig. 6 added in Methods to describe resonator-to-waveguide phase-matching control; (5) Other minor changes
Subjects: Optics (physics.optics)
[117]  arXiv:1703.06383 (replaced) [pdf, other]
Title: Manipulating polarized light with a planar slab of Black Phosphorus
Subjects: Optics (physics.optics)
[118]  arXiv:1704.06594 (replaced) [pdf, other]
Title: Selective high frequency mechanical actuation driven by the VO2 electronic instability
Comments: Main text: 6 pages, 4 figures Supplemental Material: 16 pages, 7 sections
Journal-ref: Adv. Mater. 29, 1701618 (2017)
Subjects: Applied Physics (physics.app-ph); Strongly Correlated Electrons (cond-mat.str-el)
[119]  arXiv:1705.02532 (replaced) [pdf, ps, other]
Title: Study of systematic effects in electron electric dipole moment search experiment on HfF$^+$ ion
Authors: A.N. Petrov
Subjects: Atomic Physics (physics.atom-ph)
[120]  arXiv:1705.04951 (replaced) [pdf, ps, other]
Title: The LHC Timeline: A personal recollection (1980-2012). Oral History Interview
Comments: 33 pages, 15 figures. To be published on The European Physical Journal H. New version with added text and references
Subjects: History and Philosophy of Physics (physics.hist-ph); High Energy Physics - Experiment (hep-ex)
[121]  arXiv:1705.05682 (replaced) [pdf, other]
Title: Self-compression of spatially limited laser pulses in a system of coupled light-guides
Subjects: Optics (physics.optics)
[122]  arXiv:1705.06803 (replaced) [pdf, other]
Title: Segregation of large particles in dense granular flows: A granular Saffman effect?
Subjects: Soft Condensed Matter (cond-mat.soft); Fluid Dynamics (physics.flu-dyn)
[123]  arXiv:1706.01528 (replaced) [pdf, other]
Title: Bose-Einstein Condensation in a Plasmonic Lattice
Subjects: Quantum Gases (cond-mat.quant-gas); Optics (physics.optics); Quantum Physics (quant-ph)
[124]  arXiv:1706.01565 (replaced) [pdf, other]
Title: Two-color phase-of-the-phase spectroscopy in the multiphoton regime
Comments: 6 pages, 5 figures, RevTeX 4.1
Subjects: Atomic Physics (physics.atom-ph); Optics (physics.optics); Quantum Physics (quant-ph)
[125]  arXiv:1706.04562 (replaced) [pdf, other]
Title: Quantifying genuine multipartite correlations and their pattern complexity
Comments: 4 pages, to appear in Phys. Rev. Lett
Subjects: Quantum Physics (quant-ph); Disordered Systems and Neural Networks (cond-mat.dis-nn); Information Theory (cs.IT); Adaptation and Self-Organizing Systems (nlin.AO); Data Analysis, Statistics and Probability (physics.data-an)
[126]  arXiv:1706.06446 (replaced) [pdf]
Title: The Concepts and Applications of Fractional Order Differential Calculus in Modelling of Viscoelastic Systems: A primer
Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft)
[127]  arXiv:1706.07295 (replaced) [pdf, ps, other]
Title: Non-renewal statistics for electron transport in a molecular junction with electron-vibration interaction
Authors: Daniel S. Kosov
Journal-ref: J. Chem. Phys. 147, 104109 (2017)
Subjects: Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Chemical Physics (physics.chem-ph)
[128]  arXiv:1706.09780 (replaced) [pdf, other]
Title: ENLIVE: An Efficient Nonlinear Method for Calibrationless and Robust Parallel Imaging
Comments: Submitted to Magnetic Resonance in Medicine as a Full Paper. Part of this work has been presented at the 25th ISMRM Annual Meeting. 21 pages, 8 figures
Subjects: Medical Physics (physics.med-ph)
[129]  arXiv:1707.00025 (replaced) [pdf, other]
Title: Quantum Limits to Gravity Estimation with Optomechanics
Comments: 7 pages, 3 figures; accepted for publication in Phys. Rev. A
Subjects: Quantum Physics (quant-ph); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Optics (physics.optics)
[130]  arXiv:1707.01833 (replaced) [pdf, other]
Title: The Charm of Theoretical Physics (1958-1993)
Comments: 53 pages, 12 figures, to be published in The European Physical Journal H. New version with added text and figures
Subjects: History and Philosophy of Physics (physics.hist-ph); High Energy Physics - Experiment (hep-ex); High Energy Physics - Phenomenology (hep-ph)
[131]  arXiv:1707.01882 (replaced) [pdf, other]
Title: A contemporary look at Hermann Hankel's 1861 pioneering work on Lagrangian fluid dynamics
Comments: 17 pages, see the companion paper by Villone and Rampf (2017), v2: minor revisions, accepted for publication in EPJH
Subjects: History and Overview (math.HO); Analysis of PDEs (math.AP); History and Philosophy of Physics (physics.hist-ph)
[132]  arXiv:1707.01883 (replaced) [pdf, other]
Title: Hermann Hankel's "On the general theory of motion of fluids", an essay including an English translation of the complete Preisschrift from 1861
Comments: 44 pages, see the companion paper by Frisch, Grimberg and Villone (2017), v2: minor revisions including change of title, accepted for publication in EPJH
Subjects: History and Overview (math.HO); Analysis of PDEs (math.AP); History and Philosophy of Physics (physics.hist-ph)
[133]  arXiv:1707.02189 (replaced) [pdf, other]
Title: Characterization of Chromium Compensated GaAs as an x-ray Sensor Material for Charge-Integrating Pixel Array Detectors
Comments: revised version after peer review
Subjects: Instrumentation and Detectors (physics.ins-det)
[134]  arXiv:1707.02815 (replaced) [pdf, other]
Title: Laser spectroscopy of $^{176}$Lu$^+$
Subjects: Atomic Physics (physics.atom-ph)
[135]  arXiv:1707.04936 (replaced) [pdf, ps, other]
Title: Highly accurate bound state calculations of the two-center molecular ions by using the universal variational expansion for three-body systems
Authors: Alexei M Frolov
Subjects: Atomic Physics (physics.atom-ph)
[136]  arXiv:1707.06577 (replaced) [pdf, other]
Title: Confinement effects in premelting dynamics
Subjects: Fluid Dynamics (physics.flu-dyn)
[137]  arXiv:1707.06749 (replaced) [pdf, other]
Title: Results on MeV-scale dark matter from a gram-scale cryogenic calorimeter operated above ground
Comments: 6 pages, 6 figures, v3: ancillary files added, v4: high energy spectrum (0.6-12keV) added to ancillary files
Subjects: Cosmology and Nongalactic Astrophysics (astro-ph.CO); Instrumentation and Methods for Astrophysics (astro-ph.IM); Instrumentation and Detectors (physics.ins-det)
[138]  arXiv:1708.01509 (replaced) [pdf, other]
Title: Exact Solution of the Zakharov-Shabat Scattering Problem for Doubly-Truncated Multi-Soliton Potentials
Authors: V. Vaibhav
Comments: The manuscript is revised for submission to PRE. Also, some typos have been corrected
Subjects: Computational Physics (physics.comp-ph); Numerical Analysis (math.NA); Exactly Solvable and Integrable Systems (nlin.SI)
[139]  arXiv:1708.02768 (replaced) [pdf, ps, other]
Title: Cs nDJ Rydberg-atom macrodimers formed by long-range multipole interaction
Subjects: Atomic Physics (physics.atom-ph)
[140]  arXiv:1708.04661 (replaced) [pdf, other]
Title: Characterizing Feshbach resonances in ultracold scattering calculations
Subjects: Atomic Physics (physics.atom-ph)
[141]  arXiv:1708.05203 (replaced) [pdf, other]
Title: Scattering of long water waves in a canal with rapidly varying cross-section in the presence of a current
Subjects: Fluid Dynamics (physics.flu-dyn)
[142]  arXiv:1709.00950 (replaced) [pdf, other]
Title: The Difference between Physics and Biology: The Key Role of Biomolecules
Comments: 22 pages, 2 figures. Updated version of an FQXI essay. Many edits to Section on deductive causation
Subjects: Biological Physics (physics.bio-ph)
[143]  arXiv:1709.01361 (replaced) [pdf, ps, other]
Title: Response to Comments in Exact and -exact- formulae in the theory of composites (arXiv:1708.02137v1 [math-ph], 7 August 2017)
Subjects: Applied Physics (physics.app-ph)
[144]  arXiv:1709.03448 (replaced) [pdf, other]
Title: Wide tailorability of sound absorption using acoustic metamaterials
Subjects: Applied Physics (physics.app-ph)
[145]  arXiv:1709.04391 (replaced) [pdf]
Title: Microhexcavity Plasma Panel Detectors
Authors: Alexis Mulski (1), Daniel S. Levin (1), Yan Benhamou (2), John W. Chapman (1), Achintya Das (2), Erez Etzion (2), Claudio Ferretti (1), Peter S. Friedman (3), Meny Raviv-Moshe (2), David Reikher (2), Nicholas Ristow (1) ((1) University of Michigan, Department of Physics, Ann Arbor, Michigan (2) Tel Aviv University, School of Physics and Astronomy, Tel Aviv, Israel. (3) Integrated Sensors, LLC, Ottawa Hills, Ohio)
Comments: To be included in conference proceedings for the 2017 meeting of the American Physical Society (APS) Division of Particles and Fields (DPF 2017)
Subjects: Instrumentation and Detectors (physics.ins-det); High Energy Physics - Experiment (hep-ex)
[146]  arXiv:1709.04478 (replaced) [pdf, other]
Title: Fundamental efficiency bound for coherent energy transfer in nanophotonics