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45 records · Page 3

ADCP Upsample

This R script takes reads the csv file of stream-wise velocity data and generates a new time series of with comparable but distinct noise using the Langevin method and library. It simulates a time series measured at 1/10 the sampling rate by calculating a moving average of 10, though other sampling rates can be calculated by adjusting the moving average window. A stationary signal is calculated by taking the difference of the original signal and the moving average, then normalizing by the standard deviation of the moving average. The stationary signal is used to calculate drift and diffusion coefficients. Those coefficients are used to generate a new stationary signal. The new stationary signal is un-normalized and added to the moving average (or new equivalent signal) to create a new up-sampled velocity time-series.

Green, Nathan↗

Learning effective stochastic differential equations from microscopic simulations: Linking stochastic numerics to deep learning

We identify effective stochastic differential equations (SDEs) for coarse observables of fine-grained particle- or agent-based simulations; these SDEs then provide useful coarse surrogate models of the fine scale dynamics. We approximate the drift and diffusivity functions in these effective SDEs through neural networks, which can be thought of as effective stochastic ResNets. The loss function is inspired by, and embodies, the structure of established stochastic numerical integrators (here, Euler–Maruyama and Milstein); our approximations can thus benefit from backward error analysis of these underlying numerical schemes. They also lend themselves naturally to “physics-informed” gray-box identification when approximate coarse models, such as mean field equations, are available. Existing numerical integration schemes for Langevin-type equations and for stochastic partial differential equations can also be used for training; we demonstrate this on a stochastically forced oscillator and the stochastic wave equation. Our approach does not require long trajectories, works on scattered snapshot data, and is designed to naturally handle different time steps per snapshot. We consider both the case where the coarse collective observables are known in advance, as well as the case where they must be found in a data-driven manner.

97 MATHEMATICS AND COMPUTING↗

Thermodynamics–Structure–Dynamics Correlations and Nonuniversal Effects in the Elastically Collective Activated Hopping Theory of Glass-Forming Liquids

We employ the microscopic Elastically Collective Nonlinear Langevin Equation (ECNLE) theory of activated dynamics in combination with crystal-avoiding simulations to study four inter-related questions for metastable monodisperse hard sphere fluids. The first is how significantly improved integral equation theory structural input (Modified-Verlet (MV) closure) changes the dynamical predictions of ECNLE theory. The main consequence is a modest enhancement of the importance of the collective elastic barrier relative to its local cage contribution, which increases the alpha relaxation time and fragility relative to prior results based on the Percus–Yevick closure. Second, ECNLE-MV theory predictions for the alpha time and self-diffusion constant in the metastable regime are quantitatively compared to our new simulations. The small adjustment of a numerical prefactor that enters the collective elastic barrier leads to quantitative agreement over three decades. Third, using the more accurate MV structural input, ECNLE theory is shown to predict thermodynamics–structure–dynamics “correlations” based on various long and short wavelength scalar properties all related to static two-point collective density fluctuations. The logarithm of the alpha relaxation time scales as a power law with these scalar metrics with an exponent that is significantly lower in the less dense noncooperative activated regime compared to the very dense highly cooperative regime. However, the discovered correlation of activated relaxation with a thermodynamic property (dimensionless compressibility) is not causal in ECNLE theory, but rather reflects a strong connection between the local structural quantities that quantify kinetic constraints in the theory with the amplitude of long wavelength density fluctuations. Fourth, the consequences of chemically specific nonuniversalities associated with the onset condition and relative importance of collective elasticity are studied. In conclusion, the predicted thermodynamics–structure–dynamics correlations are found to be robust, albeit with nontrivial shifts of the onset condition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

From Latent Dynamics to Meaningful Representations

While representation learning has been central to the rise of machine learning and artificial intelligence, a key problem remains in making the learnt representations meaningful. For this the typical approach is to regularize the learned representation through prior probability distributions. However such priors are usually unavailable or are ad hoc. To deal with this, recent efforts have shifted towards leveraging the insights from physical principles to guide the learning process. In this spirit, we propose a purely dynamics-constrained representation learning framework. Instead of relying on predefined probabilities, we restrict the latent representation to follow overdamped Langevin dynamics with a learnable transition density — a prior driven by statistical mechanics. We show this is a more natural constraint for representation learning in stochastic dynamical systems, with the crucial ability to uniquely identify the ground truth representation. We validate our framework for different systems including a real-world fluorescent DNA movie dataset. Here, we show that our algorithm can uniquely identify orthogonal, isometric and meaningful latent representations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neutron spin echo spectroscopy

Neutron spin echo (NSE) spectroscopy is a powerful technique used to probe the internal dynamics and diffusion processes within matter, allowing researchers to quantify how materials respond to changes in external conditions. To fully understand the bulk properties of a material, it is often crucial to investigate dynamic processes occurring on nanometre length scales and nanosecond timescales. NSE spectroscopy provides an exceptional capability to measure such dynamics across a broad spectrum of condensed matter systems, ranging from proteins and quantum magnets to catalysts. In this Primer, we present an overview of NSE spectroscopy, highlighting the instruments used, methods of data collection and representative applications in both soft-matter and hard-matter sciences.

Czakkel, Orsolya [Institut Max von Laue-Paul Lange↗

Structure and dynamical properties of two-dimensional dusty plasmas on one-dimensional periodic substrates

In the presence of the substrate, various structural and dynamical properties of two-dimensional dusty plasma (2DDP) were investigated using Langevin dynamical simulations. This paper reviews a series of results of the structural and dynamical properties of 2DDP modified by one-dimensional periodic substrates (1DPSs) as follows. First, when the depth of the 1DPS increases gradually, it is found that the static structural order of 2DDP along each potential well of the 1DPS increases first, and then decreases gradually. When the width of the 1DPS increases gradually, the particle arrangement in each potential well of the 1DPS changes from one straight row gradually to two rows, including the stable zigzag structure. Second, when there are two rows in each potential well of the 1DPS, the phonon spectra are split into two branches, corresponding to the breathing and sloshing modes, respectively. In addition, due to the pure repulsion between dust particles, from the obtained phonon spectra, the sloshing wave propagates backward at small wave numbers. Third, the calculated mean-square displacement (MSD) shown that, at the intermediate timescale between the initial ballistic and final diffusive motions, the particle motion tends to be more subdiffusive while the depth of the 1DPS increases. While the width of the 1DPS increases gradually, the long-time diffusive motion first increases, then decreases, and finally increases again, exhibiting the oscillation-like diffusion, due to the stable zigzag structure. Finally, when an external direct-current driving force is applied on all particles of 2DDP, three different depinning phases are discovered, which are the pinned, disordered plastic flow, and moving ordered states, respectively, as the driving force increases from zero. In addition, the continuous/discontinuous property of the phase transition between these different depinning states is investigated, showing that the transition property is modulated by the depth of the applied 1DPS

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Optimized utilization of COMB3 reactive potentials in LAMMPS

An investigation to optimize the application of the third-generation charge optimized many-body (COMB3) interatomic potential and associated input parameters was carried out through the study of solid–liquid interactions in classical molecular dynamics simulations. The rates of these molecular interactions are understood through the wetting rates of water nano-droplets on a bare copper (111) surface. Implementing the Langevin thermostat, the influence of simulation time step, the number of atoms in the system, the frequency at which charge equilibration is performed, and the temperature relaxation rate are all examined. The results indicate that time steps of 0.4 fs are possible when using longer relaxation times for the system temperature, which is almost double the typical time step used for reactive potentials. Additionally, the use of the charge equilibration allows for a fewer atomic layers to be used in the Cu slab. In addition, charge equilibrium schemes do not need to be performed every time step to ensure accurate charge transfer. Interestingly, the rate of wetting for the nanodroplets is dominantly dependent on the temperature relaxation time, which is predicted to significantly change the viscosity of the water droplets. This work provides a pathway for optimizing simulations using the COMB3 reactive interatomic potential.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Terahertz-field activation of polar skyrons

Unraveling collective modes arising from coupled degrees of freedom is crucial for understanding complex interactions in solids and developing new functionalities. Unique collective behaviors emerge when two degrees of freedom, ordered on distinct length scales, interact. Polar skyrmions, three-dimensional electric polarization textures in ferroelectric superlattices, disrupt the lattice continuity at the nanometer scale with nontrivial topology, leading to previously unexplored collective modes. Here, using terahertz-field excitation and femtosecond x-ray diffraction, we discover subterahertz collective modes, dubbed “skyrons”, which appear as swirling patterns of atomic displacements functioning as atomic-scale gearsets. The key to activating skyrons is the use of the THz field that couples primarily to skyrmion domain walls. Momentum-resolved time-domain measurements of diffuse scattering reveal an avoided crossing in the dispersion relation of skyrons. Atomistic simulations and dynamical phase-field modeling provide microscopic insights into the three-dimensional crystallographic and polarization dynamics. The amplitude and dispersion of skyrons are demonstrated to be controlled by sample temperature and electric-field bias. The discovery of skyrons and their coupling with terahertz fields opens avenues for ultrafast control of topological polar structures.

ferroelectrics↗