Related papers: Dynasor 2: From Simulation to Experiment Through C…
Atomistic simulations are used to test the equations of continuum contact mechanics in nanometer scale contacts. Nominally spherical tips, made by bending crystals or cutting crystalline or amorphous solids, are pressed into a flat, elastic…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Correlation remains to be one of the most widely used statistical tools for assessing the strength of relationships between data series. This paper presents a novel compositional correlation method for detecting linear and nonlinear…
While investigating quantum correlations in atomic systems, we note that single measurements contain information about these correlations. Using a simple model of measurement -- analogous to the one used in quantum optics -- we show how to…
We present a new time-dependent Density Functional approach to study the relaxational dynamics of an assembly of interacting particles subject to thermal noise. Starting from the Langevin stochastic equations of motion for the velocities of…
This dissertation is founded on the central notion that structural correlations in dense fluids, such as dense gases, liquids, and glasses, are directly related to fundamental interatomic forces. This relationship was identified early in…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure.…
Two-particle, pair-number correlation distributions on two-dimensional transverse momentum ($p_{t1},p_{t2}$) constructed from the particle production in relativistic heavy-ion collisions allow access to dynamical processes in these systems…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
Thomson scattering spectra measure the response of plasma particles to incident radiation. In warm dense matter, which is opaque to visible light, x-ray Thomson scattering (XRTS) enables a detailed probe of the electron distribution and has…
Summary: The DynaSig-ML (Dynamical Signatures - Machine Learning) Python package allows the efficient, user-friendly exploration of 3D dynamics-function relationships in biomolecules, using datasets of experimental measures from large…
Predicting and enhancing inherent properties based on molecular structures is paramount to design tasks in medicine, materials science, and environmental management. Most of the current machine learning and deep learning approaches have…
The efforts associated with parametrization of continuum-based models for crystal plasticity are a significant obstacle for the routine use of these models in materials science and engineering. While phenomenological constitutive…
We demonstrate the use of symbolic regression in deriving analytical formulas, which are needed at various stages of a typical experimental analysis in collider phenomenology. As a first application, we consider kinematic variables like the…
Multivariate functional data from a complex system are naturally high-dimensional and have complex cross-correlation structure. The complexity of data structure can be observed as that (1) some functions are strongly correlated with similar…
Machine Learning (ML) techniques are revolutionizing the way to perform efficient materials modeling. Nevertheless, not all the ML approaches allow for the understanding of microscopic mechanisms at play in different phenomena. To address…
A formalism using a double Laplace Fourier transform of the transport equation yields the return probabilities of the vacancy in the vicinity of the tracer atom in the presence of solute-vacancy interactions of arbitrary extension. Studying…
Synthetic quantum systems with interacting constituents play an important role in quantum information processing and in elucidating fundamental phenomena in many-body physics. Following impressive advances in cooling and trapping…
Tailoring microscopic details to tune bulk rheology is a key paradigm in soft matter physics, yet the vast parameter space associated with constituent interactions precludes a fully systematic approach. To address this, we have designed a…