Related papers: Kinetic rates calculation via non-equilibrium dyna…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
We introduce a new method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. Such reduced dynamics play an essential role in the study of a broad class of processes, ranging from…
Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
We introduce the coherent state mapping ring-polymer molecular dynamics (CS-RPMD), a new method that accurately describes electronic non-adiabatic dynamics with explicit nuclear quantization. This new approach is derived by using coherent…
Two kinetic models are proposed for high-temperature rarefied (or non-equilibrium) gas flows with radiation. One of the models uses the Boltzmann collision operator to model the translational motion of gas molecules, which has the ability…
Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying…
This paper proposes a sign gradient descent (SGD) algorithm for predicting the three-dimensional folded protein molecule structures under the kinetostatic compliance method (KCM). In the KCM framework, which can be used to simulate the…
In this paper, we present an efficient algorithm for the long time behavior of plasma simulations. We will focus on 4D drift-kinetic model, where the plasma's motion occurs in the plane perpendicular to the magnetic field and can be…
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate…
This technical report provides an in-depth evaluation of both established and state-of-the-art methods for simulating constrained rigid multi-body systems with hard-contact dynamics, using formulations of Nonlinear Complementarity Problems…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
The physicochemical mechanisms underlying the pyrolysis of n-hexane in a high temperature Ar-H2 environment were investigated for plasma pyrolysis process. An optimal chemical kinetics model was developed using the Reaction Mechanism…
In previous work, we introduced a method for determining convergence rates for integration methods for the kinetic Langevin equation for $M$-$\nabla$Lipschitz $m$-log-concave densities [arXiv:2302.10684, 2023]. In this article, we exploit…
We present a new method to derive kinetic equations for systems undergoing non-linear transport in the presence of memory effects. In the framework of mesoscopic nonequilibrium thermodynamics, we derive a generalized Fokker-Planck equation…
Leveraging neural implicit representation to conduct dense RGB-D SLAM has been studied in recent years. However, this approach relies on a static environment assumption and does not work robustly within a dynamic environment due to the…
We report new statistical time-series analysis tools providing significant improvements in the rapid, precision extraction of discrete state dynamics from large databases of experimental observations of molecular machines. By building…
We present a method to model the interaction and the dynamics of atoms excited to Rydberg states. We show a way to solve the optical Bloch equations for laser excitation of the frozen gas in good agreement with the experiment. A second…
Conventional kinesin is a homodimeric motor protein that is capable of walking unidirectionally along a cytoskeletal filament. While previous experiments indicated unyielding unidirectionality against an opposing load up to the so-called…
We generalise the non-affine theory of viscoelasticity for use with large, well-sampled systems of arbitrary chemical complexity. Having in mind predictions of mechanical and vibrational properties of amorphous systems with atomistic…