Related papers: Kinetic rates calculation via non-equilibrium dyna…
Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear, computationally intensive, and can be difficult to interpret, while often only…
Simulation modeling of robots, objects, and environments is the backbone for all model-based control and learning. It is leveraged broadly across dynamic programming and model-predictive control, as well as data generation for imitation,…
Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include use of static lattice phonons, quasi-harmonic approximation…
Molecular motors walk along filaments until they detach stochastically with a force-dependent unbinding rate. Here, we show that this unbinding rate can be obtained from the analysis of experimental data of molecular motors moving in…
We propose a methodology for fully automated calculation of thermal rate coefficients of gas phase chemical reactions, which is based on combining the ring polymer molecular dynamics (RPMD) with the machine-learning interatomic potentials…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…
Time-dependent kinetic models are ubiquitous in computational science and engineering. The underlying integro-differential equations in these models are high-dimensional, comprised of a six--dimensional phase space, making simulations of…
We present a new approach to calculate real-time quantum dynamics in complex systems. The formalism is based on the partitioning of a system's environment into "core" and "reservoir" modes, with the former to be treated quantum mechanically…
We present TTCF4LAMMPS, a toolkit for performing non-equilibrium molecular dynamics (NEMD) simulations to study fluid behaviour at low shear rates using the LAMMPS software. By combining direct NEMD simulations and the transient-time…
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in conformational state, scale exponentially with the relevant…
We combined Moment Tensor Potential (MTP) and Ring Polymer Molecular Dynamics (RPMD) for calculating the thermal rate constants of the OH + HBr system. We used the active learning (AL) algorithm for constructing a training set during RPMD.…
The standard two-step model of homogeneous-catalyzed reactions had been theoretically analyzed at various levels of approximations from time to time. The primary aim was to check the validity of the quasi-steady-state approximation, and…
A realistic physical model for the so called rate promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein…
Real-time lattice quantum electrodynamics (QED) provides a unique tool for simulating plasmas in the strong-field regime, where collective plasma scales are not well-separated from relativistic-quantum scales. As a toy model, we study…
In this article, we implement a recently developed non-equilibrium chemical kinetics model \cite{singhmodeldevelopment2019} based on \textit{ab initio} simulation data and perform verification studies. Direct molecular simulation data is…
A method for the discrete particle simulation of of almost rigid, sharply edged frictional particles, such as railway ballast is proposed. In difference to Molecular Dynamics algorithms, the method does not require knowledge about the…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…