Related papers: Tunneling-splittings from path-integral molecular …
The critical step in a molecular process is often a rare-event and has to be simulated by an enhanced sampling protocol. Recovering accurate dynamical estimates from such biased simulation is challenging. Girsanov reweighting is a method to…
Machine Learning Interatomic Potentials (MLIPs) are a modern computational method that allows achieving near-quantum mechanical accuracy (DFT) while still describing large-scale systems in molecular dynamics (MD) simulations. In this work,…
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…
The thermal degradation of a graphene-like two-dimensional triangular membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that the…
We describe the thermodynamic state of a highly confined single-phase and single-component fluid in a slit pore using Hill's thermodynamics of small systems. This theory was more recently named nanothermodynamics. We start by constructing…
The combination of transfer learning (TL) a low level potential energy surface (PES) to a higher level of electronic structure theory together with ring-polymer instanton (RPI) theory is explored and applied to malonaldehyde. The RPI…
A simple algorithm is described to sample permutations of identical particles in Path Integral Monte Carlo (PIMC) simulations of continuum many-body systems. The sampling strategy illustrated here is fairly general, and can be easily…
Controlling structural transitions between molecular configurations is crucial for advancing functional molecular electronics. While reversible switching of bistable two-state molecules has been achieved, creating molecular systems that can…
To take into account nuclear quantum effects on the dynamics of atoms, the path integral molecular dynamics (PIMD) method used since 1980s is based on the formalism developed by R. P. Feynman. However, the huge computation time required for…
Calorimetric determination of enthalpies of mixing ($\Delta$H$_{\rm mix}$) of multicomponent molten salts often employs empirical models that lack parameters with clear physical interpretation (e.g., coordination numbers, molar volumes, and…
The framework of bipartite stochastic thermodynamics is a powerful tool to analyze a composite system's internal thermodynamics. It has been used to study the components of different molecular machines such as ATP synthase. However, this…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
In our recent work [H. Zhang, F.X. Trias, A. Oliva, D. Yang, Y. Tan, Y. Sheng. PIBM: Particulate immersed boundary method for fluid-particle interaction problems. Powder Technology. 272(2015), 1-13.], a particulate immersed boundary method…
We investigate the influence of numerical discretization errors on computed averages in a molecular dynamics simulation of TIP4P liquid water at 300 K coupled to different deterministic (Nos\'e-Hoover and Nos\'e-Poincar\'e) and stochastic…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
Langevin dynamics sampling suffers from extremely low generation speed, fundamentally limited by numerous fine-grained iterations to converge to the target distribution. We introduce PID-controlled Langevin Dynamics (PIDLD), a novel…
This computational experiment demonstrates that chain melting in lipids is a molecular process. BOMD is certainly the best method to reproduce such dynamics properties, since the electronic contributions to the various molecular structures…
Advanced thermostats for molecular dynamics are proposed on the base of the rigorous Langevin dynamics. Because the latter accounts for the subsystem-bath interactions in details, the bath anisotropy and nonuniformity are described via the…
In this paper, we present splitting algorithms to solve multicomponent transport models with Maxwell-Stefan-diffusion approaches. The multicomponent models are related to transport problems, while we consider plasma processes, in which the…
A new theoretical method, referred to as Generalized Langevin Mode Analysis (GLMA), is proposed to analyze the mode of structural fluctuations of a biomolecule in solution. The method combines the two theories in the statistical mechanics,…