Related papers: Mapping Variable Ring Polymer Molecular Dynamics: …
We present non-convex maximal dissipation principle (NMDP), a time integration scheme for articulated bodies with simultaneous contacts. Our scheme resolves contact forces via the maximal dissipation principle (MDP). Prior MDP solvers…
We introduce a direct Boltzmann inversion method to infer the interaction potential in particle systems using as input particle configurations generated at an arbitrary state point of the system. Unlike iterative Boltzmann inversion, the…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
A novel quantum dynamical method to simulate vibronic reaction dynamics in molecules at metal surfaces is proposed. The method is based on the hierarchical quantum master equation approach and uses a discrete variable representation of the…
Modeling of dynamic processes in nuclear reactors is carried out, mainly, on the basis of the multigroup diffusion approximation for the neutron flux. The basic model includes a multidimensional set of coupled parabolic equations and…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
We develop a novel multilevel asymptotic-preserving Monte Carlo method, called Multilevel Kinetic-Diffusion Monte Carlo (ML-KDMC), for simulating the kinetic Boltzmann transport equation with a Bhatnagar-Gross-Krook (BGK) collision…
A hybrid computational method coupling the lattice-Boltzmann (LB) method and a Langevin-dynamics (LD) method is developed to simulate nanoscale particle and polymer (NPP) suspensions in the presence of both thermal fluctuation and…
In this paper, an automated Linear Parameter-Varying (LPV) model conversion approach is proposed for nonlinear dynamical systems. The proposed method achieves global embedding of the original nonlinear behavior of the system by leveraging…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
The mapping approach addresses the mismatch between the continuous nuclear phase space and discrete electronic states by creating an extended, fully continuous phase space using a set of harmonic oscillators to encode the populations and…
The Dynamic Monte Carlo (DMC) method is an established molecular simulation technique for the analysis of the dynamics in colloidal suspensions. An excellent alternative to Brownian Dynamics or Molecular Dynamics simulation, DMC is…
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Herein, epoxy resin is cured by coupling quantum chemical (QC) calculations with molecular dynamics (MD) simulations that enable parameter-free prediction of material characteristics. A polymer network is formed by the reaction between base…
Matsubara dynamics is the classical dynamics which results when imaginary-time path-integrals are smoothed; it conserves the quantum Boltzmann distribution and appears in drastically approximated form in path-integral dynamics methods such…
High-resolution simulations of particle-based kinetic plasma models typically require a high number of particles and thus often become computationally intractable. This is exacerbated in multi-query simulations, where the problem depends on…