相关论文: A Formulation of the Ring Polymer Molecular Dynami…

The position-based dynamics (PBD) algorithm is a popular and versatile technique for real-time simulation of deformable bodies, but is only applicable to forces that can be expressed as linearly compliant constraints. In this work, we…

Internal coordinate molecular dynamics (ICMD) is an efficient method for studying biopolymers, but it is readily applicable only to molecules with tree topologies, that is with no internal flexible rings. Common examples violating this…

We present a Generalized Langevin Equation for the dynamics of interacting semiflexible polymer chains, undergoing slow cooperative dynamics. The calculated Gaussian intermolecular center-of-mass and monomer potentials, wich enter the GLE,…

Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…

The third-order response lies at the heart of simulating and interpreting nonlinear spectroscopies ranging from two dimensional infrared (2D-IR) to 2D electronic (2D-ES), and 2D sum frequency generation (2D-SFG). The extra time and…

Coarse graining (CG) is an important task for efficient modeling and simulation of complex multi-scale systems, such as the conformational dynamics of biomolecules. This work presents a projection-based coarse-graining formalism for general…

This paper investigates the problem of efficient computation of physically consistent multi-contact behaviors. Recent work showed that under mild assumptions, the problem could be decomposed into simpler kinematic and centroidal dynamic…

We study the dynamics and conformation of polymers composed by active monomers. By means of Brownian dynamics simulations we show that when the direction of the self-propulsion of each monomer is aligned with the backbone, the polymer…

Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these…

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,…

We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…

G-protein-coupled receptors (GPCRs), primary targets for over one-third of approved therapeutics, rely on intricate conformational transitions to transduce signals. While Molecular Dynamics (MD) is essential for elucidating this…

Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…

We investigated the static and dynamic properties of a Rouse ring polymer modified by introducing an effective, spherically symmetric, attractive potential of entropic nature and a memory function describing the effect of dynamic…

An approach, recently proposed to calculate the nucleon generalized parton distributions (GPDs) in a constituent quark model (CQM) scenario, in which the constituent quarks are taken as complex systems, is used to obtain helicity-dependent…

Geopolymers are an emerging class of binding materials used in sustainable cements, concretes, and composites. However, despite growing research, the lack of standardised processes and stability analyses for formulating activator solutions…

It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics…

Modern implementations of path integral molecular dynamics (PIMD) simulations of distinguishable particles frequently make use of high order factorization schemes for the Boltzmann operator to expedite convergence of equilibrium averages.…

I describe a generalization of the hybrid Monte Carlo (HMC) algorithm in which the molecular dynamics (MD) steps utilize Nambu generalized Hamiltonian dynamics. Characterized by multiple Hamiltonian functions, this formalism allows me to…

This work introduces a method for generating generalized structures of amorphous polymers using simulated polymerization and molecular dynamics equilibration, with a particular focus on amorphous polymers. The techniques and algorithms used…