相关论文: Dimension-free path-integral molecular dynamics wi…

Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…

Dimensional analysis is one of the most fundamental tools for understanding physical systems. However, the construction of dimensionless variables, as guided by the Buckingham-$\pi$ theorem, is not uniquely determined. Here, we introduce…

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…

We study the numerical integration problem for functions with infinitely many variables. The function spaces of integrands we consider are weighted reproducing kernel Hilbert spaces with norms related to the ANOVA decomposition of the…

We develop a family of stabilized backward differentiation formula (sBDF) schemes of orders one through four for semilinear parabolic equations. The proposed methods are designed to achieve three properties that are rarely available…

Centroid molecular dynamics (CMD) incorporates nuclear quantum statistics into the calculation of vibrational spectra. However, when performed in Cartesian coordinates, CMD shows unphysical artifacts in certain vibrational bands, known as…

We study a model of flexible block copolymers (BCPs) in which there is an enlthalpic preference for local alignment, among like-block segments. We describe a generalization of the self-consistent field theory (SCFT) of flexible BCPs to…

Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…

Path integral quantum Monte Carlo (PIMC) is a method for estimating thermal equilibrium properties of stoquastic quantum spin systems by sampling from a classical Gibbs distribution using Markov chain Monte Carlo. The PIMC method has been…

We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition…

In this paper we present a Path Integral Monte Carlo (PIMC) simulation of the orthorhombic phase of crystalline polyethylene, using an explicit atom force field with unconstrained bond lengths and angles. This work represents a quantum…

In contrast to ordinary stochastic differential equations (SDEs), the numerical simulation of McKean-Vlasov stochastic differential equations (MV-SDEs) requires approximating the distribution law first. Based on the theory of propagation of…

We present a comprehensive new framework for handling biologically accurate models of molecular evolution. This model provides a systematic framework for studying models of molecular evolution that implement heterogeneous rates,…

An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…

Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…

We present simulations on a binary blend of bead-spring polymer chains. The introduction of monomer size disparity yields very different relaxation times for each component of the blend. Competition between two different arrest mechanisms,…

In this paper we establish a new efficient method for simulating polymer-solvent systems which combines a lattice Boltzmann approach for the fluid with a continuum molecular dynamics (MD) model for the polymer chain. The two parts are…

The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…

Excited-state molecular dynamics (ESMD) simulations near conical intersections (CIs) pose significant challenges when using machine learning potentials (MLPs). Although MLPs have gained recognition for their integration into mixed…

Gibbs samplers are popular algorithms to approximate posterior distributions arising from Bayesian hierarchical models. Despite their popularity and good empirical performances, however, there are still relatively few quantitative results…