相关论文: Associative bond swaps in molecular dynamics

Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…

Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…

Different approaches have been used in the development of system models. In addition, modeling and simulation approaches are essential for design, analysis, control, and diagnosis of complex systems. This work presents a Simulink model for…

Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body…

In this work, algorithms for the parallel computation of three-body interactions in molecular dynamics are developed. While traversals for the computation of pair interactions are readily available in the literature, here, such traversals…

Materials incorporating covalent adaptive networks (CAN), e.g., vitrimers, have received significant scientific attention due to their distinctive attributes of self-healing and stimuli-responsive properties. Different from direct…

It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…

This paper applies the multibond graph approach for rigid multibody systems to model the dynamics of general spatial mechanisms. The commonly used quick return mechanism which comprises of revolute as well as prismatic joints has been…

Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…

The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…

Three-body recombination processes are treated numerically for a system of three identical bosons. The two-body model potentials utilized support many bound states, a major leap in complexity that produces an intricate structure of sharp…

Here, we study the flow of energy between coupled simulators in a co-simulation environment using the concept of power bonds. We introduce energy residuals which are a direct expression of the coupling errors and hence the accuracy of…

We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions. We start by introducing the formalism of the new…

Non-bonded potentials are included in most force fields and therefore widely used in classical molecular dynamics simulations of materials and interfacial phenomena. It is commonplace to truncate these potentials for computational…

Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…

We consider conformation dynamics of a chain-like three-body bead-spring model, in which three point masses are connected in series by two springs and the conformation is defined by the bending angle between the two springs. Previous…

We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…

Adding dynamic bonds in polymer networks enables reprocessing and recycling; however the full impact of reversible bonds on dynamic network mechanics remains unclear. We build model dynamic networks and observe substantial deviations from…

Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…

Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…