Related papers: Extension of the simulation code ACAT to treat rea…
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate between those two states. Atomic coordinates of a macromolecule…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
A central concern of molecular dynamics simulations are the potential energy surfaces that govern atomic interactions. These hypersurfaces define the potential energy of the system, and have generally been calculated using either predefined…
This paper introduces SiQAD, a computer-aided design tool enabling the rapid design and simulation of atomic silicon dangling bond quantum dot patterns capable of computational logic. Several simulation tools are included, each able to…
The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry,…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
In this paper we study the realization of lattice models in mixtures of atomic and dipolar molecular quantum gases. We consider a situation where polar molecules form a self-assembled dipolar lattice, in which atoms or molecules of a second…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
A model for the simulation of orientational effects in straight and bent periodic atomic structures is presented. The continuum potential approximation has been adopted.The model allows the manipulation of particle trajectories by means of…
We study cavity optomechanics of a mixture of ultracold atoms with tunable nonlinear collisions. We show that atomic collisions provide linear couplings between fictitious condensate oscillators, leading to possibilities of achieving a…
Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structural changes, molecular recognition, transmembrane transport, and functional mechanisms. However, its practical bottleneck lies not only in software…
We formulate and analyze an optimization-based Atomistic-to-Continuum (AtC) coupling method for problems with point defects. Near the defect core the method employs a potential-based atomistic model, which enables accurate simulation of the…
Representing a strongly interacting multi-particle wave function in a finite product basis leads to errors. Simple rescaling of the contact interaction can preserve the low-lying energy spectrum and long-wavelength structure of wave…
We review achievements made in recent years in the field of numerical modeling of ultra-relativistic projectiles propagation in oriented crystals, radiation emission and related phenomena. This topic is highly relevant to the problem of…
The ever-increasing power of supercomputers coupled with highly scalable simulation codes have made molecular dynamics an indispensable tool in applications ranging from predictive modeling of materials to computational design and discovery…
Continual Test-Time Adaptation (CTTA) is proposed to migrate a source pre-trained model to continually changing target distributions, addressing real-world dynamism. Existing CTTA methods mainly rely on entropy minimization or…
A new class of matching condition between the atomistic and continuum regions is presented for the multi-scale modeling of crystals. They ensure the accurate passage of large scale information between the atomistic and continuum regions and…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are…