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The task of multi-dimensional numerical integration is frequently encountered in physics and other scientific fields, e.g., in modeling the effects of systematic uncertainties in physical systems and in Bayesian parameter estimation.…
Motivation: Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful…
In order to illustrate the adaptation of traditional continuum numerical techniques to the study of complex network systems, we use the equation-free framework to analyze a dynamically evolving multigraph. This approach is based on coupling…
For molecular dynamics simulations of hard particles, we define dynamic neighbors as the distinct particles that collide with a given reference one during a specific time interval. This definition allows us to determine the distribution of…
Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of…
Microbiomes are a vital part of the human body, engaging in tasks like food digestion and immune defense. Their structure and function must be understood in order to promote host health and facilitate swift recovery during disease. Due to…
Crystallization, a fundamental phase transition process governing material formation in natural and industrial contexts, involves the spontaneous emergence of long-range structural order from disordered phases. This long-range periodicity…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
The long-time behavior of many complex molecular systems is often governed by slow relaxation dynamics that can be described by a few reaction coordinates referred to as collective variables (CVs). However, identifying CVs hidden in a…
Machine-learned interatomic potentials have revolutionized molecular dynamics simulations by providing quantum-mechanical accuracy at empirical-potential speeds. The graphics processing unit molecular dynamics (GPUMD) package, featuring the…
Structures of metal nanoparticles (NPs) significantly influence their catalytic reactivities. Recent in situ experimental observations of dramatic structural changes in NPs have underscored the need to establish a dynamic structure-property…
In molecular dynamics simulations, rare events, such as protein folding, are typically studied using enhanced sampling techniques, most of which are based on the definition of a collective variable (CV) along which acceleration occurs.…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
Background: Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides…
Developing effective descriptions of the microscopic dynamics of many physical phenomena can both dramatically enhance their computational exploration and lead to a more fundamental understanding of the underlying physics. Previously, an…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…