Related papers: Interactive molecular dynamics
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 nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
We study colloidal particle dynamics of a model glass system using confocal and fluorescence microscopy as the sample evolves from a hard-sphere glass to a liquid with attractive interparticle interactions. The transition from hard-sphere…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
The ion-electron coupling properties for a ion impurity in an electron gas and for a two component plasma are carried out on the basis of a regularized electron-ion potential removing the short-range Coulomb divergence. This work is largely…
We have extended our recent molecular-dynamic simulations of memristors to include the effect of thermal inhomogeneities on mobile ionic species appearing during operation of the device. Simulations show a competition between an attractive…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
Simulating the dynamics of non-equilibrium matter under extreme conditions lies beyond the capabilities of classical computation alone. Remarkable advances in quantum information science and technology are profoundly changing how we…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…
The properties of a strongly interacting quark plasma are investigated by molecular dynamics method including non-abelian quark-quark potential. Our main goal is to study the thermalization process in this system. We find an interesting…
Machine learned interaction potentials (MLIPs) have become a critical component of large-scale, high-quality simulations for a range of chemical and biochemical systems. Yet, despite their in-distribution accuracy, molecular dynamics…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
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.…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…