Related papers: A concise introduction to molecular dynamics simul…
Videos of the molecular dynamics simulations of a colliding hard disk reactive medium. A simple event-driven algorithm is used to simulate these colliding hard disks allowing for the study of detonations at the microscopic level. This video…
We present a pedagogical work-in-progress. This textbook aims to introduce Hilbert space representations for quantum and classical dynamics, outlining the mathematical foundations, practical guidance, and Python implementation of dynamical…
The interaction of mass-selected atomic clusters and nanoparticles with surfaces attracts strong interest in view of fundamental research and technological applications. Understanding dynamics of the deposition process is important for…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
We use functional, Fr\'echet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
We create a Python GUI scripting interface working under Windows in addition to (UNIX/Linux). The GUI has been built around the Python open-source programming language. We use the Python's GUI library that so called Python Mega Widgets…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
The simulation of high-energy physics collision events is a key element for data analysis at present and future particle accelerators. The comparison of simulation predictions to data allows looking for rare deviations that can be due to…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
Simulations at the atomic scale provide a direct and effective way to understand the mechanical properties of materials. In the regime of classical mechanics, simulations for the thermodynamic properties of metals and alloys can be done by…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
We present a rigorous derivation of classical molecular dynamics (MD) from quantum molecular dynamics (QMD) that applies to the standard Hamiltonians of molecular physics with Coulomb interactions. The derivation is valid away from possible…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
Modified Newtonian dynamics (MOND) is a promising alternative to dark matter. To further test the theory, there is a need for fluid- and particle-dynamics simulations. The force in MOND is not a direct particle-particle interaction, but…