Related papers: Single-molecule motion control
We present a systematic study of the self-diffusion coefficient for a fluid of particles interacting via the square-well pair potential by means of molecular dynamics simulations in the canonical (N,V,T) ensemble. The discrete nature of the…
Biomolecular condensates provide distinct chemical environments, which control various cellular processes. The diffusive dynamics and chemical kinetics inside phase-separated condensates can be studied experimentally by fluorescently…
We report on the short-time dynamics in colloidal mixtures made up of monomers and dimers highly confined between two glass-plates. At low concentrations, the experimental measurements of colloidal motion agree well with the solution of the…
Understanding molecular state evolution is central to many disciplines, including molecular dynamics, precision measurement, and molecule-based quantum technology. Details of the evolution are obscured when observing a statistical ensemble…
Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion…
Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME), can simulate for extended spatial and temporal…
We consider the diffusion and spreading of chainlike molecules on solid surfaces. We first show that the steep spherical cap shape density profiles, observed in some submonolayer experiments on spreading polymer films, imply that the…
Single molecules are nanoscale thermodynamic systems with few degrees of freedom. Thus, the knowledge of their entropy can reveal the presence of microscopic electron transfer dynamics, that are difficult to observe otherwise. Here, we…
Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and…
In the last decade, the atomically focused beam of a scanning transmission electron microscope (STEM) was shown to induce a broad set of transformations of material structure, open pathways for probing atomic-scale reactions and…
We study the dynamics of a single-particle wave packet on a one-dimensional lattice subject to periodic random phase kicks with finite spatial correlation length. This stroboscopic setting provides a controllable model of dephasing in…
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the…
Natural phenomena frequently involve a very large number of interacting molecules moving in confined regions of space. Cellular transport by motor proteins is an example of such collective behavior. We derive a deterministic compartmental…
The ability to make electrical contact to single molecules creates opportunities to examine fundamental processes governing electron flow on the smallest possible length scales. We report experiments in which we controllably stretch…
A stochastic differential equation that describes the dynamics of single-domain magnetic particles at any temperature is derived using a classical formalism. The deterministic terms recover existing theory and the stochastic process takes…
The bulk and surface dynamics of Cu50Zr50 metallic glass were studied using classical molecular dynamics (MD) simulations. As the alloy undergoes cooling, it passes through liquid, supercooled, and glassy states. While bulk dynamics showed…
We present a new method for simulating crystal growth by energetic beam deposition. The method combines a Kinetic Monte-Carlo simulation for the thermal surface diffusion with a small scale molecular dynamics simulation of every single…
This work presents a general thermodynamic approach to describe particle diffusion on a lattice, a model used to study transport processes in solids and on surfaces. By treating each lattice site as an open thermodynamic system, the effects…
The diffusion of a Janus rod-shaped nanoparticle in a dense Lennard-Jones fluid is studied using molecular dynamics (MD) simulations. The Janus particle is modeled as a rigid cylinder whose atoms on each half-side have different interaction…
Microscopic models of reaction-diffusion processes on the cell membrane can link local spatiotemporal effects to macroscopic self-organized patterns often observed on the membrane. Simulation schemes based on the microscopic lattice method…