Related papers: Single molecule simulations in complex geometries …
The diffusion of finite-size hard-core interacting particles in two- or three-dimensional confined domains is considered in the limit that the confinement dimensions become comparable to the particle's dimensions. The result is a nonlinear…
Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five…
Molecular motors interacting with cytoskeletal filaments undergo peculiar random walks consisting of alternating sequences of directed movements along the filaments and diffusive motion in the surrounding solution. An ensemble of motors is…
Dynamical polydispersity in single-particle properties, for example a fluctuating particle size, shape, charge density, etc., is intrinsic to responsive colloids (RCs), such as biomacromolecules or microgels, but is typically not resolved…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Single polymer dynamics offers a powerful approach to study molecular-level interactions and dynamic microstructure in materials. Direct visualization of single chain dynamics has uncovered new ideas regarding the rheology and…
Understanding the quantum dynamics of strongly coupled molecule-cavity systems remains a significant challenge in molecular polaritonics. This work develops a comprehensive self-consistent model simulating electromagnetic interactions of…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
A systematic understanding of the evolution and growth dynamics of invasive solid tumors in response to different chemotherapy strategies is crucial for the development of individually optimized oncotherapy. Here, we develop a hybrid…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
In this paper we consider the mathematical relationship between nonlocal interactions of convolution type and multiple diffusive substances in high dimensions. Motivated by that the nonlocal evolution equations reproduce similar patterns to…
Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…
Various biological cells secrete diffusing chemical compounds into their environment for communication purposes. Secretion usually takes place over the cell membrane in a spatially heterogeneous manner. Mathematical models of these…
In this work we study the diffusion mechanisms in lithium disilicate melt using molecular dynamics simulation, which has an edge over other simulation methods because it can track down actual atomic rearrangements in materials once a…
The propagation of signalling molecules within cellular networks is affected by network topology, but also by the spatial arrangement of cells in the networks. Understanding the collective reaction--diffusion behaviour in space of signals…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
We present a study of the spatial correlation functions of a one-dimensional reaction-diffusion system in both equilibrium and out of equilibrium. For the numerical simulations we have employed the Gillespie algorithm dividing the system in…