Related papers: Molecular dynamics study of molecular mobility in …
Tight binding molecular dynamics simulations, with a non orthogonal basis set, are performed to study the fragmentation of carbon fullerenes doped with up to six silicon atoms. Both substitutional and adsorbed cases are considered. The…
Three problems in the statistical mechanics of models for an assembly of molecular motors interacting with cytoskeletal filaments are reviewed. First, a description of the hydrodynamical behaviour of density-density correlations in…
The transport by molecular motors along cytoskeletal filaments is studied theoretically in the presence of static defects. The movements of single motors are described as biased random walks along the filament as well as binding to and…
We show that quantum rotational wavepacket dynamics in molecules can be described by a new system-environment model, which consists of a rotational subsystem coupled to a magnetically tunable spin bath formed by the nuclear spins within the…
Routinely navigating through an ever-changing and unsteady environment, and utilizing chemical energy, molecular motors transport the cell's crucial components, such as neurotransmitters and organelles. They generate force and pull cargo,…
We model the dynamics of a processive or rotary molecular motor using a renewal processes, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation…
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for…
We propose a dynamic mechanism of a molecular machine for energy conversion, by considering a simple model describing the dynamics of two components, the head and the chain. After injection of energy to the head region, the energy is stored…
Quantum molecular dynamics is applied to study the ground state properties of nuclear matter at subsaturation densities. Clustering effects are observed as to soften the equation of state at these densities. The structure of nuclear matter…
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…
We have investigated the effect of molecular shape and charge asymmetry on the translation dynamics of confined hydrocarbon molecules having different shapes but similar kinetic diameters, inside ZSM-5 pores using molecular dynamics…
This paper focuses on studying a model for molecular motors responsible for the bending of the axoneme in the flagella of microorganisms. The model is a coupled system of partial differential equations inspired by J\"ulicher et al. or…
Molecular machines consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an engine that "transduces" input energy into…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
We propose a simple microscopic model of molecular dynamics simulation to study orientational glass in three dimensions. We present simulation results for mixtures of mildly anisotropic particles and spherical impurities. We realize fcc…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
We present a detailed analysis of the molecular kinetics of CHCl$_3$ in a range of temperatures covering the solid and liquid phases. Using nuclear quadrupolar resonance we determine the relaxation times for the molecular rotations in solid…
The flow of motor proteins on a filamental track is modelled within the the framework of lattice driven diffusive systems. Motors, considered as hopping particles, perform a highly biased asymmetric exclusion process when bound to the…