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Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
Extremely fast rotating molecules carrying significantly more energy in their rotation than in any other degree of freedom are known as "super rotors". It has been speculated that super rotors may exhibit a number of unique properties.…
Stochastic kinetic models of genetic expression are able to describe protein fluctuations. A comparative study of the canonical and a feedback model is given here by using stochastic simulation methods. The feedback model is skeleton model…
Using both atomistic and particle-based simulations, we investigate the current-driven dynamics of skyrmions on two-dimensional periodic substrates when there are multiple skyrmions per substrate minimum. At zero drive, the system forms…
Magnetic nanomaterials are considered, formed by magnetic nanomolecules with high spins. The problem of spin reversal in these materials is analyzed, which is of interest for the possible use of such materials for quantum information…
Most models designed to study the bidirectional movement of cargos as they are driven by molecular motors rely on the idea that motors of different polarities can be coordinated by external agents if arranged into a motor-cargo complex to…
A minimal design for a molecular swimmer is proposed that is a based on a mechanochemical propulsion mechanism. Conformational changes are induced by electrostatic actuation when specific parts of the molecule temporarily acquire net…
The collective behavior of chemically propelled sphere-dimer motors made from linked catalytic and noncatalytic spheres in a quasi-two-dimensional confined geometry is studied using a coarse-grained microscopic dynamical model. Chemical…
Current reversal is an intriguing phenomenon that has been central to recent experimental and theoretical investigations of transport based on ratchet mechanism. By considering a system of two interacting ratchets, we demonstrate how the…
A minimal model for coherent transport through a donor/acceptor molecular junction is presented. The two donor and acceptor sites are described by single levels energetically separated by an intramolecular tunnel barrier. In the limit of…
We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very…
We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. The theoretical results on the…
This study conducts a comprehensive investigation into the reversal mechanism of magnetic vortex cores in a nanopillar system composed of two coupled ferromagnetic dots under zero magnetic field conditions. The research employs a…
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…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of…
We analyze here the minimal conditions for directional motion (net flow in phase space) of a molecular motor placed on a mirror-symmetric environment and driven by a center-symmetric and time-periodic force field. The complete…
The appealing feature of molecular electronics is the possibility of exploiting functionality built within a single molecule. This functionality can be employed, for example, for sensing or switching purposes. Thus, ideally, the associated…
This work is part of an effort to understand the neural basis for our visual system's ability, or failure, to accurately track moving visual signals. We consider here a ring model of spiking neurons, intended as a simplified computational…