Related papers: A Three-State Thermodynamically Consistent Cross-B…
A quantitative model of the mobility of functionalized particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles anchored through…
The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a phosphate transfer, and then the…
Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the…
The glass transition is considered within two toys models, a mean field spin glass and a directed polymer in a correlated random potential. In the spin glass model there occurs a dynamical transition, where the system condenses in a state…
We study the electrical conductance $G$ and the thermopower $S$ of single-molecule junctions, and reveal signatures of different transport mechanisms: off-resonant tunneling, on-resonant coherent (ballistic) motion, and multi-step hopping.…
We present results of a simulation study of inelastic hard-disks vibrated in a vertical container. An Event-Driven Molecular Dynamics method is developed for studying the onset of convection. Varying the relevant parameters (inelasticity,…
We simulate the compression of a two-component Lennard-Jones liquid at a variety of constant temperatures using a molecular dynamics algorithm in an isobaric-isothermal ensemble. The viscosity of the liquid increases with pressure,…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Lower temperature leads to a higher probability of visiting low-energy states. This intuitive belief underlies most physics-inspired strategies for addressing hard optimization problems. For instance, the popular simulated annealing (SA)…
We study swelling and structural properties of ionic microgel suspensions within a comprehensive coarse-grained model that combines the polymeric and colloidal natures of microgels as permeable, compressible, charged spheres governed by…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
We study three different experiments that involve dry friction and periodic driving, and which employ both single and many-particle systems. These experimental set-ups, besides providing a playground for investigation of frictional effects,…
The high-pressure dynamics of a computer-modeled silica melt is studied in the framework of the mode-coupling theory of the glass transition (MCT) using static-structure input from molecular-dynamics (MD) computer simulation. The theory…
Stochastic Beta Relaxation (SBR) is a model for the dynamics of glass- forming liquids close to the glass transition singularity of the idealized mode- coupling theory (MCT) that has been derived from generic MCT-like theories by applying…
In the present contribution, we derive from kinetic theory a unified fluid model for multicomponent plasmas by accounting for the electromagnetic field influence. We deal with a possible thermal nonequilibrium of the translational energy of…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
We develop an energy-landscape based elasto-plastic model to understand the behaviour of amorphous solids under uniform and cyclic shear. Amorphous solids are modeled as being composed of mesoscopic sub-volumes, each of which may occupy…
We discuss the stick-slip motion of an elastic block sliding along a rigid substrate. We argue that for a given external shear stress this system shows a discontinuous nonequilibrium transition from a uniform stick state to uniform sliding…
The thermodynamic driving force in the self-assembly of the secondary structure of a class of donor-acceptor oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…