Related papers: Force Feedback Effects on Single Molecule Hopping …
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
Current dual-frequency magneto-optical traps for ultracold molecules are plagued by sub-Doppler heating effects, making them vastly inferior to standard atomic MOTs. Here we demonstrate theoretically that the sub-Doppler effects in such a…
We investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states)…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
We investigate the dynamics of a single-ended N-state molecular zipper based on a model originally proposed by Kittel. The molecule is driven unidirectionally towards the completely unzipped state with increasing time t, where the driving…
The Hamiltonian Mean Field (HMF) model has a low-energy phase where $N$ particles are trapped inside a cluster. Here, we investigate some properties of the trapping/untrapping mechanism of a single particle into/outside the cluster. Since…
We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
We simulate the capture process of MgF molecules into a frequency-chirped molecular MOT. Our calculations show that by chirping the frequency, the MOT capture velocity is increased by about of factor of 4 to 80 m/s, allowing for direct…
We use an optimal control protocol to cool one mode of the center of mass motion of an optically levitated nanoparticle. The feedback technique relies on exerting a Coulomb force on a charged particle with a pair of electrodes and follows…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
We present results of molecular dynamics (MD) simulations for a non-entangled polymer melt confined between two completely smooth and repulsive walls, interacting with inner particles via the potential $U_{\rm wall}\myeq (\sigma/z)^9$,…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
We study a coarse-grained model for a water monolayer that cannot crystallize due to the presence of confining interfaces, such as protein powders or inorganic surfaces. Using both Monte Carlo simulations and mean field calculations, we…
We stabilize resistance of melt-quenched amorphous Ge2Sb2Te5 (a-GST) phase change memory (PCM) line cells by substantially accelerating resistance drift and bringing it to a stop within a few minutes with application of high electric field…
Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
One-dimensional non-equilibrium models of particles subjected to a coagulation-diffusion process are important in understanding non-equilibrium dynamics, and fluctuation-dissipation relation. We consider in this paper transport properties…