Related papers: Atomistic study of macroscopic analogs to short ch…
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…
We study the continuous time quantum walk of a single particle (initially localized at a single site) on a one-dimensional spatial lattice with complex nearest neighbour and next-nearest neighbour hopping amplitudes. Complex couplings lead…
In a variety of situations, isolated polymer molecules are found in a vacuum and here we examine their properties. Angular momentum conservation is shown to significantly alter the average size of a chain and its conservation is only broken…
The ability to manipulate single atoms has opened up the door to constructing interesting and useful quantum structures from the ground up. On the one hand, nanoscale arrangements of magnetic atoms are at the heart of future quantum…
We use complete enumeration and Monte Carlo techniques to study two-dimensional self-avoiding polymer chains with quenched ``charges'' $\pm 1$. The interaction of charges at neighboring lattice sites is described by $q_i q_j$. We find that…
Jumps between neighboring minima in the energy landscape of both homopolymeric and heteropolymeric chains are numerically investigated by determining the average escape time from different valleys. The numerical results are compared to the…
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two dimensional system. Specifically, we analyse the polymer looping properties versus the SPP activity and…
A variational approach, based on a discrete representation of the chain, is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic…
We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated…
In this Letter, we study the collective behaviour of a large number of self-propelled microswimmers immersed in a fluid. Using unprecedently large-scale lattice Boltzmann simulations, we reproduce the transition to bacterial turbulence. We…
We introduce a general numerical method to compute dynamics and multi-time correlations of chains of quantum systems, where each system may couple strongly to a structured environment. The method combines the process tensor formalism for…
We consider the lattice model for an ideal-linear polymer chain to mimic the conformations of the semi-flexible homo-polymer chain. The polymer chain is assumed to confine in the fairly small area, such that the flexible chain conformations…
We investigate both numerically and analytically the effect of strong disorder on the large scale properties of the hyperbolic equations for stresses proposed in \protect\cite{bcc,wcc}. The physical mechanism that we model is the local…
We study the interplay of intrinsic-electronic and environmental factors on long-range charge transport across molecular chains with up to $N\sim 80$ monomers. We describe the molecular electronic structure of the chain with a tight-binding…
We deduce the qualitative phase diagram of a long flexible neutral polymer chain immersed in a poor solvent near an attracting surface using phenomenological arguments. The actual positions of the phase boundaries are estimated numerically…
A lattice model of the directed self-avoiding walk is used to estimate the possibility on the formation of an infinitely long linear semi-flexible copolymer chain. The copolymer chain is assumed to composed of four different types of the…
Histogram-reweighting grand canonical Monte Carlo simulations are used to obtain the critical properties of lattice chains composed of solvophilic and solvophobic monomers. The model is a modification of one proposed by Larson \emph{et al.}…
We investigate the properties of a harmonic chain in contact with a thermal bath at one end and subjected, at its other end, to a periodic force. The particles also undergo a random velocity reversal action, which results in a finite heat…