Related papers: Lattice stretching bistability and dynamic heterog…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Willis dynamic homogenization theory revealed that the effective linear momentum of elastic composites is coupled to their effective strain. % This result, which is partially due to asymmetry at the subwavelength scale, implies that…
Surfaces and structures capable of multiple stable configurations have attracted growing interest for on-demand shape morphing. In this work, we consider an elastic compliant plate coupled to a two-dimensional foundation comprising an array…
Using an analytically tractable lattice model for reaction-diffusion processes of hard-core particles we demonstrate that under nonequilibrium conditions phase coexistence may arise even if the system is effectively one-dimensional as e.g.…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
Cell-fate transition can be modeled by ordinary differential equations (ODEs) which describe the behavior of several molecules in interaction, and for which each stable equilibrium corresponds to a possible phenotype (or 'biological…
This research paper presents a 2D numerical model of an electrokinetic T-junction micromixer based on the stretching and folding theory presented by Ottino. Particle deformation was considered by simulating 2 $\mu m$ massless particles as…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
When two-dimensional van der Waals materials are stacked to build heterostructures, moir\'e patterns emerge from twisted interfaces or from mismatch in lattice constant of individual layers. Relaxation of the atomic positions is a direct,…
We consider a prototypical dynamical lattice model, namely, the discrete nonlinear Schroedinger equation on nonsquare lattice geometries. We present a systematic classification of the solutions that arise in principal six-lattice-site and…
The connection between domain relaxations at individual scales and the collective heterogeneous response in non-equilibrium systems is a topic of profound interest in recent times. In a model sys- tem of constantly driven oppositely charged…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
We study spatial correlations and structure factors in a three-state stochastic lattice gas, consisting of holes and two oppositely ``charged'' species of particles, subject to an ``electric'' field at zero total charge. The dynamics…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
Dynamical frictional phenomena are studied theoretically in a two-chain model with incommensurate structure. A perturbation theory with respect to the interchain interaction reveals the contributions from phonons excited in each chain to…
We study a one-dimensional system of strongly correlated bosons on a dynamical lattice. To this end, we extend the standard Bose-Hubbard Hamiltonian to include extra degrees of freedom on the bonds of the lattice. We show that this minimal…
The aim of this paper is to provide a construction of stationary discrete solitons in an extended one-dimensional Discrete NLS model with non-nearest neighbour interactions. These models, models of the type with long-range interactions were…