Related papers: Collapse and coexistence for a molecular braid wit…
We consider the driven dynamics of a probe particle moving through an assembly of particles with competing long-range repulsive and short-range attractive interactions, which form crystal, stripe, labyrinth, and bubble states as the ratio…
How frictional effects emerge at the microscopic level in particulate materials remains a challenging question, particularly in systems subject to thermal fluctuations due to the transient nature of interparticle contacts. Here, we directly…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
Mechanical forces influence the development and behavior of biological tissues. In many situations these forces are exerted or resisted by elastic compliant structures such as the own-tissue cellular matrix or other surrounding tissues.…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
We study the influence of atomic interactions on quantum simulations in momentum-space lattices (MSLs), where driven transitions between discrete momentum states mimic transport between sites of a synthetic lattice. Low energy atomic…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
The motion of cells in tissues is an ubiquitous phenomenon. In particular, in monolayered cell colonies in vitro, pronounced collective behavior with swirl-like motion has been observed deep within a cell colony, while at the same time, the…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
A binary mixture of super-paramagnetic colloidal particles is confined between glass plates such that the large particles become fixed and provide a two-dimensional disordered matrix for the still mobile small particles, which form a fluid.…
We evaluate the elasticity of arrested short-ranged attractive colloids by combining an analytically solvable elastic model with a hierarchical arrest scheme into a new approach, which allows to discriminate the microscopic (primary…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic…
We analyze a bubble forming system composed of particles with competing long range repulsive and short range attractive interactions driven over a quasi-one-dimensional periodic substrate. We find various pinned and sliding phases as a…
The effective interaction between charged colloidal particles confined between two planar like-charged walls is investigated using computer simulations of the primitive model describing asymmetric electrolytes. In detail, we calculate the…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in…
Particles of low velocity, travelling without dissipation in a superfluid, can interact and emit sound when they collide. We propose a minimal model in which the equations of motion of the particles, including a short-range repulsive force,…