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In a topological description of elementary matter proposed by Bilson-Thompson, the leptons and quarks of a single generation, together with the electroweak gauge bosons, are represented as elements of the framed braid group of three…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
We explore the zero-temperature behavior of an assembly of bosons interacting through a zero-range, attractive potential. Because the two-body interaction admits a bound state, the many-body model is best described by a Hamiltonian that…
In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the…
We present a numerical study of the dynamics of a non-ideal fluid subject to a density-dependent pseudo-potential characterized by a hierarchy of nested attractive and repulsive interactions. It is shown that above a critical threshold of…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…
A remarkable property of quantum mechanics in two-dimensional (2D) space is its ability to support "anyons," particles that are neither fermions nor bosons. Theory predicts that these exotic excitations can be realized as bound states…
We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength $\kappa$ of the local…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range…
We investigate the dynamics of colloids at a fluid interface driven by attractive capillary interactions. At submillimeter length scales, the capillary attraction is formally analogous to two-dimensional gravity. In particular it is a…
A crystal lattice, when confined to the surface of a cylinder, must have a periodic structure that is commensurate with the cylinder circumference. This constraint can frustrate the system, leading to oblique crystal lattices or to…
Computational methods for designing interactions between colloidal particles that induce self-assembly have received much attention for their promise to discover tailored materials. However, it often remains a challenge to translate…
In this paper, we theoretically study the electrostatic interaction between a pair of identical colloids with constant surface potentials sitting in close vicinity of each other at a fluid interface. By employing a simplified yet reasonable…
We introduce a model of friction between two contacting (stationary or co-sliding) rough surfaces, each comprising a random ensemble of polydisperse hemispherical bumps. In the simplest version of the model, the bumps experience on contact…
We study the mechanics of a reversible decohesion (unzipping) of an elastic layer subjected to quasi-static end-point loading. At the micro level the system is simulated by an elastic chain of particles interacting with a rigid foundation…
Lifetimes of bound states of protein complexes or biomolecule folded states typically decrease when subject to mechanical force. However, a plethora of biological systems exhibit the counter-intuitive phenomenon of catch bonding, where…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
Attractive colloidal particles can form a disordered elastic solid or gel when quenched into a two-phase region, if the volume fraction is sufficiently large. When the interactions are comparable to thermal energies the stress-bearing…
We use Molecular Dynamics simulations to study attractive interactions and the underlying ionic correlations between parallel like-charged rods in the absence of additional salt. For a generic bulk system of rods we identify a reduction of…