Related papers: DNA Elasticity : Topology of Self-Avoidance
The relation between force and stretch in the worm-like chain model of entropic elasticity is examined. Although no closed-form expression is valid for all values of forcing, solutions in the form of asymptotic series can be obtained under…
We propose a microscopic picture for understanding the nonlinear rheology of supercooled liquids with soft-repulsive potentials. Based on Brownian dynamics simulations of supercooled charge-stabilized colloidal suspensions, our analysis…
Constructing systems that exhibit time-scales much longer than those of the underlying components, as well as emergent dynamical and collective behavior, is a key goal in fields such as synthetic biology and materials self-assembly.…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
We analyze the phase behavior of lyotropic nematic liquid crystals in the self-organizing flow, viz. so called active nematics (AN). Their elastic properties are mutually caused by evolution of topological defects (for instance,…
Using the Wherl entropy, we study the delocalization in phase-space of energy eigenstates in the vicinity of avoided crossing in the Lipkin-Meshkov-Glick model. These avoided crossing, appearing at intermediate energies in a certain…
Despite intense interest in realizing topological phases across a variety of electronic, photonic and mechanical platforms, the detailed microscopic origin of topological behavior often remains elusive. To bridge this conceptual gap, we…
We study the mechanics and statistical physics of dislocations interacting on cylinders, motivated by the elongation of rod-shaped bacterial cell walls and cylindrical assemblies of colloidal particles subject to external stresses. The…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
The effect of disorder on flux lattices at equilibrium is studied quantitatively in the absence of free dislocations using both the Gaussian variational method and the renormalization group. Our results for the mean square relative…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
The application of a sufficiently strong strain perpendicular to the pitch axis of a monodomain cholesteric elastomer unwinds the cholesteric helix. Previous theoretical analyses of this transition ignored the effects of Frank elasticity…
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…
In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent…
Neural network models capable of storing memory have been extensively studied in computer science and computational neuroscience. The Hopfield network is a prototypical example of a model designed for associative, or content-addressable,…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
We introduce a self-consistent theory of mobility edges in nearest-neighbour tight-binding chains with quasiperiodic potentials. Demarcating boundaries between localised and extended states in the space of system parameters and energy,…
Motivated by a question about the sensitivity of knots' diffusive motion to the actual sequence of nucleotides placed on a given DNA, here we study a simple model of a sequence-reading diffusion on a stretched chain with a frozen sequence…
Coupling between axial and torsional degrees of freedom often modifies the conformation and expression of natural and synthetic filamentous aggregates. Recent studies on chiral single-walled carbon nanotubes and B-DNA reveal a reversal in…
We propose and analyze a simple variational model for dislocations at semi-coherent interfaces. The energy functional describes the competition between two terms: a surface energy induced by dislocations that compensate the lattice misfit…