Related papers: Entropic Penalties in Circular DNA Assembly
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
Dislocation nucleation is essential to our understanding of plastic deformation, ductility and mechanical strength of crystalline materials. Molecular dynamics simulation has played an important role in uncovering the fundamental mechanisms…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Topological insulators are promising for spintronics and related technologies due to their spin-momentum-locked edge states, which are protected by time-reversal symmetry. In addition to the unique fundamental physics that arises in these…
The relaxation dynamics of a polymer wound around a fixed obstacle constitutes a fundamental instance of polymer with twist and torque and it is of relevance also for DNA denaturation dynamics. We investigate it by simulations and Langevin…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
We present a novel way of modeling common envelope evolution in binary and few-body systems. We consider the common envelope inspiral as driven by a drag force with a power-law dependence in relative distance and velocity. The orbital…
We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a…
We provide a framework for a perturbative evaluation of the reduced density matrix. The method is based on a path integral in the analytically continued spacetime. It suggests an alternative to the holographic and `standard' replica trick…
The state space of a polymer molecule is analysed. We show how the size of the state space can be reduced on the basis of symmetry. In the reduced state space, the probability of a new state (termed below as class) is equal to the number of…
Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of…
We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from…
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
A binary system of classical charged particles interacting through a dipole repulsive potential and confined in a two-dimensional hardwall trap is studied by Brownian dynamics simulations. We found that the presence of small particles…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…