Related papers: A constant extension ensembles model of double-str…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
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…
Single-chain elasticity is of fundamental importance in polymer physics, as it underlies many of the unique properties of polymer systems. Recently, there has been interest in characterizing the elastic properties of catenanes, molecular…
Biofilament-motor protein complexes are ubiquitous in biology and drive the transport of cargo vital for many fundamental cellular processes. As they move, motor proteins exert compressive forces on the filaments to which they are attached,…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a…
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible polymers to…
In two-dimensional tissues, such as developing germ layers, pair-wise forces (or active stresses) arise from the contractile activity of the cytoskeleton, with dissipation provided by the three-dimensional surroundings. We show analytically…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
In this thesis we deal with the specific collective phenomena in condensed matter - striped-structures formation. Such structures are observed in different branches of condensed matter physics, like surface physics or physics of…
In development and homeostasis, multi-cellular systems exhibit spatial and temporal heterogeneity in their biochemical and mechanical properties. Nevertheless, it remains unclear how spatiotemporally heterogeneous forces affect the…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
Non-equilibrium random fluctuations of non-thermal nature are a salient feature of active matter. In this work, we consider the collective excitations of active systems at high density, focusing on a one-dimensional chain of elastically…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
We study two cross-linked polymer systems in the strong stretching regime. The first consists of two polymers sharing one endpoint, with the other two endpoints coupled by a harmonic potential. Within the weakly bending approximation, we…
Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…