Related papers: Improved Approximations for Some Polymer Extension…
We consider the force on the end of a polymer chain being pulled through a network at velocity $v$, using computer simulations. We develop algorithms for measuring the force on the end of the chain using lattice models of polymers. Our…
We consider a class of elasticity equations in ${\mathbb R}^d$ whose elastic moduli depend on $n$ separated microscopic scales, are random and expressed as a linear expansion of a countable sequence of random variables which are…
We study three quasicontinuum approximations of a lattice model for crack propagation. The influence of the approximation on the bifurcation patterns is investigated. The estimate of the modeling error is applicable to near and beyond…
We demonstrate that a semiflexible bundle of wormlike chains exhibits a state-dependent bending stiffness that alters fundamentally its scaling behavior with respect to the standard wormlike chain. We explore the equilibrium conformational…
We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe…
Systems under external confinement and constraints often show interesting properties. In this thesis, we study some systems under external confinement. We begin by finding out the probability distribution of end-to-end separation of a Worm…
We introduce a compact cluster expansion method, constructed over Jacobi and Legendre polynomials, to generate highly accurate and flexible machine-learning force fields. The constituent many-body contributions are separated, interpretable…
The derivation of Marko and Siggia's interpolation formula for the force-extension relation of the Worm-Like Chain Model (C.Bustamante, J.F.Marko, E.D.Siggia, and S.Smith, Science Vol.265, p.1599 (1994); J.F.Marko and E.D.Siggia,…
The wormlike chain model of stiff polymers is a nonlinear $\sigma$-model in one spacetime dimension in which the ends are fluctuating freely. This causes important differences with respect to the presently available theory which exists only…
We prove an almost sure CLT for spatial extension of stretched (meaning subject to a non-zero pulling force) polymers at very weak disorder in all dimensions d+1 larger than or equal to 4.
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
This paper derives a posteriori error estimators for the nonlinear first-order optimality conditions associated with the Frank-Oseen elastic free-energy model of nematic and cholesteric liquid crystals, where the required unit-length…
We study theoretically the entropic elasticity of a semi-flexible polymer, such as DNA, confined to two dimensions. Using the worm-like-chain model we obtain an exact analytical expression for the partition function of the polymer pulled at…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
We propose a method for improving approximate inference methods that corrects for the influence of loops in the graphical model. The method is applicable to arbitrary factor graphs, provided that the size of the Markov blankets is not too…
We study the swelling of a flexible linear chain composed of active particles by analytical theory and computer simulation. Three different situations are considered: a free chain, a chain confined to an external harmonic trap, and a chain…
The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that…
Using molecular dynamic simulation, we study the stretching of an adsorbed homopolymer in a poor solvent with one end held at a distance $z_e$ from the substrate. We measure the vertical force $f$ on the end of the chain as a function of…
Polymer models describing the statistics of biomolecules under confinement have applications to a wide range of single molecule experimental techniques and give insight into biologically relevant processes {\em{in vivo}}. In this paper, we…
We construct a systematic mean-field-improved coupling constant and quark loop expansion for corrections to the valence (quenched) approximation to vacuum expectation values in the lattice formulation of QCD. Terms in the expansion are…