Related papers: Nonlinear excitations in DNA: Aperiodic models vs …
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA.…
We study a nonlinear recombination model from population genetics as a combinatorial version of the Kac-Boltzmann equation from kinetic theory. Following Kac's approach, the nonlinear model is approximated by a mean field linear evolution…
The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…
Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and…
The behavior of the kink in the sine-Gordon (sG) model in the presence of periodic inhomogeneity is studied. An ansatz is proposed that allows for the construction of a reliable effective model with two degrees of freedom. Effective models…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
We experimentally probe the distribution of kink pairs resulting from driving a one-dimensional quantum Ising chain through the paramagnet-ferromagnet quantum phase transition, using a single trapped ion as a quantum simulator in momentum…
We study the crossing of the quantum phase transition in the transverse-field Ising model after modulating the magnetic field at an arbitrary rate, exploring the critical dynamics from the slow to the sudden quench regime. We do so by…
We consider a family of field-theoretic models with a real scalar field in (1+1)-dimensional space-time. The field dynamics in each model is determined by a polynomial potential with two degenerate minima. We obtain exact general formulas…
We investigate crack propagation in a simple two-dimensional visco-elastic model and find a scaling regime in the relation between the propagation velocity and energy release rate or fracture energy, together with lower and upper bounds of…
We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…
We investigate transient nonlinear localization, namely the self-excitation of energy bursts in an atomic lattice at finite temperature. As a basic model we consider the diatomic Lennard-Jones chain. Numerical simulations suggest that the…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
Phase transitions are the macroscopic manifestation of microscopic processes that drive a system towards a new state. The detailed evolution of these processes, particularly in abrupt phase transitions, are currently not fully understood.…
We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the…