Related papers: Thermodynamic relations for DNA phase transitions
Background: Acceleration of adaptation dynamics by stress-induced hypermutation has been found experimentally. Evolved evolvability is a prominent explanation. We investigate a more generally applicable explanation by a physical constraint.…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
We study a zero-range process with two species of interacting particles. We show that the steady state assumes a simple factorised form, provided the dynamics satisfy certain conditions, which we derive. The steady state exhibits a new…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
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…
Thermodynamic relations are derived from first principles of mechanics for non-equilibrium processes. Since the key role herein is played by the law of increase of entropy, the latter is analyzed at first. It is shown that its derivation…
In this Letter, we investigate the link between thermal denaturation and mechanical unzipping for two models of DNA, namely the Dauxois-Peyrard-Bishop model and a variant thereof we proposed recently. We show that the critical line that…
Mechanically induced crystallographic phase transformation that reflects dynamic stress responses of intrinsically stochastic nature is a pertinent yet much less well-understood phenomenon. We focus on understanding the physical…
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
We study by using Monte Carlo simulations the hysteresis in unzipping and rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite directions in the fixed force ensemble. The force is increased, at a constant rate from…
A simple description of thermodynamics of DMAAS and DMAGaS ferroelectric crystals by means of Landau expansion is proposed. Conditions of occurrence of phase transitions are established and their temperatures are obtained. The influence of…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and $B$ represent two different types of base pairs having two- and three-bonds,…
We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
The opening of the Y-fork - the first step of DNA replication - is shown to be a critical phenomenon under an external force at one of its ends. From the results of an equivalent delocalization in a non-hermitian quantum-mechanics problem…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…