Related papers: Thermodynamic relations for DNA phase transitions
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
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…
Equations that govern the temperature-dependence of the rate constants, Gibbs energies,enthalpies, entropies and heat capacities of activation for folding and unfolding of spontaneously-folding fixed two-state systems have been derived…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
This letter investigates the molecular dynamics of inelastic disks without external forcing. By introducing a new observation frame with a rescaled time, we observe the virtual steady states converted from asymptotic energy dissipation…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
A simple and effective approach to thermodynamics is suggested, which solves the major difficulties in the traditional presentation of the subject. The internal energy is introduced from the behavior of deformable bodies, whereas the…
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…
In order to find out whether there exists a thermodynamic description of the glass phase, the Ehrenfest relations along the glass transition line are reconsidered. It is explained that the one involving the compressibility is always…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
We consider a Brownian particle in harmonic confinement of stiffness $k$, in one dimension in the underdamped regime. The whole setup is immersed in a heat bath at temperature $T$. The center of harmonic trap is dragged under any arbitrary…
In this thesis the finite temperature transition between confined and deconfined matter is studied at zero and nonzero quark densities. The findings are relevant for the understanding of the evolution of the early Universe and contemporary…
We use a simplified model which is based on the same physics as inherent in most statistical models for nuclear multifragmentation. The simplified model allows exact calculations for thermodynamic properties of systems of large number of…
Thermodynamic properties of matter are conveniently expressed as functional relations between variables known as equations of state. Here we experimentally determine the compressibility, density and pressure equations of state for an…
Three, interrelated biologically-relevant examples of biased random walks are presented: (1) A model for DNA melting, modelled as DNA unzipping, which provides a way to illustrate the role of the Boltzmann factor in a venue well-known to…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…