Related papers: Modeling the interaction of DNA with alternating f…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally…
We present a mechanism for thermalizing a moving particle by microscopic deterministic scattering. As an example, we consider the periodic Lorentz gas. We modify the collision rules by including energy transfer between particle and…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
By assuming that not only counter-ions but DNA molecules as well are thermally distributed according to a Boltzmann law, we propose a modified Poisson-Boltzmann equation at the classical level as starting point to compute the effects of…
The basic models of helix-coil transitions in biomolecules are introduced. These include phenomenological, zipper (Bragg-Zimm) models of polypeptides, loop-entropy (Poland-Scheraga) and Hamiltonian (Peyrard-Bishop) models of homogeneous DNA…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
The cosmological evolution of a scalar field is shaped by Hubble damping. Any non-gravitational couplings of the scalar with the primordial thermal bath generically contribute additional damping. Although rarely considered, such thermal…
We explore the melting of a lattice DNA in the presence of atmospheric disorder, which mimics the crowded environment inside the cell nucleus, using Monte Carlo simulations. The disorder is modeled by randomly retaining lattice sites with…
We present an alternative method for describing the evolution of a mode of the quantized electromagnetic field in contact with a finite temperature thermal bath. We use the expansion of the field density operator in terms of coherent states…
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
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…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
We investigate the multi-order parameter phase field model of Steinbach and Pezzolla [I. Steinbach, F. Pezzolla, A generalized field method for multiphase transformations using interface fields, Physica D 134 (1999) 385-393] concerning its…
In this work we rederive the Lamb-Retherford energy shift for an atomic electron in the presence of a thermal radiation. Using the Dalibard, Dupont-Roc and Cohen-Tannoudji (DDC) formalism, where physical observables are expressed as…
A tomographic study of near-field radiative heat exchanges between a mesoscopic object and a substrate immersed in a thermal bath is carried out within the theoretical framework of fluctuational electrodynamics. By using the…
The following is a thermodynamic analysis of a III order (and some aspects of a IV order) phase transition. Such a transition can occur in a superconductor if the normal state is a diamagnet. The equation for a phase boundary in an H-T (H…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…