Related papers: Bubbles, clusters and denaturation in genomic DNA:…
A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…
Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or…
Simple self-consistent models of galaxy groups and clusters are tested against the results of high-resolution adiabatic gasdynamical simulations. We investigate two models based on the existence of a 'universal' dark matter density profile…
We numerically investigate the structures of the near-plate temperature profiles close to the bottom and top plates of turbulent Rayleigh-B\'{e}nard flow in a cylindrical sample at Rayleigh numbers Ra=10^8 to Ra=2\times10^{12} and Prandtl…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
We use molecular dynamics simulations to study a model of the gelation transition with a dynamic bond forming procedure. After establishing evidence for 3D percolation as the static universality class, we turn our attention to the dynamics…
Delamination assessment of the bridge deck plays a vital role for bridge health monitoring. Thermography as one of the nondestructive technologies for delamination detection has the advantage of efficient data acquisition. But there are…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
We present literature on abundance determinations in planetary nebulae (PN) as well as public tools that can be used to derive them. Concerning direct methods to derive abundances we discuss in some depth such issues as reddening…
We apply ideas from renormalization theory to models of cluster formation in nucleation and growth processes. We study a simple case of the Becker-Doring system of equations and show how a novel coarse-graining procedure applied to the…
A method for dimension reduction with clustering, classification, or discriminant analysis is introduced. This mixture model-based approach is based on fitting generalized hyperbolic mixtures on a reduced subspace within the paradigm of…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
We report the splitting of an oscillating DNA circuit into $\sim 700$ droplets with picoliter volumes. Upon incubation at constant temperature, the droplets display sustained oscillations that can be observed for more than a day.…
We theoretically investigated the temperature fluctuations of DNA close to denaturation and observed a strong enhancement of these fluctuations at the critical temperature. Although in a much lower frequency range, such a sharp increase was…
The Protein Data Bank (PDB) contains the atomic structures of over 105 biomolecules with better than 2.8A resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the…
Three-dimensional molecular dynamics simulations of dissipative particles (~ 10^6) are carried out for studying the clustering kinetics of granular media during cooling. The inter-connected high particle density regions are identified,…
In the framework of the Polyakov quark-meson model with two flavors, the bubble dynamics of a first-order phase transition in the region of high density and low temperature are investigated by using the homogeneous thermal nucleation…
The Poisson-Boltzmann equation (PBE) is an implicit solvent continuum model for calculating the electrostatic potential and energies of ionic solvated biomolecules. However, its numerical solution remains a significant challenge due strong…