Related papers: Base Pair Openings and Temperature Dependence of D…
The thermal conductivity of double-stranded (ds) B-DNA was systematically investigated using classical molecular dynamics (MD) simulations. The effect of changing base-pairs on the thermal conductivity of dsDNA, needed investigation at a…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…
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…
We investigate the temperature dependence of thermodynamic (density, isobaric heat capacity), dynamical (self-diffusion coefficient, shear viscosity), and dielectric properties of several water models, the commonly employed TIP3P water…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
We present the temperature dependence of alpha-relaxation times of 13 glass formers determined from broadband dielectric spectroscopy, also including data from aging measurements. The data sets partly cover relaxation-time ranges of up to…
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 predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
The velocity of polaron migration in the long poly-DNA chain (~40 base pairs) in an applied electric field has been studied within a polaron model. We found that the polaron velocity strongly depends on the polaron size. A small polaron…
We propose a new simple model for DNA denaturation bases on the pendulum model of Englander\cite{A1} and the microscopic model of Peyrard {\it et al.},\cite{A3} so called "combined model". The main parameters of our model are: the coupling…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
We study the features on the unzipping process of a modified version of the Peyrard-Bishop- Dauxois model. We show that the inclusion of a barrier in the on-site potential allows for the existence of stable domain wall solutions between…
Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity, in the framework…
Fragility, quantifying the rapidity of variation of relaxation times, is analysed for a series of model glass formers, which differ in the softness of their interparticle interactions. In an attempt to rationalize experimental observations…