Related papers: Reactive Molecular Dynamics Simulation on DNA Doub…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a broad set of design frameworks has emerged to accommodate…
This paper concentrates on relationships of formal systems with biology. The paper is based on previous papers by the author. We have freely used texts of those papers where the formulations are of use, and we have extended the concepts and…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
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 perform smoothed-particle hydrodynamical simulations of the explosion of a helium star in a close binary system, and study the effects of the explosion on the companion star as well as the effect of the presence of the companion on the…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…
Spin dipole (SD) strengths for double beta-decay (DBD) nuclei were studied experimentally for the first time by using measured cross sections of (3He,t) charge exchange reactions (CERs). Then SD nuclear matrix elements (NMEs) for low-lying…
R Coronae Borealis (RCB) stars are rare hydrogen-deficient carbon-rich variable supergiants thought to be the result of dynamically unstable white dwarf mergers. We attempt to model RCBs through all the relevant timescales by simulating a…
When binaries are injected into low-angular-momentum orbits around a central supermassive black hole (SMBH), various outcomes can occur, including binary tidal breakup, double stellar disruptions and stellar collision. We use hydrodynamical…
We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
It is well known that during homology recognition and strand exchange the double stranded DNA (dsDNA) in DNA/RecA filaments is highly extended, but the functional role of the extension has been unclear. We present an analytical model that…
We simulate the dynamics of Rydberg atoms resonantly exchanging energy via two-, three-, and four-body dipole-dipole interactions in a one-dimensional array. Using simplified models of a realistic experimental system, we study the initial…
The proton-magnetic reaction is commonly used in MRI machines with a strong magnetic field of over 1 T, while this study hypothesized that the electron magnetic reaction of hydrogen could affect the hydrogen bonds of double-stranded DNA…
Motivated by the new observed scalar boson of 126 GeV at ATLAS and CMS, various phenomena in two-Higgs-doublet model (THDM) are investigated broadly in the literature. For considering the model that possesses a solution to the massive…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…