Related papers: Reactive Molecular Dynamics Simulation on DNA Doub…
The cell cycle is an orderly sequence of events which ultimately lead to the division of a single cell into two daughter cells. In the case of DNA damage by radiation or chemicals, the damage checkpoints in the $G_{1}$ and $G_{2}$ phases of…
We propose a model for the photo-deactivation mechanism for DNA based upon accurate quantum chemical and molecular dynamical evaluations of model Watson/Crick nucleoside pairs and stacked pairs. Our results corroborate recent ultrafast…
We present the first three-dimensional (3D) simulations of the large-scale mixing that takes place in the shock-heated stellar layers ejected in the explosion of a 15.5 solar-mass blue supergiant star. The outgoing supernova shock is…
We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test…
Coherent control of OH-free radicals interacting with the spin-triplet state of a DNA molecule is investigated. A model Hamiltonian for molecular spin singlet-triplet resonance is developed. We illustrate that the spin-triplet state in DNA…
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…
We investigate the LHC phenomenology of a model where the Standard Model (SM) scalar sector is extended by two real scalar singlets. A $\mathbb{Z}_2\otimes\mathbb{Z}_2'$ discrete symmetry is imposed to reduce the number of scalar potential…
After photo-excitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we…
We investigate the hydrodynamics of the interaction of two supersonic winds in binary systems. The collision of the winds creates two shocks separated by a contact discontinuity. The overall structure depends on the momentum flux ratio eta…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
The scientific community shows a great interest in the study of DNA damage induction, DNA damage repair and the biological effects on cells and cellular systems after exposure to ionizing radiation. Several in-silico methods have been…
In dynamic force spectroscopy, a (bio-)molecular complex is subjected to a steadily increasing force until the chemical bond breaks. Repeating the same experiment many times results in a broad distribution of rupture forces, whose…
Following the recent observation of wave function revivals in large Rydberg atom quantum simulators, much effort has focused on understanding the emergence of many-body scars in non-integrable quantum systems. Here we explore the origin of…
Two-dimensional (2D) hydrodynamical simulations of progenitor evolution of a 23 solar mass star, close to core collapse (about 1 hour, in 1D), with simultaneously active C, Ne, O, and Si burning shells, are presented and contrasted to…
Using a Brownian dynamics simulation, we numerically studied the interaction of DNA with histone and proposed an octamer-rotation model to describe the process of nucleosome formation. Nucleosome disruption under stretching was also…
Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
The possibility of dynamical electroweak symmetry breaking by strong coupling gauge interaction in models with D-branes in String Theory is examined. Instead of elementary scalar Higgs doublet fields, the gauge symmetry with strong coupling…