相关论文: A molecular dynamics simulation of DNA damage indu…
We apply a recently introduced model for an independent-atom-like calculation of ion-impact electron transfer and ionization cross sections to proton collisions from water, neon, and carbon clusters. The model is based on a geometrical…
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+)…
Critical experimental design issues connecting energy transduction and inheritable information within a protocell are explored and elucidated. The protocell design utilizes a photo-driven energy transducer (a ruthenium complex) to turn…
The variation of the oxygen enhancement ratio (OER) across Linear Energy Transfer (LET) currently lacks a comprehensive mechanistic interpretation and a mechanistic model. Our earlier research revealed a significant correlation between the…
Purpose: A reliable model to simulate nuclear interactions is fundamental for Ion-therapy. We already showed how BLOB ("Boltzmann-Langevin One Body"), a model developed to simulate heavy ion interactions up to few hundreds of MeV/u, could…
The ultrafast electronic and nuclear dynamics of H2 laser-induced double ionization is studied using a time-dependent wave packet approach that goes beyond the fixed nuclei approximation. The double ionization pathways are analyzed by…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
Secondary electron cascades are responsible for significant ionizations in macroscopic samples during irradiation with X-rays. A quantitative analysis of these cascades is needed, e.g. for assessing damage in optical components at X-ray…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
A new simulation box setup is introduced for the precise description of the wavepacket evolution of two electronic systems in intense laser pulses. In this box, the regions of the hydrogen molecule H$_{2} $, and singly and doubly ionized…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
We model molecular cloud fragmentation with thin disk non-ideal magnetohydrodynamic simulations that include ambipolar diffusion and partial ionization that transitions from primarily ultraviolet dominated to cosmic ray dominated regimes.…
The processes of electron excitation, capture, and ionization were investigated in proton collisions with atomic hydrogen in the initial $n=1$ and $n=2$ states at impact energies from 1 to 300 keV. The theoretical analysis is based on the…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
Ionic liquid ion sources are a promising technology that can be used for many applications from space propulsion to focused ion beam microetching. Ionic liquid ion sources produce ion beams by extracting single ions and metastable solvated…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
We develop a kinetic reaction model for cells having irradiated DNA molecules due to ionizing radiation exposure. Our theory simultaneously accounts for the time-dependent reactions of the DNA damage, the DNA mutation, the DNA repair, and…