Related papers: A molecular dynamics simulation of DNA damage indu…
Recently, some authors have shown that a DNA molecule produces electromagnetic signals and communicates with other DNA molecules or other molecules. In fact, a DNA acts like a receiver or transmitter of radio waves. In this paper, we…
{\bf Purpose}: To develop a first principle and multi-scale model for normal tissue complication probability (NTCP) as a function of dose and LET for proton and in general for particle therapy with a goal of incorporating nano-scale…
In this work, we report a novel strategy to construct molecular diodes with a record tunable rectification ratio of as high as 10^6 using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA…
The morphology of DNA is strongly influenced by its surrounding environment, including factors such as pH, salt type and valency, and the presence of polymers. Inorganic salts are known to reduce the DNA chain length through mechanisms like…
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in…
The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
We have developed a novel methodology utilizing molecular dynamics simulations to evaluate the ionization yields of nuclear recoils in crystalline silicon. This approach enables analytical exploration of atomic-scale transport within the…
We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically…
In previous work, we constructed a statistical framework for estimating the rate of clustered ionization from charged particle radiation in DNA. This model is extended to include contributions from secondary electrons. Using a simple…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
Cancer treatment with radiotherapy aims to kill tumor cells and spare healthy tissue.Thus,the experimentally observed sparing of healthy tissue by the FLASH effect during irradiations with ultra-high dose rates (UHDR) enables clinicians to…
The differences in H2O2 production between conventional (CONV) and ultra-high dose rate (UHDR) irradiations in water radiolysis are still not fully understood. The lower levels of this radiolytic species, as a critical end product of water…
The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the…
We used a multiscale model to study the damage caused by swift heavy ions in GaN. The model combines Monte Carlo and molecular dynamics simulations to analyze the material response to the excitation initiated by a projectile. We found that…
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…
Electromagnetic interactions of protons and alpha particles are modeled in a form that is suitable for Monte Carlo simulation of the transport of charged particles. The differential cross section (DCS) for elastic collisions with neutral…
Single strand breaks are induced in DNA plasmids, pBR322 and pUC19, in aqueous media exposed to strong fields generated using ultrashort laser pulses (820 nm wavelength, 45 fs pulse duration, 1 kHz repetition rate) at intensities of 1-12 TW…