Related papers: A molecular dynamics simulation of DNA damage indu…
Purpose: Recent studies suggest ultra-high dose rate (FLASH) irradiation can spare normal tissues from radiotoxicity, while efficiently controlling the tumor, and this is known as the FLASH effect. This study performed theoretical analyses…
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…
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA…
High intensity XUV radiation from a free-electron (FEL) was used to create a nanoplasma inside ammonia clusters with the intent of studying the resulting electron-ion interactions and their interplay with plasma evolution. In a plasma-like…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Photo-ionization induced ultrafast electron dynamics is considered as a precursor to the slower nuclear dynamics associated with molecular dissociation. Here, using ab initio multielectron wave-packet propagation method, we study the…
Novel approaches to DNA sequencing and detection require the measurement of electrical currents between metal probes immersed in ionic solution. Here, we experimentally demonstrate that these systems maintain large background currents with…
Tsallis entropy and a maximum entropy principle allows to reproduce experimental data of DNA double strand breaking by electron and neutron radiation. Analytic results for the probability of finding a DNA segment of length l are obtained…
Context. While synthesis of organic molecules in molecular clouds or protoplanetary disks is complex, observations of interstellar grains, analyses of carbonaceous chondrites, and UV photochemistry experiments are rapidly developing and…
Single strand breaks are induced in DNA plasmids, pBR322 and pUC19, in aqueous media by intense ultrashort laser pulses (820 nm wavelength, 45 fs pulse duration, 1 kHz repetition rate) at intensities of 1-12 TW cm$^{-2}$. The intense laser…
Using high-quality gas phase electron scattering calculations and multiple scattering theory, we attempt to gain insights on the radiation damage to DNA induced by secondary low-energy electrons in the condensed phase, and to bridge the…
We formulate a general hybrid quantum-classical technique to describe the interaction of diatomic molecules with XUV pulses. We demonstrate the accuracy of our model in the context of the interaction of the O$_2$ molecule with an XUV pulse…
Boron-doped diamond crystals (BDD, C$_{1-x}$B$_{x}$) exhibit exceptional mechanical strength, electronic tunability, and resistance to radiation damage. This makes them promising materials for use in gamma-ray crystal-based light sources.…
The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photo damage, and is determined by the interplay of electronic couplings between…
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been…
The accurate treatment of electronic effects in multi-million atom simulations of radiation-induced collision cascades is crucial for reliable predictions of primary radiation damage. In this work, we explore the performance of a recently…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
The interaction of a free-electron-laser pulse with a moderate or large size cluster is known to create a quasi-neutral nanoplasma, which then expands on hydrodynamic timescale, i.e., $>1$ ps. To have a better understanding of ion and…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…