Related papers: Simulation and Experimental Verification of DNA Da…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
Radiation damage is an unavoidable process when performing structural investigations of biological macromolecules with X-ray sources. In crystallography this process can be limited through damage distribution in a crystal, while for single…
According to the experimental evidence damage induced by densely ionizing radiation in mammalian cells is distributed along the DNA molecule in the form of clusters. The most critical constituent of DNA damage are double-strand breaks…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
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…
We report in situ single-molecule measurements of proton-induced double-strand breaks (DSBs) in DNA immersed in water, using real-time fluorescence tracking along the entire proton path, including the Bragg peak region. By chemically…
In single particle coherent x-ray diffraction imaging experiments, performed at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray pulses to obtain single-shot diffraction patterns. The high intensity induces…
To date X-ray spectroscopy has become a routine tool that can reveal highly local and element-specific information on the electronic structure of atoms in complex environments. Here, we focus on nuclear dynamical effects in X-ray spectra…
Published survival data for V79 cells irradiated by monoenergetic protons, helium-3, carbon, and oxygen ions and for CHO cells irradiated by carbon ions have been analyzed using the probabilistic two-stage model of cell inactivation. Three…
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…
Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called…
{\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…
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…
How DNA repair enzymes find the relatively rare sites of damage is not known in great detail. Recent experiments and molecular data suggest that the individual repair enzymes do not work independently of each other, but rather interact with…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule…
Nanoprobe X-ray diffraction (nXRD) using focused synchrotron radiation is a powerful technique to study the structural properties of individual semiconductor nanowires. However, when performing the experiment under ambient conditions, the…