Related papers: Simulation and Experimental Verification of DNA Da…
Diamond is more and more used as detector material for particle detection. One argument for diamond is its higher radiation hardness compared to silicon. Since various particles have different potential for radiation damage at different…
We propose a mathematical model for estimating biological damage caused by low-dose irradiation. We understand that the Linear Non Threshold (LNT) hypothesis is realized only in the case of no recovery effects. In order to treat the…
The report contains various aspects of radiation damage in silicon detectors subjected to high intensity hadron and electromagnetic irradiation. It focuses on improvements for the foreseen LHC applications, employing oxygenation of silicon…
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…
In this paper we consider dipole-mediated correlations between DNA and enzymes in the context of their water environment. Such correlations emerge from electric dipole-dipole interactions between aromatic ring structures in DNA and in…
This paper presents a convolutional neural network (CNN)-based deep learning model, inspired from UNet with series of encoder and decoder units with skip connections, for the simulation of microwave-plasma interaction. The microwave…
The nanometric track-structure of energetic ion beams in biological media determines the direct physical damage to living cells, which is one of the main responsibles of their killing or inactivation during radiotherapy treatments or under…
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both…
In this work, experimental and data analysis procedures were developed and applied for studying amino acid crystals by means of X-ray phase measurements. It clearly demonstrated the sensitivity of invariant triplet phases to electronic…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
Understanding the three-dimensional (3D) structure and stability of DNA is fundamental for its biological function and the design of novel drugs. In this study, we introduce an improved coarse-grained (CG) model, incorporating a more…
X-ray scattering is a weak linear probe of matter. It is primarily sensitive to the position of electrons and their momentum distribution. Elastic X-ray scattering forms the basis of atomic structural determination while inelastic Compton…
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…
Modern X-ray spectroscopy has proven itself as a robust tool for probing the electronic structure of atoms in complex environments. Despite working on energy scales that are much larger than those corresponding to nuclear motions, taking…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
In the framework of the Poland Scheraga model of DNA denaturation, we derive a recursion relation for the partition function of double stranded DNA, allowing for mismatches between the two strands. This relation is studied numerically using…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of…