Related papers: Multivalent ion-mediated nucleic acid helix-helix …
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…
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…
Bayesian methods are used to constrain the density dependence of the QCD Equation of State (EoS) for dense nuclear matter using the data of mean transverse kinetic energy and elliptic flow of protons from heavy ion collisions (HIC), in the…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…
Nuclei are unique analyzers for the early stage of the space-time development of hadronization. DIS at medium energies is especially suitable for this task being sensitive to hadronization dynamics, since the production length is comparable…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity…
High energy heavy-ion collisions are proposed as a novel means to constrain stringently the high density (HD) behaviour of nuclear symmetry energy. Within an isospin-dependent hadronic transport model, it is shown for the first time that…
The dispersion interaction between a pair of parallel DNA double-helix structures is investigated by means of the van der Waals density functional (vdW-DF) method. Each double-helix structure consists of an infinite repetition of one B-DNA…
The density-functional theory proves that an ion-electron mixture can be treated as a one-component liquid interacting only via a {\it pairwise} interaction in the evaluation of the ion-ion radial distribution function (RDF), and provides a…
These lecture notes are addressed to PhD student and/or researchers who want a general overview of microscopic approaches based on mean-field and applied to nuclear dynamics. Our goal is to provide a good description of low energy heavy-ion…
The effects of ionic ordering in DNA water solutions are studied by conductivity experiments. The conductivity measurements are performed for the solutions of DNA with KCl salt in the temperature range from 28 to 70 C. Salt concentration…
We investigate the role of nuclear motion and strong-field-induced electronic couplings during the double ionization of deuterated water using momentum-resolved coincidence spectroscopy. By examining the three-body dicationic dissociation…
The nucleus-nucleus potential is calculated in the frame work of the double folding model (DFM) to obtain the Coulomb barrier parameters (barrier position and height), starting from M3Y-Reid nucleon-nucleon interaction and realistic nuclear…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
Heavy Ion Collisions (HIC) represent a unique tool to probe the in-medium nuclear interaction in regions away from saturation. In this report we present a selection of new reaction observables in dissipative collisions particularly…