Related papers: Reversible B/A Transitions in Single DNA Molecule …
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
Water plays a major role in bio-systems, greatly contributing to determine their structure, stability and even function. It is well know, for instance, that proteins require a minimum amount of water to be functionally active. Since the…
A droplet impacting a deep fluid bath is as common as rain over the ocean. If the impact is sufficiently gentle, the mediating air layer remains intact, and the droplet may rebound completely from the interface. In this work, we…
The network connectivity in liquid water is revised in terms of electronic signatures of hydrogen bonds (HBs) instead of geometric criteria, in view of recent X-ray absorption studies. The analysis is based on ab initio molecular-dynamics…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
On the surface of a vibrating liquid bath, instead of coalescing, a drop will continually bounce on a thin film of air between the drop and the free surface, giving rise to rich chaotic dynamics and quantum analog behavior. However,…
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…
Structurally disordered materials continue to pose fundamental questions, including that of how different disordered phases ("polyamorphs") can coexist and transform from one to another. As a widely studied case, amorphous silicon (a-Si)…
We present extensive molecular dynamics simulations of a liquid of symmetric dumbbells, for constant packing fraction, as a function of temperature and molecular elongation. For large elongations, translational and rotational degrees of…
Some aspects of direct ion transfer across the water/1,2-dichloroethane are analyzed using a very simple model based on thermodynamic considerations. It was concluded that ion solvation by water molecules may occur in some particular cases…
The theoretical study of deformability of special sequence of DNA double helix TATA-box is presentated. The paper elaborates on the mechanisms of abnormal deformation of DNA TATA-box double helix that cannot be explained using the standard…
Recently, it has been confirmed that long duplex DNA molecules with sizes larger than several tens of kilo-base pairs (kbp), exhibit a discrete conformational transition from an elongated coil state to a compact globule state upon the…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
The water molecule occurs in two nuclear-spin isomers that differ by the value of the total nuclear spin of the hydrogen atoms, i.e., $I=0$ for para-H$_2$O and $I=1$ for ortho-H$_2$O. Spectroscopic transitions between rovibrational states…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Fluid polyamorphism, the existence of multiple amorphous fluid states in a single-component system, has been observed or predicted in a variety of substances. A remarkable example of this phenomenon is the fluid-fluid phase transition in…
A rigorous hydrodynamic theory of the A-B transition is presented. All dissipative processes are considered. At low interface velocities, those occurring on hydrodynamic length scales, not considered hitherto, are most probably the dominant…
In the paper the behavior of density (or specific volume), the heat of evaporation and entropy per molecule for normal and heavy water on their coexistence curves is discussed. The special attention is paid on the physical nature of the…
We review recent advances in the physics of strongly interacting charged systems functioning in water at room temperature. We concentrate on the phenomena which go beyond the framework of mean field theories, whether linear Debye-Huckel or…
The present study deals with the numerical as well as asymptotic analysis of the electrohydrodynamic interaction between two deformable droplets in a confined shear flow. Considering both the phases as leaky dielectric, we have performed…