Related papers: Change of Hydration Patterns upon RNA Melting Prob…
Morphogenesis involves the transformation of initially simple shapes, such as multicellular spheroids, into more complex $3D$ shapes. These shape changes are governed by mechanical forces including molecular motor-generated forces as well…
Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations…
Something about structure of the water shell of DNA and how it can help to design of novel biologically-active molecules and potential drugs with sequence-specific binding to nucleic acids.
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic…
Interpretation of the X-ray spectra of water as evidence for its asymmetric structure has challenged the conventional symmetric nearly-tetrahedral model and initiated an intense debate about the order and symmetry of the hydrogen bond…
Changes in the medium of biological cell nucleus under ion beam action is considered as a possible cause of cell functioning disruption in the living body. As the most long-lived molecular product appeared in the cell after the passage of…
The transfer of a hydrated proton between water molecules in aqueous solution is accompanied by the large-scale structural reorganization of the environment as the proton relocates, giving rise to the Grotthus mechanism. The Zundel (H5O2+)…
Ribonucleic Acid (RNA) can fold into shapes that perform functions in the cell. These foldings are governed by Watson-Crick base pairing, namely Adenine to Uracil and Cytosine to Guanine (A-U and G-C). The properties of the H-P…
Thermal fluctuations strongly modify the large length-scale elastic behavior of crosslinked membranes, giving rise to scale-dependent elastic moduli. While thermal effects in flat membranes are well understood, many natural and artificial…
The stationary nonempirical simulations of Na+(H2O)n clusters with n in a range of 28 to 51 carried out at the density functional level with a hybrid B3LYP functional and the Born-Oppenheimer molecular dynamics modeling of the size selected…
Molecular dynamics results on water confined in a silica pore in the low hydration regime are presented. Strong layering effects are found due to the hydrophilic character of the substrate. The local properties of water are studied as…
The vibrational modes of water get significantly modified by external solutes; this becomes particularly important when the solute is hydrophobic. In this work, we examine the effects of a tiny hydrophobe, methane, on the normal modes of…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic…
2H NMR spin-lattice relaxation and line-shape analyses are performed to study the temperature-dependent dynamics of water in the hydration shells of myoglobin, elastin, and collagen.