Related papers: Change of Hydration Patterns upon RNA Melting Prob…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although the number of water molecules near the membrane fluctuates dynamically, the…
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…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as…
We use {\it ab initio} molecular dynamics simulations to study a sample of liquid silica containing 3.84 wt.% H$_2$O.We find that, for temperatures of 3000 K and 3500 K,water is almost exclusively dissolved as hydroxyl groups, the silica…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
We used high-resolution quasielastic neutron scattering spectroscopy to study the single-particle dynamics of water molecules on the surface of hydrated DNA samples. Both H2O and D2O hydrated samples were measured. The contribution of…
Recent experimental investigations into Hydra regeneration revealed a remarkable phenomenon: the morphological transformation of a tissue fragment from the incipient spherical configuration to a tube-like structure - the hallmark of a…
Binary mixtures of water with lower alcohols display non-linear phase behaviour upon mixing which are attributed to potential cluster formation at molecular level. Unravelling such elusive structures requires the investigation of…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
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…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well…
A variety of neurodegenerative diseases are associated with the formation of amyloid plaques. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Most experimental and…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…