相关论文: Ion-mediated RNA structural collapse: effect of sp…

The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of ions. For ribozymes, divalent cations are known to be more…

Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of…

Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance…

We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…

We present a molecular dynamics study of the effects of confinement on the lubrication and flow properties of ionic liquids. We use a coarse-grained salt model description of ionic liquid as a lubricant confined between finite solid plates…

We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…

Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…

Systems in which particles can self-assemble into mono- or bilayers can form variety of stable and metastable structures on a nanometer length scale. For this reason confinement has a particularly strong effect on such systems. We discuss…

Recent advances in operating and manipulating DNA have provided unique experimental possibilities in many fields of DNA research, especially in gene therapy. Researchers have deployed many techniques, experimental and theoretical, to study…

In cellular environment, confinement and macromulecular crowding play an important role on thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saito-Munoz-Eaton model for protein…

Ion specificity and related Hofmeister effects, ubiquitous in aqueous systems, can have spectacular consequences in hydrated clays, where ion-specific nanoscale surface forces can determine large scale cohesive, swelling and shrinkage…

Fundamental studies of the effect of specific ions on hydrophobic interactions are driven by the need to understand phenomena such as hydrophobically driven self-assembly or protein folding. Using beta-peptide-inspired nano-rods, we…

Recent measurements suggest the possibility to exploit ionic liquids (ILs) as smart lubricants for nano-contacts, tuning their tribological and rheological properties by charging the sliding interfaces. Following our earlier theoretical…

Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…

Methane hydrate nucleation under nanoconfinement remains poorly understood due to the complex interplay between geometric restriction and molecular ordering. Here, we investigate the structural organization of water-methane systems confined…

Nanoconfinement reduces the favorable hydration free energies of single ions, which is correlated with ion rejection and modified chemical reactivity in water-filled nanopores. Many factors contribute to the magnitude of the observed…

It is well stablished that confinement of supercooled liquids in nano-pores induces various effects as a strong modification of the dynamics and a layering of the local structure. In this work we raise the issue as how these confinement…

Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively…

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…

Folding of ribozymes into well-defined tertiary structures usually requires divalent cations. How Mg$^{2+}$ ions direct the folding kinetics has been a long-standing unsolved problem because experiments cannot detect the positions and…