Related papers: Spontaneous RNA condensation into nanoring structu…
Selected ribonucleotide sequences bind well to zwitterionic phospholipid bilayer membranes, though randomized RNAs do not. There are no evident repeated sequences in selected membrane binding RNAs. This implies small and varied motifs…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
Targeting specific technological applications requires the control of nanoparticle properties, especially the crystalline polymorph. Freezing a nanodroplet deposited on a solid substrate leads to the formation of crystalline structures. We…
To understand the mechanism of TATA-box conformational transformations we model structure mobility and find the types of conformational excitations of DNA macromolecule in heteronomous conformation. We have constructed the two-component…
Carbon nanoribbons (CNRs) are graphene (planar) structures with large aspect ratio. Carbon nanobelts (CNBs) are small graphene nanoribbons rolled up into spiral-like structures, i. e., carbon nanoscrolls (CNSs) with large aspect ratio. In…
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…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Electron scattering measurements from high-momentum nucleons in nuclei at SLAC and Jefferson Lab (JLab) have shown that these nucleons are generally associated with two-nucleon short-range correlations (2N-SRCs). These SRCs are formed when…
A facile route to prepare the nanotubes from rod-like mesogens dissolved in typical organic solvents is reported. For selected types of chiral rod-like molecules, both enantiomers as well as the racemic mixtures formed the nanotubes by slow…
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
We investigate by scattering techniques the structure of water-based soft composite materials comprising a crystal made of Pluronic block-copolymer micelles arranged in a face-centered cubic lattice and a small amount (at most 2% by volume)…
The increasing importance of RNA as a prime player in biology can hardly be overstated. Problems in RNA, such as folding and RNA-RNA interactions that drive phase separation, require cations. Because experiments alone cannot reveal the…
Nanowires are formed by indenting and subsequently retracting two pieces of sodium metal. Their cross-section gradually reduces upon retraction and the diameters can be obtained from the conductance. In previous work we have demonstrated…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
The problem of DNA$-$DNA interaction mediated by divalent counterions is studied using a generalized Grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior…
Unique nanorod precipitates with a core-shell structure are found to nucleate from the grain boundaries of a bulk nanocrystalline Al-Ni-Y alloy fabricated via powder consolidation, contributing significantly to stabilization and…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
The effects of monovalent (Na+, K+) and divalent (Mg2+, Ca2+, Mn2+) ions on the interaction between DNA and histone are studied using the molecular combing technique. Lamda-DNA molecules and DNA-histone complexes incubated with metal…