Related papers: A Coarse-Grained Model for Predicting RNA Folding …
We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and…
The transport coefficients of a dilute gas of inelastic hard spheres immersed in a molecular gas are determined. We assume that the number density of the granular gas is much smaller than that of the surrounding molecular gas, so that the…
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…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying…
We investigate coarse-grained models of suspended self-thermophoretic microswimmers. Upon heating, the Janus spheres, with hemispheres made of different materials, induce a heterogeneous local solvent temperature that causes the…
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in…
The organization of water molecules and ions between charged mineral surfaces determines the stability of colloidal suspensions and the strength of phase-separated particulate gels. In this article we assemble a density functional that…
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…
We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous…
Based on the earlier obtained equations of state for the ternary systems H2O-CO2-CaCl2 and H2O-CO2-NaCl, an equation of state for the four-component fluid system H2O-CO2-NaCl-CaCl2 is derived in terms of the Gibbs excess free energy. A…
Using Brownian dynamics (BD) simulations and an analytical approach we investigate the shear-induced, nonequilibrium dynamics of dense colloidal suspensions confined to a narrow slit-pore. Focusing on situations where the colloids arrange…
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent…
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
We study an elasticity model for compressed protein monolayers or particle rafts at a liquid interface. Based on the microscopic view of hard-core particles with soft shells, a bead-spring model is formulated and analyzed in terms of…
A new approach to modelling the behaviour of simple fluids is presented. Starting from the usual expression of the partition function of N molecules, a Fourier transformation is performed. It is argued that the N(N-1)/2 dynamical variables…
Synthesis and efficient implementation mRNA strands has been shown to have wide utility, especially recently in the development of COVID vaccines. However, the intrinsic chemical stability of mRNA poses a challenge due to the presence of…
We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…