Related papers: Ion Condensation onto Ribozyme is Site-Specific an…
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…
We discuss the distribution of ions around highly charged PEs when there is competition between monovalent and multivalent ions, pointing out that in this case the number of condensed ions is sensitive to short-range interactions, salt, and…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
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…
Quick clay is a highly sensitive soil that transforms rapidly from solid to liquid under minor stress, as a result of long-term salt leaching that drastically reduces shear strength. Stabilizing it is both costly and carbon-intensive,…
The dependence of DNA assemblies conductance on relative humidity is investigated theoretically. Following earlier suggestions, we consider the ionic conductivity through the layers of water adsorbed by DNA molecules. The increase in…
A model for the description of proton collisions from molecules composed of atoms such as hydrogen, carbon, nitrogen, oxygen and phosphorus (H, C, N, O, P) was recently extended to treat collisions with multiply charged ions with a focus on…
We study ion condensation onto a patterned surface of alternating charges. The competition between self-energy and ion-surface interactions leads to the formation of ionic crystalline structures at low temperatures. We consider different…
Water mediates electrostatic interactions via the orientation of its dipoles around ions, molecules, and interfaces. This induced water polarization consequently influences multiple phenomena. In particular, water polarization modulated by…
The uptake and sorption of charged molecules by responsive polymer membranes and hydrogels in aqueous solutions is of key importance for the development of soft functional materials. Here we investigate the partitioning of simple monoatomic…
The adsorption of anions from aqueous solution on the air/water interface controls important heterogeneous chemistry in the atmosphere and is thought to have similar physics to anion adsorption at hydrophobic interfaces more generally.…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we…
We have investigated interlayer interactions in the bilayer PtTe$_{2}$ system, which influence the electronic energy bands near the Fermi levels. Our diffusion Monte Carlo (DMC) calculations for the high-symmetry bilayer stackings (AA, AB,…
Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic…
By using single-DNA observation with fluorescence microscopy, we observed the effects of divalent and trivalent cations on the higher-order structure of giant DNA (T4 DNA with 166 kbp). It was found that divalent cations, such as Mg(2+) and…
Nanoporous carbon-based supercapacitors store electricity through adsorption of ions from the electrolyte at the surface of the electrodes. Room temperature ionic liquids, which show the largest ion concentrations among organic liquid…
Within the quasichemical approach, the hydration free energy of an ion is decomposed into a chemical term accounting for ion specific ion-water interactions within the coordination sphere and nonspecific contributions accounting for packing…
Using Brownian dynamics computer simulations we show that a two-dimensional suspension of self-propelled ("active") colloidal particles crystallizes at sufficiently high densities. Compared to the equilibrium freezing of passive particles…
We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key…