Related papers: Ion-mediated RNA structural collapse: effect of sp…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Atoms under pressure undergo a series of processes and modification of its electronic structure. Examples are the spontaneous ionization, stabilization of excited-state configurations that result in a level-crossing with the ground state of…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
We study the effects of droplet finite size on the structure of nanogel particles synthesized by random crosslinking of molecular polymers diluted in nanoemulsions. For this, we use a bead-spring computer model of polymer-like structures…
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 translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
We numerically study models of $\mathrm{H}_2$ and $\mathrm{LiH}$ molecules, aligned collinearly with the linear polarization of the external field, to elucidate the possible role of correlation in the enhanced-ionization phenomena.…
We study the impact of spatial confinement on the dynamics of three-dimensional excitation vortices with circular filaments. In a chemically active medium we observe a decreased contraction of such scroll rings and even expanding ones,…
We investigate confinement-induced resonances in atom-ion quantum mixtures confined in hybrid traps. Specifically, we consider an ion confined in a time-dependent radio-frequency Paul trap with linear geometry, while the atom is constrained…
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both…
Due to the internal structure of the nucleon, we should expect, in general, that the effective meson nucleon parameters may change in nuclear medium. We study such changes by using a chiral confining model of the nucleon. We use…
Deprivation of essential nutrients can have stark consequences for many processes in a cell. We consider amino acid starvation, which can result in bottlenecks in mRNA translation when ribosomes stall due to lack of resources, i.e. tRNAs…
The effect of fluctuations on the conductivity of ion channels is investigated. It is shown that modulation of the potential barrier at the selectivity site due to electrostatic amplification of charge fluctuations at the channel mouth…
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…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Cross-correlation signals are recorded from fluorescence photons scattered in free space off a trapped ion structure. The analysis of the signal allows for unambiguously revealing the spatial frequency, thus the distance, as well as the…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
Understanding ion-transport under molecular confinement is essential for developing next-generation energy technologies, where ionic motion often occurs within nanoscale or angstrom-scale channels. In this study, we use the model system of…
We use molecular dynamics simulations of the primitive model of electrolytes to study the ionic structure in aqueous monovalent electrolyte solutions confined by charged planar interfaces over a wide range of electrolyte concentration,…
Ion distribution in aqueous electrolytes near the interface plays critical roles in electrochemical, biological and colloidal systems and is expected to be particularly significant inside nanoconfined regions. Electroneutrality of the total…