Related papers: Ion Condensation onto Ribozyme is Site-Specific an…
We propose a mechanism for the stabilization/destabilization of cell membranes by multivalent ions with an emphasis on its implications for the division and fusion of cells. We find that multivalent cations preferentially adsorbed onto a…
Isolating neutral and charged particles from the environment is essential in precision experiments. For decades, this has been achieved by trapping ions with radio-frequency (rf) fields and neutral particles with optical fields. Recently,…
Dissipative quantum systems can under appropriate conditions exhibit bi- or multi-partite entanglement at the steady state. The presence and properties of these quantum correlations depend on the relevant model parameters. Here, we…
The formation of complexes between like-charged polyelectrolytes challenges conventional electrostatic intuition and highlights the central role of ions in mediating macromolecular organization. Here, we investigate the salt-dependent…
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…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is…
State-dependent conformational changes play a central role in molecular dynamics, yet they are often difficult to observe or simulate due to their complexity and ultrafast nature. One alternative approach is to emulate such phenomena using…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that…
We generalize the concept of charge regulation of ionic solutions, and apply it to complex fluids with mobile macro-ions having internal non-electrostatic degrees of freedom. The suggested framework provides a convenient tool for…
We determine the persistence length, $l_p$, for a bacterial group I ribozyme as a function of concentration of monovalent and divalent cations by fitting the distance distribution functions $P(r)$ obtained from small angle X-ray scattering…
Positive ions play a fundamental role in the interstellar chemistry, especially in cold environments where chemistry is believed to be mainly ion-driven. However, in contrast with neutral species, most of the cations present in the…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
The extent of contact and solvent shared ion pairs of phosphate groups with Na$^+$, Ca$^{2+}$ and Mg$^{2+}$ ions in aqueous environment and their relevance for the stability of polyanionic DNA and RNA structures is highly debated. Employing…
In this work, we addressed the effects of Y$^{3+}$ and Nd$^{3+}$ cations on the adsorption of the whey protein $\beta$-lactoglobulin (BLG) at air-water interfaces as a function of electrolyte concentration. Both cations caused very similar…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
Accurate modeling of aqueous monovalent ions is essential for understanding the function of biomolecules, such as nucleic acid stability and binding of charged drugs to protein targets. The 1D and 3D reference interaction site models (1D-…
Zinc-fingers, which widely exist in eukaryotic cell and play crucial roles in life processes, depend on the binding of zinc ion for their proper folding. To computationally study the zinc coupled folding of the zinc-fingers, charge transfer…
The ion populations most frequently adopted for diagnostics in collisional plasmas are derived from the density independent, coronal approximation. In higher density, lower temperature conditions, ionisation rates are enhanced once…