Related papers: Water-mediated correlations in DNA-enzyme interact…
Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption…
We analyze the electric dipole moments (PDMs) and static electric dipole polarizabilities of the alkali--alkaline-earth (Alk-AlkE) dimers by employing finite-field coupled-cluster methods, both in the frameworks of non-relativistic and…
A dynamical rearrangement in the electronic structure of a molecule can be driven by different phenomena, including nuclear motion, electronic coherence or electron correlation. Recording such electronic dynamics and identifying their fate…
Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological…
We develop a phenomenological vector model of polar liquids capable to describe aqueous interactions of macroscopic bodies. It is shown that a strong, long-range and orientationally dependent interaction between macroscopic objects appears…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
We study a means of creating multiparticle entanglement of neutral atoms using pairwise controlled dipole-dipole interactions in a three dimensional optical lattice. For tightly trapped atoms the dipolar interaction energy can be much…
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the…
Magnetite, a naturally abundant mineral, frequently interacts with water in both natural settings and various technical applications, making the study of its surface chemistry highly relevant. In this work, we investigate the hydrogen…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
Electric dipoles of water molecules, enclosed singly in regularly spaced nanopores of a cordierite crystal, become ordered at low temperature due to their mutual interaction and show the frequency dependence of their dielectric…
We use large-scale molecular dynamics to study dynamics at the three-phase contact line in electrowetting of water and electrolytes on no-slip substrates. Under the applied electrostatic potential the line friction at the contact line is…
We consider an electrolyte solution confined by semipermeable membranes in contact with a salt-free solvent. Membranes are uncharged, but since small counter-ions leak-out into infinite salt-free reservoirs, we observe a distance-dependent…
DNA origami is a powerful method to achieve nanoscale folded structures. Despite rapid improvements in folding and purification methods, DNA origami objects are still often produced in small quantities and studied at single molecule scale.…
We construct a model to explore the hydrodynamic interactions of active inclusions in curved biological membranes. The curved membrane is modelled as a two dimensional layer of highly viscous fluid, surrounded by external solvents of…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the…