Title: Individual behavior and pairwise interactions between microswimmers in anisotropic liquid

A motile bacterium swims by generating flow in its surrounding liquid. Anisotropy of the suspending liquid significantly modifies the swimming dynamics and corresponding flow signatures of an individual bacterium and impacts collective behavior. We study the interactions between swimming bacteria in an anisotropic environment exemplified by lyotropic chromonic liquid crystal. Our analysis reveals a significant localization of the bacteria-induced flow along a line coaxial with the bacterial body, which is due to strong viscosity anisotropy of the liquid crystal. Despite the fact that the average viscosity of the liquid crystal is two to three orders of magnitude higher than themore » viscosity of pure water, the speed of bacteria in the liquid crystal is of the same order of magnitude as in water. We show that bacteria can transport a cargo (a fluorescent particle) along a predetermined trajectory defined by the direction of molecular orientation of the liquid crystal. We demonstrate that while the hydrodynamic interaction between flagella of two close-by bacteria is negligible, the observed convergence of the swimming speeds as well as flagella waves' phase velocities may occur due to viscoelastic interaction between the bacterial bodies« less

This work presents that the 26S proteasome is a large cellular assembly that mediates the selective degradation of proteins in the nucleus and cytosol and is an established target for anticancer therapeutics. Protein substrates are typically targeted to the proteasome through modification with a polyubiquitin chain, which can be recognized by several proteasome-associated ubiquitin receptors. One of these receptors, RPN13/ADRM1, is recruited to the proteasome through direct interaction with the large scaffolding protein RPN2 within the 19S regulatory particle. To better understand the interactions between RPN13, RPN2, and ubiquitin, we used human proteins to map the RPN13-binding epitope to themore » C-terminal 14 residues of RPN2, which, like ubiquitin, binds the N-terminal pleckstrin-like receptor of ubiquitin (PRU) domain of RPN13. We also report the crystal structures of the RPN13 PRU domain in complex with peptides corresponding to the RPN2 C terminus and ubiquitin. Through mutational analysis, we validated the RPN2-binding interface revealed by our structures and quantified binding interactions with surface plasmon resonance and fluorescence polarization. In contrast to a previous report, we find that RPN13 binds ubiquitin with an affinity similar to that of other proteasome-associated ubiquitin receptors and that RPN2, ubiquitin, and the deubiquitylase UCH37 bind to RPN13 with independent energetics. In conclusion, these findings provide a detailed characterization of interactions that are important for proteasome function, indicate ubiquitin affinities that are consistent with the role of RPN13 as a proteasomal ubiquitin receptor, and have major implications for the development of novel anticancer therapeutics.« less

Presenting a relatively simple ab initio method to calculate full van der Walls interaction potentials between molecules, rules are given for the optimization of basis functions which permit the reliable evaluation of second order long range interactions. Closed expressions for the long range interaction energy are derived in which the orientational dependence is simplified to the utmost. Calculations show that even for molecules which have no dipole moment, such as ethylene, the strongly anisotropic electrostatic interactions are of the same magnitude as the dispersion interactions, but also that the anisotropic (''cross'') terms in the dispersion energy are about equal inmore » size to the corresponding ''quadratic'' terms. Even though these anisotropic forces cancel to a large extent in the cohesion energy of the ethylene crystal, they can have important effects on some of the other crystal properties.« less

In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx andmore » vdW as resulting from a large-scale AIMD simulation of (H{sub 2}O){sub 128} significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, S{sub OO}(Q), and corresponding oxygen-oxygen radial distribution function, g{sub OO}(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, P{sub OOO}(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.« less