Crowding induced switching of polymer translocation by the amalgamation of entropy and osmotic pressure.

The translocation of polymers is omnipresent in inherently crowded biological systems. We investigate the dynamics of polymer translocation through a pore in free and crowded environments using Langevin dynamics simulation. We observed a location-dependent translocation rate of monomers showcasing counterintuitive behavior in stark contrast to the bead velocity along the polymer backbone. The free energy calculation of asymmetrically placed polymers indicates a critical number of segments to direct receiver-side translocation. For one-sided crowding, we have identified a critical crowding size revealing a nonzero probability of translocation toward the crowded-side. Moreover, we have observed that shifting the polymer toward the crowded-side compensates for one-sided crowding, yielding an equal probability akin to a crowder-free system. In two-sided crowding, a slight variation in crowder size and packing fraction induces a polymer to switch its translocation direction. These conspicuous yet counter-intuitive phenomena are rationalized by minimalistic theoretical arguments based on osmotic pressure and radial entropic forces.

Bacterial cell-size changes resulting from altering the relative expression of Min proteins.

The timing of cell division, and thus cell size in bacteria, is determined in part by the accumulation dynamics of the protein FtsZ, which forms the septal ring. FtsZ localization depends on membrane-associated Min proteins, which inhibit FtsZ binding to the cell pole membrane. Changes in the relative concentrations of Min proteins can disrupt FtsZ binding to the membrane, which in turn can delay cell division until a certain cell size is reached, in which the dynamics of Min proteins frees the cell membrane long enough to allow FtsZ ring formation. Here, we study the effect of Min proteins relative expression on the dynamics of FtsZ ring formation and cell size in individual Escherichia coli bacteria. Upon inducing overexpression of minE, cell size increases gradually to a new steady-state value. Concurrently, the time required to initiate FtsZ ring formation grows as the size approaches the new steady-state, at which point the ring formation initiates as early as before induction. These results highlight the contribution of Min proteins to cell size control, which may be partially responsible for the size fluctuations observed in bacterial populations, and may clarify how the size difference acquired during asymmetric cell division is offset.

Sequence effects on internal structure of droplets of associative polymers.

Intrinsically disordered proteins (IDPs) can form liquid-like membraneless organelles, gels, and fibers in cells and in vitro. In this study, we propose a simple model of IDPs as associative polymers in poor solvent and explore the formation of transient liquid droplets and their transformation into solid-like aggregates. We use Langevin dynamics simulations of short polymers with two stickers placed symmetrically along their contour to study the effect of the primary sequence of these polymers on their organization inside condensed droplets. We observe that the shape, size, and number of sticker clusters inside the droplet change from a long cylindrical fiber to many compact clusters as one varies the location of stickers along the chain contour. Aging caused by the conversion of intramoleclular to intermolecular associations is observed in droplets of telechelic polymers but not for other sequences of associating polymers. The relevance of our results to condensates of IDPs is discussed.

Assembly along lines in boundary-driven dynamical system.

We introduce a simple dynamical rule in which each particle locates a particle that is farthest from it and moves towards it. Repeated application of this algorithm results in the formation of unusual dynamical patterns: during the process of assembly the system self-organizes into slices of low particle density separated by lines of increasingly high particle density along which most particles move. As the process proceeds, pairs of lines meet and merge with each other until a single line remains and particles move along it towards the zone of assembly. We show that this pattern is governed by particles (attractors) situated on the instantaneous outer boundary of the system and that both in two and in three dimensions the lines are formed by zigzag motion of a particle towards a pair of nearly equidistant attractors. This novel line-dominated assembly is very different from the local assembly in which particles that move towards their nearest neighbors produce point-like clusters that coalesce into new point-like clusters, etc.

Effect of Liquid State Organization on Nanostructure and Strength of Model Multicomponent Solids.

When a multicomponent liquid composed of particles with random interactions is slowly cooled below the freezing temperature, the fluid reorganizes in order to increase (decrease) the number of strong (weak) attractive interactions and solidifies into a structure composed of domains of strongly and of weakly interacting particles. Using Langevin dynamics simulations of a model system we find that the tensile strength, mode of fracture, and thermal stability of such solids differ from those of one-component solids and that these properties can be controlled by the method of preparation.

Effect of size and charge asymmetry on aggregation kinetics of oppositely charged nanoparticles.

We report a theoretical and experimental study of the aggregation kinetics of oppositely charged nanoparticles. Kinetic Monte Carlo simulations are performed for symmetric, charge-asymmetric and size-asymmetric systems of oppositely charged nanoparticles. Simulation results show that both the weight and number average aggregate size kinetics exhibit power law scaling with different exponents for small and intermediate time of evolution. The qualitative behavior of the symmetric and the size asymmetric system are the same, but the charge asymmetric system shows anomalous behavior for intermediate to high particle concentrations. We also observe a strong dependence of power law exponents on the particle concentration. Radius of gyration of the cluster that indicates how nanoparticles inside a cluster are distributed around the center of mass of the cluster shows a non-monotonic time evolution with pronounced peak at higher particle concentration. The dependence of particle concentration on aggregation kinetics as observed by predictive numerical simulation is further verified experimentally by monitoring the time evolution of aggregate size of nanoparticles assemblies of Poly (methacrylic acid) (PMMA) nanoparticles functionalized with oppositely charged ligands. These size and charge tunable asymmetric polymeric nanoparticles were synthesized by modified miniemulsion technique. The integrated approach for studying nanoparticles aggregation as described here renders new insights into super structure formation and morphology optimization which can be potentially useful in the design of new materials, such as organic photovoltaics.

Optimizing the Mass-Specific Activity of Bilirubin Oxidase Adlayers through Combined Electrochemical Quartz Crystal Microbalance and Dual Polarization Interferometry Analyses.

Two surface analysis techniques, dual polarization interferometry (DPI) and analysis by an electrochemical quartz crystal microbalance with dissipation capability (E-QCM-D), were paired to find the deposition conditions that give the highest and most stable electrocatalytic activity per adsorbed mass of enzyme. Layers were formed by adsorption from buffered solutions of bilirubin oxidase from Myrothecium verrucaria at pH 6.0 to planar surfaces, under high enzyme loading (≥1 mg mL(-1)) for contact periods of up to 2 min. Both unmodified and carboxylate-functionalized gold-coated sensors showed that a deposition solution concentration of 10-25 mg mL(-1) gave the highest activity per mass of adsorbed enzyme with an effective catalytic rate constant (k(cat)) of about 60 s(-1). The densification of adsorbed layers observed by DPI correlated with reduced bioactivity observed by parallel E-QCM-D measurements. Postadsorption changes in thickness and density observed by DPI were incorporated into Kelvin-Voigt models of the QCM-D response. The modeled response matched experimental observations when the adlayer viscosity tripled after adsorption.

Surface Characterization and in situ Protein Adsorption Studies on Carbene-Modified Polymers.

Polystyrene thin films were functionalized using a facile two-step chemical protocol involving carbene insertion followed by azo-coupling, permitting the introduction of a range of chemical functional groups, including aniline, hexyl, amine, carboxyl, phenyl, phosphonate diester, and ethylene glycol. X-ray photoelectron spectroscopy (XPS) confirmed the success of the two-step chemical modification with a grafting density of at least 1/10th of the typical loading density (10(14)-10(15)) of a self-assembled monolayer (SAM). In situ, real-time quartz crystal microbalance with dissipation (QCM-D) studies show that the dynamics of binding of bovine serum albumin (BSA) are different at each modified surface. Mass, viscoelastic, and kinetic data were analyzed, and compared to cheminformatic descriptors (i.e., c log P, polar surface area) typically used for drug discovery. Results show that functionalities may either resist or adsorb BSA, and uniquely influence its adsorption dynamics. It is concluded that carbene-based surface modification can usefully influence BSA binding dynamics in a manner consistent with, and more robust than, traditional systems based on SAM chemistry.

Effect of intrinsic curvature on semiflexible polymers.

Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influences the conformational statistics of such polymers. We give exact results for the tangent-tangent spatial correlation function C(r)=, both in two and three dimensions. Contrary to expectation, C(r) does not show any oscillatory behavior, rather decays exponentially and the effective persistence length has strong length dependence for short polymers. We also compute the distribution function P(R) of the end to end distance R and show how curved chains can be distinguished from wormlike chains using loop formation probability.