Discrete elastic model for stretching-induced flagellar polymorphs

Force-induced reversible transformations between coiled and normal polymorphs of bacterial flagella have been observed in recent optical-tweezer experiment. We introduce a discrete elastic rod model with two competing helical states governed by a fluctuating spin-like variable that represents the underlying conformational states of flagellin monomers. Using hybrid Brownian dynamics Monte-Carlo simulations, we show that a helix undergoes shape transitions dominated by domain wall nucleation and motion in response to externally applied uniaxial tension. A scaling argument for the critical force is presented in good agreement with experimental and simulation results. Stretching rate-dependent elasticity including a buckling instability are found, also consistent with the experiment

Variational theory for a single polyelectrolyte chain revisited

We reconsider the electrostatic contribution to the persistence length, $\ell_e$, of a single, infinitely long charged polymer in the presence of screening. A Gaussian variational method is employed, taking $\ell_e$ as the only variational parameter. For weakly charged and flexible chains, crumpling occurs at small length scales because conformational fluctuations overcome electrostatic repulsion. The electrostatic persistence length depends on the square of the screening length, $\ell_e\sim\kappa^{-2}$, as first argued by Khokhlov and Khachaturian by applying the Odijk-Skolnick-Fixman (OSF) theory to a string of crumpled blobs. We compare our approach to previous theoretical works (including variational formulations) and show that the result $\ell_e\sim\kappa^{-1}$ found by several authors comes from the improper use of a cutoff at small length scales. For highly charged and stiff chains, crumpling does not occur; here we recover the OSF result and validate the perturbative calculation for slightly bent rods.Comment: 11 pages, 6 figure

Dielectric boundary effects on the interaction between planar charged surfaces with counterions only

Using Monte Carlo simulations in conjunction with periodic Green’s function methods, we study the interaction between planar charged surfaces with point-like counterions only in the presence of dielectric boundaries. Based on the calculated pressure profiles, we derive phase diagrams featuring correlation-induced negative pressure and thus attraction between the plates for large coupling parameters, i.e., low temperature or high surface charge and high ion valency. The counterion density profiles for low-dielectric and high-dielectric (metallic) surfaces are very different from the idealized case of a homogeneous dielectric constant. By contrast, the phase diagrams including the critical point and the two-phase coexistence region are rather insensitive to the presence of dielectric boundary effects. The single-image approximation that has been used in simulations before is by comparison with the exact formalism shown to be very accurate for low-dielectric surfaces but not for metallic surfaces

Dielectric boundary effects on the interaction between planar charged surfaces with counterions only

Using Monte Carlo simulations in conjunction with periodic Green’s function methods, we study the interaction between planar charged surfaces with point-like counterions only in the presence of dielectric boundaries. Based on the calculated pressure profiles, we derive phase diagrams featuring correlation-induced negative pressure and thus attraction between the plates for large coupling parameters, i.e., low temperature or high surface charge and high ion valency. The counterion density profiles for low-dielectric and high-dielectric (metallic) surfaces are very different from the idealized case of a homogeneous dielectric constant. By contrast, the phase diagrams including the critical point and the two-phase coexistence region are rather insensitive to the presence of dielectric boundary effects. The single-image approximation that has been used in simulations before is by comparison with the exact formalism shown to be very accurate for low-dielectric surfaces but not for metallic surfaces

Field theory fo charged fluids and colloids

A systematic field theory is presented for charged systems. The one-loop level corresponds to the classical Debye-H\"uckel (DH) theory, and exhibits the full hierarchy of multi-body correlations determined by pair-distribution functions given by the screened DH potential. Higher-loop corrections can lead to attractive pair interactions between colloids in asymmetric ionic environments. The free energy follows as a loop-wise expansion in half-integer powers of the density; the resulting two-phase demixing region shows pronounced deviations from DH theory for strongly charged colloids.Comment: 4 pages, 2 ps figs; new version corrects some minor typo

Counterion density profiles at charged flexible membranes

Counterion distributions at charged soft membranes are studied using perturbative analytical and simulation methods in both weak coupling (mean-field or Poisson-Boltzmann) and strong coupling limits. The softer the membrane, the more smeared out the counterion density profile becomes and counterions pentrate through the mean-membrane surface location, in agreement with anomalous scattering results. Membrane-charge repulsion leads to a short-scale roughening of the membrane.Comment: 4 pages, 4 figure

Instabilities and turbulence-like dynamics in an oppositely driven binary particle mixture

Using extensive particle-based simulations, we investigate out-of-equilibrium pattern dynamics in an oppositely driven binary particle system in two dimensions. A surprisingly rich dynamical behavior including lane formation, jamming, oscillation and turbulence-like dynamics is found. The ratio of two friction coefficients is a key parameter governing the stability of lane formation. When the friction coefficient transverse to the external force direction is sufficiently small compared to the longitudinal one, the lane structure becomes unstable to shear-induced disturbances, and the system eventually exhibits a dynamical transition into a novel turbulence-like phase characterized by random convective flows. We numerically construct an out-of-equilibrium phase diagram. Statistical analysis of complex spatio-temporal dynamics of the fully nonlinear turbulence-like phase suggests its apparent reminiscence to the swarming dynamics in certain active matter systems.Comment: 6 pages, 6 figures, accepted for publication in EP

DNA-Protein Binding Rates: Bending Fluctuation and Hydrodynamic Coupling Effects

We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory focuses on two competing effects: polymer shape fluctuations, which speed up association, and the hydrodynamic coupling between the diffusing particle and the chain, which slows down association. Polymer bending fluctuations are described using a mean field dynamical theory, while the hydrodynamic coupling between polymer and particle is incorporated through a simple heuristic approximation. Both of these we validate through comparison with Brownian dynamics simulations. Neither of the effects has been fully considered before in the biophysical context, and we show they are necessary to form accurate estimates of reaction processes. The association rate depends on the stiffness of the polymer and the particle size, exhibiting a maximum for intermediate persistence length and a minimum for intermediate particle radius. In the parameter range relevant to DNA-protein binding, the rate increase is up to 100% compared to the Smoluchowski result for simple center-of-mass motion. The quantitative predictions made by the theory can be tested experimentally.Comment: 21 pages, 11 figures, 1 tabl

Thermodynamic and dynamic anomalies for a three dimensional isotropic core-softened potential

Using molecular dynamics simulations and integral equations (Rogers-Young, Percus-Yevick and hypernetted chain closures) we investigate the thermodynamic of particles interacting with continuous core-softened intermolecular potential. Dynamic properties are also analyzed by the simulations. We show that, for a chosen shape of the potential, the density, at constant pressure, has a maximum for a certain temperature. The line of temperatures of maximum density (TMD) was determined in the pressure-temperature phase diagram. Similarly the diffusion constant at a constant temperature, $D$, has a maximum at a density $\rho_{max}$ and a minimum at a density $\rho_{min}<\rho_{max}$. In the pressure-temperature phase-diagram the line of extrema in diffusivity is outside of TMD line. Although in this interparticle potential lacks directionality, this is the same behavior observed in SPC/E water.Comment: 16 page

Hydration effects turn a highly stretched polymer from an entropic into an energetic spring

Polyethylene glycol (PEG) is a structurally simple and nontoxic water-soluble polymer that is widely used in medical and pharmaceutical applications as molecular linker and spacer. In such applications, PEG’s elastic response against conformational deformations is key to its function. According to text-book knowledge, a polymer reacts to the stretching of its end-to-end separation by a decrease in entropy that is due to the reduction of available conformations, which is why polymers are commonly called entropic springs. By a combination of single-molecule force spectroscopy experiments with molecular dynamics simulations in explicit water, we show that entropic hydration effects almost exactly compensate the chain conformational entropy loss at high stretching. Our simulations reveal that this entropic compensation is due to the stretching-induced release of water molecules that in the relaxed state form double hydrogen bonds with PEG. As a consequence, the stretching response of PEG is predominantly of energetic, not of entropic, origin at high forces and caused by hydration effects, while PEG backbone deformations only play a minor role. These findings demonstrate the importance of hydration for the mechanics of macromolecules and constitute a case example that sheds light on the antagonistic interplay of conformational and hydration degrees of freedom