605 research outputs found
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,
, of a single, infinitely long charged polymer in the presence of
screening. A Gaussian variational method is employed, taking 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, , 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
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, , has a maximum
at a density and a minimum at a density .
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
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