6,456 research outputs found
Markov state modeling reveals competing collective hydrogen bond rearrangements in liquid water
We construct a Markov state model for the dynamic rearrangement of the local hydrogen bond network in liquid water. The model is based on trajectories from classical molecular dynamics simulations and accounts for the dynamics of relative angular and separation coordinates of water molecules. We analyze first the conformational subspace of three water molecules and find five well separated dynamic modes with reaction times in the 2 - 5 ps range, which correspond to different interchanges of hydrogen bond donor and acceptors, followed by an entire continuum spectrum of modes. We then analyze the switching of one hydrogen bond between two water molecules and derive the complete transition network. The most probable pathway corresponds to a direct switch without an intermediate, in agreement with previous studies. However, a considerable fraction of paths proceeds along different intermediate states that involve alternative hydrogen bonds or unbound states
Testing the relevance of effective interaction potentials between highly charged colloids in suspension
Combining cell and Jellium model mean-field approaches, Monte Carlo together
with integral equation techniques, and finally more demanding many-colloid
mean-field computations, we investigate the thermodynamic behavior, pressure
and compressibility of highly charged colloidal dispersions, and at a more
microscopic level, the force distribution acting on the colloids. The
Kirkwood-Buff identity provides a useful probe to challenge the
self-consistency of an approximate effective screened Coulomb (Yukawa)
potential between colloids. Two effective parameter models are put to the test:
cell against renormalized Jellium models
Poisson-Boltzmann Theory of Charged Colloids: Limits of the Cell Model for Salty Suspensions
Thermodynamic properties of charge-stabilised colloidal suspensions are
commonly modeled by implementing the mean-field Poisson-Boltzmann (PB) theory
within a cell model. This approach models a bulk system by a single macroion,
together with counterions and salt ions, confined to a symmetrically shaped,
electroneutral cell. While easing solution of the nonlinear PB equation, the
cell model neglects microion-induced correlations between macroions, precluding
modeling of macroion ordering phenomena. An alternative approach, avoiding
artificial constraints of cell geometry, maps a macroion-microion mixture onto
a one-component model of pseudo-macroions governed by effective interactions.
In practice, effective-interaction models are usually based on linear screening
approximations, which can accurately describe nonlinear screening only by
incorporating an effective (renormalized) macroion charge. Combining charge
renormalization and linearized PB theories, in both the cell model and an
effective-interaction (cell-free) model, we compute osmotic pressures of highly
charged colloids and monovalent microions over a range of concentrations. By
comparing predictions with primitive model simulation data for salt-free
suspensions, and with predictions of nonlinear PB theory for salty suspensions,
we chart the limits of both the cell model and linear-screening approximations
in modeling bulk thermodynamic properties. Up to moderately strong
electrostatic couplings, the cell model proves accurate in predicting osmotic
pressures of deionized suspensions. With increasing salt concentration,
however, the relative contribution of macroion interactions grows, leading
predictions of the cell and effective-interaction models to deviate. No
evidence is found for a liquid-vapour phase instability driven by monovalent
microions. These results may guide applications of PB theory to soft materials.Comment: 27 pages, 5 figures, special issue of Journal of Physics: Condensed
Matter on "Classical density functional theory methods in soft and hard
matter
Wavelet treatment of the intra-chain correlation functions of homopolymers in dilute solutions
Discrete wavelets are applied to parametrization of the intra-chain two-point
correlation functions of homopolymers in dilute solutions obtained from Monte
Carlo simulation. Several orthogonal and biorthogonal basis sets have been
investigated for use in the truncated wavelet approximation. Quality of the
approximation has been assessed by calculation of the scaling exponents
obtained from des Cloizeaux ansatz for the correlation functions of
homopolymers with different connectivities in a good solvent. The resulting
exponents are in a better agreement with those from the recent renormalisation
group calculations as compared to the data without the wavelet denoising. We
also discuss how the wavelet treatment improves the quality of data for
correlation functions from simulations of homopolymers at varied solvent
conditions and of heteropolymers.Comment: RevTeX, 19 pages, 7 PS figures. Accepted for publication in PR
Deconvolution of dynamic mechanical networks
Time-resolved single-molecule biophysical experiments yield data that contain
a wealth of dynamic information, in addition to the equilibrium distributions
derived from histograms of the time series. In typical force spectroscopic
setups the molecule is connected via linkers to a read-out device, forming a
mechanically coupled dynamic network. Deconvolution of equilibrium
distributions, filtering out the influence of the linkers, is a straightforward
and common practice. We have developed an analogous dynamic deconvolution
theory for the more challenging task of extracting kinetic properties of
individual components in networks of arbitrary complexity and topology. Our
method determines the intrinsic linear response functions of a given molecule
in the network, describing the power spectrum of conformational fluctuations.
The practicality of our approach is demonstrated for the particular case of a
protein linked via DNA handles to two optically trapped beads at constant
stretching force, which we mimic through Brownian dynamics simulations. Each
well in the protein free energy landscape (corresponding to folded, unfolded,
or possibly intermediate states) will have its own characteristic equilibrium
fluctuations. The associated linear response function is rich in physical
content, since it depends both on the shape of the well and its diffusivity---a
measure of the internal friction arising from such processes like the transient
breaking and reformation of bonds in the protein structure. Starting from the
autocorrelation functions of the equilibrium bead fluctuations measured in this
force clamp setup, we show how an experimentalist can accurately extract the
state-dependent protein diffusivity using a straightforward two-step procedure.Comment: 9 pages, 3 figures + supplementary material 14 pages, 4 figure
The osmotic pressure of charged colloidal suspensions: A unified approach to linearized Poisson-Boltzmann theory
We study theoretically the osmotic pressure of a suspension of charged
objects (e.g., colloids, polyelectrolytes, clay platelets, etc.) dialyzed
against an electrolyte solution using the cell model and linear
Poisson-Boltzmann (PB) theory. From the volume derivative of the grand
potential functional of linear theory we obtain two novel expressions for the
osmotic pressure in terms of the potential- or ion-profiles, neither of which
coincides with the expression known from nonlinear PB theory, namely, the
density of microions at the cell boundary. We show that the range of validity
of linearization depends strongly on the linearization point and proof that
expansion about the selfconsistently determined average potential is optimal in
several respects. For instance, screening inside the suspension is
automatically described by the actual ionic strength, resulting in the correct
asymptotics at high colloid concentration. Together with the analytical
solution of the linear PB equation for cell models of arbitrary dimension and
electrolyte composition explicit and very general formulas for the osmotic
pressure ensue. A comparison with nonlinear PB theory is provided. Our analysis
also shows that whether or not linear theory predicts a phase separation
depends crucially on the precise definition of the pressure, showing that an
improper choice could predict an artificial phase separation in systems as
important as DNA in physiological salt solution.Comment: 16 pages, 5 figures, REVTeX4 styl
Fine structure of the isoscalar giant quadrupole resonance in 40Ca due to Landau damping?
The fragmentation of the Isoscalar Giant Quadrupole Resonance (ISGQR) in 40Ca
has been investigated in high energy-resolution experiments using proton
inelastic scattering at E_p = 200 MeV. Fine structure is observed in the region
of the ISGQR and its characteristic energy scales are extracted from the
experimental data by means of a wavelet analysis. The experimental scales are
well described by Random Phase Approximation (RPA) and second-RPA calculations
with an effective interaction derived from a realistic nucleon-nucleon
interaction by the Unitary Correlation Operator Method (UCOM). In these results
characteristic scales are already present at the mean-field level pointing to
their origination in Landau damping, in contrast to the findings in heavier
nuclei and also to SRPA calculations for 40Ca based on phenomenological
effective interactions, where fine structure is explained by the coupling to
two-particle two-hole (2p-2h) states.Comment: Phys. Lett. B, in pres
Exotic fluids and crystals of soft polymeric colloids
We discuss recent developments and present new findings in the colloidal
description of soft polymeric macromolecular aggregates. For various
macromolecular architectures, such as linear chains, star polymers, dendrimers
and polyelectrolyte stars, the effective interactions between suitably chosen
coordinates are shown to be ultrasoft, i.e., they either remain finite or
diverge very slowly at zero separation. As a consequence, the fluid phases have
unusual characteristics, including anomalous pair correlations and mean-field
like thermodynamic behaviour. The solid phases can exhibit exotic, strongly
anisotropic as well as open crystal structures. For example, the diamond and
the A15-phase are shown to be stable at sufficiently high concentrations.
Reentrant melting and clustering transitions are additional features displayed
by such systems, resulting in phase diagrams with a very rich topology. We
emphasise that many of these effects are fundamentally different from the usual
archetypal hard sphere paradigm. Instead, we propose that these fluids fall
into the class of mean-field fluids.Comment: 22 pages, uses iopart.cls and iopart10.clo; submitted to Journal of
Physics Condensed Matter, special issue in honour of professor Peter Puse
Dissipation and spontaneous symmetry breaking in brain dynamics
We compare the predictions of the dissipative quantum model of brain with
neurophysiological data collected from electroencephalograms resulting from
high-density arrays fixed on the surfaces of primary sensory and limbic areas
of trained rabbits and cats. Functional brain imaging in relation to behavior
reveals the formation of coherent domains of synchronized neuronal oscillatory
activity and phase transitions predicted by the dissipative model.Comment: Restyled, slight changes in title and abstract, updated bibliography,
J. Phys. A: Math. Theor. Vol. 41 (2008) in prin
Initial State Dependence of the Breakup of Weakly Bound Carbon Isotopes
The one-neutron nuclear breakup from the Carbon isotopes C and
C, is calculated as an example of application of the theory of transfer
to the continuum reactions in the formulation which includes spin coupling.
The effect of the energy sharing between the parallel and transverse neutron
momentum distributions is taken into account thus resulting in a theory which
is more general than sudden eikonal approaches. Both effects are necessary to
understand properly the breakup from not too weakly bound orbitals.
Breakup which leaves the core into an excited state below particle threshold is
also considered. The core-target interaction is treated in the smooth cut-off
approximation. By comparing to presently available experimental data we show
how to make some hypothesis on the quantum numbers and occupancy of the neutron
initial state. Possible ambiguities in the interpretation of inclusive cross
sections are discussed.Comment: 22 RevTeX pages,3 ps figures. Phys. Rev. C, accepte
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