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 $^{19}$C and $^{17}$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 $l_i>1$ 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