arXiv subjects

Peter G. Wolynes

Publications and source records attributed to Peter G. Wolynes.

At least 55 records · Page 3Linked to original sources

arXiv2008

Constructing explicit magnetic analogies for the dynamics of glass forming liquids

By defining a spatially varying replica overlap parameter for a supercooled liquid referenced to an ensemble of fiducial liquid state configurations we explicitly construct a constrained replica free energy functional that maps directly onto an Ising Hamiltonian with both random fields and random interactions whose statistics depend on liquid structure. Renormalization group results for random magnets when combined with these statistics for the Lennard-Jones glass suggest that discontinuous replica symmetry breaking would occur if a liquid with short range interactions could be equilibrated at a sufficiently low temperature where its mean field configurational entropy would vanish, even though the system strictly retains a finite configurational entropy.

cond-mat.soft↗

arXiv2008

Replica theory for fluctuations of the activation barriers in glassy systems

We consider the problem of slow activation dynamics in glassy systems undergoing a random first order phase transition. Using an effective potential approach to supercooled liquids, we determine the spectrum of activation barriers for entropic droplets. We demonstrate that fluctuations of the configurational entropy and of the liquid glass surface tension are crucial to achieve an understanding of the barrier fluctuations in glassy systems and thus are ultimatively responsible for the broad spectrum of excitations and heterogeneous dynamics in glasses. In particular we derive a relation between the length scale for dynamic heterogeneity and the related barrier fluctuations. Diluted entropic droplets are shown to have a Gaussian distribution of barriers, strongly suggesting that non-Gaussian behavior results from droplet-droplet interactions.

cond-mat.dis-nn↗

arXiv2008

On the surface of glasses

Dynamics near the surface of glasses is generally much faster than in the bulk. Neglecting static perturbations of structure at the surface, we use random first order transition theory to show the free energy barrier for activated motion near a free surface should be half that of the bulk at the same temperature. The increased mobility allows the surface layers to descend much further on the energy landscape than the bulk ordinarily does. The simplified RFOT calculation however predicts a limiting value for the configurational entropy a vapor deposited glass may reach as a function of deposition rate. We sketch how mode coupling effects extend the excess free surface mobility into the bulk so that the glass transition temperature is measurably perturbed at depths greater than the naive length scale of dynamic cooperativity.

cond-mat.soft↗

arXiv2008

Hopping induced continuous diffusive dynamics below the non-ergodic transition

In low temperature supercooled liquid, below the ideal mode coupling theory transition temperature, hopping and continuous diffusion are seen to coexist. We present a theory which incorporates interaction between the two processes and shows that hopping can induce continuous diffusion in the otherwise frozen liquid. Several universal features arise from nonlinear interactions between the continuous diffusive dynamics (described here by the mode coupling theory (MCT)) and the activated hopping (described here by the random first order transition theory). We apply the theory to real systems (Salol) to show that the theory correctly predicts the temperature dependence of the non-exponential stretching parameter, $β$, and the primary $α$ relaxation timescale, $τ$. The study explains why, even below the ergodic to non-ergodic transition, the dynamics is well described by MCT. The non-linear coupling between the two dynamical processes modifies the relaxation behavior of the structural relaxation from what would be predicted by a theory with a complete static Gaussian barrier distribution in a manner that may be described as a facilitation effect. Furthermore, the theory explains the observed variation of the stretching exponent $β$ with the fragility parameter, $D$.

cond-mat.stat-mech↗

arXiv2008

Protein Structure Prediction Using Basin-Hopping

Associative memory Hamiltonian structure prediction potentials are not overly rugged, thereby suggesting their landscapes are like those of actual proteins. In the present contribution we show how basin-hopping global optimization can identify low-lying minima for the corresponding mildly frustrated energy landscapes. For small systems the basin-hopping algorithm succeeds in locating both lower minima and conformations closer to the experimental structure than does molecular dynamics with simulated annealing. For large systems the efficiency of basin-hopping decreases for our initial implementation, where the steps consist of random perturbations to the Cartesian coordinates. We implemented umbrella sampling using basin-hopping to further confirm when the global minima are reached. We have also improved the energy surface by employing bioinformatic techniques for reducing the roughness or variance of the energy surface. Finally, the basin-hopping calculations have guided improvements in the excluded volume of the Hamiltonian, producing better structures. These results suggest a novel and transferable optimization scheme for future energy function development.

q-bio.BM↗

arXiv2007

Intermolecular Forces and the Glass Transition

Random first order transition theory is used to determine the role of attractive and repulsive interactions in the dynamics of supercooled liquids. Self-consistent phonon theory, an approximate mean field treatment consistent with random first order transition theory, is used to treat individual glassy configurations, while the liquid phase is treated using common liquid state approximations. The transition temperature $T^{*}_{A} $, the temperature where the onset of activated behavior is predicted by mean field theory, the lower crossover temperature $T_{c}^{*}$ where barrierless motions actually occur through fractal or stringy motions, and $T^{*}_{K} $, the Kauzmann temperature, are calculated in addition to $T^{*}_{g} $, the glass transition temperature that corresponds to laboratory cooling rates. Both the isobaric and isochoric behavior in the supercooled regime are studied, providing results for $ΔC_{V} $ and $ΔC_{p} $ that can be used to calculate the fragility as a function of density and pressure, respectively. The predicted variations in the $α$-relaxation time with temperature and density conform to the empirical density-temperature scaling relations found by Casalini and Roland. We thereby demonstrate the microscopic origin of their observations. Finally, the relationship first suggested by Sastry between the spinodal temperature and the Kauzmann temperatures, as a function of density, is examined. The present microscopic calculations support the existence of an intersection of these two temperatures at sufficiently low temperatures.

cond-mat.soft↗

arXiv2007

Dynamical Heterogeneity and the interplay between activated and mode coupling dynamics in supercooled liquids

We present a theoretical analysis of the dynamic structure factor (DSF) of a liquid at and below the mode coupling critical temperature $T_c$, by developing a self-consistent theoretical treatment which includes the contributions both from continuous diffusion, described using general two coupling parameter ($F_{12}$) mode coupling theory (MCT), and from the activated hopping, described using the random first order transition (RFOT) theory, incorporating the effect of dynamical heterogeneity. The theory is valid over the whole temperature plane and shows correct limiting MCT like behavior above $T_{c}$ and goes over to the RFOT theory near the glass transition temperature, $T_{g}$. Between $T_{c}$ and $T_{g}$, the theory predicts that neither the continuous diffusion, described by pure mode coupling theory, nor the hopping motion alone suffices but both contribute to the dynamics while interacting with each other. We show that the interplay between the two contributions conspires to modify the relaxation behavior of the DSF from what would be predicted by a theory with a complete static Gaussian barrier distribution in a manner that may be described as a facilitation effect. Close to $T_c$, coupling between the short time part of MCT dynamics and hopping reduces the stretching given by the F$_{12}$-MCT theory significantly and accelerates structural relaxation. As the temperature is progressively lowered below $T_c$, the equations yield a crossover from MCT dominated regime to the hopping dominated regime. In the combined theory the dynamical heterogeneity is modified because the low barrier components interact with the MCT dynamics to enhance the relaxation rate below $T_c$ and reduces the stretching that would otherwise arise from an input static barrier height distribution.

cond-mat.stat-mech↗

arXiv2006

Comparison of some recent Excitation Chain Arguments with the Random First Order Transition Theory of Supercooled Liquids and Experiment

We compare a recent excitation chain argument for the glass transition with the earlier random first order transition theory. The key equation determining the activation barriers and size of cooperatively rearranging regions has the same scaling form in both approaches. The random first order transition theory unambiguously predicts the coefficients in the equation giving results that agree with experiment vis a vis the correlation of activation barriers with thermodynamics and that also agree with experimental determination of correlation lengths following the prescription of Berthier et al. The excitation chain approach, while containing more adjustable parameters accommodates those experimental findings only by using unphysical values for those adjustable parameters.

cond-mat.soft↗

arXiv2006

A variational approach to the stochastic aspects of cellular signal transduction

Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process noisy signals. The essential difficulty associated with the master equation approach to solving the stochastic chemical kinetics problem is the enormous number of ordinary differential equations involved. In this work, we show how to achieve tremendous reduction in the dimensionality of specific reaction cascade dynamics by solving variationally an equivalent quantum field theoretic formulation of stochastic chemical kinetics. The present formulation avoids cumbersome commutator computations in the derivation of evolution equations, making more transparent the physical significance of the variational method. We propose novel time-dependent basis functions which work well over a wide range of rate parameters. We apply the new basis functions to describe stochastic signaling in several enzymatic cascades and compare the results so obtained with those from alternative solution techniques. The variational ansatz gives probability distributions that agree well with the exact ones, even when fluctuations are large and discreteness and nonlinearity are important. A numerical implementation of our technique is many orders of magnitude more efficient computationally compared with the traditional Monte Carlo simulation algorithms or the Langevin simulations.

q-bio.QM↗

arXiv2006

Statistical Mechanics of a Cat's Cradle

It is believed that, much like a cat's cradle, the cytoskeleton can be thought of as a network of strings under tension. We show that both regular and random bond-disordered networks having bonds that buckle upon compression exhibit a variety of phase transitions as a function of temperature and extension. The results of self-consistent phonon calculations for the regular networks agree very well with computer simulations at finite temperature. The analytic theory also yields a rigidity onset (mechanical percolation) and the fraction of extended bonds for random networks. There is very good agreement with the simulations by Delaney et al. (Europhys. Lett. 2005). The mean field theory reveals a nontranslationally invariant phase with self-generated heterogeneity of tautness, representing ``antiferroelasticity''.

cond-mat.soft↗

arXiv2006

Protein Structure Prediction: The Next Generation

Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein structure prediction, in particular the development of coarse grained models. We survey results from blind structure prediction. We explore how second generation prediction energy functions can be developed by introducing information from an ensemble of previously simulated structures. This procedure relies on the assumption of a funnelled energy landscape keeping with the principle of minimal frustration. First generation simulated structures provide an improved input for associative memory energy functions in comparison to the experimental protein structures chosen on the basis of sequence alignment.

q-bio.BM↗

arXiv2005

Absolute Rate Theories of Epigenetic Stability

Spontaneous switching events in most characterized genetic switches are rare, resulting in extremely stable epigenetic properties. We show how simple arguments lead to theories of the rate of such events much like the absolute rate theory of chemical reactions corrected by a transmission factor. Both the probability of the rare cellular states that allow epigenetic escape, and the transmission factor, depend on the rates of DNA binding and unbinding events and on the rates of protein synthesis and degradation. Different mechanisms of escape from the stable attractors occur in the nonadiabatic, weakly adiabatic and strictly adiabatic regimes, characterized by the relative values of those input rates.

q-bio.MN↗

arXiv2005

The Shapes of Cooperatively Rearranging Regions in Glass Forming Liquids

The shapes of cooperatively rearranging regions in glassy liquids change from being compact at low temperatures to fractal or ``stringy'' as the dynamical crossover temperature from activated to collisional transport is approached from below. We present a quantitative microscopic treatment of this change of morphology within the framework of the random first order transition theory of glasses. We predict a correlation of the ratio of the dynamical crossover temperature to the laboratory glass transition temperature, and the heat capacity discontinuity at the glass transition, Delta C_p. The predicted correlation agrees with experimental results for the 21 materials compiled by Novikov and Sokolov.

cond-mat.soft↗

arXiv2005

Thermodynamic- Kinetic Correlations in Supercooled Liquids- A Critical Survey of Experimental Data and Predictions of the Random First Order Transition Theory of Glasses

Thermodynamics and kinetics are thought to be linked in glass transitions. The quantitative predictions of -relaxation activation barriers provided by the theory of glasses based on random first order transitions are compared with experiment for 44 substances. The agreement found between the predicted activation energies near Tg and experiment is excellent. These predictions depend on the configurational heat capacity change on vitrification and the entropy of melting the crystal which are experimental inputs.

cond-mat.soft↗

arXiv2005

Electrodynamics of Amorphous Media at Low Temperatures

Amorphous solids exhibit intrinsic, local structural transitions, that give rise to the well known quantum-mechanical two-level systems at low temperatures. We explain the microscopic origin of the electric dipole moment of these two-level systems: The dipole emerges as a result of polarization fluctuations between near degenerate local configurations, which have nearly frozen in at the glass transition. An estimate of the dipole's magnitude, based on the random first order transition theory, is obtained and is found to be consistent with experiment. The interaction between the dipoles is estimated and is shown to contribute significantly to the Grüneisen parameter anomaly in low $T$ glasses. In completely amorphous media, the dipole moments are expected to be modest in size despite their collective origin. In partially crystalline materials, however, very large dipoles may arise, possibly explaining the findings of Bauer and Kador, J. Chem. Phys. {\bf 118}, 9069 (2003).

cond-mat.dis-nn↗

arXiv2005

The Microscopic Quantum Theory of Low Temperature Amorphous Solids

The quantum excitations in glasses have long presented a set of puzzles for condensed matter physicists. A common view is that they are largely disordered analogs of elementary excitations in crystals, supplemented by two level systems which are chemically local entities coming from disorder. A radical revision of this picture argues that the excitations in low temperature glasses are deeply connected to the energy landscape of the glass when it vitrifies: the excitations are not low excited states built on a single ground state but locally defined resonances, high in the energy spectrum of a solid. According to a semiclassical analysis, the two level systems involve resonant collective tunneling motions of around two hundred molecular units which are relics of the mosaic of cooperative motions at the glass transition temperature $T_g$. The density of states of the TLS is determined by $T_g$ and the mosaic's length scale, which is a weak function of the cooling rate. The universality of phonon scattering in insulating glasses is explained. The Boson Peak and the plateau in thermal conductivity, observed at higher temperatures, are also quantitatively understood within the picture as arising from the same cooperative motions, but now accompanied by thermal activation of the mosaic's vibrational modes. The dynamics of some of the local structural transitions have significant quantum corrections to the semiclassical picture. These corrections lead to a deviation of the heat capacity and conductivity from the standard tunneling model results and explain the anomalous time dependence of the heat capacity. Interaction between tunneling centers contributes to the large and negative value of the Grüneisen parameter often observed in glasses.

cond-mat.dis-nn↗

arXiv2005

Bridging the Gap Between the Mode Coupling and the Random First Order Transition Theories of Structural Relaxation in Liquids

A unified treatment of structural relaxation in a deeply supercooled glassy liquid is developed which extends the existing mode coupling theory (MCT) by incorporating the effects of activated events by using the concepts from the random first order transition (RFOT) theory. We show how the decay of the dynamic structure factor is modified by localized activated events (called instantons) which lead to the spatial reorganization of molecules in the region where the instanton pops up. The instanton vertex added to the usual MCT depicts the probability and consequences of such an event which can be derived from the random first order transition theory. The vertex is proportional to $exp(-A/s_{c})$ where $s_{c}$ is the configurational entropy. Close to the glass transition temperature, $T_{g}$, since $s_{c}$ is diminishing, the activated process slows beyond the time window and this eventually leads to an arrest of the structural relaxation as expected for glasses. The combined treatment describes the dynamic structure factor in deeply supercooled liquid fairly well, with a hopping dominated decay following the MCT plateau.

cond-mat.dis-nn↗

arXiv2005

Activated events in glasses: the structure of entropic droplets

Using an effective potential approach, we present a replica instanton theory for the dynamics of entropic droplets in glassy systems. Replica symmetry breaking in the droplet interface leads to a length scale dependent reduction of the droplet surface tension and changes the character of the dynamical heterogeneity and activated dynamics in glasses.

cond-mat.dis-nn↗