arXiv subjects

Herbert Levine

Publications and source records attributed to Herbert Levine.

At least 91 records · Page 5Linked to original sources

arXiv2002

Non-native beta-sheet formation: insights into protein amyloidosis

Protein amyloidosis is a cytopathological process characterized by the formation of highly beta-sheet-rich fibrils. How this process occurs and how to prevent/treat the associated diseases are not completely understood. Here, we carry out a theoretical investigation of sequence-independent beta-sheet formation, based on recent findings regarding the cooperativity of hydrogen-bond network formation. Our results strongly suggest that in vivo beta-sheet aggregation is induced by inter-sheet stacking dynamics. This leads to a prediction for the minimal length of susceptible polymer needed to form such an aggregate. Remarkably, the prediction corresponds quite well with the critical lengths detected in poly-glutamine-related diseases. Our work therefore provides a theoretical framework capable of understanding the underlying mechanism and shedding light on therapy strategies of protein amyloidosis.

cond-mat.soft↗

arXiv2001

Mode I fracture in a nonlinear lattice with viscoelastic forces

We study Mode I fracture in a viscoelastic lattice model with a nonlinear force law, with a focus on the velocity and linear stability of the steady-state propagating solution. This study is a continuation both of the study of the piece-wise linear model in Mode I, and the study of more general nonlinear force laws in Mode III fracture. At small driving, there is a strong dependency of the velocity curve on the dissipation and a strong sensitivity to the smoothness of the force law at large dissipation. At large driving we calculate, via a linear stability analysis, the critical velocity for the onset of instability as a function of the smoothness, the dissipation and the ratio of lattice spacing to critical extension. This critical velocity is seen to be very sensitive to these parameters. We confirm our calculations via direct numerical simulations of the initial value problem.

cond-mat.mtrl-sci↗

arXiv2001

Mechanisms underlying sequence-independent beta-sheet formation

We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation effects and the angular dependence (on the protein backbone) of hydrogen bond formation. The thermodynamics of this model is studied by comparing the restricted partition functions obtained by "unfreezing" successively larger segments of the native beta-sheet structure. Our results suggest that solvation dynamics together with the aforementioned angular dependence gives rise to a generic cooperativity in this class of systems; this result explains why pathological aggregates involving beta-sheet cores can form from many different proteins. Our work provides the foundation for the construction of phenomenological models to investigate the competition between native folding and non-specific aggregation.

cond-mat.soft↗

arXiv2001

Phase-Field Model of Mode III Dynamic Fracture

We introduce a phenomenological continuum model for mode III dynamic fracture that is based on the phase-field methodology used extensively to model interfacial pattern formation. We couple a scalar field, which distinguishes between ``broken'' and ``unbroken'' states of the system, to the displacement field in a way that consistently includes both macroscopic elasticity and a simple rotationally invariant short scale description of breaking. We report two-dimensional simulations that yield steady-state crack motion in a strip geometry above the Griffith threshold.

cond-mat.soft↗

arXiv2001

Microscopic Selection of Fluid Fingering Pattern

We study the issue of the selection of viscous fingering patterns in the limit of small surface tension. Through detailed simulations of anisotropic fingering, we demonstrate conclusively that no selection independent of the small-scale cutoff (macroscopic selection) occurs in this system. Rather, the small-scale cutoff completely controls the pattern, even on short time scales, in accord with the theory of microscopic solvability. We demonstrate that ordered patterns are dynamically selected only for not too small surface tensions. For extremely small surface tensions, the system exhibits chaotic behavior and no regular pattern is realized.

nlin.PS↗

arXiv2000

Nonlinear lattice model of viscoelastic Mode III fracture

We study the effect of general nonlinear force laws in viscoelastic lattice models of fracture, focusing on the existence and stability of steady-state Mode III cracks. We show that the hysteretic behavior at small driving is very sensitive to the smoothness of the force law. At large driving, we find a Hopf bifurcation to a straight crack whose velocity is periodic in time. The frequency of the unstable bifurcating mode depends on the smoothness of the potential, but is very close to an exact period-doubling instability. Slightly above the onset of the instability, the system settles into a exactly period-doubled state, presumably connected to the aforementioned bifurcation structure. We explicitly solve for this new state and map out its velocity-driving relation.

cond-mat.mtrl-sci↗

arXiv2000

Self-organization in systems of self-propelled particles

We investigate a discrete model consisting of self-propelled particles that obey simple interaction rules. We show that this model can self-organize and exhibit coherent localized solutions in one- and in two-dimensions.In one-dimension, the self-organized solution is a localized flock of finite extent in which the density abruptly drops to zero at the edges.In two-dimensions, we focus on the vortex solution in which the particles rotate around a common center and show that this solution can be obtained from random initial conditions, even in the absence of a confining boundary. Furthermore, we develop a continuum version of our discrete model and demonstrate that the agreement between the discrete and the continuum model is excellent.

cond-mat.soft↗

arXiv2000

Steady-state mode III cracks in a viscoelastic lattice model

We extend the Slepyan solution of the problem of a steady-state crack in an infinite ideally brittle lattice model to include dissipation in the form of Kelvin viscosity. As a demonstration of this technique, based on the Wiener-Hopf method, we apply the method to mode III cracks in a square lattice. We use this solution to find the critical velocity at which the steady-state solution becomes inconsistent due to additional bond-breaking; this point signaling the onset of complex dynamical behavior.

cond-mat.mtrl-sci↗

arXiv2000

Steady-state mode I cracks in a viscoelastic triangular lattice

We continue our study of the exact solutions for steady-state cracks in ideally brittle viscoelastic lattice models by focusing on mode I in a triangular system. The issues we address include the crack velocity versus driving curve as well as the onset of additional bond-breaking, signaling the emergence of complex spatio-temporal behavior. Somewhat surprisingly, the critical velocity for this transition becomes a decreasing function of the dissipation for sufficiently large values thereof. At the end, we briefly discuss the possible relevance of our findings for experiments on mode I crack instabilities.

cond-mat.mtrl-sci↗

arXiv1999

Discrete stochastic modeling of calcium channel dynamics

We propose a simple discrete stochastic model for calcium dynamics in living cells. Specifically, the calcium concentration distribution is assumed to give rise to a set of probabilities for the opening/closing of channels which release calcium thereby changing those probabilities. We study this model in one dimension, analytically in the mean-field limit of large number of channels per site N, and numerically for small N. As the number of channels per site is increased, the transition from a non-propagating region of activity to a propagating one changes in nature from one described by directed percolation to that of deterministic depinning in a spatially discrete system. Also, for a small number of channels a propagating calcium wave can leave behind a novel fluctuation-driven state, in a parameter range where the limiting deterministic model exhibits only single pulse propagation.

patt-sol↗

arXiv1999

Two State Behavior in a Solvable Model of $β$-hairpin folding

Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $β$-hairpin, motivated by the fact that folding of a $β$-hairpin captures much of the basic physics of protein folding. We argue that the coupling of ``primary'' backbone stiffness and ``secondary'' contact formation (similar to the coupling between the ``secondary'' and ``tertiary'' structure in globular proteins), caused for example by side-chain packing regularities, is responsible for producing an all-or-none 2-state $β$-hairpin formation. We also develop a recursive relation to compute the phase diagram and single exponential folding/unfolding rate arising via a dominant transition state.

cond-mat.soft↗

arXiv1999

A Thermodynamic Model for Receptor Clustering

Intracellular signaling often arises from ligand-induced oligomerization of cell surface receptors. This oligomerization or clustering process is fundamentally a cooperative behavior between near-neighbor receptor molecules; the properties of this cooperative process clearly affects the signal transduction. Recent investigations have revealed the molecular basis of receptor-receptor interactions, but a simple theoretical framework for using this data to predict cluster formation has been lacking. Here, we propose a simple, coarse-grained, phenomenological model for ligand-modulated receptor interactions and discuss its equilibrium properties via mean-field theory. The existence of a first-order transition for this model has immediate implications regarding the robustness of the cellular signaling response.

cond-mat.soft↗

arXiv1999

Self-organized Vortex State in Two-dimensional Dictyostelium Dynamics

We present results of experiments on the dynamics of Dictyostelium discoideum in a novel set-up which constraints cell motion to a plane. After aggregation, the amoebae collect into round ''pancake" structures in which the cells rotate around the center of the pancake. This vortex state persists for many hours and we have explicitly verified that the motion is not due to rotating waves of cAMP. To provide an alternative mechanism for the self-organization of the Dictyostelium cells, we have developed a new model of the dynamics of self-propelled deformable objects. In this model, we show that cohesive energy between the cells, together with a coupling between the self-generated propulsive force and the cell's configuration produces a self-organized vortex state. The angular velocity profiles of the experiment and of the model are qualitatively similar. The mechanism for self-organization reported here can possibly explain similar vortex states in other biological systems.

patt-sol↗

arXiv1999

Arrested Cracks in Nonlinear Lattice Models of Brittle Fracture

We generalize lattice models of brittle fracture to arbitrary nonlinear force laws and study the existence of arrested semi-infinite cracks. Unlike what is seen in the discontinuous case studied to date, the range in driving displacement for which these arrested cracks exist is very small. Also, our results indicate that small changes in the vicinity of the crack tip can have an extremely large effect on arrested cracks. Finally, we briefly discuss the possible relevance of our findings to recent experiments.

cond-mat.soft↗

arXiv1998

Steady-State Cracks in Viscoelastic Lattice Models

We study the steady-state motion of mode III cracks propagating on a lattice exhibiting viscoelastic dynamics. The introduction of a Kelvin viscosity $η$ allows for a direct comparison between lattice results and continuum treatments. Utilizing both numerical and analytical (Wiener-Hopf) techniques, we explore this comparison as a function of the driving displacement $Δ$ and the number of transverse sites $N$. At any $N$, the continuum theory misses the lattice-trapping phenomenon; this is well-known, but the introduction of $η$ introduces some new twists. More importantly, for large $N$ even at large $Δ$, the standard two-dimensional elastodynamics approach completely misses the $η$-dependent velocity selection, as this selection disappears completely in the leading order naive continuum limit of the lattice problem.

cond-mat.soft↗

arXiv1998

Interfacial Velocity Corrections due to Multiplicative Noise

The problem of velocity selection for reaction fronts has been intensively investigated, leading to the successful marginal stability approach for propagation into an unstable state. Because the front velocity is controlled by the leading edge which perforce has low density, it is interesting to study the role that finite particle number fluctuations have on this picture. Here, we use the well-known mapping of discrete Markov processes to stochastic differential equations and focus on the front velocity in the simple $A+A \stackrel{\leftarrow}{\to} A$ system. Our results are consistent with a recent (heuristic) proposal that $v_{MS} - v \sim {1\over \ln^2 {N}}$.

cond-mat.soft↗

arXiv1997

Mutator Dynamics on a Smooth Evolutionary Landscape

We investigate a model of evolutionary dynamics on a smooth landscape which features a ``mutator'' allele whose effect is to increase the mutation rate. We show that the expected proportion of mutators far from equilibrium, when the fitness is steadily increasing in time, is governed solely by the transition rates into and out of the mutator state. This results is a much faster rate of fitness increase than would be the case without the mutator allele. Near the fitness equilibrium, however, the mutators are severely suppressed, due to the detrimental effects of a large mutation rate near the fitness maximum. We discuss the results of a recent experiment on natural selection of E. coli in the light of our model.

patt-sol↗

arXiv1997

Unicellular algal growth: A biomechanical approach to cell wall dynamics

We present a model for unicellular algal growth as motivated by several experiments implicating the importance of calcium ions and ``loosening'' enzymes in morphogenesis. A growing cell at rest in a diffusive calcium solution is viewed as an elastic shell on short timescales. For a given turgor pressure, we calculate the stressed shapes of the wall elements whose elastic properties are determined by Young's modulus and the thickness of the wall. The local enzyme concentration then determines the rate at which the unstressed shape of a wall element relaxes toward its stressed shape. The local wall thickness is calculated from the calcium-mediated addition of material and thinning due to elongation. We use this model to calculate growth rates for small perturbations to a circular cell. We find an instability related to modulations of the wall thickness, leading to growth rates which peak at a finite wave number.

patt-sol↗