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James P. Sethna

Publications and source records attributed to James P. Sethna.

At least 91 records · Page 5Linked to original sources

Collective Motion of Moshers at Heavy Metal Concerts

Human collective behavior can vary from calm to panicked depending on social context. Using videos publicly available online, we study the highly energized collective motion of attendees at heavy metal concerts. We find these extreme social gatherings generate similarly extreme behaviors: a disordered gas-like state called a mosh pit and an ordered vortex-like state called a circle pit. Both phenomena are reproduced in flocking simulations demonstrating that human collective behavior is consistent with the predictions of simplified models.

physics.soc-ph↗

Scaling theory of continuum dislocation dynamics in three dimensions: Self-organized fractal pattern formation

We focus on mesoscopic dislocation patterning via a continuum dislocation dynamics theory (CDD) in three dimensions (3D). We study three distinct physically motivated dynamics which consistently lead to fractal formation in 3D with rather similar morphologies, and therefore we suggest that this is a general feature of the 3D collective behavior of geometrically necessary dislocation (GND) ensembles. The striking self-similar features are measured in terms of correlation functions of physical observables, such as the GND density, the plastic distortion, and the crystalline orientation. Remarkably, all these correlation functions exhibit spatial power-law behaviors, sharing a single underlying universal critical exponent for each type of dynamics.

cond-mat.stat-mech↗

From damage percolation to crack nucleation through finite size criticality

We present a unified theory of fracture in disordered brittle media that reconciles apparently conflicting results reported in the literature. Our renormalization group based approach yields a phase diagram in which the percolation fixed point, expected for infinite disorder, is unstable for finite disorder and flows to a zero-disorder nucleation-type fixed point, thus showing that fracture has mixed first order and continuous character. In a region of intermediate disorder and finite system sizes, we predict a crossover with mean-field avalanche scaling. We discuss intriguing connections to other phenomena where critical scaling is only observed in finite size systems and disappears in the thermodynamic limit.

cond-mat.stat-mech↗

Critical Casimir forces in cellular membranes

Recent experiments suggest that membranes of living cells are tuned close to a miscibility critical point in the 2D Ising universality class. We propose that one role for this proximity to criticality in live cells is to provide a conduit for relatively long-ranged critical Casimir forces. Using techniques from conformal field theory we calculate potentials of mean force between membrane bound inclusions mediated by their local interactions with the composition order parameter. We verify these calculations using Monte-Carlo where we also compare critical and off-critical results. Our findings suggest that membrane bound proteins experience weak yet long range forces mediated by critical composition fluctuations in the plasma membranes of living cells.

q-bio.QM↗

Structural Susceptibility and Separation of Time Scales in the van der Pol Oscillator

We use an extension of the van der Pol oscillator as an example of a system with multiple time scales to study the susceptibility of its trajectory to polynomial perturbations in the dynamics. A striking feature of many nonlinear, multi-parameter models is an apparently inherent insensitivity to large magnitude variations in certain linear combinations of parameters. This phenomenon of "sloppiness" is quantified by calculating the eigenvalues of the Hessian matrix of the least-squares cost function which typically span many orders of magnitude. The van der Pol system is no exception: Perturbations in its dynamics show that most directions in parameter space weakly affect the limit cycle, whereas only a few directions are stiff. With this study we show that separating the time scales in the van der Pol system leads to a further separation of eigenvalues. Parameter combinations which perturb the slow manifold are stiffer and those which solely affect the transients in the dynamics are sloppier.

math.NA↗

Geodesic acceleration and the small-curvature approximation for nonlinear least squares

It has been shown numerically that the performance of the Levenberg-Marquardt algorithm can be improved by including a second order correction known as the geodesic acceleration. In this paper we give the method a more sound theoretical foundation by deriving the geodesic acceleration correction without using differential geometry and showing that the traditional convergence proofs can be adapted to incorporate geodesic acceleration. Unlike other methods which include second derivative information, the geodesic acceleration does not attempt to improve the Gauss-Newton approximate Hessian, but rather is an extension of the small-residual approximation to cubic order. In deriving geodesic acceleration, we note that the small-residual approximation is complemented by a small-curvature approximation. This latter approximation provides a much broader justification for the Gauss-Newton approximate Hessian and Levenberg-Marquardt algorithm. In particular, it is justifiable even if the best fit residuals are large, is dependent only on the model and not on the data being fit, and is applicable for the entire course of the algorithm and not just the region near the minimum.

math.OC↗

Improvements to the Levenberg-Marquardt algorithm for nonlinear least-squares minimization

When minimizing a nonlinear least-squares function, the Levenberg-Marquardt algorithm can suffer from a slow convergence, particularly when it must navigate a narrow canyon en route to a best fit. On the other hand, when the least-squares function is very flat, the algorithm may easily become lost in parameter space. We introduce several improvements to the Levenberg-Marquardt algorithm in order to improve both its convergence speed and robustness to initial parameter guesses. We update the usual step to include a geodesic acceleration correction term, explore a systematic way of accepting uphill steps that may increase the residual sum of squares due to Umrigar and Nightingale, and employ the Broyden method to update the Jacobian matrix. We test these changes by comparing their performance on a number of test problems with standard implementations of the algorithm. We suggest that these two particular challenges, slow convergence and robustness to initial guesses, are complimentary problems. Schemes that improve convergence speed often make the algorithm less robust to the initial guess, and vice versa. We provide an open source implementation of our improvements that allow the user to adjust the algorithm parameters to suit particular needs.

physics.data-an↗

Is dislocation flow turbulent in deformed crystals?

Intriguing analogies were found between a model of plastic deformation in crystals and turbulence in fluids. A study of this model provides remarkable explanations of known experiments and predicts fractal dislocation pattern formation. Further, the challenges encountered resemble those in turbulence, which is exemplified in a comparison with the Rayleigh-Taylor instability.

physics.comp-ph↗

Avalanche Spatial Structure and Multivariable Scaling Functions; Sizes, Heights, Widths, and Views through Windows

We introduce a systematic method for extracting multivariable universal scaling functions and critical exponents from data. We exemplify our insights by analyzing simulations of avalanches in an interface using simulations from a driven quenched Kardar-Parisi-Zhang (qKPZ) equation. We fully characterize the spatial structure of these avalanches- we report universal scaling functions for size, height and width distributions, and also local front heights. Furthermore, we resolve a problem that arises in many imaging experiments of crackling noise and avalanche dynamics, where the observed distributions are strongly distorted by a limited field of view. Through artificially windowed data, we show these distributions and their multivariable scaling functions may be written in terms of two control parameters, the window size and the characteristic length scale of the dynamics. For the entire system and the windowed distributions we develop accurate parameterizations for the universal scaling functions, including corrections to scaling and systematic error bars, facilitated by a novel software environment SloppyScaling.

cond-mat.stat-mech↗

Fracture strength of disordered media: Universality, interactions and tail asymptotics

We study the asymptotic properties of fracture strength distributions of disordered elastic media by a combination of renormalization group, extreme value theory, and numerical simulation. We investigate the validity of the `weakest-link hypothesis' in the presence of realistic long-ranged interactions in the random fuse model. Numerical simulations indicate that the fracture strength is well described by the Duxbury-Leath-Beale (DLB) distribution which is shown to flow asymptotically to the Gumbel distribution. We explore the relation between the extreme value distributions and the DLB type asymptotic distributions, and show that the universal extreme value forms may not be appropriate to describe the non-universal low-strength tail.

cond-mat.stat-mech↗

Dielectric breakdown and avalanches at non-equilibrium metal-insulator transitions

Motivated by recent experiments on the finite temperature Mott transition in VO2 films, we propose a classical coarse-grained dielectric breakdown model where each degree of freedom represents a nanograin which transitions from insulator to metal with increasing temperature and voltage at random thresholds due to quenched disorder. We describe the properties of the resulting non-equilibrium metal-insulator transition and explain the universal characteristics of the resistance jump distribution. We predict that by tuning voltage, another critical point is approached, which separates a phase of "bolt"-like avalanches from percolation-like ones.

cond-mat.str-el↗

Nucleation at the DNA supercoiling transition

Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of order 10^4 Hz. We reconcile this with experiments that have measured hopping rates of order 10 Hz by noting that the viscosity of the bead used to manipulate the DNA limits the measured rate. We find that the intrinsic bending caused by disorder in the base-pair sequence is important for understanding the free energy barrier that governs the transition. Both analytic and numerical methods are used in the calculations. We provide extensive details on the numerical methods for simulating the elastic rod model with and without disorder.

physics.bio-ph↗

The geometry of nonlinear least squares with applications to sloppy models and optimization

Parameter estimation by nonlinear least squares minimization is a common problem with an elegant geometric interpretation: the possible parameter values of a model induce a manifold in the space of data predictions. The minimization problem is then to find the point on the manifold closest to the data. We show that the model manifolds of a large class of models, known as sloppy models, have many universal features; they are characterized by a geometric series of widths, extrinsic curvatures, and parameter-effects curvatures. A number of common difficulties in optimizing least squares problems are due to this common structure. First, algorithms tend to run into the boundaries of the model manifold, causing parameters to diverge or become unphysical. We introduce the model graph as an extension of the model manifold to remedy this problem. We argue that appropriate priors can remove the boundaries and improve convergence rates. We show that typical fits will have many evaporated parameters. Second, bare model parameters are usually ill-suited to describing model behavior; cost contours in parameter space tend to form hierarchies of plateaus and canyons. Geometrically, we understand this inconvenient parametrization as an extremely skewed coordinate basis and show that it induces a large parameter-effects curvature on the manifold. Using coordinates based on geodesic motion, these narrow canyons are transformed in many cases into a single quadratic, isotropic basin. We interpret the modified Gauss-Newton and Levenberg-Marquardt fitting algorithms as an Euler approximation to geodesic motion in these natural coordinates on the model manifold and the model graph respectively. By adding a geodesic acceleration adjustment to these algorithms, we alleviate the difficulties from parameter-effects curvature, improving both efficiency and success rates at finding good fits.

cond-mat.stat-mech↗

A minimal model of plasma membrane heterogeneity requires coupling cortical actin to criticality

We present a minimal model of plasma membrane heterogeneity that combines criticality with connectivity to cortical cytoskeleton. Our model is motivated by recent observations of micron-sized critical fluctuations in plasma membrane vesicles that are detached from their cortical cytoskeleton. We incorporate criticality using a conserved order parameter Ising model coupled to a simple actin cytoskeleton interacting through point-like pinning sites. Using this minimal model, we recapitulate several experimental observations of plasma membrane raft heterogeneity. Small (r~20nm) and dynamic fluctuations at physiological temperatures arise from criticality. Including connectivity to cortical cytoskeleton disrupts large fluctuations, prevents macroscopic phase separation at low temperatures (T<=22°C), and provides a template for long lived fluctuations at physiological temperature (T=37°C). Cytoskeleton-stabilized fluctuations produce significant barriers to the diffusion of some membrane components in a manner that is weakly dependent on the number of pinning sites and strongly dependent on criticality. More generally, we demonstrate that critical fluctuations provide a physical mechanism to organize and spatially segregate membrane components by providing channels for interaction over large distances.

q-bio.SC↗

Beyond power laws: Universality in the average avalanche shape

We report the measurement of multivariable scaling functions for the temporal average shape of Barkhausen noise avalanches, and show that they are consistent with the predictions of simple mean-field theories. We bypass the confounding factors of time-retarded interactions (eddy currents) by measuring thin permal- loy films, and bypass thresholding effects and amplifier distortions by applying Wiener deconvolution. We find experimental shapes that are approximately symmetric, and track the evolution of the scaling function. We solve a mean- field theory for the magnetization dynamics and calculate the form of the scaling function in the presence of a demagnetizing field and a finite field ramp-rate, yielding quantitative agreement with the experiment.

cond-mat.dis-nn↗

Superheating field of superconductors within Ginzburg-Landau theory

We study the superheating field of a bulk superconductor within Ginzburg-Landau theory, which is valid near the critical temperature. We calculate, as functions of the Ginzburg-Landau parameter $κ$, the superheating field $\Hsh$ and the critical momentum $k_c$ characterizing the wavelength of the instability of the Meissner state to flux penetration. By mapping the two-dimensional linear stability theory into a one-dimensional eigenfunction problem for an ordinary differential equation, we solve the problem numerically. We demonstrate agreement between the numerics and analytics, and show convergence to the known results at both small and large $κ$. We discuss the implications of the results for superconducting RF cavities used in particle accelerators.

cond-mat.supr-con↗

Bending crystals: Emergence of fractal dislocation structures

We provide a minimal continuum model for mesoscale plasticity, explaining the cellular dislocation structures observed in deformed crystals. Our dislocation density tensor evolves from random, smooth initial conditions to form self-similar structures strikingly similar to those seen experimentally - reproducing both the fractal morphologies and some features of the scaling of cell sizes and misorientations analyzed experimentally. Our model provides a framework for understanding emergent dislocation structures on the mesoscale, a bridge across a computationally demanding mesoscale gap in the multiscale modeling program, and a new example of self-similar structure formation in non-equilibrium systems.

cond-mat.mtrl-sci↗

Adaptive mutation of biochemical reaction constants: Fisher's geometrical model without pleiotropy

The distribution of fitness effects of adaptive mutations remains poorly understood, both empirically and theoretically. We study this distribution using a version of Fisher's geometrical model without pleiotropy, such that each mutation affects only a single trait. We are motivated by the notion of an organism's chemotype, the set of biochemical reaction constants that govern its molecular constituents. From physical considerations, we expect the chemotype to be of high dimension and to exhibit very little pleiotropy. Our model generically predicts striking cusps in the distribution of the fitness effects of arising and fixed mutations. It further predicts that a single element of the chemotype should comprise all mutations at the high-fitness ends of these distributions. Using extreme value theory, we show that the two cusps with the highest fitnesses are typically well-separated, even when the chemotype possesses thousands of elements; this suggests a means to observe these cusps experimentally. More broadly, our work demonstrates that new insights into evolution can arise from the chemotype perspective, a perspective between the genotype and the phenotype.

q-bio.PE↗