arXiv subjects

James P. Sethna

Publications and source records attributed to James P. Sethna.

At least 127 records · Page 7Linked to original sources

arXiv2006

Digital Material: a flexible atomistic simulation code

The complexities of today's materials simulations demand computer codes which are both powerful and highly flexible. A researcher should be able to readily choose different geometries, different materials and different algorithms without having to write low-level code and recompile each time. We describe a molecular dynamics (MD) code, called Digital Material, in which we have sought to maximize flexibility without sacrificing efficiency. Our approach starts from the software engineering concept of Design Patterns and involves dividing the work of an MD simulation into well-defined components. The bulk of this paper is taken up with a detailed description of the different components, their interfaces and implementations and the reasoning behind these. The level of detail is not at the line-by-line level, but at such a level that a reader could implement a similar code sharing the same design principles.

cond-mat.other↗

arXiv2005

Random-Field Ising Models of Hysteresis

This is a review article of our work on hysteresis, avalanches, and criticality. We provide an extensive introduction to scaling and renormalization--group ideas, and discuss analytical and numerical results for size distributions, correlation functions, magnetization, avalanche durations and average avalanche shapes, and power spectra. We focus here on applications to magnetic Barkhausen noise.

cond-mat.mtrl-sci↗

arXiv2004

The statistical mechanics of complex signaling networks : nerve growth factor signaling

It is becoming increasingly appreciated that the signal transduction systems used by eukaryotic cells to achieve a variety of essential responses represent highly complex networks rather than simple linear pathways. While significant effort is being made to experimentally measure the rate constants for individual steps in these signaling networks, many of the parameters required to describe the behavior of these systems remain unknown, or at best, estimates. With these goals and caveats in mind, we use methods of statistical mechanics to extract useful predictions for complex cellular signaling networks. To establish the usefulness of our approach, we have applied our methods towards modeling the nerve growth factor (NGF)-induced differentiation of neuronal cells. Using our approach, we are able to extract predictions that are highly specific and accurate, thereby enabling us to predict the influence of specific signaling modules in determining the integrated cellular response to the two growth factors. We show that extracting biologically relevant predictions from complex signaling models appears to be possible even in the absence of measurements of all the individual rate constants. Our methods also raise some interesting insights into the design and possible evolution of cellular systems, highlighting an inherent property of these systems wherein particular ''soft'' combinations of parameters can be varied over wide ranges without impacting the final output and demonstrating that a few ''stiff'' parameter combinations center around the paramount regulatory steps of the network. We refer to this property -- which is distinct from robustness -- as ''sloppiness.''

q-bio.MN↗

arXiv2004

Mean field approaches to the totally asymmetric exclusion process with quenched disorder and large particles

The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles (ribosomes) have spatial extent, covering more than one lattice site. Realistic, nonuniform gene sequences lead to quenched disorder in the particle hopping rates. We study the totally asymmetric exclusion process with large particles and quenched disorder via several mean field approaches and compare the mean field results with Monte Carlo simulations. Mean field equations obtained from the literature are found to be reasonably effective in describing this system. A numerical technique is developed for computing the particle current rapidly. The mean field approach is extended to include two-point correlations between adjacent sites. The two-point results are found to match Monte Carlo simulations more closely.

cond-mat.stat-mech↗

arXiv2003

Meissner Effect and Constraints

We notice some beautiful geometrical defects found in liquid crystals, and explain them by imposing a constraint. We study the way constraints can occur, and introduce the concept of massive fields. We develop the theory of magnetic field expulsion in superconductors as an example. We notice strong analogies with the formation of grain boundaries in crystals, and realize that we do not understand crystals very deeply

cond-mat↗

arXiv2003

Scaling in Plasticity-Induced Cell-Boundary Microstructure: Fragmentation and Rotational Diffusion

We develop a simple computational model for cell boundary evolution in plastic deformation. We study the cell boundary size distribution and cell boundary misorientation distribution that experimentally have been found to have scaling forms that are largely material independent. The cell division acts as a source term in the misorientation distribution which significantly alters the scaling form, giving it a linear slope at small misorientation angles as observed in the experiments. We compare the results of our simulation to two closely related exactly solvable models which exhibit scaling behavior at late times: (i) fragmentation theory and (ii) a random walk in rotation space with a source term. We find that the scaling exponents in our simulation agree with those of the theories, and that the scaling collapses obey the same equations, but that the shape of the scaling functions depend upon the methods used to measure sizes and to weight averages and histograms.

cond-mat.mtrl-sci↗

arXiv2003

Fracture of Notched Single Crystal Silicon

We study atomistically the fracture of single crystal silicon at atomically sharp notches with opening angles of 0 degrees (a crack), 70.53 degrees, 90 degrees and 125.3 degrees. Such notches occur in silicon that has been formed by etching into microelectromechanical structures and tend to be the initiation sites for failure by fracture of these structures. Analogous to the stress intensity factor of traditional linear elastic fracture mechanics which characterizes the stress state in the limiting case of a crack, there exists a similar parameter K for the case of the notch. In the case of silicon, a brittle material, this characterization appears to be particularly valid. We use three interatomic potentials: a modified Stillinger-Weber potential, the Environment-Dependent Interatomic Potential (EDIP), and the modified embedded atom method (MEAM). Of these, MEAM gives critical K-values closest to experiment. In particular the EDIP potential leads to unphysical ductile failure in most geometries. Because the units of K depend on the notch angle, the shape of the K versus angle plot depends on the units used. In particular when an atomic length unit is used the plot is almost flat, showing--in principle from macroscopic observations alone--the association of an atomic length scale to the fracture process.

cond-mat.mtrl-sci↗

arXiv2002

Crack Growth Laws from Symmetry

Reviewing work done in collaboration with Jennifer Hodgdon, we derive the most general crack growth law allowed by symmetry for mixed-mode three-dimensional fracture. We do so using the system developed in condensed matter physics to derive new laws that emerge on long length and time scales. In our derivation, we provide a symmetry interpretation for the three modes of fracture, we rederive the law giving the crack growth direction in two dimensional fracture, and we derive a growth law appropriate for three dimensional simulations. We briefly discuss related work subsequent to ours, incorporating disorder, dynamics, and other internal variables.

cond-mat.mtrl-sci↗

arXiv2002

Enhanced mesoscopic fluctuations in the crossover between random matrix ensembles

In random-matrix ensembles that interpolate between the three basic ensembles (orthogonal, unitary, and symplectic), there exist correlations between elements of the same eigenvector and between different eigenvectors. We study such correlations, using a remarkable correspondence between the interpolating ensembles late in the crossover and a basic ensemble of finite size. In small metal grains or semiconductor quantum dots, the correlations between different eigenvectors lead to enhanced fluctuations of the electron-electron interaction matrix elements which become parametrically larger than the non-universal fluctuations.

cond-mat.mes-hall↗

arXiv2001

Universal Pulse Shape Scaling Function and Exponents: A Critical Test for Avalanche Models applied to Barkhausen Noise

In order to test if the universal aspects of Barkhausen noise in magnetic materials can be predicted from recent variants of the non-equilibrium zero temperature Random Field Ising Model (RFIM), we perform a quantitative study of the universal scaling function derived from the Barkhausen pulse shape in simulations and experiment. Through data collapses and scaling relations we determine the critical exponents $τ$ and $1/σνz$ in both simulation and experiment. Although we find agreement in the critical exponents, we find differences between theoretical and experimental pulse shape scaling functions as well as between different experiments.

cond-mat.stat-mech↗

arXiv2001

Noise in disordered systems: The power spectrum and dynamic exponents in avalanche models

For a long time, it has been known that the power spectrum of Barkhausen noise had a power-law decay at high frequencies. Up to now, the theoretical predictions for this decay have been incorrect, or have only applied to a small set of models. In this paper, we describe a careful derivation of the power spectrum exponent in avalanche models, and in particular, in variations of the zero-temperature random-field Ising model. We find that the naive exponent, (3-tau)/(sigma nu z), which has been derived in several other papers, is in general incorrect for small tau, when large avalanches are common. (tau is the exponent describing the distribution of avalanche sizes, and (sigma nu z) is the exponent describing the relationship between avalanche size and avalanche duration.) We find that for a large class of avalanche models, including several models of Barkhausen noise, the correct exponent for tau<2 is 1/(sigma nu z). We explicitly derive the mean-field exponent of 2. In the process, we calculate the average avalanche shape for avalanches of fixed duration and scaling forms for a number of physical properties.

cond-mat.dis-nn↗

arXiv2001

Formal Considerations about Fracture: Nucleation and Growth

In this paper, we'll answer several abstract, formal questions about the nature of crack growth and nucleation. Bringing a field theory point of view to fracture illuminates things in what I hope will be an entertaining way. Formally, what is the crack nucleation rate? Fracture is an instability of elastic theory under tension. For thermally nucleated cracks, there is an analogy with supercooled liquids. Here the crack nucleation rate can be thought of as an imaginary part of the free energy - giving the decay rate of the metastable, stretched material. As an amusing consequence, we can formally calculate the asymptotic form for the high-order nonlinear elastic coefficients, and explicitly show that elastic theory has zero radius of convergence. Formally, can we derive the the crack growth laws from symmetry? We can describe mixed-mode three-dimensional fracture as a moving curve in space, decorated with a description of the local crack plane, and driven by the stress intensity factors along the crack. Imposing the symmetries gives us the form of the crack growth laws in two dimensions, explaining the (well-known) fact that cracks under shear (mode II) abruptly turn until the stress becomes purely extensional (mode I). The form of the crack growth law in three dimensions will be derived, and linear stability analysis for mixed-mode fracture will be briefly summarized, with connection to factory-roof morphologies.

cond-mat.mtrl-sci↗

arXiv2001

Crackling Noise

Crackling noise arises when a system responds to changing external conditions through discrete, impulsive events spanning a broad range of sizes. A wide variety of physical systems exhibiting crackling noise have been studied, from earthquakes on faults to paper crumpling. Because these systems exhibit regular behavior over many decades of sizes, their behavior is likely independent of microscopic and macroscopic details, and progress can be made by the use of very simple models. The fact that simple models and real systems can share the same behavior on a wide range of scales is called universality. We illustrate these ideas using results for our model of crackling noise in magnets, explaining the use of the renormalization group and scaling collapses. This field is still developing: we describe a number of continuing challenges.

cond-mat.stat-mech↗

arXiv2000

Dislocation Kinks in Copper: Widths, Barriers, Effective Masses, and Quantum Tunneling

We calculate the widths, migration barriers, effective masses, and quantum tunneling rates of kinks and jogs in extended screw dislocations in copper, using an effective medium theory interatomic potential. The energy barriers and effective masses for moving a unit jog one lattice constant are close to typical atomic energies and masses: tunneling will be rare. The energy barriers and effective masses for the motion of kinks are unexpectedly small due to the spreading of the kinks over a large number of atoms. The effective masses of the kinks are so small that quantum fluctuations will be important. We discuss implications for quantum creep, kink--based tunneling centers, and Kondo resonances.

cond-mat.mtrl-sci↗

arXiv1999

Hysteresis, Avalanches, and Noise: Numerical Methods

In studying the avalanches and noise in a model of hysteresis loops we have developed two relatively straightforward algorithms which have allowed us to study large systems efficiently. Our model is the random-field Ising model at zero temperature, with deterministic albeit random dynamics. The first algorithm, implemented using sorted lists, scales in computer time as O(N log N), and asymptotically uses N (sizeof(double)+ sizeof(int)) bits of memory. The second algorithm, which never generates the random fields, scales in time as O(N \log N) and asymptotically needs storage of only one bit per spin, about 96 times less memory than the first algorithm. We present results for system sizes of up to a billion spins, which can be run on a workstation with 128MB of RAM in a few hours. We also show that important physical questions were resolved only with the largest of these simulations.

cond-mat.dis-nn↗

arXiv1998

Disorder-Induced Critical Phenomena in Hysteresis: Numerical Scaling in Three and Higher Dimensions

We present numerical simulations of avalanches and critical phenomena associated with hysteresis loops, modeled using the zero-temperature random-field Ising model. We study the transition between smooth hysteresis loops and loops with a sharp jump in the magnetization, as the disorder in our model is decreased. In a large region near the critical point, we find scaling and critical phenomena, which are well described by the results of an epsilon expansion about six dimensions. We present the results of simulations in 3, 4, and 5 dimensions, with systems with up to a billion spins (1000^3).

cond-mat.dis-nn↗

arXiv1998

Simulations of energetic beam deposition: from picoseconds to seconds

We present a new method for simulating crystal growth by energetic beam deposition. The method combines a Kinetic Monte-Carlo simulation for the thermal surface diffusion with a small scale molecular dynamics simulation of every single deposition event. We have implemented the method using the effective medium theory as a model potential for the atomic interactions, and present simulations for Ag/Ag(111) and Pt/Pt(111) for incoming energies up to 35 eV. The method is capable of following the growth of several monolayers at realistic growth rates of 1 monolayer per second, correctly accounting for both energy-induced atomic mobility and thermal surface diffusion. We find that the energy influences island and step densities and can induce layer-by-layer growth. We find an optimal energy for layer-by-layer growth (25 eV for Ag), which correlates with where the net impact-induced downward interlayer transport is at a maximum. A high step density is needed for energy induced layer-by-layer growth, hence the effect dies away at increased temperatures, where thermal surface diffusion reduces the step density. As part of the development of the method, we present molecular dynamics simulations of single atom-surface collisions on flat parts of the surface and near straight steps, we identify microscopic mechanisms by which the energy influences the growth, and we discuss the nature of the energy-induced atomic mobility.

cond-mat.mtrl-sci↗

arXiv1997

Pulsed sputtering during homoepitaxial surface growth: layer-by-layer forever

The homoepitaxial growth of initially flat surfaces has so far always led to surfaces which become rougher and rougher as the number of layers increases: even in systems exhibiting ``layer by layer'' growth the registry of the layers is gradually lost. We propose that pulsed glancing-angle sputtering, once per monolayer, can in principle lead to layer-by-layer growth that continues indefinitely, if one additional parameter is controlled. We illustrate our suggestion with a fairly realistic simulation of the growth of a Pt (111) surface, coupled with a simplified model for the sputtering process.

cond-mat.mtrl-sci↗