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James P. Sethna

Publications and source records attributed to James P. Sethna.

At least 73 records · Page 4Linked to original sources
arXiv2016

The weirdest martensite: Smectic liquid crystal microstructure and Weyl-Poincaré invariance

Smectic liquid crystals are remarkable, beautiful examples of materials microstructure, with ordered patterns of geometrically perfect ellipses and hyperbolas. The solution of the complex problem of filling three-dimensional space with domains of focal conics under constraining boundary conditions yields a set of strict rules, which are similar to the compatibility conditions in a martensitic crystal. Here we present the rules giving compatible conditions for the concentric circle domains found at two-dimensional smectic interfaces with planar boundary conditions. Using configurations generated by numerical simulations, we develop a clustering algorithm to decompose the planar boundaries into domains. The interfaces between different domains agree well with the smectic compatibility conditions. We also discuss generalizations of our approach to describe the full three-dimensional smectic domains, where the variant symmetry group is the Weyl-Poincaré group of Lorentz boosts, translations, rotations, and dilatations.

cond-mat.soft↗
arXiv2015

Visualization, coarsening and flow dynamics of focal conic domains in simulated Smectic-A liquid crystals

Smectic liquid crystals vividly illustrate the subtle interplay of broken translational and orientational symmetries, by exhibiting defect structures forming geometrically perfect confocal ellipses and hyperbolas. Here, we develop and numerically implement an effective theory to study the dynamics of focal conic domains in smectic-A liquid crystals. We use the information about the smectic's structure and energy density provided by our simulations to develop several novel visualization tools for the focal conics. Our simulations accurately describe both simple and extensional shear, which we compare to experiments, and provide additional insight into the coarsening dynamics of focal conic domains.

cond-mat.soft↗
arXiv2015

Overshoot during phenotypic switching of cancer cell populations

The dynamics of tumor cell populations is hotly debated: do populations derive hierarchically from a subpopulation of cancer stem cells (CSCs), or are stochastic transitions that mutate differentiated cancer cells to CSCs important? Here we argue that regulation must also be important. We sort human melanoma cells using three distinct cancer stem cell (CSC) markers - CXCR6, CD271 and ABCG2 - and observe that the fraction of non-CSC-marked cells first overshoots to a higher level and then returns to the level of unsorted cells. This clearly indicates that the CSC population is homeostatically regulated. Combining experimental measurements with theoretical modeling and numerical simulations, we show that the population dynamics of cancer cells is associated with a complex miRNA network regulating the Wnt and PI3K pathways. Hence phenotypic switching is not stochastic, but is tightly regulated by the balance between positive and negative cells in the population. Reducing the fraction of CSCs below a threshold triggers massive phenotypic switching, suggesting that a therapeutic strategy based on CSC eradication is unlikely to succeed.

q-bio.CB↗
arXiv2015

Information Geometry and the Renormalization Group

Information theoretic geometry near critical points in classical and quantum systems is well understood for exactly solvable systems. Here we show that renormalization group flow equations can be used to construct the information metric and its associated quantities near criticality, for both classical and quantum systems, in an universal manner. We study this metric in various cases and establish its scaling properties in several generic examples. Scaling relations on the parameter manifold involving scalar quantities are studied, and scaling exponents are identified. The meaning of the scalar curvature and the invariant geodesic distance in information geometry is established and substantiated from a renormalization group perspective.

cond-mat.stat-mech↗
arXiv2015

Scaling theory for the jamming transition

We propose a scaling ansatz for the elastic energy of a system near the critical jamming transition in terms of three relevant fields: the compressive strain $Δϕ$ relative to the critical jammed state, the shear strain $ε$, and the inverse system size $1/N$. We also use $ΔZ$, the number of contacts relative to the minimum required at jamming, as an underlying control parameter. Our scaling theory predicts new exponents, exponent equalities and scaling collapses for energy, pressure and shear stress that we verify with numerical simulations of jammed packings of soft spheres. It also yields new insight into why the shear and bulk moduli exhibit different scalings; the difference arises because the shear stress vanishes as $1/\sqrt{N}$ while the pressure approaches a constant in the thermodynamic limit. The success of the scaling ansatz implies that the jamming transition exhibits an emergent scale invariance, and that it should be possible to develop a renormalization-group theory for jamming.

cond-mat.soft↗
arXiv2015

Crossover behavior in interface depinning

We study the crossover scaling behavior of the height-height correlation function in interface depinning in random media. We analyze experimental data from a fracture experiment and simulate an elastic line model with non-linear couplings and disorder. Both exhibit a crossover between two different universality classes. For the experiment, we fit a functional form to the universal crossover scaling function. For the model, we vary the system size and the strength of the non-linear term, and describe the crossover between the two universality classes with a multiparameter scaling function. Our method provides a general strategy to extract scaling properties in depinning systems exhibiting crossover phenomena.

cond-mat.stat-mech↗
arXiv2015

Shielding superconductors with thin films

Determining the optimal arrangement of superconducting layers to withstand large amplitude AC magnetic fields is important for certain applications such as superconducting radiofrequency cavities. In this paper, we evaluate the shielding potential of the superconducting film/insulating film/superconductor (SIS') structure, a configuration that could provide benefits in screening large AC magnetic fields. After establishing that for high frequency magnetic fields, flux penetration must be avoided, the superheating field of the structure is calculated in the London limit both numerically and, for thin films, analytically. For intermediate film thicknesses and realistic material parameters we also solve numerically the Ginzburg-Landau equations. It is shown that a small enhancement of the superheating field is possible, on the order of a few percent, for the SIS' structure relative to a bulk superconductor of the film material, if the materials and thicknesses are chosen appropriately.

physics.acc-ph↗
arXiv2015

"Irregularization" of Systems of Conservation Laws

We explore new ways of regulating defect behavior in systems of conservation laws. Contrary to usual regularization schemes (such as a vanishing viscosity limit), which attempt to control defects by making them smoother, our schemes result in defects which are \textit{more singular}, and we thus refer to such schemes as "irregularizations". In particular, we seek to produce \textit{delta shock} defects which satisfy a condition of \textit{stationarity}. We are motivated to pursue such exotic defects by a physical example arising from dislocation dynamics in materials physics, which we describe.

math.AP↗
arXiv2015

You Can Run, You Can Hide: The Epidemiology and Statistical Mechanics of Zombies

We use a popular fictional disease, zombies, in order to introduce techniques used in modern epidemiology modelling, and ideas and techniques used in the numerical study of critical phenomena. We consider variants of zombie models, from fully connected continuous time dynamics to a full scale exact stochastic dynamic simulation of a zombie outbreak on the continental United States. Along the way, we offer a closed form analytical expression for the fully connected differential equation, and demonstrate that the single person per site two dimensional square lattice version of zombies lies in the percolation universality class. We end with a quantitative study of the full scale US outbreak, including the average susceptibility of different geographical regions.

q-bio.PE↗
arXiv2015

Sloppiness and Emergent Theories in Physics, Biology, and Beyond

Large scale models of physical phenomena demand the development of new statistical and computational tools in order to be effective. Many such models are `sloppy', i.e., exhibit behavior controlled by a relatively small number of parameter combinations. We review an information theoretic framework for analyzing sloppy models. This formalism is based on the Fisher Information Matrix, which we interpret as a Riemannian metric on a parameterized space of models. Distance in this space is a measure of how distinguishable two models are based on their predictions. Sloppy model manifolds are bounded with a hierarchy of widths and extrinsic curvatures. We show how the manifold boundary approximation can extract the simple, hidden theory from complicated sloppy models. We attribute the success of simple effective models in physics as likewise emerging from complicated processes exhibiting a low effective dimensionality. We discuss the ramifications and consequences of sloppy models for biochemistry and science more generally. We suggest that the reason our complex world is understandable is due to the same fundamental reason: simple theories of macroscopic behavior are hidden inside complicated microscopic processes.

cond-mat.stat-mech↗
arXiv2014

Fracture strength: Stress concentration, extreme value statistics and the fate of the Weibull distribution

The fracture strength distribution of materials is often described in terms of the Weibull law which can be derived by using extreme value statistics if elastic interactions are ignored. Here, we consider explicitly the interplay between elasticity and disorder and test the asymptotic validity of the Weibull distribution through numerical simulations of the two-dimensional random fuse model. Even when the local fracture strength follows the Weibull distribution, the global failure distribution is dictated by stress enhancement at the tip of the cracks and sometimes deviates from the Weibull law. Only in the case of a pre-existing power law distribution of crack widths do we find that the failure strength is Weibull distributed. Contrary to conventional assumptions, even in this case, the Weibull exponent can not be simply inferred from the exponent of the initial crack width distribution. Our results thus raise some concerns on the applicability of the Weibull distribution in most practical cases.

cond-mat.stat-mech↗
arXiv2014

Mechanical Properties of Growing Melanocytic Nevi and the Progression to Melanoma

Melanocytic nevi are benign proliferations that sometimes turn into malignant melanoma in a way that is still unclear from the biochemical and genetic point of view. Diagnostic and prognostic tools are then mostly based on dermoscopic examination and morphological analysis of histological tissues. To investigate the role of mechanics and geometry in the morpholgical dynamics of melanocytic nevi, we study a computation model for cell proliferation in a layered non-linear elastic tissue. Numerical simulations suggest that the morphology of the nevus is correlated to the initial location of the proliferating cell starting the growth process and to the mechanical properties of the tissue. Our results also support that melanocytes are subject to compressive stresses that fluctuate widely in the nevus and depend on the growth stage. Numerical simulations of cells in the epidermis releasing matrix metalloproteinases display an accelerated invasion of the dermis by destroying the basal membrane. Moreover, we suggest experimentally that osmotic stress and collagen inhibit growth in primary melanoma cells while the effect is much weaker in metastatic cells. Knowing that morphological features of nevi might also reflect geometry and mechanics rather than malignancy could be relevant for diagnostic purposes

q-bio.TO↗
arXiv2013

Theoretical Field Limits for Multi-Layer Superconductors

The SIS structure---a thin superconducting film on a bulk superconductor separated by a thin insulating film---was propsed as a method to protect alternative SRF materials from flux penetration by enhancing the first critical field $B_{c1}$. In this work, we show that in fact $B_{c1}$ = 0 for a SIS structure. We calculate the superheating field $B_{sh}$, and we show that it can be enhanced slightly using the SIS structure, but only for a small range of film thicknesses and only if the film and the bulk are different materials. We also show that using a multilayer instead of a single thick layer is detrimental, as this decreases $B_{sh}$ of the film. We calculate the dissipation due to vortex penetration above the $B_{sh}$ of the film, and find that it is unmanageable for SRF applications. However, we find that if a gradient in the phase of the order parameter is introduced, SIS structures may be able to shield large DC and low frequency fields. We argue that the SIS structure is not beneficial for SRF cavities, but due to recent experiments showing low-surface-resistance performance above $B_{c1}$ in cavities made of superconductors with small coherence lengths, we argue that enhancement of $B_{c1}$ is not necessary, and that bulk films of alternative materials show great promise.

physics.acc-ph↗
arXiv2013

Senescent Cells in Growing Tumors: Population Dynamics and Cancer Stem Cells

Tumors are defined by their intense proliferation, but sometimes cancer cells turn senescent and stop replicating. In the stochastic cancer model in which all cells are tumorigenic, senescence is seen as the result of random mutations, suggesting that it could represent a barrier to tumor growth. In the hierarchical cancer model a subset of the cells, the cancer stem cells, divide indefinitely while other cells eventually turn senescent. Here we formulate cancer growth in mathematical terms and obtain predictions for the evolution of senescence. We perform experiments in human melanoma cells which are compatible with the hierarchical model and show that senescence is a reversible process controlled by survivin. We conclude that enhancing senescence is unlikely to provide a useful therapeutic strategy to fight cancer, unless the cancer stem cells are specifically targeted

q-bio.TO↗
arXiv2013

Universal scaling function for the two-dimensional Ising model in an external field: A pragmatic approach

We report an effective functional form for the spin-spin correlation function of the 2D Ising model as a function of temperature and field. Although the Ising model has been well studied, no analytical result for the spin-spin correlation function exists for arbitrary magnetic fields and temperatures. We show the validity of our form by comparison with simulations using the Wolff algorithm, and obtain remarkable precision by including analytic corrections to scaling. Given recent interest in comparing biomembrane heterogeneity to Ising criticality, our spin-spin correlation function may be used as a predictive quantitative measure for FRET or NMR membrane experiments.

cond-mat.stat-mech↗
arXiv2013

Quasi-periodic events in crystal plasticity and the self-organized avalanche oscillator

When external stresses in a system - physical, social or virtual - are relieved through impulsive events, it is natural to focus on the attributes of these avalanches. However, during the quiescent periods in between, stresses may be relieved through competing processes, such as slowly flowing water between earthquakes or thermally activated dislocation flow between plastic bursts. Such unassuming, smooth responses can have dramatic effects on the avalanche properties. Here we report a thorough experimental investigation of slowly compressed Ni microcrystals, covering three orders of magnitude in nominal strain rate, that exhibits unconventional quasi-periodic avalanche bursts and higher critical exponents as the strain rate is decreased. Our analytic and computational study naturally extends dislocation avalanche modeling to incorporate dislocation relaxations and reveals the emergence of the self-organized avalanche oscillator, a novel critical state exhibiting oscillatory approaches toward a depinning critical point. We demonstrate that the predictions of our theory are faithfully exhibited in our experiments.

cond-mat.stat-mech↗
arXiv2013

Parameter Space Compression Underlies Emergent Theories and Predictive Models

We report a similarity between the microscopic parameter dependance of emergent theories in physics and that of multiparameter models common in other areas of science. In both cases, predictions are possible despite large uncertainties in the microscopic parameters because these details are compressed into just a few governing parameters that are sufficient to describe relevant observables. We make this commonality explicit by examining parameter sensitivity in a hopping model of diffusion and a generalized Ising model of ferromagnetism. We trace the emergence of a smaller effective model to the development of a hierarchy of parameter importance quantified by the eigenvalues of the Fisher Information Matrix. Strikingly, the same hierarchy appears ubiquitously in models taken from diverse areas of science. We conclude that the emergence of effective continuum and universal theories in physics is due to the same parameter space hierarchy that underlies predictive modeling in other areas of science.

cond-mat.stat-mech↗