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Leonard M. Sander

Publications and source records attributed to Leonard M. Sander.

At least 37 records · Page 2Linked to original sources
arXiv2009

Fluctuations and Dispersal Rates in Population Dyanmics

Dispersal of species to find a more favorable habitat is important in population dynamics. Dispersal rates evolve in response to the relative success of different dispersal strategies. In a simplified deterministic treatment (J. Dockery, V. Hutson, K. Mischaikow, et al., J. Math. Bio. 37, 61 (1998)) of two species which differ only in their dispersal rates the slow species always dominates. We demonstrate that fluctuations can change this conclusion and can lead to dominance by the fast species or to coexistence, depending on parameters. We discuss two different effects of fluctuations, and show that our results are consistent with more complex treatments that find that selected dispersal rates are not monotonic with the cost of migration.

q-bio.PE↗
arXiv2008

The Micromechanics of Three Dimensional Collagen-I Gels

We study the micromechanics of collagen-I gel with the goal of bridging the gap between theory and experiment in the study of biopolymer networks. Three-dimensional images of fluorescently labeled collagen are obtained by confocal microscopy and the network geometry is extracted using a 3d network skeletonization algorithm. Each fiber is modeled as a worm-like-chain that resists stretching and bending, and each cross-link is modeled as torsional spring. The stress-strain curves of networks at three different densities are compared to rheology measurements. The model shows good agreement with experiment, confirming that strain stiffening of collagen can be explained entirely by geometric realignment of the network, as opposed to entropic stiffening of individual fibers. The model also suggests that at small strains, cross-link deformation is the main contributer to network stiffness whereas at large strains, fiber stretching dominates. Since this modeling effort uses networks with realistic geometries, this analysis can ultimately serve as a tool for understanding how the mechanics of fibers and cross-links at the microscopic level produce the macroscopic properties of the network. While the focus of this paper is on the mechanics of collagen, we demonstrate a framework that can be applied to many biopolymer networks.

cond-mat.soft↗
arXiv2008

A generalized voter model on complex networks

We study a generalization of the voter model on complex networks, focusing on the scaling of mean exit time. Previous work has defined the voter model in terms of an initially chosen node and a randomly chosen neighbor, which makes it difficult to disentangle the effects of the stochastic process itself relative to the network structure. We introduce a process with two steps, one that selects a pair of interacting nodes and one that determines the direction of interaction as a function of the degrees of the two nodes and a parameter $α$ which sets the likelihood of the higher degree node giving its state. Traditional voter model behavior can be recovered within the model. We find that on a complete bipartite network, the traditional voter model is the fastest process. On a random network with power law degree distribution, we observe two regimes. For modest values of $α$, exit time is dominated by diffusive drift of the system state, but as the high nodes become more influential, the exit time becomes becomes dominated by frustration effects. For certain selection processes, a short intermediate regime occurs where exit occurs after exponential mixing.

cond-mat.stat-mech↗
arXiv2008

Harmonic Measure for Percolation and Ising Clusters Including Rare Events

We obtain the harmonic measure of the hulls of critical percolation clusters and Ising-model Fortuin-Kastelyn clusters using a biased random-walk sampling technique which allows us to measure probabilities as small as 10^{-300}. We find the multifractal D(q) spectrum including regions of small and negative q. Our results for external hulls agree with Duplantier's theoretical predictions for D(q) and his exponent -23/24 for the harmonic measure probability distribution. For the complete hull, we find the probability decays with an exponent of -1 for both systems.

cond-mat.stat-mech↗
arXiv2008

Fast kinetic Monte Carlo simulation of strained heteroepitaxy in three dimensions

Accelerated algorithms for simulating the morphological evolution of strained heteroeptiaxy based on a ball and spring lattice model in three dimensions are explained. We derive exact Green's function formalisms for boundary values in the associated lattice elasticity problems. The computational efficiency is further enhanced by using a superparticle surface coarsening approximation. Atomic hoppings simulating surface diffusion are sampled using a multi-step acceptance-rejection algorithm. It utilizes quick estimates of the atomic elastic energies from extensively tabulated values modulated by the local strain. A parameter controls the compromise between accuracy and efficiency of the acceptance-rejection algorithm.

cond-mat.stat-mech↗
arXiv2008

A generalized Cahn-Hilliard equation for biological applications

Recently we considered a stochastic discrete model which describes fronts of cells invading a wound \cite{KSS}. In the model cells can move, proliferate, and experience cell-cell adhesion. In this work we focus on a continuum description of this phenomenon by means of a generalized Cahn-Hilliard equation (GCH) with a proliferation term. As in the discrete model, there are two interesting regimes. For subcritical adhesion, there are propagating "pulled" fronts, similarly to those of Fisher-Kolmogorov equation. The problem of front velocity selection is examined, and our theoretical predictions are in a good agreement with a numerical solution of the GCH equation. For supercritical adhesion, there is a nontrivial transient behavior, where density profile exhibits a secondary peak. To analyze this regime, we investigated relaxation dynamics for the Cahn-Hilliard equation without proliferation. We found that the relaxation process exhibits self-similar behavior. The results of continuum and discrete models are in a good agreement with each other for the different regimes we analyzed.

cond-mat.stat-mech↗
arXiv2006

The role of cell-cell adhesion in wound healing

We present a stochastic model which describes fronts of cells invading a wound. In the model cells can move, proliferate, and experience cell-cell adhesion. We find several qualitatively different regimes of front motion and analyze the transitions between them. Above a critical value of adhesion and for small proliferation large isolated clusters are formed ahead of the front. This is mapped onto the well-known ferromagnetic phase transition in the Ising model. For large adhesion, and larger proliferation the clusters become connected (at some fixed time). For adhesion below the critical value the results are similar to our previous work which neglected adhesion. The results are compared with experiments, and possible directions of future work are proposed.

q-bio.CB↗
arXiv2005

The role of discrete-particle noise in the Ostwald ripening

We investigate the role of discrete-particle noise in interface-controlled Ostwald ripening. We introduce the noise within the framework of the Becker-Doering equations, and employ both Monte Carlo simulations and direct numerical solution of these equations. We find that the noise drives the system towards a unique scaling regime describable by a limiting solution of a classical continuum theory due to Lifshitz, Slyozov and Wagner. The convergence towards the scaling solution is extremely slow, and we report a systematic deviation between the observed small correction to scaling and a theoretical prediction of this quantity.

cond-mat.stat-mech↗
arXiv2005

A stochastic model for wound healing

We present a discrete stochastic model which represents many of the salient features of the biological process of wound healing. The model describes fronts of cells invading a wound. We have numerical results in one and two dimensions. In one dimension we can give analytic results for the front speed as a power series expansion in a parameter, p, that gives the relative size of proliferation and diffusion processes for the invading cells. In two dimensions the model becomes the Eden model for p near 1. In both one and two dimensions for small p, front propagation for this model should approach that of the Fisher-Kolmogorov equation. However, as in other cases, this discrete model approaches Fisher-Kolmogorov behavior slowly.

q-bio.CB↗
arXiv2005

Dynamics and pattern formation in invasive tumor growth

In this work, we study the in-vitro dynamics of the most malignant form of the primary brain tumor: Glioblastoma Multiforme. Typically, the growing tumor consists of the inner dense proliferating zone and the outer less dense invasive region. Experiments with different types of cells show qualitatively different behavior. Wild-type cells invade a spherically symmetric manner, but mutant cells are organized in tenuous branches. We formulate a model for this sort of growth using two coupled reaction-diffusion equations for the cell and nutrient concentrations. When the ratio of the nutrient and cell diffusion coefficients exceeds some critical value, the plane propagating front becomes unstable with respect to transversal perturbations. The instability threshold and the full phase-plane diagram in the parameter space are determined. The results are in a good agreement with experimental findings for the two types of cells.

q-bio.CB↗
arXiv2005

Island, pit and groove formation in strained heteroepitaxy

We study the morphological evolution of strained heteroepitaxial films using a kinetic Monte Carlo method in three dimensions. The elastic part of the problem uses a Green's function method. Isolated islands are observed under deposition conditions for deposition rates slow compared with intrinsic surface roughening rates. They are semi-spherical and truncated conical for high and low temperature cases respectively. Annealing of films at high temperature leads to the formation of closely packed islands consistent with an instability theory. At low temperature, pits form via a layer-by-layer nucleation mechanism and subsequently develop into grooves.

cond-mat.stat-mech↗
arXiv2005

Random walks, diffusion limited aggregation in a wedge, and average conformal maps

We investigate diffusion-limited aggregation (DLA) in a wedge geometry. Arneodo and collaborators have suggested that the ensemble average of DLA cluster density should be close to the noise-free selected Saffman-Taylor finger. We show that a different, but related, ensemble average, that of the conformal maps associated with random clusters, yields a non-trivial shape which is also not far from the Saffman-Taylor finger. However, we have previously demonstrated that the same average of DLA in a channel geometry is not the Saffman-Taylor finger. This casts doubt on the idea that the average of noisy diffusion-limited growth is governed by a simple transcription of noise-free results.

cond-mat.stat-mech↗
arXiv2004

Kinetic pinning and biological antifreezes

Biological antifreezes protect cold-water organisms from freezing. An example are the antifreeze proteins (AFPs) that attach to the surface of ice crystals and arrest growth. The mechanism for growth arrest has not been heretofore understood in a quantitative way. We present a complete theory based on a kinetic model. We use the `stones on a pillow' picture. Our theory of the suppression of the freezing point as a function of the concentration of the AFP is quantitatively accurate. It gives a correct description of the dependence of the freezing point suppression on the geometry of the protein, and might lead to advances in design of synthetic AFPs.

cond-mat.mtrl-sci↗
arXiv2004

Growth by Random Walker Sampling, and Scaling of the Dielectric Breakdown Model

Random walkers absorbing on a boundary sample the Harmonic Measure linearly and independently: we discuss how the recurrence times between impacts enable non-linear moments of the measure to be estimated. From this we derive a new technique to simulate Dielectric Breakdown Model growth which is governed nonlinearly by the Harmonic Measure. Recurrence times are shown to be accurate and effective in probing the multifractal growth measure of diffusion limited aggregation. For the Dielectric Breakdown Model our new technique grows large clusters efficiently and we are led to significantly revise earlier exponent estimates. Previous results by two conformal mapping techniques were less converged than expected, and in particular a recent theoretical suggestion of superuniversality is firmly refuted.

cond-mat.stat-mech↗
arXiv2004

Extinction times for birth-death processes: exact results, continuum asymptotics, and the failure of the Fokker-Planck approximation

We consider extinction times for a class of birth-death processes commonly found in applications, where there is a control parameter which determines whether the population quickly becomes extinct, or rather persists for a long time. We give an exact expression for the discrete case and its asymptotic expansion for large values of the population. We have results below the threshold, at the threshold, and above the threshold (where there is a quasi-stationary state and the extinction time is very long.) We show that the Fokker-Planck approximation is valid only quite near the threshold. We compare our analytical results to numerical simulations for the SIS epidemic model, which is in the class that we treat. This is an interesting example of the delicate relationship between discrete and continuum treatments of the same problem.

q-bio.PE↗
arXiv2003

Diffusion-limited aggregation in channel geometry

We performed extensive numerical simulation of diffusion-limited aggregation in two dimensional channel geometry. Contrary to earlier claims, the measured fractal dimension D = 1.712 +- 0.002 and its leading correction to scaling are the same as in the radial case. The average cluster, defined as the average conformal map, is similar but not identical to Saffman-Taylor fingers.

cond-mat.stat-mech↗
arXiv2002

Competing roughening mechanisms in strained heteroepitaxy: a fast kinetic Monte Carlo study

We study the morphological evolution of strained heteroepitaxial films using kinetic Monte Carlo simulations in two dimensions. A novel Green's function approach, analogous to boundary integral methods, is used to calculate elastic energies efficiently. We observe island formation at low lattice misfit and high temperature that is consistent with the Asaro-Tiller-Grinfeld instability theory. At high misfit and low temperature, islands or pits form according to the nucleation theory of Tersoff and LeGoues.

cond-mat.mtrl-sci↗