arXiv subjects

Andrew J. Bernoff

Publications and source records attributed to Andrew J. Bernoff.

11 recordsLinked to original sources

arXiv2026

A weighted model of perception and decision-making between targets of finite size

Recent research grounded in experiments has connected neural ring models of vision to how animals navigate a complex landscape of attractive targets. In this paper we investigate the mathematical and biological implications of a three-stage model where animals pre-process visual stimuli to identify a discrete set of targets, process this input to select the dominant targets, and then post-process this information to navigate the landscape. Incorporating finite target sizes and a neural density allows consistent target acquisition and pursuit reflecting what is seen in nature. Mathematically, we show this model corresponds to an energy minimization problem, simplifying both its analysis and numerical implementation. Biologically, we argue that the model is physiologically motivated, reproduces experimental observations, and presents a fairly direct pathway to decoding neural geometry via empirical data. Our results also demonstrate an analysis pipeline for future model extensions and suggest specific avenues for experimental research to test and parameterize our quantitative framework.

q-bio.NC↗

arXiv2026

The three-dimensional Neumann Green's function for general surfaces: singular asymptotics and boundary integral methods

We present an asymptotic analysis and high-order boundary integral method for the three-dimensional Neumann Green's function in general closed and smooth geometries. The Neumann Green's function is a fundamental quantity which arises in numerous fields of science and engineering. In the application of singular perturbation methods to strongly localized reactions and diffusive transport, the Green's function plays the key role in mediating global dynamics. However, this essential quantity can only be determined in closed-form for a limited set of geometries. The Green's function for the Laplacian is an elliptic problem with a Dirac forcing term. Accurate resolution of the solution requires a careful decomposition into a singular and a regular part. The bulk scenario is where the source is placed off surface and the singularity is given by the free-space function. In the surface case, where the source is placed at a curved point on the boundary, we use asymptotic analysis to determine a three-term singularity structure. With explicit knowledge of these singularities, we develop a high-order boundary integral method for the determination of the remaining regular part. To resolve the singular boundary data, our integral method uses a custom discretization with Duffy patches near the source. We validate our method using several test cases in which closed-form solutions can be developed, including spheres, prolate spheroids and constructed domains. We demonstrate the applicability of our method to address some open problems in narrow capture theory.

math.NA↗

arXiv2024

Kinetic Monte Carlo methods for three-dimensional diffusive capture problems in exterior domains

Cellular scale decision making is modulated by the dynamics of signalling molecules and their diffusive trajectories from a source to small absorbing sites on the cellular surface. Diffusive capture problems are computationally challenging due to the complex geometry and the applied boundary conditions together with intrinsically long transients that occur before a particle is captured. This paper reports on a particle-based Kinetic Monte Carlo (KMC) method that provides rapid accurate simulation of arrival statistics for (i) a half-space bounded by a surface with a finite collection of absorbing traps and (ii) the domain exterior to a convex cell again with absorbing traps. We validate our method by replicating classical results and in addition, newly developed boundary homogenization theories and matched asymptotic expansions on capture rates. In the case of non-spherical domains, we describe a new shielding effect in which geometry can play a role in sharpening cellular estimates on the directionality of diffusive sources.

math.NA↗

arXiv2020

Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry

Locusts are significant agricultural pests. Under favorable environmental conditions flightless juveniles may aggregate into coherent, aligned swarms referred to as hopper bands. These bands are often observed as a propagating wave having a dense front with rapidly decreasing density in the wake. A tantalizing and common observation is that these fronts slow and steepen in the presence of green vegetation. This suggests the collective motion of the band is mediated by resource consumption. Our goal is to model and quantify this effect. We focus on the Australian plague locust, for which excellent field and experimental data is available. Exploiting the alignment of locusts in hopper bands, we concentrate solely on the density variation perpendicular to the front. We develop two models in tandem; an agent-based model that tracks the position of individuals and a partial differential equation model that describes locust density. In both these models, locust are either stationary (and feeding) or moving. Resources decrease with feeding. The rate at which locusts transition between moving and stationary (and vice versa) is enhanced (diminished) by resource abundance. This effect proves essential to the formation, shape, and speed of locust hopper bands in our models. From the biological literature we estimate ranges for the ten input parameters of our models. Sobol sensitivity analysis yields insight into how the band's collective characteristics vary with changes in the input parameters. By examining 4.4 million parameter combinations, we identify biologically consistent parameters that reproduce field observations. We thus demonstrate that resource-dependent behavior can explain the density distribution observed in locust hopper bands. This work suggests that feeding behaviors should be an intrinsic part of future modeling efforts.

nlin.AO↗

arXiv2017

Numerical approximation of diffusive capture rates by planar and spherical surfaces with absorbing pores

In 1977 Berg & Purcell published a landmark paper entitled "Physics of Chemoreception" which examined how a bacterium can sense a chemical attractant in the fluid surrounding it. At small scales the attractant molecules move by Brownian motion and diffusive processes dominate. This example is the archetype of diffusive signaling problems where an agent moves via a random walk until it either strikes or eludes a target. Berg & Purcell modeled the target as a sphere with a set of small circular targets (pores) that can capture a diffusing agent. They argued that, in the limit of small radii and wide spacing, each pore could be modeled independently as a circular pore on an infinite plane. Using a known exact solution, they showed the capture rate to be proportional to the combined perimeter of the pores. In this paper we study how to improve this approximation by including inter-pore competition effects and verify this result numerically for a finite collection of pores on a plane or sphere. Asymptotically we have found the corrections to the Berg-Purcell formula that account for enhancement of capture due to the curvature of the spherical target and inhibition of capture due to spatial interactions of the pores. Numerically we develop a spectral boundary element method for the exterior mixed Neumann-Dirichlet boundary value problem. Our formulation reduces the problem to a linear integral equation, specifically a Neumann to Dirichlet map, which is supported only on the individual pores. The difficulty is that both the kernel and the flux are singular, a notorious obstacle in such problems. A judicious choice of singular boundary elements allows us to resolve the flux singularity at the edge of the pore. In biological systems there can be thousands of receptors whose radii are 0.1% the cell radius. Our numerics resolve this realistic limit with an accuracy of roughly one part in 10^8.

math.AP↗

arXiv2016

Biological aggregation driven by social and environmental factors: A nonlocal model and its degenerate Cahn-Hilliard approximation

Biological aggregations such as insect swarms and bird flocks may arise from a combination of social interactions and environmental cues. We focus on nonlocal continuum equations, which are often used to model aggregations, and yet which pose significant analytical and computational challenges. Beginning with a particular nonlocal aggregation model [Topaz et al., Bull. Math. Bio., 2006], we derive the minimal well-posed long-wave approximation, which is a degenerate Cahn-Hilliard equation. Energy minimizers of this reduced, local model retain many salient features of those of the nonlocal model, especially for large populations and away from an aggregation's boundaries. Using the Cahn-Hilliard model as a testbed, we investigate the degree to which an external potential modeling food sources can be used to suppress peak population density, which is essential for controlling locust outbreaks. A random distribution of food sources tends to increase peak density above its intrinsic value, while a periodic pattern of food sources can decrease it.

nlin.PS↗

arXiv2015

Energy Driven Pattern Formation in Planar Dipole-Dipole Systems in the Presence of Weak Noise

We study pattern formation in planar fluid systems driven by intermolecular cohesion (which manifests as a line tension) and dipole-dipole repulsion which are observed in physical systems including ferrofluids in Hele-Shaw cells and Langmuir layers. When the dipolar repulsion is sufficiently strong, domains undergo forked branching reminiscent of viscous fingering. A known difficulty with these models is that the energy associated with dipole-dipole interactions is singular at small distances. Following previous work, we demonstrate how to ameliorate this singularity and show that in the macroscopic limit, only the relative scale of the microscopic details of a system are relevant, and develop an expression for the system energy that depends only on a generalized line tension, Λ, that in turn depends logarithmically on that scale. We conduct numerical studies that use energy minimization to find equilibrium states. Following the subcritical bifurcations from the circle, we find a few highly symmetric stable shapes, but nothing that resembles the observed diversity of experimental and dynamically simulated domains. The application of a weak random background to the energy landscape stabilizes a smörgåsbord of domain morphologies recovering the diversity observed experimentally. With this technique, we generate a large sample of qualitatively realistic shapes and use them to create an empirical model for extracting Λ using only a shape's perimeter and morphology with high accuracy.

cond-mat.soft↗

arXiv2013

Social aggregation in pea aphids: Experimental measurement and stochastic modeling

An ongoing challenge in the mathematical modeling of biological aggregations is to strengthen the connection between models and biological data by quantifying the rules that individuals follow. We model aggregation of the pea aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the motion of aphids walking in a featureless circular arena in order to deduce individual-level rules. We observe that each aphid transitions stochastically between a moving and a stationary state. Moving aphids follow a correlated random walk. The probabilities of motion state transitions, as well as the random walk parameters, depend strongly on distance to an aphid's nearest neighbor. For large nearest neighbor distances, when an aphid is essentially isolated, its motion is ballistic with aphids moving faster, turning less, and being less likely to stop. In contrast, for short nearest neighbor distances, aphids move more slowly, turn more, and are more likely to become stationary; this behavior constitutes an aggregation mechanism. From the experimental data, we estimate the state transition probabilities and correlated random walk parameters as a function of nearest neighbor distance. With the individual-level model established, we assess whether it reproduces the macroscopic patterns of movement at the group level. To do so, we consider three distributions, namely distance to nearest neighbor, angle to nearest neighbor, and percentage of population moving at any given time. For each of these three distributions, we compare our experimental data to the output of numerical simulations of our nearest neighbor model, and of a control model in which aphids do not interact socially. Our stochastic, social nearest neighbor model reproduces salient features of the experimental data that are not captured by the control.

q-bio.QM↗

arXiv2012

Locust Dynamics: Behavioral Phase Change and Swarming

Locusts exhibit two interconvertible behavioral phases, solitarious and gregarious. While solitarious individuals are repelled from other locusts, gregarious insects are attracted to conspecifics and can form large aggregations such as marching hopper bands. Numerous biological experiments at the individual level have shown how crowding biases conversion towards the gregarious form. To understand the formation of marching locust hopper bands, we study phase change at the collective level, and in a quantitative framework. Specifically, we construct a partial integrodifferential equation model incorporating the interplay between phase change and spatial movement at the individual level in order to predict the dynamics of hopper band formation at the population level. Stability analysis of our model reveals conditions for an outbreak, characterized by a large scale transition to the gregarious phase. A model reduction enables quantification of the temporal dynamics of each phase, of the proportion of the population that will eventually gregarize, and of the time scale for this to occur. Numerical simulations provide descriptions of the aggregation's structure and reveal transiently traveling clumps of gregarious insects. Our predictions of aggregation and mass gregarization suggest several possible future biological experiments.

q-bio.QM↗

arXiv2010

A primer of swarm equilibria

We study equilibrium configurations of swarming biological organisms subject to exogenous and pairwise endogenous forces. Beginning with a discrete dynamical model, we derive a variational description of the corresponding continuum population density. Equilibrium solutions are extrema of an energy functional, and satisfy a Fredholm integral equation. We find conditions for the extrema to be local minimizers, global minimizers, and minimizers with respect to infinitesimal Lagrangian displacements of mass. In one spatial dimension, for a variety of exogenous forces, endogenous forces, and domain configurations, we find exact analytical expressions for the equilibria. These agree closely with numerical simulations of the underlying discrete model.The exact solutions provide a sampling of the wide variety of equilibrium configurations possible within our general swarm modeling framework. The equilibria typically are compactly supported and may contain $δ$-concentrations or jump discontinuities at the edge of the support. We apply our methods to a model of locust swarms, which are observed in nature to consist of a concentrated population on the ground separated from an airborne group. Our model can reproduce this configuration; quasi-two-dimensionality of the model plays a critical role.

nlin.PS↗

arXiv2007

A model for rolling swarms of locusts

We construct an individual-based kinematic model of rolling migratory locust swarms. The model incorporates social interactions, gravity, wind, and the effect of the impenetrable boundary formed by the ground. We study the model using numerical simulations and tools from statistical mechanics, namely the notion of H-stability. For a free-space swarm (no wind and gravity), as the number of locusts increases, it approaches a crystalline lattice of fixed density if it is H-stable, and in contrast becomes ever more dense if it is catastrophic. Numerical simulations suggest that whether or not a swarm rolls depends on the statistical mechanical properties of the corresponding free-space swarm. For a swarm that is H-stable in free space, gravity causes the group to land and form a crystalline lattice. Wind, in turn, smears the swarm out along the ground until all individuals are stationary. In contrast, for a swarm that is catastrophic in free space, gravity causes the group to land and form a bubble-like shape. In the presence of wind, the swarm migrates with a rolling motion similar to natural locust swarms. The rolling structure is similar to that observed by biologists, and includes a takeoff zone, a landing zone, and a stationary zone where grounded locusts can rest and feed.

q-bio.PE↗