arXiv subjects

Ulrich Dobramysl

Publications and source records attributed to Ulrich Dobramysl.

At least 19 recordsLinked to original sources

arXiv2025

Agent-based Monte Carlo simulations for reaction-diffusion models, population dynamics, and epidemic spreading

We provide an overview of Monte Carlo algorithms based on Markovian stochastic dynamics of interacting and reacting many-particle systems not in thermal equilibrium. These agent-based simulations are an effective way of introducing students to current research without requiring much prior knowledge or experience. By starting from the direct visualization of the data, students can gain immediate insight into emerging macroscopic features of a complex system and subsequently apply more sophisticated data analysis to quantitatively characterize its rich dynamical properties, both in the stationary and transient regimes. We utilize simulations of reaction-diffusion systems, stochastic models for population dynamics and epidemic spreading, to exemplify how interdisciplinary computational research can be effectively utilized in bottom-up undergraduate and graduate education through learning by doing. We also give helpful hints for the practical implementation of Monte Carlo algorithms, provide sample codes, explain some typical data analysis tools, and describe various potential error sources and pitfalls and tips for avoiding them.

cond-mat.stat-mech↗

arXiv2024

Argentine ants regulate traffic flow with stopped individuals

We investigated the emerging traffic patterns of Argentine ants (Linepithema humile) as they navigated a narrow bridge between their nest and a food source. By tracking ant movements in experiments with varying bridge widths and colony sizes and analyzing the resulting trajectories, we discovered that a small subset of ants stopped for long periods of time, acting as obstacles and affecting traffic flow. Interestingly, the fraction of these stopped ants increased with wider bridges, suggesting a mechanism to reduce traffic flow to a narrower section of the bridge. To quantify transport efficiency, we measured the average speed of the ants on the bridge as a function of the pressure of ants arriving at the bridge, finding this relationship to be an increasing but saturating function of the pressure. We developed an agent-based model for ant movement and interactions to better understand these dynamics. Including stopped agents in the model was crucial to explaining the experimental observations. We further validated our hypothesis by introducing artificial obstacles on the bridges and found that our simulations accurately mirrored the experimental data when these obstacles were included. These findings provide new insights into how Argentine ants self-organize to manage traffic, highlighting a unique form of dynamic obstruction that enhances traffic flow in high-density conditions. This study advances our understanding of self-regulation in biological traffic systems and suggests potential applications for managing human traffic in congested environments.

q-bio.PE↗

arXiv2023

Perturbative Field-Theoretical Analysis of Three-Species Cyclic Predator-Prey Models

We apply a perturbative Doi--Peliti field-theoretical analysis to the stochastic spatially extended symmetric Rock-Paper-Scissors (RPS) and May--Leonard (ML) models, in which three species compete cyclically. Compared to the two-species Lotka--Volterra predator-prey (LV) model, according to numerical simulations, these cyclical models appear to be less affected by intrinsic stochastic fluctuations. Indeed, we demonstrate that the qualitative features of the ML model are insensitive to intrinsic reaction noise. In contrast, and although not yet observed in numerical simulations, we find that the RPS model acquires significant fluctuation-induced renormalizations in the perturbative regime, similar to the LV model. We also study the formation of spatio-temporal structures in the framework of stability analysis and provide a clearcut explanation for the absence of spatial patterns in the RPS system, whereas the spontaneous emergence of spatio-temporal structures features prominently in the LV and the ML models.

cond-mat.stat-mech↗

arXiv2020

Computational methods and fast hybrid stochastic simulations for triangulation sensing and identifying principles of cell navigation in the brain

Brownian simulations can be used to generate statistics relevant for studying molecular interactions or trafficking. However, the concurrent simulation of many Brownian trajectories at can become computationally intractable. Replacing detailed Brownian simulations by a rate model was the basis of Gillespie's algorithm, but requires one to disregard spatial information. However, this information is crucial in molecular and cellular biology. Alternatively one can use a hybrid approach, generating Brownian paths only in a small region where the spatial organization is relevant and avoiding it in the remainder of the domain. Here we review the recent progress of hybrid methods and simulations in the context of cell sensing and guidance via external chemical gradients. Specifically, we highlight the reconstruction of the location of a point source in 2D and 3D from diffusion fluxes arriving at narrow windows located on the cell. We discuss cases in which these windows are located on the boundary of the 2D or 3D half-space, on a disk in free space, inside a 2D corridor, or a 3D ball. The hybrid method in question performs Brownian simulations only inside a region of interest. It uses the Neumann-Green's function for the mentioned geometries to generate exact mappings exit and entry points when the trajectory leaves the region, thus avoiding the explicit computation of Brownian paths in an infinite domain. Matched asymptotics is used to compute the probability fluxes to small windows and we review how such an approach can be used to reconstruct the location of a point source and estimating the uncertainty in the source reconstruction due to an additive perturbation present in the fluxes. We also review the influence of various window configurations on the source position recovery. Finally, we discuss potential applications in developmental cell biology and possible computational principles.

cond-mat.stat-mech↗

arXiv2020

Critical Scaling and Aging near the Flux Line Depinning Transition

We utilize Langevin molecular dynamics simulations to study dynamical critical behavior of magnetic flux lines near the depinning transition in type-II superconductors subject to randomly distributed attractive point defects. We employ a coarse-grained elastic line Hamiltonian for the mutually repulsive vortices and purely relaxational kinetics. In order to infer the stationary-state critical exponents for the continuous non-equilibrium depinning transition at zero temperature T = 0 and at the critical driving current density j_c, we explore two-parameter scaling laws for the flux lines' gyration radius and mean velocity as functions of the two relevant scaling fields T and j - j_c. We also investigate critical aging scaling for the two-time height auto-correlation function in the early-time non-equilibrium relaxation regime to independently measure critical exponents. We provide numerical exponent values for the distinct universality classes of non-interacting and repulsive vortices.

cond-mat.stat-mech↗

arXiv2019

Triangulation sensing: how cells recover a source from diffusing particles in three dimensions

How can cells embedded into a gradient concentration triangulate the position of the source and migrate toward their final destination? The source triangulation requires to recover the three dimensional coordinates of the source from the fluxes of diffusing cues at narrow windows (receptors) located on the surface of a cell. We develop here a method to address this question and we show in the limit of fast binding rate to the receptors, that at least three receptors are necessary. We solve the steady-state diffusion equation using an asymptotic approach, which agrees with hybrid stochastic-analytical simulations. Interestingly, with an accuracy of few percent, the source cannot be located if it is located at a distance tens of time the size of the cell. Finally, the precision of the source recovery increases with the number of receptors.

q-bio.CB↗

arXiv2018

Dynamical regimes of vortex flow in type-II superconductors with parallel twin boundaries

We explore the dynamics of driven magnetic flux lines in disordered type-II superconductors in the presence of twin boundaries oriented parallel to the direction of the applied magnetic field, using a three-dimensional elastic line model simulated with Langevin molecular dynamics. The lines are driven perpendicular to the planes to model the effect of an electric current applied parallel to the planes and perpendicular to the magnetic field. A study of the long-time non-equilibrium steady states for varying sample orientation and thickness reveals a rich collection of dynamical regimes spanning the depinning crossover region that separates the pinned and moving-lattice states of vortex matter. We observe the emergence of a preferred direction for the ordering of the Abrikosov lattice in the free-flowing vortex regime due to asymmetric pinning by the planar defects. We have performed novel direct measurements of flux line excitations such as half-loops and double kinks to aid the characterization of the topologically rich flux flow profile.

cond-mat.supr-con↗

arXiv2017

Stochastic population dynamics in spatially extended predator-prey systems

Spatially extended population dynamics models that incorporate intrinsic noise serve as case studies for the role of fluctuations and correlations in biological systems. Including spatial structure and stochastic noise in predator-prey competition invalidates the deterministic Lotka-Volterra picture of neutral population cycles. Stochastic models yield long-lived erratic population oscillations stemming from a resonant amplification mechanism. In spatially extended predator-prey systems, one observes noise-stabilized activity and persistent correlations. Fluctuation-induced renormalizations of the oscillation parameters can be analyzed perturbatively. The critical dynamics and the non-equilibrium relaxation kinetics at the predator extinction threshold are characterized by the directed percolation universality class. Spatial or environmental variability results in more localized patches which enhances both species densities. Affixing variable rates to individual particles and allowing for trait inheritance subject to mutations induces fast evolutionary dynamics for the rate distributions. Stochastic spatial variants of cyclic competition with rock-paper-scissors interactions illustrate connections between population dynamics and evolutionary game theory, and demonstrate how space can help maintain diversity. In two dimensions, three-species cyclic competition models of the May-Leonard type are characterized by the emergence of spiral patterns whose properties are elucidated by a mapping onto a complex Ginzburg-Landau equation. Extensions to general food networks can be classified on the mean-field level, which provides both a fundamental understanding of ensuing cooperativity and emergence of alliances. Novel space-time patterns emerge as a result of the formation of competing alliances, such as coarsening domains that each incorporate rock-paper-scissors competition games.

cond-mat.stat-mech↗

arXiv2017

Evolutionary dynamics and competition stabilize three-species predator-prey communities

We perform individual-based Monte Carlo simulations in a community consisting of two predator species competing for a single prey species, with the purpose of studying biodiversity stabilization in this simple model system. Predators are characterized with predation efficiency and death rates, to which Darwinian evolutionary adaptation is introduced. Competition for limited prey abundance drives the populations' optimization with respect to predation efficiency and death rates. We study the influence of various ecological elements on the final state, finding that both indirect competition and evolutionary adaptation are insufficient to yield a stable ecosystem. However, stable three-species coexistence is observed when direct interaction between the two predator species is implemented.

q-bio.PE↗

arXiv2017

Mixed analytical-stochastic simulation method for the recovery of a Brownian gradient source from probability fluxes to small windows

Is it possible to recover the position of a source from the steady-state fluxes of Brownian particles to small absorbing windows located on the boundary of a domain? To address this question, we develop a numerical procedure to avoid tracking Brownian trajectories in the entire infinite space. Instead, we generate particles near the absorbing windows, computed from the analytical expression of the exit probability. When the Brownian particles are generated by a steady-state gradient at a single point, we compute asymptotically the fluxes to small absorbing holes distributed on the boundary of half-space and on a disk in two dimensions, which agree with stochastic simulations. We also derive an expression for the splitting probability between small windows using the matched asymptotic method. Finally, when there are more than two small absorbing windows, we show how to reconstruct the position of the source from the diffusion fluxes. The present approach provides a computational first principle for the mechanism of sensing a gradient of diffusing particles, a ubiquitous problem in cell biology.

q-bio.CB↗

arXiv2016

Flux line relaxation kinetics following current quenches in disordered type-II superconductors

We investigate the relaxation dynamics of magnetic vortex lines in type-II superconductors following rapid changes of the external driving current by means of an elastic line model simulated with Langevin molecular dynamics. A system of flux vortices in a sample with randomly distributed point-like defects is subjected to an external current of appropriate strength for a sufficient period of time so as to be in a moving non-equilibrium steady state. The current is then instantaneously lowered to a value that pertains to either the moving or pinned regime. The ensuing relaxation of the flux lines is studied via one-time observables such as their mean velocity and radius of gyration. We have in addition measured the two-time flux line height autocorrelation function to investigate dynamical scaling and aging behavior in the system, which in particular emerge after quenches into the glassy pinned state.

cond-mat.supr-con↗

arXiv2016

Steric effects induce geometric remodeling of actin bundles in filopodia

Filopodia are ubiquitous fingerlike protrusions, spawned by many eukaryotic cells, to probe and interact with their environments. Polymerization dynamics of actin filaments, comprising the structural core of filopodia, largely determine their instantaneous lengths and overall lifetimes. The polymerization reactions at the filopodial tip require transport of G-actin, which enter the filopodial tube from the filopodial base and diffuse toward the filament barbed ends near the tip. Actin filaments are mechanically coupled into a tight bundle by cross-linker proteins. Interestingly, many of these proteins are relatively short, restricting the free diffusion of cytosolic G-actin throughout the bundle and, in particular, its penetration into the bundle core. To investigate the effect of steric restrictions on G-actin diffusion by the porous structure of filopodial actin filament bundle, we used a particle-based stochastic simulation approach. We discovered that excluded volume interactions result in partial and then full collapse of central filaments in the bundle, leading to a hollowed-out structure. The latter may further collapse radially due to the activity of cross-linking proteins, hence producing conical-shaped filament bundles. Interestingly, electron microscopy experiments on mature filopodia indeed frequently reveal actin bundles that are narrow at the tip and wider at the base. Overall, our work demonstrates that excluded volume effects in the context of reaction-diffusion processes in porous networks may lead to unexpected geometric growth patterns and complicated, history-dependent dynamics of intermediate metastable configurations.

q-bio.SC↗

arXiv2016

Particle-based Multiscale Modeling of Calcium Puff Dynamics

Intracellular calcium is regulated in part by the release of Ca$^{2+}$ ions from the endoplasmic reticulum via inositol-4,5-triphosphate receptor (IP$_3$R) channels (among other possibilities such as RyR and L-type calcium channels). The resulting dynamics are highly diverse, lead to local calcium "puffs" as well as global waves propagating through cells, as observed in {\it Xenopus} oocytes, neurons, and other cell types. Local fluctuations in the number of calcium ions play a crucial role in the onset of these features. Previous modeling studies of calcium puff dynamics stemming from IP$_3$R channels have predominantly focused on stochastic channel models coupled to deterministic diffusion of ions, thereby neglecting local fluctuations of the ion number. Tracking of individual ions is computationally difficult due to the scale separation in the Ca$^{2+}$ concentration when channels are in the open or closed states. In this paper, a spatial multiscale model for investigating of the dynamics of puffs is presented. It couples Brownian motion (diffusion) of ions with a stochastic channel gating model. The model is used to analyze calcium puff statistics. Concentration time traces as well as channel state information are studied. We identify the regime in which puffs can be found and develop a mean-field theory to extract the boundary of this regime. Puffs are only possible when the time scale of channel inhibition is sufficiently large. Implications for the understanding of puff generation and termination are discussed.

q-bio.SC↗

arXiv2015

Disordered vortex matter out of equilibrium: a Langevin molecular dynamics study

We discuss the use of Langevin molecular dynamics in the investigation of the non-equilibrium properties of disordered vortex matter. Our special focus is set on values of system parameters that are realistic for disordered high-$T_c$ superconductors such as YBCO. Using a discretized elastic line model, we study different aspects of vortices far from thermal equilibrium. On the one hand we investigate steady-state properties of driven magnetic flux lines in a disordered environment, namely the current-voltage characteristics, the gyration radius, and the pinning time statistics. On the other hand we study the complex relaxation processes and glassy-like dynamics that emerge in type-II superconductors due to the intricate competition between the long-range vortex-vortex repulsion and flux pinning due to randomly placed point defects. To this end we consider different types of sudden perturbations: temperature, magnetic field, and external current quenches.

cond-mat.stat-mech↗

arXiv2015

Relaxation dynamics of vortex lines in disordered type-II superconductors following magnetic field and temperature quenches

We study the effects of rapid temperature and magnetic field changes on the non-equilibrium relaxation dynamics of magnetic vortex lines in disordered type-II superconductors by employing an elastic line model and performing Langevin molecular dynamics simulations. In a previously equilibrated system, either the temperature is suddenly changed, or the magnetic field is instantaneously altered which is reflected in adding or removing flux lines to or from the system. The subsequent aging properties are investigated in samples with either randomly distributed point-like or extended columnar defects, which allows to distinguish the complex relaxation features that result from either type of pinning centers. One-time observables such as the radius of gyration and the fraction of pinned line elements are employed to characterize steady-state properties, and two-time correlation functions such as the vortex line height autocorrelations and their mean-square displacement are analyzed to study the non-linear stochastic relaxation dynamics in the aging regime.

cond-mat.stat-mech↗

arXiv2014

Pinning time statistics for vortex lines in disordered environments

We study the pinning dynamics of magnetic flux (vortex) lines in a disordered type-II superconductor. Using numerical simulations of a directed elastic line model, we extract the pinning time distributions of vortex line segments. We compare different model implementations for the disorder in the surrounding medium: discrete, localized pinning potential wells that are either attractive and repulsive or purely attractive, and whose strengths are drawn from a Gaussian distribution; as well as continuous Gaussian random potential landscapes. We find that both schemes yield power law distributions in the pinned phase as predicted by extreme-event statistics, yet they differ significantly in their effective scaling exponents and their short-time behavior.

cond-mat.stat-mech↗

arXiv2013

Environmental vs demographic variability in stochastic predator-prey models

In contrast to the neutral population cycles of the deterministic mean-field Lotka--Volterra rate equations, including spatial structure and stochastic noise in models for predator-prey interactions yields complex spatio-temporal structures associated with long-lived erratic population oscillations. Environmental variability in the form of quenched spatial randomness in the predation rates results in more localized activity patches. Population fluctuations in rare favorable regions in turn cause a remarkable increase in the asymptotic densities of both predators and prey. Very intriguing features are found when variable interaction rates are affixed to individual particles rather than lattice sites. Stochastic dynamics with demographic variability in conjunction with inheritable predation efficiencies generate non-trivial time evolution for the predation rate distributions, yet with overall essentially neutral optimization.

q-bio.PE↗

arXiv2013

Relaxation dynamics in type-II superconductors with point-like and correlated disorder

We employ an elastic line model to investigate the steady-state properties and non-equilibrium relaxation kinetics of magnetic vortex lines in disordered type-II superconductors using Langevin molecular dynamics (LMD). We extract the dependence of the mean vortex line velocity and gyration radius as well as the mean-square displacement in the steady state on the driving current, and measure the vortex density and height autocorrelations in the aging regime. We study samples with either randomly distributed point-like or columnar attractive pinning centers, which allows us to distinguish the complex relaxation features of interacting flux lines subject to extended vs. uncorrelated disorder. Additionally, we find that our new LMD findings match earlier Monte Carlo (MC) simulation data well, verifying that these two microscopically quite distinct simulation methods lead to macroscopically very similar results for non-equilibrium vortex matter.

cond-mat.supr-con↗