arXiv subjects

Yoav G. Pollack

Publications and source records attributed to Yoav G. Pollack.

12 recordsLinked to original sources

arXiv2026

Determination of active forces in actomyosin systems as inverse source problems for the Stokes equation

The identification of forces and stresses is a central task in biophysics research: Knowledge on forces is key to understanding dynamic processes in active biological systems that are able to self-organize and display emergent properties by converting energy into mechanical work. The aim of this paper is to identify forces generated by a filament-motor network of F-actin and myosin -- actomyosin -- and exerted on the surrounding fluid, therefore causing a fluid flow. In particular, we evaluate optical microscopy data stemming from two different physical settings, confined and non-confined active gels. As a theoretical model, we use the Stokes equation together with an incompressibility condition and suitable boundary conditions reflecting the physical settings. The problem of determining the forces from knowledge on the fluid flow is formulated as an inverse source problem. Due to experimental limitations, only incomplete data are available. We provide a rigorous analysis of the forward problems and the impact of missing data, derive the adjoints of the forward operators needed for regularization, and demonstrate our methods on both synthetic and experimentally measured data.

physics.flu-dyn↗

arXiv2025

Dimensionality and confinement reshape competition in cellular renewing active matter

Cellular renewing active matter - assemblies of proliferating and apoptotic cells - underlies tissue homeostasis, morphogenesis, and clonal competition. Previous work in one-dimensional periodic systems identified a fitness advantage associated with rapid dead-cell clearance, an "opportunistic" competition mechanism. Extending this framework, we study two-dimensional cellular aggregates and show that dimensionality modifies the interplay between competition mechanisms for clones with different clearance rates: in 2D, opportunistic and homeostatic-pressure-based competition jointly shape clonal selection, to varying degrees. We then introduce an explicit circular confinement to probe how boundaries modulate this interplay. While opportunistic competition persists, distinct timescale-dependent behaviors emerge through weakened homeostatic-pressure-based competition near boundaries. Structural analysis reveals that confinement promotes tangential alignment and spatially heterogeneous homeostatic pressure, thereby reshaping competitive outcomes at tissue edges. Our study connects newly discovered competition mechanisms with more realistic biological contexts, highlighting how dimensionality and spatial constraints influence tissue structures and modulate competition in heterogeneous cell populations, with implications for tumor growth dynamics and tissue development.

cond-mat.soft↗

arXiv2025

Hackathons for biophysics education: simulating the cytoskeleton

Hackathons are intensive innovation-oriented events where participants work in teams to solve problems or create projects in as little as 24 or 48 hours. These events are common in startup culture, open source communities and mainstream industry. Here we examine how hackathons can be ported to academic teaching, specifically in computational biophysics. We propose hackathons as a teaching modality distinct from traditional courses and structured workshops. In particular, we suggest they can offer a low-stakes platform for students to overcome entry barriers to computational tools or to explore new topics, disciplines, and skills beyond their academic comfort zone. We tested this format in two computational biophysics hackathons on the Göttingen campus in 2023 and 2024, providing practical insights and a preliminary evaluation. To the best of our knowledge, the 2024 event is the first public hackathon dedicated to Biophysics. This paper explores the benefits of the hackathon format for teachers and researchers and provides guidelines for running a hackathon adapted to a teaching goal.

physics.ed-ph↗

arXiv2024

A minimal model of smoothly dividing disk-shaped cells

Replication through cell division is one of the most fundamental processes of life and a major driver of dynamics in systems ranging from bacterial colonies to embryogenesis, tissues and tumors. While regulation often plays a role in shaping self-organization, mounting evidence suggests that many biologically relevant behaviors exploit principles based on a limited number of physical ingredients, and particle-based models have become a popular platform to reconstitute and investigate these emergent dynamics. However, incorporating division into such models often leads to aberrant mechanical fluctuations that hamper physically meaningful analysis. Here, we present a minimal model focusing on mechanical consistency during division. Cells are comprised of two nodes, overlapping disks which separate from each other during cell division, resulting in transient dumbbell shapes. Internal degrees of freedom, cell-cell interactions and equations of motion are designed to ensure force continuity at all times, including through division, both for the dividing cell itself as well as interaction partners, while retaining the freedom to define arbitrary anisotropic mobilities. As a benchmark, we also translate an established model of proliferating spherocylinders with similar dynamics into our theoretical framework. Numerical simulations of both models demonstrate force continuity of the new disk cell model and quantify our improvements. We also investigate some basic collective behaviors related to alignment and orientational order and find consistency both between the models and with the literature. A reference implementation of the model is freely available as a package in the Julia programming language based on $\mathit{InPartS}$. Our model is ideally suited for the investigation of mechanical observables such as velocities and stresses, and is easily extensible with additional features.

cond-mat.soft↗

arXiv2017

How Generic are the Robust Theoretical Aspects of Jamming in Hard Sphere Models?

In very recent work the mean field theory of the jamming transition in infinite dimensional hard spheres models was presented. Surprisingly, this theory predicts quantitatively numerically determined characteristics of jamming in two and three dimensions. This is a rare and unusual finding. Here we argue that this agreement in non-generic: only for hard sphere models it happens that sufficiently close to jamming the effective interactions are in agreement with mean-field theory, justifying the truncation of many body interactions (which is the exact protocol in infinite dimensions). Any softening of the bare hard sphere interactions results in effective interactions that are not mean-field all the way to jamming, making the discussed phenomenon non generic.

cond-mat.soft↗

arXiv2017

Reply to Comment on `What Determines the Static Force Chains in Stressed Granular Media?'

The formalism proposed in Phys. Rev. Lett. 116, 078001 (2016) for determination of the normal and tangential inter-particle forces in frictional disks from visual data was criticized in a comment to that paper. However the theory developed in the original publication is aimed at finding the forces when provided with accurate measurements while the comment addresses a different problem, being the statistics of forces in a configuration with uncertainty of the relevant parameters. We address this difference in perspectives and point out that even with experimental errors one can improve the results using an iterative procedure proposed in Phys. Rev. E. Rapid Communication, 93, 060601(R) (2016).

cond-mat.soft↗

arXiv2016

Emergent Inter-particle Interactions in Thermal Amorphous Solids

Amorphous media at finite temperatures, be them liquids, colloids or glasses, are made of interacting particles that move chaotically due to thermal energy, colliding and scattering continuously off each other. When the average configuration in these systems relaxes only at long times, one can introduce {\em effective interactions} that keep the {\em mean positions} in mechanical equilibrium. We introduce a new framework to determine these effective force-laws that define an effective Hessian that can be employed to discuss stability properties and density of states of the amorphous system. We exemplify the approach with a thermal glass of hard spheres; these feel zero forces when not in contact and infinite forces when they touch. The present approach recaptures the effective interactions which for sufficiently dense spheres at temperature $T$ depends on the gap $h$ between spheres as $T/h$ [C. Brito and M. Wyart, Europhys. Lett. 76 149 (2006)]. In systems at lower densities or with longer microscopic interaction (say like Lennard-Jones), the emergent force laws will include ternary, quaternary and generally higher order many-body terms, even if the microscopic interactions are strictly binary.

cond-mat.soft↗

arXiv2016

Determining the Inter-Particle Force-Laws in Amorphous Solids from a Visual Image

We consider the problem of how to determine the force laws in an amorphous system of interacting particles. Given the positions of the centers of mass of the constituent particles we propose a new algorithm to determine the inter-particle force-laws. Having $n$ different types of constituents we determine the coefficients in the Laurent polynomials for the $n(n+1)/2$ possibly different force-laws. A visual providing the particle positions in addition to a measurement of the pressure is all that is required. The algorithm proposed includes a part that can correct for experimental errors in the positions of the particles. Such a correction of unavoidable measurement errors is expected to benefit many experiments in the field.

cond-mat.soft↗

arXiv2016

Scaling Theory of the Mechanical Properties of Amorphous Nano-Films

Numerical Simulations are employed to create amorphous nano-films of a chosen thickness on a crystalline substrate which induces strain on the film. The films are grown by a vapor deposition technique which was recently developed to create very stable glassy films. Using the exact relations between the Hessian matrix and the shear and bulk moduli we explore the mechanical properties of the nano-films as a function of the density of the substrate and the film thickness. The existence of the substrate dominates the mechanical properties of the combined substrate-film system. Scaling concepts are then employed to achieve data collapse in a wide range of densities and film thicknesses.

cond-mat.soft↗

arXiv2016

What determines static force chains in stressed granular media?

The determination of the normal and transverse (frictional) inter-particle forces within a granular medium is a long standing, taunting, and yet unresolved problem. We present a new formalism which employs the knowledge of the external forces and the orientations of contacts between particles (of any given sizes), to compute all the inter-particle forces. Having solved this problem we exemplify the efficacy of the formalism showing that the force chains in such systems are determined by an expansion in the eigenfunctions of a newly defined operator.

cond-mat.soft↗

arXiv2015

The Static Lengthscale Characterizing the Glass Transition at Lower Temperatures

The existence of a static lengthscale that grows in accordance with the dramatic slowing down observed at the glass transition is a subject of intense interest. A recent publication compared two proposals for this length scale, one based on the point-to-set correlation technique and the other on the scale where the lowest eigenvalue of the Hessian matrix becomes sensitive to disorder. The conclusion was that both approaches lead to the same lengthscale, but the former is easier to measure at higher temperatures and the latter at lower temperatures. But even after using both methods together, the range of increase in the observed lengthscales was limited by the relaxation times reachable by standard molecular dynamics techniques (i.e. about 4-5 orders of magnitude). In this paper we therefore attempt to explore the typical scale at even lower temperatures, testing for this purpose two approaches, one based on the idea of vapor deposition and the other on a swap Monte Carlo technique. We conclude that the first approach does not help in getting to lower temperatures, but the second one does so quite effectively. We can reach a typical lengthscale that grows in accordance with at least $15$ orders of magnitude increase in the relaxation time, competing with the best experimental conditions. We conclude by discussing the relationship between the observed lengthscale and various models of the relaxation time.

cond-mat.stat-mech↗

arXiv2013

Direct Measurement of Random Fields in the $LiHo_xY_{1-x}F_4$ Crystal

The random field Ising model (RFIM) is central to the study of disordered systems. Yet, for a long time it eluded realization in ferromagnetic systems because of the difficulty to produce locally random magnetic fields. Recently it was shown that in anisotropic dipolar magnetic insulators, the archetypal of which is the $LiHo_xY_{1-x}F_4$ system, the RFIM can be realized in both ferromagnetic and spin glass phases. The interplay between an applied transverse field and the offdiagonal terms of the dipolar interaction produce effective longitudinal fields, which are random in sign and magnitude as a result of spatial dilution. In this paper we use exact numerical diagonalization of the full Hamiltonian of Ho pairs in $LiHo_xY_{1-x}F_4$ to calculate the effective longitudinal field beyond the perturbative regime. In particular, we find that nearby spins can experience an effective field larger than the intrinsic dipolar broadening (of quantum states in zero field) which can therefore be evidenced in experiments. We then calculate the magnetization and susceptibility under several experimental protocols, and show how these protocols can produce direct measurement of the effective longitudinal field.

cond-mat.dis-nn↗