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L. L. Bonilla

Publications and source records attributed to L. L. Bonilla.

At least 19 recordsLinked to original sources

Early stages of collective cell invasion: Biomechanics

The early stages of the collective invasion may occur by single mesenchymal cells or hybrid epithelial-mesenchymal cell groups that detach from cancerous tissue. Tumors may also emit invading protrusions of epithelial cells, which could be led (or not) by a basal cell. Here we devise a novel fractional step cellular Potts model comprising passive and active cells able to describe these different types of collective invasion before cells start proliferating. Cells moving toward stiffness gradients (durotaxis) and active forces pulling them away from the tumor have different symmetry properties under cellular extension and retraction that sometimes hamper collective invasion when put together. Thus, these forces are included in different half steps of the fractional step method. Compared with a single step method, fractional step produces more realistic collective invasion scenarios with little extra computational effort. Biochemical mechanisms that determine how cells acquire their different phenotypes and cellular proliferation will be incorporated to the model in future publications.

cond-mat.stat-mech

Whodunnit? The case of midge swarms

As collective states of animal groups go, swarms of midge insects pose a number of puzzling questions. Their ordering polarization parameter is quite small and the insects are weakly coupled among themselves but strongly coupled to the swarm. In laboratory studies (free of external perturbations), the correlation length is small, whereas midge swarms exhibit strong correlations, scale free behavior and power laws for correlation length, susceptibility and correlation time in field studies. Data for the dynamic correlation function versus time collapse to a single curve only for small values of time scaled with the correlation time. Is there a theory that explains these disparate observations? Among the existing theories, whodunnit? Here we review and discuss several models proposed in the literature and extend our own one, the harmonically confined Vicsek model, to anisotropic confinement. Numerical simulations of the latter produce elongated swarm shapes and values of the static critical exponents between those of the two dimensional and isotropic three dimensional models. The new values agree better with those measured in natural swarms.

cond-mat.stat-mech

Charging capacitors using diodes at different temperatures. II Numerical studies

This study is presented in a series of two papers. The first paper is an analytical study. This is the second paper, and here we numerically study the thermal energy harvesting capability of two electronic circuits. The first circuit consists of a diode and capacitor in series. We solve the time-dependent Fokker-Planck equation and show the capacitor initially charges and then discharges to zero. The peak charge on the capacitor increases with temperature, capacitance, and diode quality. The second circuit has two current loops with one small capacitor, two storage capacitors, and two diodes wired in opposition. When the diodes are held at different temperatures we observe a non-zero steady-state charge is accumulated on both storage capacitors. The magnitude of the stored charges are nearly equal but the signs are opposite. When resistors are used in place of diodes there is no transient and no steady-state charge buildup. Numerical studies for the time-independent Fokker-Planck equation are presented and confirm the steady state charges.

cond-mat.stat-mech

Charging capacitors using diodes at different temperatures. I Theor

Nonlinear elements in a rectifying circuit can be used to harvest energy from thermal fluctuations either steadily or transitorily. We study an energy harvesting system comprising a small variable capacitor (e.g., free standing graphene) wired to two diodes and two storage capacitors that may be kept at different temperatures (or at a single one) and use two current loops. The system reaches very rapidly a quasi stationary state with constant overall charge while the difference of the charges at the storage capacitors evolves much more slowly to its stationary value. In this paper, we extract an exponentially small factor out of the solution of the Fokker-Planck equation and use a Chapman-Enskog procedure to describe the long evolution of the marginal probability density for the charge difference, from the quasi stationary state to the final stationary state (thermal equilibrium for equal temperatures). The second paper of this series shows that the results of the perturbation procedure compare well with direct numerical simulations. For a specific form of the diodes' nonlinear mobilities, we can approximate the quasi stationary state by Gaussian functions and further study the evolution of the marginal probability density. The latter adopts the shape of a slowly expanding pulse (comprising left and right moving wave fronts whose fore edges become sharper as time elapses) in the space of charge differences that leaves the final stationary state behind it.

cond-mat.stat-mech

Exact solutions of the harmonically confined Vicsek model

The discrete time Vicsek model confined by a harmonic potential explains many aspects of swarm formation in insects. We have found exact solutions of this model without alignment noise in two or three dimensions. They are periodic or quasiperiodic (invariant circle) solutions with positions on a circular orbit or on several concentric orbits and exist for quantized values of the confinement. There are period 2 and period 4 solutions on a line for a range of confinement strengths and period 4 solutions on a rhombus. These solutions may have polarization one, although there are partially ordered period 4 solutions and totally disordered (zero polarization) period 2 solutions. We have explored the linear stability of the exact solutions in two dimensions using the Floquet theorem and verified the stability assignements by direct numerical simulations.

physics.bio-ph

Power laws of natural swarms are fingerprints of an extended critical region

Collective biological systems display power laws for macroscopic quantities and are fertile probing grounds for statistical physics. Besides power laws, natural insect swarms present strong scale-free correlations, suggesting closeness to phase transitions. Swarms exhibit {\em imperfect} dynamic scaling: their dynamical correlation functions collapse into single curves when written as functions of the scaled time $tξ^{-z}$ ($ξ$: correlation length, $z$: dynamic exponent), but only for short times. Triggered by markers, natural swarms are not invariant under space translations. Measured static and dynamic critical exponents differ from those of equilibrium and many nonequilibrium phase transitions. Here, we show that: (i) the recently discovered scale-free-chaos phase transition of the harmonically confined Vicsek model has a novel extended critical region for $N$ (finite) insects that contains several critical lines. (ii) As alignment noise vanishes, there are power laws connecting critical confinement and noise that allow calculating static critical exponents for fixed $N$. These power laws imply that the unmeasurable confinement strength is proportional to the perception range measured in natural swarms. (iii) Observations of natural swarms occur at different times and under different atmospheric conditions, which we mimic by considering mixtures of data on different critical lines and $N$. Unlike results of other theoretical approaches, our numerical simulations reproduce the previously described features of natural swarms and yield static and dynamic critical exponents that agree with observations.

cond-mat.stat-mech

Scale-free chaos in the 2D harmonically confined Vicsek model

Animal motion and flocking are ubiquitous nonequilibrium phenomena that are often studied within active matter. In examples such as insect swarms, macroscopic quantities exhibit power laws with measurable critical exponents and ideas from phase transitions and statistical mechanics have been explored to explain them. The widely used Vicsek model with periodic boundary conditions has an ordering phase transition but the corresponding homogeneous ordered or disordered phases are different from observations of natural swarms. If a harmonic potential (instead of a periodic box) is used to confine particles, the numerical simulations of the Vicsek model display periodic, quasiperiodic and chaotic attractors. The latter are scale free on critical curves that produce power laws and critical exponents. Here we investigate the scale-free-chaos phase transition in two space dimensions. We show that the shape of the chaotic swarm on the critical curve reflects the split between core and vapor of insects observed in midge swarms and that the dynamic correlation function collapses only for a finite interval of small scaled times, as also observed. We explain the algorithms used to calculate the largest Lyapunov exponents, the static and dynamic critical exponents and compare them to those of the three-dimensional model.

cond-mat.soft

Soliton approximation in continuum models of leader-follower behavior

Complex biological processes involve collective behavior of entities (bacteria, cells, animals) over many length and time scales and can be described by discrete models that track individuals or by continuum models involving densities and fields. We consider hybrid stochastic agent-based models of branching morphogenesis and angiogenesis (new blood vessel creation from pre-existing vasculature), which treat cells as individuals that are guided by underlying continuous chemical and/or mechanical fields. In these descriptions, leader (tip) cells emerge from existing branches and follower (stalk) cells build the new sprout in their wake. Vessel branching and fusion (anastomosis) occur as a result of tip and stalk cell dynamics. Coarse-graining these hybrid models in appropriate limits produces continuum partial differential equations (PDEs) for endothelial cell densities that are more analytically tractable. While these models differ in nonlinearity, they produce similar equations at leading order when chemotaxis is dominant. We analyze this leading order system in a simple quasi-one-dimensional geometry and show that the numerical solution of the leading order PDE is well described by a soliton wave that evolves from vessel to source. This wave is an attractor for intermediate times until it arrives at the hypoxic region releasing the growth factor. The mathematical techniques used here thus identify common features of discrete and continuum approaches and provide insight into general biological mechanisms governing their collective dynamics.

cond-mat.soft

Charging capacitors from thermal fluctuations using diodes

We theoretically consider a graphene ripple as a Brownian particle coupled to an energy storage circuit. When circuit and particle are at the same temperature, the second law forbids harvesting energy from the thermal motion of the Brownian particle, even if the circuit contains a rectifying diode. However, when the circuit contains a junction followed by two diodes wired in opposition, the approach to equilibrium may become ultraslow. Detailed balance is temporarily broken as current flows between the two diodes and charges storage capacitors. The energy harvested by each capacitor comes from the thermal bath of the diodes while the system obeys the first and second laws of thermodynamics.

cond-mat.mes-hall

Mean field theory of chaotic insect swarms

The harmonically confined Vicsek model displays qualitative and quantitative features observed in natural insect swarms. It exhibits a scale free transition between single and multicluster chaotic phases. Finite size scaling indicates that this unusual phase transition occurs at zero confinement [Physical Review E 107, 014209 (2023)]. While the evidence of the scale-free-chaos phase transition comes from numerical simulations, here we present its mean field theory. Analytically determined critical exponents are those of the Landau theory of equilibrium phase transitions plus dynamical critical exponent $z=1$ and a new critical exponent $φ=0.5$ for the largest Lyapunov exponent. The phase transition occurs at zero confinement and noise in the mean field theory. The noise line of zero largest Lyapunov exponents informs observed behavior: (i) the qualitative shape of the swarm (on average, the center of mass rotates slowly at the rate marked by the winding number and its trajectory fills compactly the space, similarly to the observed condensed nucleus surrounded by vapor), and (ii) the critical exponents resemble those observed in natural swarms. Our predictions include power laws for the frequency of the maximal spectral amplitude and the winding number.

cond-mat.stat-mech

Scale free chaos in the confined Vicsek flocking model

The Vicsek model encompasses the paradigm of active dry matter. Motivated by collective behavior of insects in swarms, we have studied finite size effects and criticality in the three dimensional, harmonically confined Vicsek model. We have discovered a phase transition that exists for appropriate noise and small confinement strength. On the critical line of confinement versus noise, swarms are in a state of scale-free chaos characterized by minimal correlation time, correlation length proportional to swarm size and topological data analysis. The critical line separates dispersed single clusters from confined multicluster swarms. Scale-free chaotic swarms occupy a compact region of space and comprise a recognizable `condensed' nucleus and particles leaving and entering it. Susceptibility, correlation length, dynamic correlation function and largest Lyapunov exponent obey power laws. The critical line and a narrow criticality region close to it move simultaneously to zero confinement strength for infinitely many particles. At the end of the first chaotic window of confinement, there is another phase transition to infinitely dense clusters of finite size that may be termed flocking black holes.

cond-mat.stat-mech

Bifurcation theory captures band formation in the Vicsek model of flock formation

Collective behavior occurs ubiquitously in nature and it plays a key role in bacterial colonies, mammalian cells or flocks of birds. Here, we examine the average density and velocity of self-propelled particles, which are described by a system of partial differential equations near the flocking transition of the Vicsek model. This agent-based model illustrates the trend towards flock formation of animals that align their velocities to an average of those of their neighbors. Near the flocking transition, particle density and velocity obey partial differential equations that include a parameter $ε$ measuring the distance to the bifurcation point. We have obtained analytically the Riemann invariants in one and two spatial dimensions for the hyperbolic ($ε=0$) and parabolic ($ε\neq 0$) system and, under periodic initial-boundary value conditions, we show that the solutions include wave trains. Additionally, we have found wave trains having oscillation frequencies that agree with those predicted by a linearization approximation and that may propagate at angles depending on the initial condition. The wave amplitudes increase with time for the hyperbolic system but are stabilized to finite values for the parabolic system. To integrate the partial differential equations, we design a basic numerical scheme which is first order in time and space. To mitigate numerical dissipation and ensure good resolution of the wave features, we also use a high order accurate WENO5 reconstruction procedure in space and a third order accurate Runge-Kutta scheme in time. Comparisons with direct simulations of the Vicsek model confirm these predictions.

cond-mat.stat-mech

Uncovering spatio-temporal patterns in semiconductor superlattices by efficient data processing tools

Time periodic patterns in a semiconductor superlattice, relevant to microwave generation, are obtained upon numerical integration of a known set of drift-diffusion equations. The associated spatio-temporal transport mechanisms are uncovered by applying (to the computed data) two recent data processing tools, known as the higher order dynamic mode decomposition and the spatio-temporal Koopman decomposition. Outcomes include a clear identification of the asymptotic self-sustained oscillations of the current density (isolated from the transient dynamics) and an accurate description of the electric field traveling pulse in terms of its dispersion diagram. In addition, a preliminary version of a novel data-driven reduced order model is constructed, which allows for extremely fast online simulations of the system response over a range of different configurations.

cond-mat.mtrl-sci

Designing hyperchaos and intermittency in semiconductor superlattices

Weakly coupled semiconductor superlattices under dc voltage bias are excitable systems with many degrees of freedom that may exhibit spontaneous chaos at room temperature and act as fast physical random number generator devices. Superlattices with identical periods exhibit current self-oscillations due to the dynamics of charge dipole waves but chaotic oscillations exist on narrow voltage intervals. They disappear easily due to variation in structural growth parameters. Based on numerical simulations, we predict that inserting two identical sufficiently separated wider wells increases superlattice excitability by allowing wave nucleation at the modified wells and more complex dynamics. This system exhibits hyperchaos and varieties of intermittent chaos in extended dc voltage ranges. Unlike in ideal superlattices, our chaotic attractors are robust and resilient against noises and against controlled random disorder due to growth fluctuations.

cond-mat.mes-hall

Tracking collective cell motion by topological data analysis

By modifying and calibrating an active vertex model to experiments, we have simulated numerically a confluent cellular monolayer spreading on an empty space and the collision of two monolayers of different cells in an antagonistic migration assay. Cells are subject to inertial forces and to active forces that try to align their velocities with those of neighboring ones. In agreement with experiments, spreading tests exhibit finger formation in the moving interfaces, swirls in the velocity field, and the polar order parameter and correlation and swirl lengths increase with time. Cells inside the tissue have smaller area than those at the interface, as observed in recent experiments. In antagonistic migration assays, a population of fluidlike Ras cells invades a population of wild type solidlike cells having shape parameters above and below the geometric critical value, respectively. Cell mixing or segregation depends on the junction tensions between different cells. We reproduce experimentally observed antagonistic migration assays by assuming that a fraction of cells favor mixing, the others segregation, and that these cells are randomly distributed in space. To characterize and compare the structure of interfaces between cell types or of interfaces of spreading cellular monolayers in an automatic manner, we apply topological data analysis to experimental data and to numerical simulations. We use time series of numerical simulation data to automatically group, track and classify advancing interfaces of cellular aggregates by means of bottleneck or Wasserstein distances of persistent homologies. These topological data analysis techniques are scalable and could be used in studies involving large amounts of data. Besides applications to wound healing and metastatic cancer, these studies are relevant for tissue engineering, biological effects of materials, tissue and organ regeneration.

cond-mat.soft

Integrodifference master equation describing actively growing blood vessels in angiogenesis

We study a system of particles in a two-dimensional geometry that move according to a reinforced random walk with transition probabilities dependent on the solutions of reaction-diffusion equations for the underlying fields. A birth process and a history-dependent killing process are also considered. This system models tumor-induced angiogenesis, the process of formation of blood vessels induced by a growth factor released by a tumor. Particles represent vessel tip cells, whose trajectories constitute the growing vessel network. New vessels appear and may fuse with existing ones during their evolution. Thus, the system is described by tracking the density of active tips, calculated as an ensemble average over many realizations of the stochastic process. Such density satisfies a novel discrete master equation with source and sink terms. The sink term is proportional to a space-dependent and suitably fitted killing coefficient. Results are illustrated studying two influential angiogenesis models.

q-bio.TO

Two dimensional soliton in tumor induced angiogenesis

Ensemble averages of a stochastic model show that, after a formation stage, the tips of active blood vessels in an angiogenic network form a moving two dimensional stable diffusive soliton, which advances toward sources of growth factor. Here we use methods of multiple scales to find the diffusive soliton as a solution of a deterministic equation for the mean density of active endothelial cells tips. We characterize the diffusive soliton shape in a general geometry, and find that its vector velocity and the trajectory of its center of mass along curvilinear coordinates solve appropriate collective coordinate equations. The vessel tip density predicted by the soliton compares well with that obtained by ensemble averages of simulations of the stochastic model.

cond-mat.stat-mech

Fluctuation-induced current from freestanding graphene: toward nanoscale energy harvesting

At room temperature, micron-sized sheets of freestanding graphene are in constant motion even in the presence of an applied bias voltage. We quantify the out-of-plane movement by collecting the displacement current using a nearby small-area metal electrode and present a Langevin model for the motion coupled to a circuit containing diodes. The system reaches thermal equilibrium and the rates of heat, work, and entropy production tend quickly to zero. However, there is power generated by graphene which is equal to the power dissipated by the load resistor. The exact power formula is similar to Nyquist's noise power formula, except that the rate of change of diode resistance significantly boosts the output power, and the movement of the graphene shifts the power spectrum to lower frequencies.

cond-mat.mes-hall