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L. L. Bonilla

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

At least 37 records · Page 2Linked to original sources

Active Ornstein-Uhlenbeck particles

Active Ornstein-Uhlenbeck particles (AOUPs) are overdamped particles in an interaction potential subject to external Ornstein-Uhlenbeck noises. They can be transformed into a system of underdamped particles under additional velocity dependent forces and subject to white noise forces. There has been some discussion in the literature on whether AOUPs can be in equilibrium for particular interaction potentials and how far from equilibrium they are in the limit of small persistence time. By using a theorem on the time reversed form of the AOUP Langevin-Ito equations, I prove that they have an equilibrium probability density invariant under time reversal if and only if their smooth interaction potential has zero third derivatives. In the limit of small persistence Ornstein-Uhlenbeck time $τ$, a Chapman-Enskog expansion of the Fokker-Planck equation shows that the probability density has a local equilibrium solution in the particle momenta modulated by a reduced probability density that varies slowly with the position. The reduced probability density satisfies a continuity equation in which the probability current has an asymptotic expansion in powers of $τ$. Keeping up to $O(τ)$ terms, this equation is a diffusion equation, which has an equilibrium stationary solution with zero current. However, $O(τ^2)$ terms contain fifth and sixth order spatial derivatives and the continuity equation no longer has a zero current stationary solution. The expansion of the overall stationary solution now contains odd terms in the momenta, which clearly shows that it is not an equilibrium.

cond-mat.soft↗

Crossover between parabolic and hyperbolic scaling, oscillatory modes and resonances near flocking

A stability and bifurcation analysis of a kinetic equation indicates that the flocking bifurcation of the two-dimensional Vicsek model exhibits an interplay between parabolic and hyperbolic behavior. For box sizes smaller than a certain large value, flocking appears continuously from a uniform disordered state at a critical value of the noise. Because of mass conservation, the amplitude equations describing the flocking state consist of a scalar equation for the density disturbance from the homogeneous particle density (particle number divided by box area) and a vector equation for a current density. These two equations contain two time scales. At the shorter scale, they are a hyperbolic system in which time and space scale in the same way. At the longer, diffusive, time scale, the equations are parabolic. The bifurcating solution depends on the angle and is uniform in space as in the normal form of the usual pitchfork bifurcation. We show that linearization about the latter solution is described by a Klein-Gordon equation in the hyperbolic time scale. Then there are persistent oscillations with many incommensurate frequencies about the bifurcating solution, they produce a shift in the critical noise and resonate with a periodic forcing of the alignment rule. These predictions are confirmed by direct numerical simulations of the Vicsek model.

cond-mat.soft↗

Two dimensional collective electron magnetotransport, oscillations and chaos in a semiconductor superlattice

When quantized, traces of classically chaotic single particle systems include eigenvalue statistics and scars in eigenfuntions. Since 2001, many theoretical and experimental works have argued that classically chaotic single electron dynamics influences and controls collective electron transport. For transport in semiconductor superlattices under tilted magnetic and electric fields, these theories rely on a reduction to a one-dimensional self-consistent drift model. A two-dimensional theory based on self-consistent Boltzmann transport does not support that single electron chaos influences collective transport. This theory agrees with existing experimental evidence of current self-oscillations, predicts spontaneous collective chaos via a period doubling scenario and it could be tested unambiguously by measuring the electric potential inside the superlattice under a tilted magnetic field.

cond-mat.mes-hall↗

Bifurcation analysis and phase diagram of a spin-string model with buckled states

We analyze a one-dimensional spin-string model, in which string oscillators are linearly coupled to their two nearest neighbors and to Ising spins representing internal degrees of freedom. String-spin coupling induces a long-range ferromagnetic interaction among spins that competes with a spin-spin antiferromagnetic coupling. As a consequence, the complex phase diagram of the system exhibits different flat rippled and buckled states, with first or second order transition lines between states. The two-dimensional version of the model has a similar phase diagram, which has been recently used to explain the rippled to buckled transition observed in scanning tunnelling microscopy experiments with suspended graphene sheets. Here we describe in detail the phase diagram of the simpler one-dimensional model and phase stability using bifurcation theory. This gives additional insight into the physical mechanisms underlying the different phases and the behavior observed in experiments.

cond-mat.stat-mech↗

Critical radius and temperature for buckling in graphene

In this work, we find an analytical flat-membrane solution to the saddle point equations, derived by Guinea et al. [Phys. Rev. B 89, 125428 (2014)], for the case of a suspended graphene membrane of circular shape. We also find how different buckled membrane solutions bifurcate from the flat membrane at critical temperatures and membrane radii. The saddle point equations take into account electron-phonon coupling and this coupling provides a residual stress even for a flat graphene layer. Below a critical temperature (which is exceedingly high for an infinite layer) or above a critical size that depend on boundary conditions, different buckling modes that may be the germ of rippling appear. Our results provide the opportunity to develop new feasible experiments dealing with buckling in small suspended graphene membranes that could verify them. These experiments may also be used to fit the phonon-electron coupling constant or the bending energy.

cond-mat.mes-hall↗

Soliton-like attractor for blood vessel tip density in angiogenesis

Recently, numerical simulations of a stochastic model have shown that the density of vessel tips in tumor induced angiogenesis adopts a soliton-like profile [Sci. Rep. 6, 31296 (2016)]. In this work, we derive and solve the equations for the soliton collective coordinates that indicate how the soliton adapts its shape and velocity to varying chemotaxis and diffusion. The vessel tip density can be reconstructed from the soliton formulas. While the stochastic model exhibits large fluctuations, we show that the location of the maximum vessel tip density for different replicas follows closely the soliton peak position calculated either by ensemble averages or by solving an alternative deterministic description of the density. The simple soliton collective coordinate equations may also be used to ascertain the response of the vessel network to changes in the parameters and thus to control it.

physics.bio-ph↗

Stochastic Model of Tumor-induced Angiogenesis: Ensemble Averages and Deterministic Equations

A recent conceptual model of tumor-driven angiogenesis including branching, elongation, and anastomosis of blood vessels captures some of the intrinsic multiscale structures of this complex system, yet allowing to extract a deterministic integro-partial differential description of the vessel tip density [Phys. Rev. E 90, 062716 (2014)]. Here we solve the stochastic model, show that ensemble averages over many realizations correspond to the deterministic equations, and fit the anastomosis rate coefficient so that the total number of vessel tips evolves similarly in the deterministic and ensemble averaged stochastic descriptions.

q-bio.TO↗

Wavelength selection of rippling patterns in myxobacteria

Rippling patterns of myxobacteria appear in starving colonies before they aggregate to form fruiting bodies. These periodic traveling cell density waves arise from the coordination of individual cell reversals, resulting from an internal clock regulating them, and from contact signaling during bacterial collisions. Here we revisit a mathematical model of rippling in myxobacteria due to Igoshin et al.\ [Proc. Natl. Acad. Sci. USA {\bf 98}, 14913 (2001) and Phys. Rev. E {\bf 70}, 041911 (2004)]. Bacteria in this model are phase oscillators with an extra internal phase through which they are coupled to a mean-field of oppositely moving bacteria. Previously, patterns for this model were obtained only by numerical methods and it was not possible to find their wavenumber analytically. We derive an evolution equation for the reversal point density that selects the pattern wavenumber in the weak signaling limit, show the validity of the selection rule by solving numerically the model equations and describe other stable patterns in the strong signaling limit. The nonlocal mean-field coupling tends to decohere and confine patterns. Under appropriate circumstances, it can annihilate the patterns leaving a constant density state via a nonequilibrium phase transition reminiscent of destruction of synchronization in the Kuramoto model.

cond-mat.stat-mech↗

Measuring strain and rotation fields at the dislocation core in graphene

Strain fields, dislocations and defects may be used to control electronic properties of graphene. By using advanced imaging techniques with high-resolution transmission electron microscopes, we have measured the strain and rotation fields about dislocations in monolayer graphene with single-atom sensitivity. These fields differ qualitatively from those given by conventional linear elasticity. However, atom positions calculated from two dimensional (2D) discrete elasticity and three dimensional discrete periodized Föppl-von Kármán equations (dpFvKEs) yield fields close to experiments when determined by geometric phase analysis. 2D theories produce symmetric fields whereas those from experiments exhibit asymmetries. Numerical solutions of dpFvKEs provide strain and rotation fields of dislocation dipoles and pairs that also exhibit asymmetries and, compared with experiments, may yield information on out-of-plane displacements of atoms. While discrete theories need to be solved numerically, analytical formulas for strains and rotation about dislocations can be obtained from 2D Mindlin's hyperstress theory. These formulas are very useful for fitting experimental data and provide a template to ascertain the importance of nonlinear and nonplanar effects. Measuring the parameters of this theory, we find two characteristic lengths between three and four times the lattice spacings that control dilatation and rotation about a dislocation. At larger distances from the dislocation core, the elastic fields decay to those of conventional elasticity. Our results may be relevant for strain engineering in graphene and other 2D materials of current interest.

cond-mat.mes-hall↗

Theory of force-extension curve for modular proteins and DNA hairpins

We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by the elongations of each of the units. The system free energy includes a double-well potential for each unit and an elastic nearest neighbor interaction between them. Minimizing the free energy yields the system equilibrium properties whereas its dynamics is given by (overdamped) Langevin equations for the elongations, in which friction and noise amplitude are related by the fluctuation-dissipation theorem. Our results, both for the equilibrium and the dynamical situations, include analytical and numerical descriptions of the system force-extension curves under force or length control, and agree very well with actual experiments in biomolecules. Our conclusions also apply to other physical systems comprising a number of metastable units, such as storage systems or semiconductor superlattices.

cond-mat.stat-mech↗

Hybrid modeling of tumor-induced angiogenesis

When modeling of tumor-driven angiogenesis, a major source of analytical and computational complexity is the strong coupling between the kinetic parameters of the relevant stochastic branching-and-growth of the capillary network, and the family of interacting underlying fields. To reduce this complexity, we take advantage of the system intrinsic multiscale structure: we describe the stochastic dynamics of the cells at the vessel tip at their natural mesoscale, whereas we describe the deterministic dynamics of the underlying fields at a larger macroscale. Here, we set up a conceptual stochastic model including branching, elongation, and anastomosis of vessels and derive a mean field approximation for their densities. This leads to a deterministic integro-partial differential system that describes the formation of the stochastic vessel network. We discuss the proper capillary injecting boundary conditions and include the results of relevant numerical simulations.

q-bio.TO↗

Dynamics of optically injected currents in carbon nanotubes

We consider theoretically the dynamics of electric currents optically injected in carbon nanotubes. Although the plasma oscillations are not seen in these systems, the main effect on the carrier's motion is due to strongly nonuniform space-charge Coulomb forces produced by time-dependent separation of injected electron and hole densities. We calculate evolution of the dipole moment characterizing the time- and coordinate-dependent charge density distributions and analyze different regimes of the dynamics. The developed time-dependent dipole moment leads to a dipole radiation in the THz frequency range for typical parameters of injected currents.

cond-mat.mes-hall↗

Protein unfolding and refolding as transitions through virtual states

Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a bistable potential, weakly connected by harmonic spring linkers. Multistability of equilibrium extensions provides the characteristic sawtooth force-extension curve. We show that abrupt or stepwise unfolding and refolding under force-clamp conditions involve transitions through virtual states (which are quasi-stationary domain configurations) modified by thermal noise. These predictions agree with experimental observations.

cond-mat.stat-mech↗

Noise enhanced spontaneous chaos in semiconductor superlattices at room temperature

Physical systems exhibiting fast spontaneous chaotic oscillations are used to generate high-quality true random sequences in random number generators. The concept of using fast practical entropy sources to produce true random sequences is crucial to make storage and transfer of data more secure at very high speeds. While the first high-speed devices were chaotic semiconductor lasers, the discovery of spontaneous chaos in semiconductor superlattices at room temperature provides a valuable nanotechnology alternative. Spontaneous chaos was observed in 1996 experiments at temperatures below liquid nitrogen. Here we show spontaneous chaos at room temperature appears in idealized superlattices for voltage ranges where sharp transitions between different oscillation modes occur. Internal and external noises broaden these voltage ranges and enhance the sensitivity to initial conditions in the superlattice snail-shaped chaotic attractor thereby rendering spontaneous chaos more robust.

cond-mat.mes-hall↗

Influence of primary particle density in the morphology of agglomerates

Agglomeration processes occur in many different realms of science such as colloid and aerosol formation or formation of bacterial colonies. We study the influence of primary particle density in agglomerate structure using diffusion-controlled Monte Carlo simulations with realistic space scales through different regimes (DLA and DLCA). The equivalence of Monte Carlo time steps to real time scales is given by Hirsch's hydrodynamical theory of Brownian motion. Agglomerate behavior at different time stages of the simulations suggests that three indices (fractal exponent, coordination number and eccentricity index) characterize agglomerate geometry. Using these indices, we have found that the initial density of primary particles greatly influences the final structure of the agglomerate as observed in recent experimental works.

cond-mat.soft↗

Sawtooth patterns in biomolecules force-extension curves: an equilibrium-statistical-mechanics theory

We analyze the force-extension curve for a general class of systems, which are described at the mesoscopic level by a free energy depending on the extension of its components. Similarly to what is done in real experiments, the total length of the system is the controlled parameter. This imposes a global constraint in the minimization procedure leading to the equilibrium values of the extensions. As a consequence, the force-extension curve has multiple branches in a certain range of forces. The stability of these branches is governed by the free energy: there are a series of first-order phase transitions at certain values of the total length, in which the free energy itself is continuous but its first derivative, the force, has a finite jump. This behavior is completely similar to the one observed in real experiments with biomolecules like proteins, and other complex systems.

physics.bio-ph↗

Ripples in a graphene membrane coupled to Glauber spins

We propose a theory of ripples in suspended graphene sheets based on two-dimensional elasticity equations that are made discrete on the honeycomb lattice and then periodized. At each point carbon atoms are coupled to Ising spins whose values indicate the atoms local trend to move vertically off-plane. The Ising spins are in contact with a thermal bath and evolve according to Glauber dynamics. In the limit of slow spin flip compared to membrane vibrations, ripples with no preferred orientation appear as long-lived metastable states for any temperature. Numerical solutions confirm this picture.

cond-mat.mes-hall↗

Model of ripples in graphene

We propose a model of ripples in suspended graphene sheets based on plate equations that are made discrete with the periodicity of the honeycomb lattice and then periodized. In addition, the equation for the displacements with respect to the planar configuration contains a double-well site potential, a nonlinear friction and a multiplicative white noise term satisfying the fluctuation-dissipation theorem. The nonlinear friction terms agree with those proposed by Eichler et al [Nature Nanotech. {\bf 6}, 339 (2011)] to explain their experiments with a graphene resonator. The site double-well potential indicates that the carbon atoms at each lattice point have equal probability to move upward or downward off-plane. For the considered parameter values, the relaxation time due to friction is much larger than the periods of membrane vibrations and the noise is quite small. Then ripples with no preferred orientation appear as long-lived metastable states for any temperature. Numerical solutions confirm this picture.

cond-mat.mes-hall↗