arXiv subjects

Jorge Vinals

Publications and source records attributed to Jorge Vinals.

At least 19 recordsLinked to original sources

arXiv2025

Biomechanics of orientationally ordered epithelial tissue

Organogenesis involves large deformations and complex shape changes that require elaborate mechanical regulation. Models of tissue biomechanics have been introduced to account for the coupling between mechanical response and biochemical processes. Recent experimental evidence indicates that the mechanical response of epithelial tissue is strongly anisotropic, with the degree of anisotropy being correlated with the existence of long range orientational order of cytoskeletal organization across the tissue. A theoretical framework is introduced that captures the dynamic feedback between tissue elastic response and cytoskeletal reorganization under stress. Within the linear regime for small and uniform applied strains, the shear modulus is effectively reduced by the nematic order in cytoskeletal alignment induced by the applied strain. This prediction agrees with experimental observations of epithelial response in lithographically patterned micro tissues.

cond-mat.soft↗

arXiv2025

A computational study of nematic core structure and disclination interactions in elastically anisotropic nematics

A singular potential method in the Q tensor order parameter representation of a nematic liquid crystal is used to study the equilibrium configuration of a disclination dipole. Unlike the well studied isotropic limit (the so called one constant approximation), we focus on the case of anisotropic Frank elasticity (bend/splay elastic constant contrast). Prior research has established that the singular potential method provides an accurate description of the tensor order parameter profile in the vicinity of a disclination core of a highly anisotropic lyotropic chromonic liquid crystal. This research is extended here to two interacting disclinations forming a dipole configuration. The director angle is shown to decay in the far field inversely with distance to the dipole as is the case in the isotropic limit, but with a different angular dependence. Therefore elastic constant anisotropy modifies the elastic screening between disclinations, with implications for the study of ensembles of defects as seen, for example, in active matter in the extended system limit.

cond-mat.soft↗

arXiv2025

Integrated Experiment and Simulation Co-Design: A Key Infrastructure for Predictive Mesoscale Materials Modeling

The design of structural & functional materials for specialized applications is being fueled by rapid advancements in materials synthesis, characterization, manufacturing, with sophisticated computational materials modeling frameworks that span a wide spectrum of length & time scales in the mesoscale between atomistic & continuum approaches. This is leading towards a systems-based design methodology that will replace traditional empirical approaches, embracing the principles of the Materials Genome Initiative. However, several gaps remain in this framework as it relates to advanced structural materials:(1) limited availability & access to high-fidelity experimental & computational datasets, (2) lack of co-design of experiments & simulation aimed at computational model validation,(3) lack of on-demand access to verified and validated codes for simulation and for experimental analyses, & (4) limited opportunities for workforce training and educational outreach. These shortcomings stifle major innovations in structural materials design. This paper describes plans for a community-driven research initiative that addresses current gaps based on best-practice recommendations of leaders in mesoscale modeling, experimentation & cyberinfrastructure obtained at an NSF-sponsored workshop dedicated to this topic. The proposal is to create a hub for Mesoscale Experimentation and Simulation co-Operation (hMESO)-that will (I) provide curation and sharing of models, data, & codes, (II) foster co-design of experiments for model validation with systematic uncertainty quantification, & (III) provide a platform for education & workforce development. It will engage experimental & computational experts in mesoscale mechanics and plasticity, along with mathematicians and computer scientists with expertise in algorithms, data science, machine learning, & large-scale cyberinfrastructure initiatives.

cond-mat.mtrl-sci↗

arXiv2022

The propagation of infection fronts in spatially distributed compartment models in epidemiology

Spatio-temporal extensions of familiar compartment models for disease transmission incorporating diffusive behavior, or interactions between individuals at separate locations, are explored. The models considered have the character of reaction-diffusion systems, which allow familiar techniques to be applied. The focus is largely on the appearance of soliton-like moving fronts that spread infection to previously uninfected regions. Near threshold dynamical critical behavior and a degree of universality are revealed. Extending two of the models to include a simple nonlinearity in the strength of the binary interaction between a susceptible individual and an infected one, we find the possibility of static coexistence between spatial regions with different levels of infection and an analogy with first-order transitions in thermodynamics.

physics.bio-ph↗

arXiv2022

Elasticity versus phase field driven motion in the phase field crystal model

The inherent inconsistency in identifying the phase field in the phase field crystal Theory with the material mass and, simultaneously, with material distortion is discussed. In its current implementation, elastic relaxation in the phase field crystal occurs on a diffusive time scale through a dissipative permeation mode. The very same phase field distortion that is included in solid elasticity drives diffusive motion, resulting in a non physical relaxation of the phase field crystal. We present two alternative theories to remedy this shortcoming. In the first case, it is assumed that the phase field only determines the incompatible part of the elastic distortion, and therefore one is free to specify an additional compatible distortion so as to satisfy mechanical equilibrium at all times (in the quasi static limit). A numerical solution of the new model for the case of a dislocation dipole shows that, unlike the classical phase field crystal model, it can account for the known law of relative motion of the two dislocations in the dipole. The physical origin of the compatible strain in this new theory remains to be specified. Therefore, a second theory is presented in which an explicit coupling between independent distortion and phase field accounts for the time dependence of the relaxation of fluctuations in both. Preliminary details of its implementation are also given.

cond-mat.mtrl-sci↗

arXiv2018

A connection between Living Liquid Crystals and electrokinetic phenomena in nematic fluids

We develop a formal analogy between configurational stresses in two distinct physical systems, and study the flows that they induce when the configurations of interest include topological de- fects. The two systems in question are electrokinetic flows in a nematic fluid under an applied electrostatic field, and the motion of self propelling or active particles in a nematic matrix (a living liquid crystal). The mapping allows the extension, within certain limits, of existing results on trans- port in electrokinetic systems to self propelled transport. We study motion induced by a pair of point defects in a dipole configuration, and steady rotating flows due to a swirling vortex nematic director pattern. The connection presented allows the design of electrokinetic experiments that correspond to particular active matter configurations that may, however, be easier to conduct and control in the laboratory.

cond-mat.soft↗

arXiv2016

Electrokinetic flows in liquid crystal thin films with fixed anchoring

We study ionic and mass transport in a liquid crystalline fluid film in its nematic phase under an applied electrostatic field. Both analytic and numerical solutions are given for some prototypical configurations of interest in electrokinetics: Thin films with spatially nonuniform nematic director that are either periodic or comprise a set of isolated disclinations. We present a quantitative description of the mechanisms inducing spatial charge separation in the nematic, and of the structure and magnitude of the resulting flows. The fundamental solutions for the charge distribution and flow velocities induced by disclinations of topological charge $m=-1/2, 1/2$ and $1$ are given. These solutions allow the analysis of several designer flows, such as "pusher" flows created by three colinear disclinations, the flow induced by an immersed spherical particle (equivalent to an $m=1$ defect) and its accompanying $m=-1$ hyperbolic hedgehog defect, and the mechanism behind nonlinear ionic mobilities when the imposed field is perpendicular to the line joining the defects.

cond-mat.soft↗

arXiv2015

Liquid Crystals with Patterned Molecular Orientation as an Electrolytic Active Medium

Transport of fluids and particles at the microscale is an important theme both in fundamental and applied science. One of the most successful approaches is to use an electric field, which requires the system to carry or induce electric charges. We describe a versatile approach to generate electrokinetic flows by using a liquid crystal (LC) with surface-patterned molecular orientation as an electrolyte. The surface patterning is produced by photo-alignment. In the presence of an electric field, the spatially varying orientation induces space charges that trigger flows of the LC. The active patterned LC electrolyte converts the electric energy into the LC flows and transport of embedded particles of any type (fluid, solid, gaseous) along a predesigned trajectory, posing no limitation on the electric nature (charge, polarizability) of these particles and interfaces. The patterned LC electrolyte exhibits a quadratic field dependence of the flow velocities; it induces persistent vortices of controllable rotation speed and direction that are quintessential for micro- and nanoscale mixing applications.

cond-mat.soft↗

arXiv2015

Impact of lattice rotation on dislocation motion

We introduce a phenomenological theory of dislocation motion appropriate for two dimensional lattices. A coarse grained description is proposed that involves as primitive variables local lattice rotation and Burgers vector densities along distinguished slip systems of the lattice. We then use symmetry considerations to propose phenomenological equations for both defect energies and their dissipative motion. As a consequence, the model includes explicit dependences on the local state of lattice orientation, and allows for differential defect mobilities along distinguished directions. Defect densities and lattice rotation need to determined self consistently and we show specific results for both square and hexagonal lattices. Within linear response, dissipative equations of motion for the defect densities are derived which contain defect mobilities that depend nonlocally on defect distribution.

cond-mat.mtrl-sci↗

arXiv2013

The role of viscoelastic contrast in orientation selection of block copolymer lamellar phases under oscillatory shear

The mesoscale rheology of a lamellar phase of a block copolymer is modeled as a structured fluid of uniaxial symmetry. The model predicts a viscoelastic response that depends on the angle between the the local lamellar planes and velocity gradients. We focus on the stability under oscillatory shear of a two layer configuration comprising a parallel and a perpendicularly oriented domain, so that the two layers have a different viscoelastic modulus $G^{*}(ω)$. A long wave, low Reynolds number expansion is introduced to analytically obtain the region of stability. When the response of the two layers is purely viscous, we recover earlier results according to which the interface is unstable for non zero Reynolds number flows when the thinner layer is more viscous. On the other hand, when viscoelasticity is included, we find that the interface can become unstable even for zero Reynolds number. The interfacial instability is argued to dynamically favor perpendicular relative to parallel orientation, and hence we suggest that the perpendicular orientation would be selected in a multi domain configuration in the range of frequency $ω$ in which viscoelastic contrast among orientations is appreciable.

cond-mat.soft↗

arXiv2011

Anisotropic diffusion and hydrodynamic effects on lamellar relaxation and grain boundary motion in a model of a block copolymer

We consider the effects of anisotropic diffusion and hydrodynamic flows on the relaxation time scales of the lamellar phase of a diblock copolymer. We first extend the two-fluid model of a polymer solution to a block copolymer, and include a tensor mobility for the diffusive relaxation of monomer composition which is consistent with the uniaxial symmetry of the lamellar phase. The resulting equation is coupled to the momentum conservation equation, allowing also for a dissipative stress tensor for a uniaxial fluid. We then study the linear relaxation of weakly perturbed lamellae, and the motion of a tilt grain boundary separating two semi-infinite domains. We find that anisotropic diffusion has a negligible effect on the linear relaxation of the layered phase (in the long wavelenght limit), whereas the introduction of hydrodynamic flows considerably speeds the decay to a rate proportional to $Q^{2}$, where $Q\ll 1$ is the wavenumber of a transverse perturbation to the lamellar phase (diffusive relaxation scales as $Q^{4}$ instead). On the other hand, grain boundary motion is siginificantly affected by anisotropic diffusion because of the coupling between undulation and permeation diffusive modes within the grain boundary region.

cond-mat.soft↗

arXiv2009

Pitchfork and Hopf bifurcation thresholds in stochastic equations with delayed feedback

The bifurcation diagram of a model stochastic differential equation with delayed feedback is presented. We are motivated by recent research on stochastic effects in models of transcriptional gene regulation. We start from the normal form for a pitchfork bifurcation, and add multiplicative or parametric noise and linear delayed feedback. The latter is sufficient to originate a Hopf bifurcation in that region of parameters in which there is a sufficiently strong negative feedback. We find a sharp bifurcation in parameter space, and define the threshold as the point in which the stationary distribution function p(x) changes from a delta function at the trivial state x=0 to p(x) ~ x^alpha at small x (with alpha = -1 exactly at threshold). We find that the bifurcation threshold is shifted by fluctuations relative to the deterministic limit by an amount that scales linearly with the noise intensity. Analytic calculations of the bifurcation threshold are also presented in the limit of small delay tau -> 0 that compare quite favorably with the numerical solutions even for tau = 1.

cond-mat.stat-mech↗

arXiv2008

Pitchfork and Hopf bifurcation threshold in stochastic equations with delayed feedback

The bifurcation diagram of a model nonlinear Langevin equation with delayed feedback is obtained numerically. We observe both direct and oscillatory bifurcations in different ranges of model parameters. Below threshold, the stationary distribution function p(x) is a delta function at the trivial state x=0. Above threshold, p(x) ~ x^alpha at small x, with alpha = -1 at threshold, and monotonously increasing with the value of the control parameter above threshold. Unlike the case without delayed feedback, the bifurcation threshold is shifted by fluctuations by an amount that scales linearly with the noise intensity. With numerical information about time delayed correlations, we derive an analytic expression for p(x) which is in good agreement with the numerical results.

cond-mat.stat-mech↗

arXiv2006

Grain boundary dynamics in stripe phases of non potential systems

We describe numerical solutions of two non potential models of pattern formation in nonequilibrium systems to address the motion and decay of grain boundaries separating domains of stripe configurations of different orientations. We first address wavenumber selection because of the boundary, and possible decay modes when the periodicity of the stripe phases is different from the selected wavenumber for a stationary boundary. We discuss several decay modes including long wavelength undulations of the moving boundary as well as the formation of localized defects and their subsequent motion. We find three different regimes as a function of the distance to the stripe phase threshold and initial wavenumber, and then correlate these findings with domain morphology during domain coarsening in a large aspect ratio configuration.

cond-mat.soft↗

arXiv2006

Stability of parallel/perpendicular domain boundaries in lamellar block copolymers under oscillatory shear

We introduce a model constitutive law for the dissipative stress tensor of lamellar phases to account for low frequency and long wavelength flows. Given the uniaxial symmetry of these phases, we argue that the stress tensor must be the same as that of a nematic but with the local order parameter being the slowly varying lamellar wavevector. This assumption leads to a dependence of the effective dynamic viscosity on orientation of the lamellar phase. We then consider a model configuration comprising a domain boundary separating laterally unbounded domains of so called parallel and perpendicularly oriented lamellae in a uniform, oscillatory, shear flow, and show that the configuration can be hydrodynamically unstable for the constitutive law chosen. It is argued that this instability and the secondary flows it creates can be used to infer a possible mechanism for orientation selection in shear experiments.

cond-mat.soft↗

arXiv2006

Orientation selection in lamellar phases by oscillatory shears

In order to address the selection mechanism that is responsible for the unique lamellar orientation observed in block copolymers under oscillatory shears, we use a constitutive law for the dissipative part of the stress tensor that respects the uniaxial symmetry of a lamellar phase. An interface separating two domains oriented parallel and perpendicular to the shear is shown to be hydrodynamically unstable, a situation analogous to the thin layer instability of stratified fluids under shear. The resulting secondary flows break the degeneracy between parallel and perpendicular lamellar orientation, leading to a preferred perpendicular orientation in certain ranges of parameters of the polymer and of the shear.

cond-mat.soft↗

arXiv2004

Tilt grain boundary instabilities in three dimensional lamellar patterns

We identify a finite wavenumber instability of a 90$^{\circ}$ tilt grain boundary in three dimensional lamellar phases which is absent in two dimensional configurations. Both a stability analysis of the slowly varying amplitude or envelope equation for the boundary, and a direct numerical solution of an order parameter model equation are presented. The instability mode involves two dimensional perturbations of the planar base boundary, and is suppressed for purely one dimensional perturbations. We find that both the most unstable wavenumbers and their growth rate increase with $ε$, the dimensionless distance away from threshold of the lamellar phase.

cond-mat.soft↗

arXiv2003

Shear induced grain boundary motion for lamellar phases in the weakly nonlinear regime

We study the effect of an externally imposed oscillatory shear on the motion of a grain boundary that separates differently oriented domains of the lamellar phase of a diblock copolymer. A direct numerical solution of the Swift-Hohenberg equation in shear flow is used for the case of a transverse/parallel grain boundary in the limits of weak nonlinearity and low shear frequency. We focus on the region of parameters in which both transverse and parallel lamellae are linearly stable. Shearing leads to excess free energy in the transverse region relative to the parallel region, which is in turn dissipated by net motion of the boundary toward the transverse region. The observed boundary motion is a combination of rigid advection by the flow and order parameter diffusion. The latter includes break up and reconnection of lamellae, as well as a weak Eckhaus instability in the boundary region for sufficiently large strain amplitude that leads to slow wavenumber readjustment. The net average velocity is seen to increase with frequency and strain amplitude, and can be obtained by a multiple scale expansion of the governing equations.

cond-mat.soft↗