arXiv subjects

Shahriar Shadkhoo

Publications and source records attributed to Shahriar Shadkhoo.

7 recordsLinked to original sources

arXiv2025

Boundaries Program Deformation in Isolated Active Networks

Cellular structures must organize themselves within strict physical constraints, operating with finite resources and well-defined boundaries. Classical systems demonstrate only passive responses to boundaries, from surface energy minimization in soap films to strain distributions in elastic networks. Active matter fundamentally alters this paradigm - internally generated stresses create a bidirectional coupling between boundary geometry and mass conservation that enables dynamic control over network organization. Here we demonstrate boundary geometry actively directs network deformation in reconstituted microtubule-kinesin systems, revealing a programmable regime of shape transformation through controlled boundary manipulation. A coarse-grained theoretical framework reveals how boundary geometry couples to internal stress fields via mass conservation, producing distinct dynamical modes that enable engineered deformations. The emergence of shape-preserving and shape-changing regimes, predicted by theory and confirmed through experiments, establishes boundary geometry as a fundamental control parameter for active materials. The control principle based on boundaries advances both the understanding of biological organization and enables design of synthetic active matter devices with programmable deformation.

cond-mat.soft↗

arXiv2024

Force Propagation in Active Cytoskeletal Networks

In biological systems, molecular-scale forces and motions are pivotal for enabling processes like motility, shape change, and replication. These forces and motions are organized, amplified, and transmitted across macroscopic scales by active materials such as the cytoskeleton, which drives micron-scale cellular movement and re-organization. Despite the integral role of active materials, understanding how molecular-scale interactions alter macroscopic structure and force propagation remains elusive. This knowledge gap presents challenges to the harnessing and regulation of such dynamics across diverse length scales. Here, we demonstrate how mediating the bundling of microtubules can shift active matter between a global force-transmitting phase and a local force-dissipating phase. A fivefold increase in microtubule effective length results in the transition from local to global phase with a hundredfold increase in velocity autocorrelation. Through theory and simulation, we identify signatures of a percolation-driven transition between the two phases. This provides evidence for how force propagation can be generated when local molecular interactions reach a sufficient length scale. We show that force propagation in the active matter system enables material transport. Consequently, we demonstrate that the global phase is capable of facilitating millimeter-scale human cell transport and manipulation, as well as powering the movement of aqueous droplets. These findings underscore the potential for designing active materials capable of force organization and transmission. Our results lay the foundation for further exploration into the organization and propagation of forces/stresses in biological systems, thereby paving the way for the engineering of active materials in synthetic biology and soft robotics.

cond-mat.soft↗

arXiv2024

Theoretical Limits of Energy Extraction in Active Fluids

Active materials form a class of far-from-equilibrium systems that are driven internally and exhibit self-organization which can be harnessed to perform mechanical work. Inspired by experiments on synthetic active networks we examine limits of work extraction from an active viscoelastic medium by analyzing the transport of a particle. The active viscoelastic material possesses an equilibrium density where the active and passive forces are balanced out. In one dimension, a gliding activation front (AF) that converts a passive to an active medium, provides active energy at a constant rate, which is injected into the system at one end and propagates to the other. We demonstrate that there exists a maximum velocity of the AF, above which the activated region fails to deliver the transport power. We hypothesize, and intuitively argue based on the limit cases, that the feasibility and the velocity of transport can be interpreted in terms of the velocity of an equilibration Domain Wall of the field, which is set by two parameters: a measure of activity, and the viscoelastic timescale. The phase diagram comprises Transport and No-Transport sectors, namely for any pair of the two parameters, there exists a threshold velocity of the AF above which the particle transport becomes impossible. Constructing the phase diagram we find that there are regions of the phase diagram for which the threshold velocity of the AF diverges. Larger viscoelastic timescale makes the transport region more accessible, and increases the transport velocity therein. Also, we find that increasing the velocity of AF results in larger extracted power but smaller transport coefficient; the ratio of the transport velocity and that of the AF. Our model provides a framework for understanding the energetics of transport phenomena in biology, and designing efficient mechanisms of transport in synthetic active materials.

cond-mat.soft↗

arXiv2021

Programming Boundary Deformation Patterns in Active Networks

Active materials take advantage of their internal sources of energy to self-organize in an automated manner. This feature provides a novel opportunity to design micron-scale machines with minimal required control. However, self-organization goes hand in hand with predetermined dynamics that are hardly susceptible to environmental perturbations. Therefore utilizing this feature of active systems requires harnessing and directing the macroscopic dynamics to achieve specific functions; which in turn necessitates understanding the underlying mechanisms of active forces. Here we devise an optical control protocol to engineer the dynamics of active networks composed of microtubules and light-activatable motor proteins. The protocol enables carving activated networks of different shapes, and isolating them from the embedding solution. Studying a large set of shapes, we observe that the active networks contract in a shape-preserving manner that persists over the course of contraction. We formulate a coarse-grained theory and demonstrate that self-similarity of contraction is associated with viscous-like active stresses. These findings help us program the dynamics of the network through manipulating the light intensity in space and time, and maneuver the network into bending in specific directions, as well as temporally alternating directions. Our work improves understanding the active dynamics in contractile networks, and paves a new path towards engineering the dynamics of a large class of active materials.

cond-mat.soft↗

arXiv2020

Persistent fluid flows defined by active matter boundaries

Biological systems achieve precise control over ambient fluids through the self-organization of active protein structures including flagella, cilia, and cytoskeletal networks. In active structures individual proteins consume chemical energy to generate force and motion at molecular length scales. Self-organization of protein components enables the control and modulation of fluid flow fields on micron scales. The physical principles underlying the organization and control of active-matter driven fluid flows are poorly understood. Here, we apply an optically-controlled active-matter system composed of microtubule filaments and light-switchable kinesin motor proteins to analyze the emergence of persistent flow fields in a model active matter system. Using light, we form contractile microtubule networks of varying shape. We analyze the fluid flow fields generated by a wide range of microtubule network geometries and explain the resulting flow fields within a unified theoretical framework. We specifically demonstrate that the geometry of microtubule flux at the boundary of contracting microtubule networks predicts the steady-state fluid flow fields across polygonal network geometries through finite-element simulations. Our work provides a foundation for programming microscopic fluid-flows with controllable active matter and could enable the engineering of versatile and dynamic microfluidic devices.

cond-mat.soft↗

arXiv2019

The Role of Intracellular Interactions in the Collective Polarization of Tissues and its Interplay with Cellular Geometry

Planar cell polarity (PCP), the coherent in-plane polarization of a tissue on multicellular length scales, provides directional information that guides a multitude of developmental processes at cellular and tissue levels. While it is manifest that cells utilize both intracellular and intercellular mechanisms, how the two produce the collective polarization remains an active area of investigation. We study the role of intracellular interactions in the large-scale spatial coherence of cell polarities, and scrutinize the role of intracellular interactions in the emergence of tissue-wide polarization. We demonstrate that nonlocal cytoplasmic interactions are necessary and sufficient for the robust long-range polarization, and are essential to the faithful detection of weak directional signals. In the presence of nonlocal interactions, signatures of geometrical information in tissue polarity become manifest. We investigate the deleterious effects of geometric disorder, and determine conditions on the cytoplasmic interactions that guarantee the stability of polarization. These conditions get progressively more stringent upon increasing the geometric disorder. Another situation where the role of geometrical information might be evident is elongated tissues. Strikingly, our model recapitulates an observed influence of tissue elongation on the orientation of polarity. Eventually, we introduce three classes of mutants: lack of membrane proteins, cytoplasmic proteins, and local geometrical irregularities. We adopt core-PCP as a model pathway, and interpret the model parameters accordingly, through comparing the in silico and in vivo phenotypes. This comparison helps us shed light on the roles of the cytoplasmic proteins in cell-cell communication, and make predictions regarding the cooperation of cytoplasmic and membrane proteins in long-range polarization.

physics.bio-ph↗

arXiv2014

Bose-Einstein Condensates: a model system for particle solvation?

We propose that impurities in Bose-Einstein condensates can serve as a minimal laboratory system to explore the effects of quantum and thermal fluctuations on solvation. Specifically, we show that the role of quantum fluctuations in the formation of solvation shells and the breakdown of linear response theory can be explored in detail.

cond-mat.quant-gas↗