arXiv subjects

M. Reza Shaebani

Publications and source records attributed to M. Reza Shaebani.

At least 19 recordsLinked to original sources

arXiv2025

Optimal chirality enhances long-range fluctuation-induced interactions in active fluids

Understanding interactions between chiral active particles -- self-propelling and self-rotating entities -- is crucial for uncovering how chiral active matter self-organizes into dynamic structures. Although fluctuation-induced forces in nonequilibrium active systems can drive structure formation, the role of chirality remains largely unexplored. We investigate effective fluctuation-induced forces between intruders immersed in chiral active fluids and reveal that the impact of chirality depends sensitively on particle shape. For circular particles, increasing the self-rotation to self-propulsion ratio suppresses the interaction, reflecting a transition from rotating flocks to localized spinners. Contrarily, a striking collective behavior emerges for rodlike particles: vortices spontaneously form around the intruders, most pronounced at an optimal chiral angle where the mean curvature of particle trajectories matches the intruder boundary curvature, maximizing the effective force. We map the attractive and repulsive force regimes across chirality, propulsion, and intruder separation, offering new insights and principles for designing and controlling self-assembled active systems.

cond-mat.soft↗

arXiv2022

Yielding and Strain Stiffening in Entangled Assemblies of Frictional Granular Chains

Packings of macroscopic granular chains capture some of the essential aspects of molecular polymer systems and have been suggested as a paradigm to understand the physics on a molecular scale. However, here we demonstrate that the interparticle friction $μ$ in granular chain packings, which has no counterpart in polymer systems, leads to a nontrivial yielding and rheological response. Based on discrete element simulations we study the nonlinear rheology of random packings of granular chains under large amplitude oscillatory shear. We find that the maximum stress and the penetration depth of the shear deformation into the material bulk are nonmonotonic functions of friction with extrema at intermediate values of $μ$. We also show that the regularly repeated gaps between the adjacent grains, which are special to commercial granular chains, broaden the shear zone and enhance the entanglements in the system by promoting the interlocking events between chains. These topological constraints can significantly increase the degree of strain stiffening. Our findings highlight the differences between the physics of granular chain packings and molecular polymer systems.

cond-mat.soft↗

arXiv2022

Distinct Speed and Direction Memories of Migrating Dendritic Cells Diversify Their Search Strategies

Migrating cells exhibit various motility patterns, resulting from different migration mechanisms, cell properties, or cell-environment interactions. The complexity of cell dynamics is reflected, e.g., in the diversity of the observed forms of velocity autocorrelation function -- that has been widely served as a measure of diffusivity and spreading -- . By analyzing the dynamics of migrating dendritic cells in vitro, we disentangle the contributions of direction and speed to the velocity autocorrelation. We find that the ability of cells to maintain their speed or direction of motion is unequal, reflected in power-law decays of speed and direction autocorrelation functions with different exponents. The larger power-law exponent of the speed autocorrelation function indicates that the cells lose their speed memory considerably faster than the direction memory. Using numerical simulations, we investigate the influence of speed and direction memories as well as the direction-speed cross-correlation on the search time of a persistent random walker to find a randomly located target in confinement. Although the direction memory and direction-speed coupling play the major roles, we find that the speed autocorrelation can be also tuned to minimize the search time. Adopting an optimal speed memory can reduce the search time even up to 10% compared to uncorrelated spontaneous speeds. Our results suggest that migrating cells can improve their search efficiency, especially in crowded environments, through the directional or speed persistence or the speed-direction correlation.

physics.bio-ph↗

arXiv2022

Orientational Memory of Active Particles in Multistate Non-Markovian Processes

The orientational memory of particles can serve as an effective measure of diffusivity, spreading, and search efficiency in complex stochastic processes. We develop a theoretical framework to describe the decay of directional correlations in a generic class of stochastic active processes consisting of distinct states of motion characterized by their persistence and switching probabilities between the states. For exponentially distributed sojourn times, the orientation autocorrelation is analytically derived and the characteristic times of its crossovers are obtained in terms of the persistence of each state and the switching probabilities. We show how non-exponential sojourn-time distributions of interest, such as Gaussian and power-law distributions, can result from history-dependent transitions between the states. The relaxation behavior of the correlation function in such non-Markovian processes is governed by the history-dependence of the switching probabilities and cannot be solely determined by the mean sojourn times of the states.

cond-mat.soft↗

arXiv2022

Kinematics of Persistent Random Walkers with Two Distinct Modes of Motion

We study the stochastic motion of active particles that undergo spontaneous transitions between two distinct modes of motion. Each mode is characterized by a velocity distribution and an arbitrary (anti-)persistence. We present an analytical formalism to provide a quantitative link between these two microscopic statistical properties of the trajectory and macroscopically observable transport quantities of interest. For exponentially distributed residence times in each state, we derive analytical expressions for the initial anomalous exponent, the characteristic crossover time to the asymptotic diffusive dynamics, and the long-term diffusion constant. We also obtain an exact expression for the time evolution of the mean square displacement over all time scales and provide a recipe to obtain higher displacement moments. Our approach enables us to disentangle the combined effects of velocity, persistence, and switching probabilities between the two states on the kinematics of particles in a wide range of stochastic active/passive processes and to optimize the transport quantities of interest with respect to any of the particle dynamics properties.

cond-mat.stat-mech↗

arXiv2022

Universal Transition to Wide Shear Zones in Entangled Macroscale Chains or Ropes

Macroscale chains have been proposed to give insight into the physics of molecular polymer systems. Nevertheless, understanding the rheological response of systems of quasi-one-dimensional semiflexible materials, such as bead-chain packings, is currently a great challenge. We study the nonlinear rheology of random assemblies of macroscale chains -- including steel bead chains and cooked spaghetti -- under oscillatory shear. We show that a universal transition from localized to wide shear zones occurs upon increasing the strain amplitude, for a wide range of lengths, flexibilities, and other structural parameters of the constituent elements. The critical strain amplitude coincides with the onset of strain stiffening development in the system. We obtain scaling laws for transition sharpness, shear-zone width, and stiffness enhancement as a function of chain length. Our findings suggest that the entanglements between the constituent elements strengthen when approaching the critical strain amplitude and rapidly become long range, even spanning the entire finite system for long enough chains. We show that the nonlinear rheological response is governed by the interplay between increasing stored elastic forces due to entanglements and increasing contribution of dissipation with shear rate and interlocking between chains.

cond-mat.soft↗

arXiv2021

Striped Patterns in Radially Driven Suspensions with Open Boundaries

We study the motion of radially driven fluid-immersed particles in a novel Hele-Shaw cell with open boundaries. The initially uniform suspension forms a striped pattern within a specific range of horizontal oscillation frequencies and for sufficiently large amplitudes. We observe that the initial coarsening dynamics of the stripes gradually slows down and the pattern reaches a steady state after a few minutes. The distance between the stripes in the steady state exhibits an exponentially saturating increase with increased oscillation amplitude or frequency. The width of the stripes decreases as a power-law with the frequency while its amplitude dependence follows a logistic function. We propose a mechanism -- based on the interplay between shear stress, hydrodynamic interactions, and frictional forces -- to link the structural characteristics of the stripes to the properties of the oscillatory external drive.

cond-mat.soft↗

arXiv2021

Evolution of shear zones in granular packings under pressure

Stress transmission in realistic granular media often occurs under external load and in the presence of boundary slip. We investigate shear localization in a split-bottom Couette cell with smooth walls subject to a confining pressure experimentally and by means of numerical simulations. We demonstrate how the characteristics of the shear zone, such as its center position and width, evolve as the confining pressure and wall slip modify the local effective friction coefficient of the material. For increasing applied pressure, the shear zone evolves toward the center of the cylinder and grows wider and the angular velocity reduces compared to the driving rate of the bottom disk. Moreover, the presence of slip promotes the transition from open shear zones at the top surface to closed shear zones inside the bulk. We also systematically vary the ratio of the effective friction near the bottom plate and in the bulk in simulations and observe the resulting impact on the surface flow profile. Besides the boundary conditions and external load, material properties such as grain size are also known to influence the effective friction coefficient. However, our numerical results reveal that the center position and width of the shear zone are insignificantly affected by the choice of the grain size as far as it remains small compared to the radius of the rotating bottom disk.

cond-mat.soft↗

arXiv2021

Transient anomalous diffusion in run-and-tumble dynamics

We study the stochastic dynamics of a particle with two distinct motility states. Each one is characterized by two parameters: one represents the average speed and the other represents the persistence quantifying the tendency to maintain the current direction of motion. We consider a run-and-tumble process, which is a combination of an active fast motility mode (persistent motion) and a passive slow mode (diffusion). Assuming stochastic transitions between the two motility states, we derive an analytical expression for the time evolution of the mean square displacement. The interplay of the key parameters and the initial conditions as for instance the probability of initially starting in the run or tumble state leads to a variety of transient regimes of anomalous transport on different time scales before approaching the asymptotic diffusive dynamics. We estimate the crossover time to the long-term diffusive regime and prove that the asymptotic diffusion constant is independent of initially starting in the run or tumble state.

cond-mat.stat-mech↗

arXiv2020

Persistence-Speed Coupling Enhances the Search Efficiency of Migrating Immune Cells

Migration of immune cells within the human body allows them to fulfill their main function of detecting pathogens. Adopting an optimal navigation and search strategy by these cells is of crucial importance to achieve an efficient immune response. Analyzing the dynamics of dendritic cells in our in vitro experiments reveals that the directional persistence of these cells is highly correlated with their migration speed, and that the persistence-speed coupling enables the migrating cells to reduce their search time. We introduce theoretically a new class of random search optimization problems by minimizing the mean first-passage time (MFPT) with respect to the strength of the coupling between influential parameters such as speed and persistence length. We derive an analytical expression for the MFPT in a confined geometry and verify that the correlated motion improves the search efficiency if the mean persistence length is sufficiently shorter than the confinement size. In contrast, a positive persistence-speed correlation even increases the MFPT at long persistence length regime, thus, such a strategy is disadvantageous for highly persistent active agents.

cond-mat.soft↗

arXiv2020

Cell-Type-Specific Differences in KDEL Receptor Clustering in Mammalian Cells

In eukaryotic cells, KDEL receptors (KDELRs) facilitate the retrieval of endoplasmic reticulum (ER) luminal proteins from the Golgi compartment back to the ER. Apart from the well-documented retention function, recent findings reveal that the cellular KDELRs have more complex roles, e.g. in cell signalling, protein secretion, cell adhesion and tumorigenesis. Furthermore, several studies suggest that a sub-population of KDELRs is located at the cell surface, where they could form and internalize KDELR/cargo clusters after K/HDEL-ligand binding. However, so far it has been unclear whether there are cell-type- or species-specific differences in KDELR clustering. By comparing ligand-induced KDELR clustering in different mouse and human cell lines via live cell imaging, we show that macrophage cell lines from both species do not develop any clusters. Using RT-qPCR experiments and numerical analysis, we address the role of KDELR expression as well as endocytosis and exocytosis rates on the receptor clustering at the plasma membrane and discuss how the efficiency of directed transport to preferred docking sites on the membrane influences the exponent of the power-law distribution of the cluster size.

physics.bio-ph↗

arXiv2019

Trapping in and escape from branched structures of neuronal dendrites

We present a coarse-grained model for stochastic transport of noninteracting chemical signals inside neuronal dendrites and show how first-passage properties depend on the key structural factors affected by neurodegenerative disorders or aging: the extent of the tree, the topological bias induced by segmental decrease of dendrite diameter, and the trapping probabilities in biochemical cages and growth cones. We derive an exact expression for the distribution of first-passage times, which follows a universal exponential decay in the long-time limit. The asymptotic mean first-passage time exhibits a crossover from power-law to exponential scaling upon reducing the topological bias. We calibrate the coarse-grained model parameters and obtain the variation range of the mean first-passage time when the geometrical characteristics of the dendritic structure evolve during the course of aging or neurodegenerative disease progression (A few disorders are chosen and studied for which clear trends for the pathological changes of dendritic structure have been reported in the literature). We prove the validity of our analytical approach under realistic fluctuations of structural parameters, by comparing to the results of Monte Carlo simulations. Moreover, by constructing local structural irregularities, we analyze the resulting influence on transport of chemical signals and formation of heterogeneous density patterns. Since neural functions rely on chemical signal transmission to a large extent, our results open the possibility to establish a direct link between the disease progression and neural functions.

physics.bio-ph↗

arXiv2019

Flagellar number governs bacterial spreading and transport efficiency

Peritrichous bacteria synchronize and bundle their flagella to actively swim while disruption of the bundle leads to tumbling. It is still not known whether the number of flagella represents an evolutionary adaptation towards optimizing bacterial navigation. Here, we study the swimming dynamics of differentially flagellated Bacillus subtilis strains in a quasi-two-dimensional system. We find that decreasing the number of flagella N reduces the average turning angle between two successive run phases and enhances the duration and directional persistence of the run phase. As a result, having less flagella is beneficial for long-distance transport and fast spreading, while having a lot of flagella is advantageous for the processes which require localization and slow dynamics, such as biofilm formation. We develop a two-state random walk model that incorporates spontaneous switchings between the states and yields exact analytical expressions for transport properties, in remarkable agreement with experiments. The results of numerical simulations based on our two-state model suggest that the efficiency of searching and exploring the environment is optimized at intermediate values of N. The optimal choice of N, for which the search time is minimized, decreases with increasing the size of the environment in which the bacteria swim.

physics.bio-ph↗

arXiv2018

Unraveling the structure of treelike networks from first-passage times of lazy random walkers

We study the problem of random search in finite networks with a tree topology, where it is expected that the distribution of the first-passage time F(t) decays exponentially. We show that the slope of the exponential tail is independent of the initial conditions of entering the tree in general, and scales exponentially or as a power law with the extent of the tree L, depending on the tendency p to jump toward the target node. It is unfeasible to uniquely determine L and p from measuring the tail slope or the mean first-passage time (MFPT) of an ordinary diffusion along the tree. To unravel the structure, we consider lazy random walkers that take steps with probability m when jumping on the nodes and return with probability q from the leaves. By deriving an exact analytical expression for the MFPT of the intermittent random walk, we verify that the structural information of the tree can be uniquely extracted by measuring the MFPT for two randomly chosen types of tracer particles with distinct experimental parameters m and q. We also address the applicability of our approach in the presence of disorder in the structure of the tree or statistical uncertainty in the experimental parameters.

cond-mat.stat-mech↗

arXiv2017

Compaction of Quasi One-Dimensional Elastoplastic Materials

Insight in the crumpling or compaction of one-dimensional objects is of great importance for understanding biopolymer packaging and designing innovative technological devices. By compacting various types of wires in rigid confinements and characterizing the morphology of the resulting crumpled structures, here we report how friction, plasticity, and torsion enhance disorder, leading to a transition from coiled to folded morphologies. In the latter case, where folding dominates the crumpling process, we find that reducing the relative wire thickness counter-intuitively causes the maximum packing density to decrease. The segment-size distribution gradually becomes more asymmetric during compaction, reflecting an increase of spatial correlations. We introduce a self-avoiding random walk model and verify that the cumulative injected wire length follows a universal dependence on segment size, allowing for the prediction of the efficiency of compaction as a function of material properties, container size, and injection force.

cond-mat.soft↗

arXiv2017

Cargo binding promotes KDEL receptor clustering at the mammalian cell surface

Transmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor cluster formation has been described for a wide variety of receptors, ranging from chemotactic receptors in bacteria to growth factor and neurotransmitter receptors in mammalian cells, a mechanistic understanding of the underlying molecular processes is still puzzling. In an attempt to fill this gap we followed a combined experimental and theoretical approach by dissecting and modulating cargo binding, internalization and cellular response mediated by KDEL receptors (KDELRs) at the mammalian cell surface after interaction with a model cargo/ligand. Using a fluorescent variant of ricin toxin A chain as KDELR-ligand, eGFP-RTA (H/KDEL), we demonstrate that cargo binding induces dose-dependent receptor cluster formation at and subsequent internalization from the membrane which is associated and counteracted by anterograde and microtubule-assisted receptor transport to preferred docking sites at the plasma membrane. By means of analytical arguments and extensive numerical simulations we show that cargo-synchronized receptor transport from and to the membrane is causative for KDELR/cargo cluster formation at the mammalian cell surface.

q-bio.SC↗

arXiv2017

Tracking of plus-ends reveals microtubule functional diversity in different cell types

Many cellular processes are tightly connected to the dynamics of microtubules (MTs). While in neuronal axons MTs mainly regulate intracellular trafficking, they participate in cytoskeleton reorganization in many other eukaryotic cells, enabling the cell to efficiently adapt to changes in the environment. We show that the functional differences of MTs in different cell types and regions is reflected in the dynamic properties of MT tips. Using plus-end tracking proteins EB1 to monitor growing MT plus-ends, we show that MT dynamics and life cycle in axons of human neurons significantly differ from that of fibroblast cells. The density of plus-ends, as well as the rescue and catastrophe frequencies increase while the growth rate decreases toward the fibroblast cell margin. This results in a rather stable filamentous network structure and maintains the connection between nucleus and membrane. In contrast, plus-ends are uniformly distributed along the axons and exhibit diverse polymerization run times and spatially homogeneous rescue and catastrophe frequencies, leading to MT segments of various lengths. The probability distributions of the excursion length of polymerization and the MT length both follow nearly exponential tails, in agreement with the analytical predictions of a two-state model of MT dynamics.

q-bio.SC↗

arXiv2016

Run-and-pause dynamics of cytoskeletal motor proteins

Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and effectively stationary phase in which it detaches from the filaments and performs passive diffusion in the vicinity of the detachment point due to cytoplasmic crowding. The transition rates between motion and pause phases are asymmetric in general, and considerably affected by changes in environmental conditions which influences the efficiency of cargo delivery to specific targets. By considering the motion of molecular motor on a single filament as well as a dynamic filamentous network, we present an analytical model for the dynamics of self-propelled particles which undergo frequent pause phases. The interplay between motor processivity, structural properties of filamentous network, and transition rates between the two states of motility drastically changes the dynamics: multiple transitions between different types of anomalous diffusive dynamics occur and the crossover time to the asymptotic diffusive or ballistic motion varies by several orders of magnitude. We map out the phase diagrams in the space of transition rates, and address the role of initial conditions of motion on the resulting dynamics.

physics.bio-ph↗