arXiv subjects

Zahra Mokhtari

Publications and source records attributed to Zahra Mokhtari.

7 recordsLinked to original sources

arXiv2023

Active motion of tangentially-driven polymers in periodic array of obstacles

We computationally investigate the active transport of tangentially-driven polymers with varying degrees of flexibility and activity in two-dimensional square lattices of obstacles. Tight periodic confinement induces notable conformational changes and distinct modes of transport for flexible and stiff active filaments. It leads to localization and caging of flexible polymers inside the inter-obstacle pores, while promoting more elongated conformations and enhanced diffusion for stiff polymers at low to moderate activity levels. The migration of flexible active polymers occurs via hopping events, where they unfold to move from one cage to another. In contrast, stiff chains travel mainly in straight paths within inter-obstacle channels, while occasionally changing their direction of motion. Both the duration of caging and persistent directed migration within the channels decrease with increasing the activity level. As a consequence, at high active forces polymers overcome confinement effects and transport within inter-obstacle pores as swiftly as those in free space. We explain the center of mass dynamics of semiflexible polymers in terms of active force and obstacle packing fraction by developing an approximate analytical theory.

cond-mat.soft↗

arXiv2023

CRC-ICM: Colorectal Cancer Immune Cell Markers Pattern Dataset

Colorectal Cancer (CRC) is the second most common cause of cancer death in the world, ad can be identified by the location of the primary tumor in the large intestine: right and left colon, and rectum. Based on the location, CRC shows differences in chromosomal and molecular characteristics, microbiomes incidence, pathogenesis, and outcome. It has been shown that tumors on left and right sides also have different immune landscape, so the prognosis may be different based on the primary tumor locations. It is widely accepted that immune components of the tumor microenvironment (TME) plays a critical role in tumor development. One of the critical regulatory molecules in the TME is immune checkpoints that as the gatekeepers of immune responses regulate the infiltrated immune cell functions. Inhibitory immune checkpoints such as PD-1, Tim3, and LAG3, as the main mechanism of immune suppression in TME overexpressed and result in further development of the tumor. The images of this dataset have been taken from colon tissues of patients with CRC, stained with specific antibodies for CD3, CD8, CD45RO, PD-1, LAG3 and Tim3. The name of this dataset is CRC-ICM and contains 1756 images related to 136 patients. The initial version of CRC-ICM is published on Elsevier Mendeley dataset portal, and the latest version is accessible via: https://databiox.com

q-bio.TO↗

arXiv2023

Effects of inertia on conformation and dynamics of tangentially-driven active filaments

Active filament-like systems propelling along their backbone exist across the scales ranging from motor-driven bio-filaments to worms and robotic chains. In macroscopic active filaments such as chain of robots, in contrast to their microscopic counterparts, inertial effects on their motion cannot be ignored. Nonetheless, consequences of interplay between inertia and flexibility on shape and dynamics of active filaments remain unexplored. Here, we examine inertial effects on flexible tangentially-driven active polymer model pertinent to above examples and we determine the conditions under which inertia becomes important. Performing Langevin dynamics simulations of active polymers with underdamped and overdamped dynamics for a wide range of contour lengths and activities, we uncover striking inertial effects on conformation and dynamics at high activities. Inertial collisions increase the persistence length of active polymers and remarkably alter their scaling behavior. In stark contrast to passive polymers, inertia leaves its fingerprint at long times by an enhanced diffusion of the center of mass. We rationalize inertia-induced enhanced dynamics by analytical calculations of center of mass velocity correlations, applicable to any active polymer model, which reveal significant contributions from active force fluctuations convoluted by inertial relaxation.

cond-mat.soft↗

arXiv2022

Dynamics of bacteria scanning a porous environment

It has recently been reported that bacteria, such as E.coli and P. putida, perform distinct modes of motion when placed in porous media as compared to dilute regions or free space. This has led us to suggest an efficient strategy for active particles in a disordered environment: reorientations are suppressed in locally dilute regions and intensified in locally dense ones. Thereby the local geometry determines the optimal path of the active agent and substantially accelerates the dynamics for up to two orders of magnitude. We observe a non-monotonic behavior of the diffusion coefficient in dependence on the tumbling rate and identify a localisation transition, either by increasing the density of obstacles or by decreasing the reorientation rate.

cond-mat.soft↗

arXiv2021

Spontaneous trail formation in populations of auto-chemotactic walkers

We study the formation of trails in populations of self-propelled agents that make oriented deposits of pheromones and also sense such deposits to which they then respond with gradual changes of their direction of motion. Based on extensive off-lattice computer simulations aiming at the scale of insects, e.g., ants, we identify a number of emerging stationary patterns and obtain qualitatively the non-equilibrium state diagram of the model, spanned by the strength of the agent--pheromone interaction and the number density of the population. In particular, we demonstrate the spontaneous formation of persistent, macroscopic trails, and highlight some behaviour that is consistent with a dynamic phase transition. This includes a characterisation of the mass of system-spanning trails as a potential order parameter. We also propose a dynamic model for a few macroscopic observables, including the sub-population size of trail-following agents, which captures the early phase of trail formation.

cond-mat.soft↗

arXiv2020

A Novel Ramp Metering Approach Based on Machine Learning and Historical Data

The random nature of traffic conditions on freeways can cause excessive congestions and irregularities in the traffic flow. Ramp metering is a proven effective method to maintain freeway efficiency under various traffic conditions. Creating a reliable and practical ramp metering algorithm that considers both critical traffic measures and historical data is still a challenging problem. In this study we use machine learning approaches to develop a novel real-time prediction model for ramp metering. We evaluate the potentials of our approach in providing promising results by comparing it with a baseline traffic-responsive ramp metering algorithm.

eess.SY↗

arXiv2019

Dynamics of active filaments in porous media

The motion of active polymers in a porous medium is shown to depend critically on flexibilty, activity and degree of polymerization. For given Peclet number, we observe a transition from localisation to diffusion as the stiffness of the chains is increased. Whereas stiff chains move almost unhindered through the porous medium, flexible ones spiral and get stuck. Their motion can be accounted for by the model of a continuous time random walk with a renewal process corresponding to unspiraling. The waiting time distribution is shown to develop heavy tails for decreasing stiffness, resulting in subdiffusive and ultimately caged behaviour.

cond-mat.soft↗