arXiv subjects

Mahdi Zarif

Publications and source records attributed to Mahdi Zarif.

7 recordsLinked to original sources

arXiv2024

Machine Learning Assisted Sorting of Active Microswimmers

Active matter systems being in a non-equilibrium state, exhibit complex behaviors such as self-organization and giving rise to emergent phenomena. There are many examples of active particles with biological origins, including bacteria and spermatozoa, or with artificial origins, such as self-propelled swimmers and Janus particles. The ability to manipulate active particles is vital for their effective application e.g. separating motile spermatozoa from nonmotile and dead ones, to increase fertilization chance. In this study, we proposed a mechanism -- an apparatus -- to sort and demix active particles based on their motility values (Pèclet number). Initially, using Brownian simulations we demonstrated the feasibility of sorting self-propelled particles. Following this, we employed machine learning methods, supplemented with data from comprehensive simulations that we conducted for this study, to model the complex behavior of active particles. This enabled us to sort them based on their Pèclet number. Finally, we evaluated the performance of the developed models and showed their effectiveness in demixing and sorting the active particles. Our findings can find applications in various fields, including physics, biology, and biomedical science, where the sorting and manipulation of active particles play a pivotal role.

cond-mat.soft↗

arXiv2023

Thermodynamics, structure and dynamics of cylindrically confined hard spheres: The role of excess helical twist

Hard spheres confined to narrow quasi-one-dimensional cylindrical channels form perfect helical structures at close packing. Here, we use molecular dynamics simulation to show that the thermodynamics, structure and dynamics of the fluid below close packing are dominated by the presence of topological defects that reverse the local twist direction of the helix. When compressed from a random, low density state, or decompressed from high density ordered states with zero excess helical twist, the system equilibrates to an achiral fluid that exhibits two heat capacity maxima along the equation of state. The low density heat capacity maximum corresponds to the onset of helix formation and the high density maximum occurs when the system rapidly loses defects in a Schottky-like anomaly. The local twist auto-correlation function in the achiral fluid exhibits a stretched exponential decay and the structural relaxation times undergo a fragile-to-strong crossover located at the high density heat capacity maximum. We also study the effect of excess helical twist by using initial starting configurations consisting of two helical domains with opposite twist directions of different lengths. This leads to the formation of topologically protected states that are characterized by the presence of loosely bound defect pairs which become more tightly bound with increasing excess helical twist. The local twist auto-correlation function in the chiral fluid decays as a power law at long times. The possible kinetic or thermodynamic origin of this topological protection is discussed.

cond-mat.soft↗

arXiv2023

Is there a Granular Potential?

Granular materials, such as sand or grain, exhibit many structural and dynamic characteristics similar to those observed in molecular systems, despite temperature playing no role in their properties. This has led to an effort to develop a statistical mechanics for granular materials that has focused on establishing an equivalent to the microcanonical ensemble and a temperature-like thermodynamic variable. Here, we expand on these ideas by introducing a granular potential into the Edwards ensemble, as an analogue to the chemical potential, and explore its properties using a simple model of a granular system. A simple kinetic Monte Carlo simulation of the model shows the effect of mass transport leading to equilibrium and how this is connected to the redistribution of volume in the system. An exact analytical treatment of the model shows that the compactivity and the ratio of the granular potential to the compactivity determine the equilibrium between two open systems that are able to exchange volume and particles, and that mass moves from high to low values of this ratio. Analysis of the granular potential shows that adding a particle to the system increases the entropy at high compactivity, but decreases the entropy at low compactivity. Finally, we demonstrate the use of a small system thermodynamics method for the measurement of granular potential differences.

cond-mat.soft↗

arXiv2021

Inherent Structure Landscape of Hard Spheres Confined to Narrow Cylindrical Channels

The inherent structure landscape for a system of hard spheres confined to a hard cylindrical channel, such that spheres can only contact their first and second neighbours, is studied using an analytical model that extends previous results [Phys. Rev. Lett. 115, 025702 (2015)] to provide a comprehensive picture of jammed packings over a range of packing densities. In the model, a packing is described as an arrangement of $k$ helical sections, separated by defects, that have alternating helical twist directions and where all spheres satisfy local jamming constraints. The structure of each helical section is determined by a single helical twist angle, and a jammed packing is obtained by minimizing the length of the channel per particle with respect to the $k$ helical section angles. An analysis of a small system of $N=20$ spheres shows that the basins on the inherent structure landscape associated with these helical arrangements split into a number of distinct jammed states separated by low barriers giving rise to a degree of hierarchical organization. The model accurately predicts the geometric properties of packings generated using the Lubachevsky and Stillinger compression scheme ($N=10^4$) and provides insight into the nature of the probability distribution of helical section lengths.

cond-mat.soft↗

arXiv2021

Effective interactions between inclusions in a chiral active bath inside a channel

Colloidal inclusions suspended in a bath of smaller particles experience an effective bath-mediated attraction at small intersurface separations, which is known as the depletion interaction. In an active bath of nonchiral self-propelled particles, the effective force changes from attraction to repulsion; an effect that is suppressed, when the active bath particles are chiral. Using Brownian Dynamics simulations, we study the effects of channel confinement and bath chirality on the effective forces and torques that are mediated between two inclusions that may be fixed within the channel or may be allowed to rotate freely as a rigid dimer around its center of mass. We show that the confinement has a strong effect on the effective interactions, depending on the orientation of the dimer relative to the channel walls. The active particle chirality leads to a force imbalance and, hence, a net torque on the inclusion dimer, which we investigate as a function of the bath chirality strength and the channel height.

cond-mat.soft↗

arXiv2020

Mapping diffusivity of narrow channels into one-dimension

The diffusion of particles trapped in long narrow channels occurs predominantly in one dimension. Here, molecular dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks, confined to long, narrow, structureless channels with hard walls in the no-passing regime. We show that the diffusion coefficient obtained from the mean squared displacement can be mapped onto the exact results for the diffusion of the strictly one-dimensional hard rod system through an effective occupied volume fraction obtained from either the equation of state or a geometric projection of the particle interaction diameters.

cond-mat.soft↗

arXiv2019

Confinement-induced alternating interactions between inclusions in an active fluid

In a system of colloidal inclusions suspended in a thermalized bath of smaller particles, the bath engenders an attractive force between the inclusions, arising mainly from entropic origins, known as the depletion force. In the case of active bath particles, the nature of the bath-mediated force changes dramatically from an attractive to a repulsive one, as the strength of particle activity is increased. We study such bath-mediated effective interactions between colloidal inclusions in a bath of self-propelled Brownian particles, being confined in a narrow planar channel. Confinement is found to have a strong effect on the interaction between colloidal particles, however, this mainly depends on the colloidal orientation inside the channel. Effect of the confinement on the interaction of colloidal disk is controlled by the layering of active particles on the surface boundaries. This can emerge as a competitive factor, involving the tendencies of the channel walls and the colloidal inclusions in accumulating the active particles in their own proximity.

cond-mat.soft↗