arXiv subjects

Jalal Sarabadani

Publications and source records attributed to Jalal Sarabadani.

At least 19 recordsLinked to original sources

arXiv2026

Confinement-Induced Optimization of Fluctuation-Induced Forces in Active Fluids

Active matter generates nonequilibrium fluctuations that mediate effective interactions between immersed objects. While fluctuation-induced (FI) forces in active fluids depend on activity, density, and geometry, their dependence on confinement remains poorly understood. We study FI forces between fixed intruders in two-dimensional active fluids composed of self-propelled circular or rodlike particles using Langevin dynamics simulations. We find that the FI force exhibits a pronounced nonmonotonic dependence on intruder separation, reaching a maximum at an optimal gap size well beyond the depletion regime, in contrast to the commonly assumed monotonic decay. This optimal confinement is robust across parameters and is more pronounced for elongated particles. The effect arises from a confinement-controlled balance between particle transport and crowding: narrow gaps hinder exchange between inner and outer regions, whereas large separations effectively decouple the intruders. At intermediate distances, enhanced crowding around the intruders generates maximal collision-rate asymmetries, leading to the strongest effective interactions. These results identify confinement geometry as a key control parameter for FI forces in active matter.

cond-mat.soft↗

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↗

arXiv2025

Driven Polymer Translocation through a Nanopore from a Confining Channel

We consider the dynamics of pore-driven polymer translocation through a nanopore to semi-infinite space when the chain is initially confined and equilibrated in a narrow channel. To this end, we use Langevin dynamics (LD) simulations and iso-flux tension propagation (IFTP) theory to characterize local and global dynamics of the translocating chain. The dynamics of the process can be described by the IFTP theory in very good agreement with the LD simulations for all values of confinement in the channel. The theory reveals that for channels with size comparable to or less than the end-to-end distance of the unconfined chain, in which the blob theory works, the scaling form of the translocation time depends on both the chain contour length as well as the channel width. %originating from the confinement of the spatial fluctuations of the chain inside the channel. Conversely, for a very narrow channel the translocation time only depends on the chain contour length and is similar to that of a rod due to the absence of spatial chain fluctuations.

cond-mat.soft↗

arXiv2024

Structural dynamics and optimal transport of an active polymer

We study the spontaneous configuration transitions of an active semi-flexible polymer between {\it spiral} and {\it non-spiral} states, and show that the configuration dynamics is fully described by a {\it subcritical pitchfork} bifurcation. Exploiting the fact that active polymer barely moves in {\it spiral} states and exhibits net displacements in {\it non-spiral} states, we theoretically prove that the motion of the active polymer is consistent with a {\it run-and-tumble}-like dynamics. Moreover, we find that there exists an {\it optimal} self-propelling {\it force}, at which the probabilities of finding the polymer in the {\it spiral} and {\it non-spiral} state become equal, that maximizes the diffusion coefficient.

cond-mat.soft↗

arXiv2023

Electroosmotic Flow in Different Phosphorus Nanochannels

The electrokinetic transport in a neutral system consists of an aqueous NaCl solution confined in a nanochannel with two similar parallel phosphorene walls, and is investigated for different black, blue, red, and green phosphorene allotropes in the presence of an external electric field in the directions $x$ (parallel to the walls roughness axis) and $y$ (perpendicular to the walls roughness axis). The results show that irrespective of the electric field direction, the thickness of the Stern layer increases with the increase in the magnitude of the negative electric surface charge density (ESCD) on the nanochannel walls, and it also increases with the increase in the roughness ratio for different allotropes. Moreover, three different regimes of Debye--Hückel (DH), intermediate, and flow reversal appear as the absolute value of the negative ESCD on the walls grows. With the increase in the absolute value of the negative ESCD, in the DH regime, the flow velocity grows, then in the intermediate regime, it decreases, and finally, at sufficiently high ESCD, the flow reversal occurs. When the external electric field is applied in the $y$ direction, the dynamics of the system are slower than that of the $x$ direction; therefore, the flow reversal occurs at the smaller absolute values of the negative ESCD.

cond-mat.soft↗

arXiv2023

Molecular Dynamics Study of Electro-Osmotic Flow in a Nanochannel with Molybdenum Disulfide Walls

The electro-osmotic flow (EOF) in a neutral system consisting of an aqueous NaCl solution confined in a nanochannel with two parallel Molybdenum disulfide ($\textrm{MoS}_{\textrm{2}}$) walls and in the presence of an external electric field parallel to the channel walls, is investigated for the first time. The results indicate that the thickness of the Stern layer grows as the negative electric surface charge density on the nanochannel walls increases. The Stern layer becomes thinner as the salt concentration is increased. Moreover, the EOF occurs under the no-slip condition on the walls. In addition, by increasing the surface charge density the average of the flow velocity across the nanochannel initially grows (Debye--H$\ddot{\textrm{u}}$ckel regime) and reaches its maximum value. Then, by further increasing the surface charge density the water flow rate decreases (intermediate regime), and gets the zero value and becomes negative (reverse flow regime) at even larger values of the surface charge densities. Comparing the results of the previous work wherein the channels are composed of the black phosphorene walls with those of the present study for a channel composed of $\textrm{MoS}_{\textrm{2}}$ surfaces, show that for the latter case the reverse flow occurs at a lower surface charge density and with a greater value of the peak velocity with respect to the change in the surface charge density for the former case.

cond-mat.soft↗

arXiv2022

Polymer translocation in an environment of active rods

We consider the dynamics of a translocation process of a flexible linear polymer through a nanopore into an environment of active rods in the {\it trans} side. Using Langevin dynamics simulations we find that the rods facilitate translocation to the {\it trans} side even when there are initially more monomers on the {\it cis} than on the {\it trans} side. Structural analysis of the translocating polymer reveals that active rods induce a folded structure to the {\it trans}-side subchain in the case of successful translocation events. By keeping the initial number of monomers on the {\it cis}-side subchain fixed, we map out a state diagram for successful events as a function of the rod number density for a variety of system parameters. This reveals competition between facilitation by the rods at low densities and crowding that hinders translocation at higher densities.

cond-mat.soft↗

arXiv2022

Translocation of an Active Polymer into a Circular Cavity

Translocation dynamics of an active semi-flexible polymer through a nano-pore into a rigid two dimensional circular cavity, and the polymer packing dynamics have been studied by using Langevin dynamics (LD) simulations. The results show that the force exponent $β$, for regime of small cavity radius, i.e. $R \ll R_{\textrm{g}}$, where $R_{\textrm{g}}$ is the gyration radius of the passive semi-flexible polymer in two dimensional free space, is $β=-1$, while for large values of $R \gg R_{\textrm{g}}$ the asymptotic value of the force exponent is $β\approx -0.92$. The force exponent is defined by the scaling form of the average translocation time $\langle τ\rangle \propto F_{\textrm{sp}}^β$, where $F_{\textrm{sp}}$ is the self-propelling force. Moreover, using the definition of the turning number for the polymer inside the cavity, it has been found that at the end of translocation process for small value of $R$ and in the strong force limit the polymer configuration is more regular than the case in which the value of $R$ is large or the force is weak.

cond-mat.soft↗

arXiv2022

Driven polymer translocation into a channel: Iso-flux tension propagation theory and Langevin dynamics simulations

Iso-flux tension propagation (IFTP) theory and Langevin dynamics (LD) simulations are employed to study the dynamics of channel-driven polymer translocation in which a polymer translocates into a narrow channel and the monomers in the channel experience a driving force $f_{\rm c}$. In the high driving force limit, regardless of the channel width, IFTP theory predicts $τ\propto f_{\textrm{c}}^β$ for the translocation time, where $β=-1$ is the force scaling exponent. Moreover, LD data show that for a very narrow channel fitting only a single file of monomers, the entropic force due to the subchain inside the channel does not play a significant role in the translocation dynamics, and the force exponent $β= -1$ regardless of the force magnitude. As the channel width increases the number of possible spatial configurations of the subchain inside the channel becomes significant, and the resulting entropic force causes the force exponent to drop below unity.

cond-mat.soft↗

arXiv2020

Polymer translocation through nanopore assisted by an environment of active rods

We use a combination of computer simulations and iso-flux tension propagation (IFTP) theory to investigate translocation dynamics of a flexible linear polymer through a nanopore into an environment composed of repulsive active rods in 2D. We demonstrate that the rod activity induces a crowding effect on the polymer, leading to a time-dependent net force that facilitates translocation into the active environment. Incorporating this force into the IFTP theory for pore-driven translocation allows us to characterise translocation dynamics in detail and derive a scaling form for the average translocation time as $\tildeτ \sim \tilde{L}_{\textrm{r}}^ν / \tilde{F}_{\textrm{SP}} $, where $\tilde{L}_{\textrm{r}}$ and $\tilde{F}_{\textrm{SP}}$ are the rod length and self-propelling force acting on the rods, respectively, and $ν$ is the Flory exponent.

cond-mat.soft↗

arXiv2020

Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics

We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension propagation (IFTP) theory with electrostatics for a negatively charged biopolymer pulled through a nanopore embedded in a similarly charged anionic membrane. We show that for the realistic case such as a single-stranded DNA, the translocation dynamics at low salt where screening is weak and at finite negative membrane charge is unexpectedly accelerated despite the large repulsive electrostatic interactions between the polymer coil on the {\it cis} side and the charged membrane. This is due to the rapid release of the electrostatic potential energy of the coil during translocation, leading to an effectively attractive force that assists end-driven translocation. The speedup results in non-monotonic polymer length and membrane charge dependence of the exponent $α$ characterizing the translocation time $τ\propto N_0^α$ of the polymer with length $N_0$. In the regime of long polymers $N_0\gtrsim500$, the translocation exponent exceeds its upper limit $α=2$ previously observed for the same system without electrostatic interactions.

cond-mat.soft↗

arXiv2019

Pulling a folded polymer through a nanopore

We investigate the translocation dynamics of a folded linear polymer which is pulled through a nanopore by an external force. To this end, we generalize the iso-flux tension propagation (IFTP) theory for end-pulled polymer translocation to include the case of two segments of the folded polymer traversing simultaneously trough the pore. Our theory is extensively benchmarked with corresponding Molecular Dynamics (MD) simulations. The translocation process for a folded polymer can be divided into two main stages. In the first stage, both branches are traversing the pore and their dynamics is coupled. If the branches are not of equal length, there is a second stage where translocation of the shorter branch has been completed. Using the assumption of equal monomer flux of both branches, we analytically derive the equations of motion for both branches and characterise the translocation dynamics in detail from the average waiting time and its scaling form. Moreover, MD simulations are used to study additional details of translocation dynamics such as the translocation time distribution and individual monomer velocities.

cond-mat.soft↗

arXiv2018

Theoretical modeling of polymer translocation: From the electrohydrodynamics of short polymers to the fluctuating long polymers

The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer fluctuations. In this review, we discuss the modeling of polymer translocation in the distinct regimes of short and long polymers where these two effects decouple. For the case of short polymers where polymer fluctuations are negligible, we present a stiff polymer model including the details of the electrohydrodynamic forces on the translocating molecule. We first show that the electrohydrodynamic theory can accurately characterize the hydrostatic pressure dependence of the polymer translocation velocity and time in pressure-voltage-driven polymer trapping experiments. Then, we discuss the electrostatic correlation mechanisms responsible for the experimentally observed DNA mobility inversion by added multivalent cations in solid-state pores, and the rapid growth of polymer capture rates by added monovalent salt in $α$-Hemolysin pores. In the opposite regime of long polymers where polymer fluctuations prevail, we review the iso-flux tension propagation (IFTP) theory which can characterize the translocation dynamics at the level of single segments. The IFTP theory is valid for a variety of polymer translocation and pulling scenarios. We discuss the predictions of the theory for fully flexible and rodlike pore-driven and end-pulled translocation scenarios, where exact analytic results can be derived for the scaling of the translocation time with chain length and driving force.

cond-mat.soft↗

arXiv2018

Theory of pore-driven and end-pulled polymer translocation dynamics through a nanopore: An overview

We review recent progress on the theory of dynamics of polymer translocation through a nanopore based on the iso-flux tension propagation (IFTP) theory. We investigate both pore-driven translocation of flexible and a semi-flexible polymers, and the end-pulled case of flexible chains by means of the IFTP theory and extensive molecular dynamics (MD) simulations. The validity of the IFTP theory can be quantified by the waiting time distributions of the monomers which reveal the details of the dynamics of the translocation process. The IFTP theory allows a parameter-free description of the translocation process and can be used to derive exact analytic scaling forms in the appropriate limits, including the influence due to the pore friction that appears as a finite-size correction to asymptotic scaling. We show that in the case of pore-driven semi-flexible and end-pulled polymer chains the IFTP theory must be augmented with an explicit {\it trans} side friction term for a quantitative description of the translocation process.

cond-mat.soft↗

arXiv2018

Dielectric trapping of biopolymers translocating through insulating membranes

Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time can be extended via the dielectric trapping of the polymer. In dilute salt conditions, the dielectric contrast between the low permittivity membrane and large permittivity solvent gives rise to attractive interactions between the cis and trans portions of the polymer. This self-attraction acts as a dielectric trap that can enhance the translocation time by orders of magnitude. We also find that electrostatic interactions result in the piecewise scaling of the translocation time $τ$ with the polymer length $L$. In the short polymer regime $L\lesssim10$ nm where the external drift force dominates electrostatic polymer interactions, the translocation is characterized by the drift behavior $τ\sim L^2$. In the intermediate length regime $10\;{\rm nm}\lesssim L\lesssimκ_{\rm b}^{-1}$ where $κ_{\rm b}$ is the Debye-Hückel screening parameter, the dielectric trap takes over the drift force. As a result, increasing polymer length leads to quasi-exponential growth of the translocation time. Finally, in the regime of long polymers $L\gtrsimκ_{\rm b}^{-1}$ where salt screening leads to the saturation of the dielectric trap, the translocation time grows linearly as $τ\sim L$. This strong departure from the drift behavior highlights the essential role played by electrostatic interactions in polymer translocation.

cond-mat.soft↗

arXiv2017

Dynamics of end-pulled polymer translocation through a nanopore

We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory to include friction arising from the trans side subchain. The theory reveals a complicated scenario of multiple scaling regimes depending on the configurations of the cis and the trans side subchains. In the limit of high driving forces $f$ such that the trans subchain is strongly stretched, the theory is in excellent agreement with molecular dynamics simulations and allows an exact analytic solution for the scaling of the translocation time $τ$ as a function of the chain length $N_0$ and $f$. In this regime the asymptotic scaling exponents for $τ \sim N_0^α f^β$ are $α=2$, and $β=-1$. The theory reveals significant correction-to-scaling terms arising from the cis side subchain and pore friction, which lead to a very slow approach to $α=2$ from below as a function of increasing $N_0$.

cond-mat.soft↗

arXiv2016

Driven translocation of a semi-flexible polymer through a nanopore

We study the driven translocation of a semi-flexible polymer through a nanopore by means of a modified version of the iso-flux tension propagation theory (IFTP), and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a finite persistence length $\tilde{\ell}_p$ the {\it trans} side friction must be explicitly taken into account to properly describe the translocation process. In addition, the scaling of the end-to-end distance $R_N$ as a function of the chain length $N$ must be known. To this end, we first derive a semi-analytic scaling form for $R_N$, which reproduces the limits of a rod, an ideal chain, and an excluded volume chain in the appropriate limits. We then quantitatively characterize the nature of the {\it trans} side friction based on MD simulations of semi-flexible chains. Augmented with these two factors, the modified IFTP theory shows that there are three main regimes for the scaling of the average translocation time $τ\propto N^α$. In the stiff chain (rod) limit $N/\tilde{\ell}_p \ll 1$, {$α= 2$}, which continuously crosses over in the regime $ 1 < N/\tilde{\ell}_p < 4$ towards the ideal chain behavior with {$α= 3/2$}, which is reached in the regime $N/\tilde{\ell}_p \sim 10^2$. Finally, in the limit $N/\tilde{\ell}_p \gg 10^6$ the translocation exponent approaches its symptotic value $1+ν$, where $ν$ is the Flory exponent. Our results are in good agreement with available simulations and experimental data.

cond-mat.soft↗

arXiv2016

Non-monotonic Casimir interaction: The role of amplifying dielectrics

The normal and the lateral Casimir interactions between corrugated ideal metallic plates in the presence of an amplifying or an absorptive dielectric slab has been studied by the path-integral quantization technique. The effect of the amplifying slab, which is located between corrugated conductors, is to increase the normal and lateral Casimir interactions, while the presence of the absorptive slab diminishes the interactions. These effects are more pronounced if the thickness of the slab increases, and also if the slab comes closer to one of the bounding conductors. When both bounding ideal conductors are flat, the normal Casimir force is non-monotonic in the presence of the amplifying slab and the system has a stable mechanical equilibrium state, while the force is attractive and is weakened by intervening the absorptive dielectric slab in the cavity. By replacing one of the flat conductors by a flat ideal permeable plate the force becomes non-monotonic and the system has an unstable mechanical equilibrium state in the presence of either an amplifying or an absorptive slab. When the left side plate is conductor and the right one is permeable, the force is non-monotonic in the presence of a double-layer DA (dissipative-amplifying) dielectric slab with a stable mechanical equilibrium state, while it is purely repulsive in the presence of a double-layer AD (amplifying-dissipative) dielectric slab.

cond-mat.mes-hall↗