arXiv subjects

Gili Bisker

Publications and source records attributed to Gili Bisker.

9 recordsLinked to original sources

arXiv2025

Near-infrared fluorescent nanoprobes for irreversibility in nonequilibrium actomyosin networks

Actomyosin networks operate far from equilibrium, yet detecting the onset of motor-driven irreversible dynamics remains challenging. Here, we embed near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) within reconstituted actin networks, and use their nonphotobleaching emission to optically report ATP-powered myosin contractile activity. G-actin-dispersed SWCNTs are incorporated into polymerized F-actin without perturbing network assembly, enabling long-term, single-emitter fluorescence monitoring. Upon myosin addition, the NIR fluorescence levels of individual SWCNTs exhibit enhanced temporal fluctuations, and population-level statistics reveal deviations from equilibrium behaviour. The index of dispersion (IOD) distributions shift and broaden relative to equilibrium baselines, and the Kullback-Leibler divergence between IOD distributions systematically increases with increasing motor activity. Stationarity analysis further shows a dose-dependent increase in the fraction of nonstationary fluorescence traces, indicating the emergence of irreversible, time-evolving dynamics. These results establish SWCNTs as minimally invasive optical probes of irreversibility in nonequilibrium actomyosin assemblies, with broad applicability to other active biopolymer systems.

physics.bio-ph↗

arXiv2024

Dissipative self-assembly of patchy particles under nonequilibrium drive: a computational study

Inspired by biology and implemented using nanotechnology, the self-assembly of patchy particles has emerged as a pivotal mechanism for constructing complex structures that mimic natural systems with diverse functionalities. Here, we explore the dissipative self-assembly of patchy particles under nonequilibrium conditions, with the aim of overcoming the constraints imposed by equilibrium assembly. Utilizing extensive Monte Carlo (MC) and Molecular Dynamics (MD) simulations, we provide insight into the effects of external forces that mirror natural and chemical processes on the assembly rates and the stability of the resulting assemblies comprising $8$, $10$, and $13$ patchy particles. Implemented by a favorable bond-promoting drive in MC or a pulsed square wave potential in MD, our simulations reveal the role these external drives play in accelerating assembly kinetics and enhancing structural stability, evidenced by a decrease in the time to first assembly and an increase in the duration the system remains in an assembled state. Through the analysis of an order parameter, entropy production, bond dynamics, and interparticle forces, we unravel the underlying mechanisms driving these advancements. We also validated our key findings by simulating a larger system of $100$ patchy particles. Our comprehensive results not only shed light on the impact of external stimuli on self-assembly processes but also open a promising pathway for expanding the application by leveraging patchy particles for novel nanostructures.

cond-mat.soft↗

arXiv2022

Utilizing time-series measurements for entropy production estimation in partially observed systems

Estimating the dissipation, or the entropy production rate (EPR), can provide insights into the underlying mechanisms of nonequilibrium driven processes. Experimentally, however, only partial information can be accessed, and the ability to estimate the EPR varies depending on the available data. Here, we test different degrees of observed information stemming from coarse-grained time-series trajectory data, and apply several EPR estimators. Given increasing amount of information, we show a hierarchy of lower bounds on the total EPR. Further, we present a novel approach for utilizing waiting times in hidden states to provide a tighter lower bound on the total EPR.

cond-mat.stat-mech↗

arXiv2022

Universal bounds on entropy production inferred from observed statistics

Nonequilibrium processes break time-reversal symmetry and generate entropy. Living systems are driven out-of-equilibrium at the microscopic level of molecular motors that exploit chemical potential gradients to transduce free energy to mechanical work, while dissipating energy. The amount of energy dissipation, or the entropy production rate (EPR), sets thermodynamic constraints on cellular processes. Practically, calculating the total EPR in experimental systems is challenging due to the limited spatiotemporal resolution and the lack of complete information on every degree of freedom. Here, we propose a new inference approach for a tight lower bound on the total EPR given partial information, based on an optimization scheme that uses the observed transitions and waiting times statistics. We introduce hierarchical bounds relying on the first- and second-order transitions, and the moments of the observed waiting time distributions, and apply our approach to two generic systems of a hidden network and a molecular motor, with lumped states. Finally, we show that a lower bound on the total EPR can be obtained even when assuming a simpler network topology of the full system.

cond-mat.stat-mech↗

arXiv2022

Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining

This paper shows an estimation of a lower bound on the total entropy production rate(EPR) for a system following Langevin dynamics with a single observed variable coarse-grained into a few discrete states, by invoking the underlying broken time-reversal symmetry. We estimate the irreversibility in waiting time distributions of the partially observed system and find the effect of spatial resolution on the mean dwell-time asymmetry and the EPR.

cond-mat.stat-mech↗

arXiv2022

Comment on "Inferring broken detailed balance in the absence of observable currents"

In this reply, we resolve the apparent discrepancy raised in the "Comment on Inferring broken detailed balance in the absence of observable currents" [arXiv:2112.08978v1]. We stress that the non-instantaneous transition paths originate from the choice of a decimation process non-local in time, in contrast to the decimation process described in our original work, which commutes with time-reversal. Therefore, the example using such a non-local decimation procedure, which indeed gives rise to spurious time-irreversibility, does not invalidate our main result, which was rigorously derived and proven mathematically. We hope this reply highlights the subtlety of the different choices for decimating time series data which is pivotal for a correct understanding of the thermodynamics of small systems.

cond-mat.stat-mech↗

arXiv2019

Inferring broken detailed balance in the absence of observable currents

Identifying dissipation is essential for understanding the physical mechanisms underlying nonequilibrium processes. {In living systems, for example, the dissipation is directly related to the hydrolysis of fuel molecules such as adenosine triphosphate (ATP)}. Nevertheless, detecting broken time-reversal symmetry, which is the hallmark of dissipative processes, remains a challenge in the absence of observable directed motion, flows, or fluxes. Furthermore, quantifying the entropy production in a complex system requires detailed information about its dynamics and internal degrees of freedom. Here we introduce a novel approach to detect time irreversibility and estimate the entropy production from time-series measurements, even in the absence of observable currents. We apply our technique to two different physical systems, namely, a partially hidden network and a molecular motor. Our method does not require complete information about the system dynamics and thus provides a new tool for studying nonequilibrium phenomena.

cond-mat.stat-mech↗

arXiv2017

Hierarchical Bounds on Entropy Production Inferred from Partial Information

Systems driven away from thermal equilibrium constantly deliver entropy to their environment. Determining this entropy production requires detailed information about the system's internal states and dynamics. However, in most practical scenarios, only a part of a complex experimental system is accessible to an external observer. In order to address this challenge, two notions of partial entropy production have been introduced in the literature as a way to assign an entropy production to an observed subsystem: one due to Shiraishi and Sagawa [Phys. Rev. E 91, 012130 (2015)] and another due to Polettini and Esposito [arXiv:1703.05715 (2017)]. We show that although both of these schemes provide a lower bound on the total entropy production, the latter -- which utilizes an effective thermodynamics description-- gives a better estimate of the total dissipation. Using this effective thermodynamic framework, we establish a partitioning of the total entropy production into two contributions that individually verify integral fluctuation theorems: an observable partial entropy production and a hidden entropy production assigned to the unobserved subsystem. Our results offer broad implications for both theoretical and empirical systems when only partial information is available.

cond-mat.stat-mech↗

arXiv2006

Bubbles in Planetary Nebulae and Clusters of Galaxies: Jet Bending

We study the bending of jets in binary stellar systems. A compact companion accretes mass from the slow wind of the mass-losing primary star, forms an accretion disk, and blows two opposite jets. These fast jets are bent by the slow wind. Disregarding the orbital motion, we find the dependence of the bending angle on the properties of the slow wind and the jets. Bending of jets is observed in planetary nebulae which are thought to be the descendants of interacting binary stars. For example, in some of these planetary nebulae the two bubbles (lobes) which are inflated by the two opposite jets, are displaced to the same side of the symmetry axis of the nebula. Similar displacements are observed in bubble pairs in the center of some clusters and groups of galaxies. We compare the bending of jets in binary stellar systems with that in clusters of galaxies.

astro-ph↗