Aishani Ghosal

@niser.ac.in

Assistant Professor and School of Chemical Sciences
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Aishani Ghosal


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https://researchid.co/aishanighosal

EDUCATION

IISc Bangalore

RESEARCH, TEACHING, or OTHER INTERESTS

Physical and Theoretical Chemistry, Biophysics, Statistical and Nonlinear Physics
17

Scopus Publications

139

Scholar Citations

7

Scholar h-index

6

Scholar i10-index

Scopus Publications

  • A first passage time study of bacterial eradication under the influence of antibacterial agents
    Nafisa Siddiqui, Shivangi Chourasia, Aishani Ghosal, Rati Sharma
    Computational Biology and Chemistry, 2026
  • Identification and quantification of irreversibility in stochastic systems
    Aishani Ghosal, Gili Bisker
    Physical Chemistry Chemical Physics, 2026
    This review summarizes methods for estimating entropy production rates from observed trajectories and coarse-grained time series.
  • Practical considerations for accurate estimation of diffusion parameters from single-particle tracking in living cells
    Aishani Ghosal, Yu-Huan Wang, Nguyen Nguyen, Laura Troyer, Sangjin Kim
    Journal of Chemical Physics, 2025
    Advances in fluorescence microscopy have enabled high-resolution tracking of individual biomolecules in living cells. However, accurate estimation of diffusion parameters from single-particle trajectories remains challenging due to static and dynamic localization errors inherent in these measurements. While previous studies have characterized how such errors affect mean-squared displacement (MSD) analysis, practical guidelines for minimizing them during data acquisition and correcting them during analysis are still lacking. Here, we combine theoretical modeling and simulations to evaluate how exposure time and sampling rate influence the accuracy of MSD-based inference under fractional Brownian motion (FBM), a canonical model of anomalous diffusion. We demonstrate that decoupling exposure and sampling times enables escape from the error-prone regime, thus improving inference accuracy, and that incorporating an offset in nonlinear MSD fitting substantially improves the estimation of the anomalous diffusion exponent. We validate this framework using trajectories of cytoplasmic particles in Escherichia coli, recovering consistent diffusion parameters across multiple datasets. We further prove that the framework extends beyond FBM to general cases of subdiffusion, thereby offering practical strategies to improve both experimental design and data analysis in single-particle tracking of live or synthetic systems.
  • Dissipation rates from experimental uncertainty
    Aishani Ghosal, Jason R. Green
    Physical Review Research, 2025
    Active matter and driven systems exhibit statistical fluctuations in density and particle positions that are an indirect indicator of dissipation across length and time scales. Here, we quantitatively relate these fluctuations to a thermodynamic speed limit that constrains the rates of heat and entropy production in nonequilibrium processes. By reparametrizing the speed limit set by the Fisher information, we show how to infer these dissipation rates from directly observable or controllable quantities. This approach can use available experimental data as input and avoid the need for analytically solvable microscopic models or full time-dependent probability distributions. The heat rate we predict agrees with experimental measurements for a pulled Brownian particle and a microtubule active gel, which validates the approach and suggests potential for the design of experiments.
  • Utilizing time-series measurements for entropy-production estimation in partially observed systems
    Uri Kapustin, Aishani Ghosal, Gili Bisker
    Physical Review Research, 2024
    Estimating the dissipation, or the entropy-production rate (EPR), can provide insights into the underlying mechanisms of nonequilibrium-driven processes. However, in practical experimental settings, precise quantification of the EPR can be challenging, as only partial information is typically accessible. Here, we explore the relationship between the observed information and the accuracy of EPR estimation. We employ a range of coarse-grained time-series trajectory data, simulating scenarios where varying degrees of information are available. We discover a hierarchy of lower bounds on the total EPR, demonstrating that an increasing amount of information can be leveraged for obtaining tighter EPR estimation, underscoring the critical role of exploiting the available data. Moreover, we introduce a technique for utilizing waiting times within hidden states and tightening the lower bound on the total EPR for some cases. This approach highlights the potential of hidden features within the data to provide valuable insights into the dissipative dynamics of complex systems. Published by the American Physical Society 2024
  • Universal bounds on entropy production inferred from observed statistics
    Eden Nitzan, Aishani Ghosal, Gili Bisker
    Physical Review Research, 2023
    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 an 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.
  • Entropy production rates for different notions of partial information
    Aishani Ghosal, Gili Bisker
    Journal of Physics D Applied Physics, 2023
    Experimentally monitoring the dynamics of a physical system, one cannot possibly resolve all the microstates or all the transitions between them. Theoretically, these partially observed systems are modeled by considering only the observed states and transitions while the rest are hidden, by merging microstates into a single mesostate, or by decimating unobserved states. The deviation of a system from thermal equilibrium can be characterized by a non-zero value of the entropy production rate (EPR). Based on the partially observed information of the states or transitions, one can only infer a lower bound on the total EPR. Previous studies focused on several approaches to optimize the lower bounds on the EPR, fluctuation theorems associated with the apparent EPR, information regarding the network topology inferred from partial information, etc. Here, we calculate partial EPR values of Markov chains driven by external forces from different notions of partial information. We calculate partial EPR from state-based coarse-graining, namely decimation and two lumping protocols with different constraints, either preserving transition flux, or the occupancy number correlation function. Finally, we compare these partial EPR values with the EPR inferred from the observed cycle affinity. Our results can further be extended to other networks and various external driving forces.
  • Model studies on motion of respiratory droplets driven through a face mask
    Rahul Karmakar, Aishani Ghosal, J. Chakrabarti
    Epl, 2023
    Face masks are used to intercept respiratory droplets to prevent spreading of air-borne diseases. Designing face masks with better efficiency needs microscopic understanding on how respiratory droplets move through a mask. Here we study a simple model on the interception of droplets by a face mask. The mask is treated as a polymeric network in an asymmetric confinement, while the droplet is taken as a micrometer-sized tracer colloidal particle, subject to driving force that mimics the breathing. We study numerically, using the Langevin dynamics, the tracer particle permeation through the polymeric network. We show that the permeation is an activated process following an Arrhenius dependence on temperature. The potential energy profile responsible for the activation process increases with tracer size, tracer bead interaction, network rigidity and decreases with the driving force and confinement length. A deeper energy barrier led to better efficiency to intercept the tracer particles of a given size in the presence of driving force at room temperature. Our studies may help to design masks with better efficiency.
  • Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining
    Aishani Ghosal, Gili Bisker
    Physical Chemistry Chemical Physics, 2022
    A lower bound on the total entropy production rate is inferred from the time-irreversibility in partially observed and coarsed-grained systems operating far from equilibrium.
  • Statistics of reaction flux and dynamical activity associated with a diffusion-influenced ligand-binding reaction
    Aishani Ghosal
    Journal of Physical Chemistry B, 2021
    In this paper, we consider a macromolecule with two competitive binding sites where a ligand can bind to and gives rise to a unicyclic reaction network consisting of four states-(i) a single state with both binding sites vacant, (ii) two states with one bound site and one free binding site, and (iii) an another single state with both sites occupied. We obtain probability densities of the time-integrated current along the clockwise direction and the dynamical activity or mean number of jumps between different states for finite times at a fast diffusion limit. On the other hand, in the diffusion-limited case, ligand diffusion between the two binding sites directly connects the mono-ligated states-changing the reaction scheme. Addition of the new reaction channel alters the precision of ligand occupancy to a single site, the mean dynamical activity, and the mean entropy production rate. All of these quantities are calculated with varying degrees of competition between the two sites for ligands, and we find that increase in the competition between the two sites decreases all above-mentioned additive functionals. The upper bound of precision associated with a single-site ligand occupancy for a diffusion-influenced reaction network is set by the mean dynamical activity (mean entropy production rate) at small (large) ligand concentrations at the steady-state limit.
  • Fluctuation relations for flow-driven trapped colloids and implications for related polymeric systems
    Aishani Ghosal, Binny J. Cherayil
    European Physical Journal B, 2019
  • Anomalies in the coil-stretch transition of flexible polymers
    Aishani Ghosal, Binny J. Cherayil
    Journal of Chemical Physics, 2018
  • The effects of slit-like confinement on flow-induced polymer deformation
    Aishani Ghosal, Binny J. Cherayil
    Journal of Chemical Physics, 2017
  • Polymer extension under flow: Some statistical properties of the work distribution function
    Aishani Ghosal, Binny J. Cherayil
    Journal of Chemical Physics, 2016
  • Polymer extension under flow: A path integral evaluation of the free energy change using the Jarzynski relation
    Aishani Ghosal, Binny J. Cherayil
    Journal of Chemical Physics, 2016
  • The distribution of heat fluctuations in resistively-coupled dual temperature heat baths
    A Ghosal, B J Cherayil
    Journal of Statistical Mechanics Theory and Experiment, 2016
  • Anomalous lifetime statistics of ligand-receptor binding in a tethered polymer system
    A Ghosal, B J Cherayil
    Journal of Statistical Mechanics Theory and Experiment, 2015

RECENT SCHOLAR PUBLICATIONS

  • BPS2026–Principles of client enrichment through scaffold-client interactions in biomolecular condensates
    A Ghosal, L Case, T GrandPre
    Biophysical Journal 125 (4), 285a-286a , 2026
    2026
  • Principles of Client Enrichment in Multicomponent Biomolecular Condensates
    A Ghosal, NE Lea, LB Case, T GrandPre
    arXiv:2601.11450v1 , 2026
    2026
  • A first passage time study of bacterial eradication under the influence of antibacterial agents
    N Siddiqui, S Chourasia, A Ghosal, R Sharma
    Computational Biology and Chemistry 122, 108889 , 2026
    2026
  • Identification and quantification of irreversibility in stochastic systems
    A Ghosal, G Bisker
    Physical Chemistry Chemical Physics 28 (16), 9840-9866 , 2026
    2026
  • Practical considerations for accurate estimation of diffusion parameters from single-particle tracking in living cells
    A Ghosal, YH Wang, N Nguyen, L Troyer, S Kim
    The Journal of Chemical Physics 163 (13), 134202 , 2025
    2025
    Citations: 3
  • Practical considerations for accurate estimation of diffusion parameters from single-particle tracking in living cells
    A Ghosal, YH Wang, N Nguyen, L Troyer, S Kim
    bioRxiv 2025.06.12.659344 , 2025
    2025
    Citations: 3
  • Dissipation rates from experimental uncertainty
    A Ghosal, JR Green
    Physical Review Research 7 (1), L012078 , 2025
    2025
    Citations: 5
  • Utilizing time-series measurements for entropy-production estimation in partially observed systems
    U Kapustin, A Ghosal, G Bisker
    Physical Review Research 6 (2), 023039 , 2024
    2024
    Citations: 18
  • Dissipation rates from experimental uncertainty
    A Ghosal, JR Green
    https://arxiv.org/abs/2406.05333 , 2024
    2024
  • Universal bounds on entropy production inferred from observed statistics
    E Nitzan, A Ghosal, G Bisker
    Physical Review Research 5 (4), 043251 , 2023
    2023
    Citations: 23
  • Entropy production rates for different notions of partial information
    A Ghosal, G Bisker
    https://doi.org/10.1088/1361-6463/acc957 , 2023
    2023
    Citations: 14
  • Model studies on motion of respiratory droplets driven through a face mask
    R Karmakar, A Ghosal, J Chakrabarti
    Europhysics Letters 141 (2), 27001 , 2023
    2023
    Citations: 5
  • Inferring entropy production rate from partially observed Langevin dynamics systems under coarse-graining
    A Ghosal, G Bisker, AG Team, GB Team
    APS March Meeting Abstracts 2022, W09. 010 , 2022
    2022
  • Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining
    A Ghosal, G Bisker
    Physical Chemistry Chemical Physics 24 (39), 24021-24031 , 2022
    2022
    Citations: 26
  • Statistics of reaction flux and dynamical activity associated with a diffusion-influenced ligand-binding reaction
    A Ghosal
    The Journal of Physical Chemistry B 125 (7), 1760-1767 , 2021
    2021
    Citations: 2
  • Fluctuation relations for flow-driven trapped colloids and implications for related polymeric systems
    A Ghosal, BJ Cherayil
    The European Physical Journal B 92 (11), 243 , 2019
    2019
    Citations: 7
  • Anomalies in the coil-stretch transition of flexible polymers
    A Ghosal, BJ Cherayil
    The Journal of Chemical Physics 148 (9) , 2018
    2018
    Citations: 5
  • The effects of slit-like confinement on flow-induced polymer deformation
    A Ghosal, BJ Cherayil
    The Journal of Chemical Physics 147 (6) , 2017
    2017
    Citations: 3
  • Polymer extension under flow: Some statistical properties of the work distribution function
    A Ghosal, BJ Cherayil
    The Journal of Chemical Physics 145 (20) , 2016
    2016
    Citations: 6
  • Polymer extension under flow: A path integral evaluation of the free energy change using the Jarzynski relation
    A Ghosal, BJ Cherayil
    The Journal of Chemical Physics 144 (21) , 2016
    2016
    Citations: 10

MOST CITED SCHOLAR PUBLICATIONS

  • Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining
    A Ghosal, G Bisker
    Physical Chemistry Chemical Physics 24 (39), 24021-24031 , 2022
    2022
    Citations: 26
  • Universal bounds on entropy production inferred from observed statistics
    E Nitzan, A Ghosal, G Bisker
    Physical Review Research 5 (4), 043251 , 2023
    2023
    Citations: 23
  • Utilizing time-series measurements for entropy-production estimation in partially observed systems
    U Kapustin, A Ghosal, G Bisker
    Physical Review Research 6 (2), 023039 , 2024
    2024
    Citations: 18
  • Entropy production rates for different notions of partial information
    A Ghosal, G Bisker
    https://doi.org/10.1088/1361-6463/acc957 , 2023
    2023
    Citations: 14
  • The distribution of heat fluctuations in resistively-coupled dual temperature heat baths
    A Ghosal, BJ Cherayil
    Journal of Statistical Mechanics: Theory and Experiment 2016 (4), 043201 , 2016
    2016
    Citations: 12
  • Polymer extension under flow: A path integral evaluation of the free energy change using the Jarzynski relation
    A Ghosal, BJ Cherayil
    The Journal of Chemical Physics 144 (21) , 2016
    2016
    Citations: 10
  • Fluctuation relations for flow-driven trapped colloids and implications for related polymeric systems
    A Ghosal, BJ Cherayil
    The European Physical Journal B 92 (11), 243 , 2019
    2019
    Citations: 7
  • Polymer extension under flow: Some statistical properties of the work distribution function
    A Ghosal, BJ Cherayil
    The Journal of Chemical Physics 145 (20) , 2016
    2016
    Citations: 6
  • Dissipation rates from experimental uncertainty
    A Ghosal, JR Green
    Physical Review Research 7 (1), L012078 , 2025
    2025
    Citations: 5
  • Model studies on motion of respiratory droplets driven through a face mask
    R Karmakar, A Ghosal, J Chakrabarti
    Europhysics Letters 141 (2), 27001 , 2023
    2023
    Citations: 5
  • Anomalies in the coil-stretch transition of flexible polymers
    A Ghosal, BJ Cherayil
    The Journal of Chemical Physics 148 (9) , 2018
    2018
    Citations: 5
  • Practical considerations for accurate estimation of diffusion parameters from single-particle tracking in living cells
    A Ghosal, YH Wang, N Nguyen, L Troyer, S Kim
    The Journal of Chemical Physics 163 (13), 134202 , 2025
    2025
    Citations: 3
  • Practical considerations for accurate estimation of diffusion parameters from single-particle tracking in living cells
    A Ghosal, YH Wang, N Nguyen, L Troyer, S Kim
    bioRxiv 2025.06.12.659344 , 2025
    2025
    Citations: 3
  • The effects of slit-like confinement on flow-induced polymer deformation
    A Ghosal, BJ Cherayil
    The Journal of Chemical Physics 147 (6) , 2017
    2017
    Citations: 3
  • Statistics of reaction flux and dynamical activity associated with a diffusion-influenced ligand-binding reaction
    A Ghosal
    The Journal of Physical Chemistry B 125 (7), 1760-1767 , 2021
    2021
    Citations: 2
  • BPS2026–Principles of client enrichment through scaffold-client interactions in biomolecular condensates
    A Ghosal, L Case, T GrandPre
    Biophysical Journal 125 (4), 285a-286a , 2026
    2026
  • Principles of Client Enrichment in Multicomponent Biomolecular Condensates
    A Ghosal, NE Lea, LB Case, T GrandPre
    arXiv:2601.11450v1 , 2026
    2026
  • A first passage time study of bacterial eradication under the influence of antibacterial agents
    N Siddiqui, S Chourasia, A Ghosal, R Sharma
    Computational Biology and Chemistry 122, 108889 , 2026
    2026
  • Identification and quantification of irreversibility in stochastic systems
    A Ghosal, G Bisker
    Physical Chemistry Chemical Physics 28 (16), 9840-9866 , 2026
    2026
  • Dissipation rates from experimental uncertainty
    A Ghosal, JR Green
    https://arxiv.org/abs/2406.05333 , 2024
    2024