Higher actin contractility and cargo-loaded clathrin pits create midplane-peaked apico-basal tension profiles in HeLa cells Tanmoy Ghosh, Anisha Majhi, Avijit Kundu, Ayan Banerjee, Bidisha Sinha Cell Reports Physical Science, 2026 <h2>Summary</h2> Slow equilibration of local mechanical perturbations on the cell membrane could ideally create inhomogeneities in the mechanical state of the cell membrane, affecting its function. However, very few reports measure mechanical heterogeneities or connect them to cellular functional state. In this work, we employ optical-trap-based dual-tension measurements (per cell) to first reveal an actin-dependent tension gradient with low apical tensions. In the same cells, interference reflection microscopy reveals heterogeneous tension distribution at the base. Super-resolution imaging and fluorescence-lifetime (Flipper-TR) measurements reveal the midplane to be more contractile and tensed while confirming an actomyosin-contractility-dependent apical tension gradient and ruling out a direct contribution of actin-membrane linkages. Cargo-loaded clathrin-coated pits are bigger and denser at the tensed midplane. Inhibiting their formation suppresses the rise in midplane tension but accentuates the apical tension gradient. Thus, the tension profile is created by the actomyosin contractility profile but further tuned by its crosstalk with clathrin-mediated endocytosis.
Irreversibility of mesoscopic processes with hydrodynamic interactions Biswajit Das, Sreekanth K. Manikandan, Shuvojit Paul, Avijit Kundu, Supriya Krishnamurthy, Ayan Banerjee Physical Review E, 2025 Optically confined colloidal particles, when placed in close proximity, form a dissipatively coupled system through hydrodynamic interactions. The role of such interactions influencing irreversibility and energy dissipation in out-of-equilibrium systems is often not well deciphered. Here, we demonstrate-through the estimation of the entropy production rate-that the nonequilibrium features of the system with such interactions vary depending on the nature of external driving, and importantly, on the level of coarse graining. Crucially, we show that coarse graining reverses the dependence of the measured entropy production rate on the strength of the hydrodynamic interactions. Furthermore, we clarify that such interactions do not violate energy balance at the level of individual trajectories, as was believed earlier. Our results highlight a previously unnoticed effect of coarse graining in nonequilibrium systems, and have implications for the inference of entropy production in experimental contexts.
Mechano-regulation by clathrin pit-formation and passive cholesterol-dependent tubules during de-adhesion Tithi Mandal, Arikta Biswas, Tanmoy Ghosh, Sreekanth Manikandan, Avijit Kundu, Ayan Banerjee, Dhrubaditya Mitra, Bidisha Sinha Cellular and Molecular Life Sciences, 2024 Adherent cells ensure membrane homeostasis during de-adhesion by various mechanisms, including endocytosis. Although mechano-chemical feedbacks involved in this process have been studied, the step-by-step build-up and resolution of the mechanical changes by endocytosis are poorly understood. To investigate this, we studied the de-adhesion of HeLa cells using a combination of interference reflection microscopy, optical trapping and fluorescence experiments. We found that de-adhesion enhanced membrane height fluctuations of the basal membrane in the presence of an intact cortex. A reduction in the tether force was also noted at the apical side. However, membrane fluctuations reveal phases of an initial drop in effective tension followed by saturation. The area fractions of early (Rab5-labelled) and recycling (Rab4-labelled) endosomes, as well as transferrin-labelled pits close to the basal plasma membrane, also transiently increased. On blocking dynamin-dependent scission of endocytic pits, the regulation of fluctuations was not blocked, but knocking down AP2-dependent pit formation stopped the tension recovery. Interestingly, the regulation could not be suppressed by ATP or cholesterol depletion individually but was arrested by depleting both. The data strongly supports Clathrin and AP2-dependent pit-formation to be central to the reduction in fluctuations confirmed by super-resolution microscopy. Furthermore, we propose that cholesterol-dependent pits spontaneously regulate tension under ATP-depleted conditions.
Experimental verification of arcsine laws in mesoscopic nonequilibrium systems Raunak Dey, Avijit Kundu, Biswajit Das, Ayan Banerjee Physical Review E, 2022 A large number of processes in the mesoscopic world occur out of equilibrium, where the time evolution of a system becomes immensely important since it is driven principally by dissipative effects. Nonequilibrium steady states (NESS) represent a crucial category in such systems, where relaxation timescales are comparable to the operational timescales. In this study, we employ a model NESS stochastic system, which is comprised of a colloidal microparticle optically trapped in a viscous fluid, externally driven by a temporally correlated noise, and show that time-integrated observables such as the entropic current, the work done on the system or the work dissipated by it, follow the three Lévy arcsine laws [A. C. Barato et al., Phys. Rev. Lett. 121, 090601 (2018)0031-900710.1103/PhysRevLett.121.090601], in the large time limit. We discover that cumulative distributions converge faster to arcsine distributions when it is near equilibrium and the rate of entropy production is small, because in that case the entropic current has weaker temporal autocorrelation. We study this phenomenon by changing the strength of the added noise as well as by perturbing our system with a flow field produced by a microbubble at close proximity to the trapped particle. We confirm our experimental findings with theoretical simulations of the systems. Our work provides an interesting insight into the NESS statistics of the meso-regime, where stochastic fluctuations play a pivotal role.
Nonmonotonic skewness of currents in nonequilibrium steady states Sreekanth K. Manikandan, Biswajit Das, Avijit Kundu, Raunak Dey, Ayan Banerjee, Supriya Krishnamurthy Physical Review Research, 2022 Measurements of any property of a microscopic system are bound to show significant deviations from the average, due to thermal fluctuations. For time-integrated currents such as heat, work or entropy production in a steady state, it is in fact known that there will be long stretches of fluctuations both above as well as below the average, occurring equally likely at large times. In this paper we show that for any finite-time measurement in a non-equilibrium steady state - rather counter-intuitively - fluctuations below the average are more probable. This discrepancy is higher when the system is further away from equilibrium. For overdamped diffusive processes, there is even an optimal time when time-integrated current fluctuations mostly lie below the average. We demonstrate that these effects result from the non-monotonic skewness of current fluctuations and provide evidence that they are easily observable in experiments. We also discuss their extensions to discrete space Markov jump processes and implications to biological and synthetic microscopic engines.
Single-shot wideband active microrheology using multiple-sinusoid modulated optical tweezers Avijit Kundu, Raunak Dey, Shuvojit Paul, Ayan Banerjee Physical Review Fluids, 2021 Optically trapped colloidal probes have been widely used for active microrheology of viscoelastic fluids over the last decade. A significant issue which arises is measurement of complex viscoelastic parameters over a wide frequency range and a short time. We use a combination of square and sinusoidal waves to spatially modulate the trapped probe over a frequency range spanning five decades, and use the phase response to calculate complex viscoelastic parameters with high signal to noise in a little over three minutes. We test our method over a wide variety of linear viscoelastic samples at different concentrations, and find good agreement of the measured parameters with known values.
Quantitative analysis of non-equilibrium systems from short-time experimental data Sreekanth K. Manikandan, Subhrokoli Ghosh, Avijit Kundu, Biswajit Das, Vipin Agrawal, Dhrubaditya Mitra, Ayan Banerjee, Supriya Krishnamurthy Communications Physics, 2021 Estimating entropy production directly from experimental trajectories is of great current interest but often requires a large amount of data or knowledge of the underlying dynamics. In this paper, we propose a minimal strategy using the short-time Thermodynamic Uncertainty Relation (TUR) by means of which we can simultaneously and quantitatively infer the thermodynamic force field acting on the system and the (potentially exact) rate of entropy production from experimental short-time trajectory data. We benchmark this scheme first for an experimental study of a colloidal particle system where exact analytical results are known, prior to studying the case of a colloidal particle in a hydrodynamical flow field, where neither analytical nor numerical results are available. In the latter case, we build an effective model of the system based on our results. In both cases, we also demonstrate that our results match with those obtained from another recently introduced scheme.
Simultaneous Random Number Generation and Optical Tweezers Calibration Employing a Learning Algorithm Based on the Brownian Dynamics of a Trapped Colloidal Particle Raunak Dey, Subhrokoli Ghosh, Avijit Kundu, Ayan Banerjee Frontiers in Physics, 2021 True random number generators are in high demand for secure cryptographic algorithms. Unlike algorithmically generated pseudo-random numbers they are unclonable and non-deterministic. A particle following Brownian dynamics as a result of the stochastic Ornstein-Uhlenbeck process is a source of true randomness because the collisions with the ambient molecules are probabilistic in nature. In this paper, we trap colloidal particles in water using optical tweezers and record its confined Brownian motion in real-time. Using a segment of the initial incoming data we train our learning algorithm to measure the values of the trap stiffness and diffusion coefficient and later use those parameters to extract the “white” noise term in the Langevin equation. The random noise is temporally delta correlated, with a flat spectrum. We use these properties in an inverse problem of trap-calibration to extract trap stiffnesses, compare it with standard equipartition of energy technique, and show it to scale linearly with the power of the trapping laser. Interestingly, we get the best random number sequence for the best calibration. We test the random number sequence, which we have obtained, using standard tests of randomness and observe the randomness to improve with increasing sampling frequencies. This method can be extended to the trap-calibration for colloidal particles confined in complex fluids, or active particles in simple or complex environments so as to provide a new and accurate analytical methodology for studying Brownian motion dynamics using the newly-emerged but robust machine learning platform.
Random number extraction from optically trapped Brownian oscillator using an iterative algorithm Raunak Dey, Avijit Kundu, Subhrokoli Ghosh, Ayan Banerjee Proceedings of SPIE the International Society for Optical Engineering, 2021 True random number generators are in high demand for secure cryptographic algorithms. Unlike algorithmically generated pseudo-random numbers, they are unclonable and non-deterministic. In this paper, we extract the white noise from stochastic Brownian Markov trajectories and use it to generate random numbers that qualify NIST standard tests of randomness. We trap colloidal particles in water using optical tweezers and record its confined Brownian motion in real-time. Next, in a two-step process, we use the initial section of incoming data to train and calibrate our iterative algorithm on the trap stiffness and viscosity of the solution based on the autocorrelation and power spectrum properties of the noise; then, we extract random arrays from the next section of the data. Interestingly, we get the best random number sequence for the best calibration. We test the random number sequence, which we have obtained, using standard randomness tests and observing the randomness to improve with increasing sampling frequencies.1 In the next steps, we extend this method to a wider class of processes, such as an optically trapped particle modulated by a square pulse or an external colored noise generated by an Ornstein Uhlenbeck process – we estimate the timescale of both the modulation and viscous effect using our algorithm.
Higher actin contractility and cargo-loaded clathrin pits create midplane-peaked apico-basal tension profiles in HeLa cells T Ghosh, A Majhi, A Kundu, A Banerjee, B Sinha Cell Reports Physical Science 7 (1) , 2026 2026
Irreversibility of mesoscopic processes with hydrodynamic interactions B Das, SK Manikandan, S Paul, A Kundu, S Krishnamurthy, A Banerjee Physical Review E 112 (2), L023401 , 2025 2025 Citations: 5
A System for Carrying Out Active Microrheology to Probe Viscoelasticity of Protein DAB Dr. Kaushik Sengupta, Ms. Chandrayee Mukherjee, Mr. Avijit Kundu, Mr ... IN Patent 539,208 , 2024 2024
Mechano-regulation by clathrin pit-formation and passive cholesterol-dependent tubules during de-adhesion T Mandal, A Biswas, T Ghosh, S Manikandan, A Kundu, A Banerjee, ... Cellular and Molecular Life Sciences: CMLS 81 (1), 43 , 2024 2024 Citations: 10
Experimental verification of arcsine laws in mesoscopic nonequilibrium systems R Dey, A Kundu, B Das, A Banerjee Physical Review E 106 (5), 054113 , 2022 2022 Citations: 7
Nonmonotonic skewness of currents in nonequilibrium steady states SK Manikandan, B Das, A Kundu, R Dey, A Banerjee, S Krishnamurthy Physical Review Research 4 (4), 043067 , 2022 2022 Citations: 8
Quantitative analysis of non-equilibrium systems from short-time experimental data SK Manikandan, S Ghosh, A Kundu, B Das, V Agrawal, D Mitra, ... Communications Physics 4 (1), 258 , 2021 2021 Citations: 43
Single-shot wideband active microrheology using multiple-sinusoid modulated optical tweezers A Kundu, R Dey, S Paul, A Banerjee Physical Review Fluids 6 (12), 123301 , 2021 2021 Citations: 5
Microrheology over a broad frequency range probing multiple-sinusoid oscillating optical tweezer A Kundu, R Dey, S Paul, A Banerjee Optical Trapping and Optical Micromanipulation XVIII 11798, 31-39 , 2021 2021
Random number extraction from optically trapped Brownian oscillator using an iterative algorithm R Dey, A Kundu, S Ghosh, A Banerjee Optical Trapping and Optical Micromanipulation XVIII 11798, 40-52 , 2021 2021
Simultaneous random number generation and optical tweezers calibration employing a learning algorithm based on the brownian dynamics of a trapped colloidal particle R Dey, S Ghosh, A Kundu, A Banerjee Frontiers in Physics 8, 576948 , 2021 2021 Citations: 7
Active microrheology using pulsed optical tweezers to probe viscoelasticity of lamin A C Mukherjee, A Kundu, R Dey, A Banerjee, K Sengupta Soft matter 17 (28), 6787-6796 , 2021 2021 Citations: 17
Probing medium viscoelasticity using signal transmission through coupled harmonic oscillators A Kundu, A Kundu, R Dey, ABT Shuvojit Paul APS March Meeting Abstracts 2021, S17. 012 , 2021 2021
Single-shot phase-sensitive wideband active microrheology of viscoelastic fluids using pulse-scanned optical tweezers S Paul, A Kundu, A Banerjee Journal of Physics: Condensed Matter 31 (50), 504001 , 2019 2019 Citations: 8
Measurement of Van der Waals force using oscillating optical tweezers A Kundu, S Paul, S Banerjee, A Banerjee Applied Physics Letters 115 (12) , 2019 2019 Citations: 27
Measurement of Van der Waals force using optical tweezers A Kundu, S Paul, S Banerjee, A Banerjee Optical Trapping and Optical Micromanipulation XVI 11083, 159-163 , 2019 2019
Active microrheology to determine viscoelastic parameters of Stokes-Oldroyd B fluids using optical tweezers S Paul, A Kundu, A Banerjee Journal of Physics Communications 3 (3), 035002 , 2019 2019 Citations: 18
Fast Bayesian inference of optical trap stiffness and particle diffusion S Bera, S Paul, R Singh, D Ghosh, A Kundu, A Banerjee, R Adhikari Scientific reports 7 (1), 41638 , 2017 2017 Citations: 50
MOST CITED SCHOLAR PUBLICATIONS
Fast Bayesian inference of optical trap stiffness and particle diffusion S Bera, S Paul, R Singh, D Ghosh, A Kundu, A Banerjee, R Adhikari Scientific reports 7 (1), 41638 , 2017 2017 Citations: 50
Quantitative analysis of non-equilibrium systems from short-time experimental data SK Manikandan, S Ghosh, A Kundu, B Das, V Agrawal, D Mitra, ... Communications Physics 4 (1), 258 , 2021 2021 Citations: 43
Measurement of Van der Waals force using oscillating optical tweezers A Kundu, S Paul, S Banerjee, A Banerjee Applied Physics Letters 115 (12) , 2019 2019 Citations: 27
Active microrheology to determine viscoelastic parameters of Stokes-Oldroyd B fluids using optical tweezers S Paul, A Kundu, A Banerjee Journal of Physics Communications 3 (3), 035002 , 2019 2019 Citations: 18
Active microrheology using pulsed optical tweezers to probe viscoelasticity of lamin A C Mukherjee, A Kundu, R Dey, A Banerjee, K Sengupta Soft matter 17 (28), 6787-6796 , 2021 2021 Citations: 17
Mechano-regulation by clathrin pit-formation and passive cholesterol-dependent tubules during de-adhesion T Mandal, A Biswas, T Ghosh, S Manikandan, A Kundu, A Banerjee, ... Cellular and Molecular Life Sciences: CMLS 81 (1), 43 , 2024 2024 Citations: 10
Nonmonotonic skewness of currents in nonequilibrium steady states SK Manikandan, B Das, A Kundu, R Dey, A Banerjee, S Krishnamurthy Physical Review Research 4 (4), 043067 , 2022 2022 Citations: 8
Single-shot phase-sensitive wideband active microrheology of viscoelastic fluids using pulse-scanned optical tweezers S Paul, A Kundu, A Banerjee Journal of Physics: Condensed Matter 31 (50), 504001 , 2019 2019 Citations: 8
Experimental verification of arcsine laws in mesoscopic nonequilibrium systems R Dey, A Kundu, B Das, A Banerjee Physical Review E 106 (5), 054113 , 2022 2022 Citations: 7
Simultaneous random number generation and optical tweezers calibration employing a learning algorithm based on the brownian dynamics of a trapped colloidal particle R Dey, S Ghosh, A Kundu, A Banerjee Frontiers in Physics 8, 576948 , 2021 2021 Citations: 7
Irreversibility of mesoscopic processes with hydrodynamic interactions B Das, SK Manikandan, S Paul, A Kundu, S Krishnamurthy, A Banerjee Physical Review E 112 (2), L023401 , 2025 2025 Citations: 5
Single-shot wideband active microrheology using multiple-sinusoid modulated optical tweezers A Kundu, R Dey, S Paul, A Banerjee Physical Review Fluids 6 (12), 123301 , 2021 2021 Citations: 5
Higher actin contractility and cargo-loaded clathrin pits create midplane-peaked apico-basal tension profiles in HeLa cells T Ghosh, A Majhi, A Kundu, A Banerjee, B Sinha Cell Reports Physical Science 7 (1) , 2026 2026
A System for Carrying Out Active Microrheology to Probe Viscoelasticity of Protein DAB Dr. Kaushik Sengupta, Ms. Chandrayee Mukherjee, Mr. Avijit Kundu, Mr ... IN Patent 539,208 , 2024 2024
Microrheology over a broad frequency range probing multiple-sinusoid oscillating optical tweezer A Kundu, R Dey, S Paul, A Banerjee Optical Trapping and Optical Micromanipulation XVIII 11798, 31-39 , 2021 2021
Random number extraction from optically trapped Brownian oscillator using an iterative algorithm R Dey, A Kundu, S Ghosh, A Banerjee Optical Trapping and Optical Micromanipulation XVIII 11798, 40-52 , 2021 2021
Probing medium viscoelasticity using signal transmission through coupled harmonic oscillators A Kundu, A Kundu, R Dey, ABT Shuvojit Paul APS March Meeting Abstracts 2021, S17. 012 , 2021 2021
Measurement of Van der Waals force using optical tweezers A Kundu, S Paul, S Banerjee, A Banerjee Optical Trapping and Optical Micromanipulation XVI 11083, 159-163 , 2019 2019
