Avijit Kundu

@sfu.ca

Postdoctoral Fellow, Physics
Simon Fraser University



                 

https://researchid.co/vagabond

RESEARCH, TEACHING, or OTHER INTERESTS

Statistical and Nonlinear Physics, Biophysics

13

Scopus Publications

171

Scholar Citations

7

Scholar h-index

5

Scholar i10-index

Scopus Publications

  • 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, and Bidisha Sinha
    Springer Science and Business Media LLC
    AbstractAdherent 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, and Ayan Banerjee
    American Physical Society (APS)
    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, and Supriya Krishnamurthy
    American Physical Society (APS)
    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, and Ayan Banerjee
    American Physical Society (APS)

  • 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, and Supriya Krishnamurthy
    Springer Science and Business Media LLC
    AbstractEstimating 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.

  • Active microrheology using pulsed optical tweezers to probe viscoelasticity of lamin A
    C. Mukherjee, A. Kundu, R. Dey, A. Banerjee, and K. Sengupta
    Royal Society of Chemistry (RSC)
    Schematic showing measurement of the viscoelasticity of purified protein sample in vitro with the help of pulsed optical tweezers and subsequent derivation of G′ & G′′.

  • 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, and Ayan Banerjee
    Frontiers Media SA
    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.

  • Microrheology over a broad frequency range probing multiple-sinusoid oscillating optical tweezer
    Avijit Kundu, Raunak Dey, Shuvojit Paul, and Ayan Banerjee
    SPIE
    We provide a multiple-sinusoid modulated optical tweezers based method to perform microrheology of a sample over a large frequency band in a one shot. So we feed the trapped particle with a square wave and a superposition of multiple-sinusoid of specific frequency and amplitude to achieve our purpose towards active microrheology. To maintain the SNR upto a certain level for the entire frequency range we increase the amplitude at high frequency in our setup. We measure the parameters of the complex fluid by extracting the phase responses at each frequency of the particle with a high SNR value compared to passive microrheology. We perform this method for a various concentrations of polyacrylamide-water solution and obtain a good agreement of the fluid parameters with the theoretical values.

  • Random number extraction from optically trapped Brownian oscillator using an iterative algorithm
    Raunak Dey, Avijit Kundu, Subhrokoli Ghosh, and Ayan Banerjee
    SPIE
    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.

  • Single-shot phase-sensitive wideband active microrheology of viscoelastic fluids using pulse-scanned optical tweezers
    Shuvojit Paul, Avijit Kundu, and Ayan Banerjee
    IOP Publishing
    We present a fast phase sensitive active microrheology technique exploring the phase response of a microscopic probe particle trapped in a linear viscoelastic fluid using optical tweezers under an external perturbation. Thus, we experimentally determine the cumulative response of the probe to an entire repertoire of sinusoidal excitations simultaneously by applying a spatial square pulse as an excitation to the trapped probe. The square pulse naturally contains the fundamental sinusoidal frequency component and higher odd harmonics, so that we measure the phase response of the probe over a wide frequency band in a single shot, with the band being tunable over the spectrum by choosing suitable experimental parameters. We then determine the responses to individual harmonics using a lock-in algorithm, and compare the phase shifts to those obtained theoretically by solving the equation of motion of the probe particle confined in a harmonic potential in the fluid in the presence of a sinusoidal perturbation. We go on to relate the phase response of the probe to the complex shear modulus , and proceed to verify our technique in a mixture of polyacrylamide and water, which we compare with known values in literature and obtain very good agreement. Our method increases the robustness of active microrheology in general and ensures that any drifts in time are almost entirely ruled out from the data, with the added advantage of high speed and ease of use.

  • Measurement of Van der Waals force using oscillating optical tweezers
    Avijit Kundu, Shuvojit Paul, Soumitro Banerjee, and Ayan Banerjee
    AIP Publishing
    We employ oscillating optical tweezers as a probe to measure the surface forces between polystyrene and silica. Thus, we modulate a trapped polystyrene particle with an external sinusoidal force in close proximity (∼80 nm) of a silica surface. The particle motion is influenced by several factors which include an increased drag force according to Faxen's correction, a spurious force that comes into play due to the diffusion coefficient of the medium becoming position dependent, and finally, the London-Van der Waals (LVdW) force which becomes substantial when the particle approaches the surface. By accounting for the other forces from the analytically known results, we are able to directly quantify the LVdW force from the experimentally measured amplitude of the oscillating particle. Thereby, we determine the Hamaker constant H for the LVdW force between polystyrene and silica, and obtain a good agreement with the value reported in the literature. Our method is general in nature and can be extended toward probing other surface effects or other interaction forces using oscillating optical tweezers.

  • Measurement of Van der Waals force using optical tweezers
    Avijit Kundu, Shuvojit Paul, Soumitro Banerjee, and Ayan Banerjee
    SPIE
    Surface effects are crucial in several mesoscopic phenomena, especially those concerning biological entities. Here we determine the effects of Van der Waals forces at relatively long range ( 80 nm) by optically trapping a probe particle close to a large silica particle and modulating the spatial position of the probe employing oscillating optical tweezers. This method has greater signal-to-noise in the experimentally measured probe-response as compare to that obtained from measurements of Brownian fluctuations. We quantify the H-value experimentally by analyzing the amplitude response of a single trapped particle in comparison to numerically expected results by employing chi-square fitting, and obtain good agreement with the known H-value for the system.

  • Fast Bayesian inference of optical trap stiffness and particle diffusion
    Sudipta Bera, Shuvojit Paul, Rajesh Singh, Dipanjan Ghosh, Avijit Kundu, Ayan Banerjee, and R. Adhikari
    Springer Science and Business Media LLC
    AbstractBayesian inference provides a principled way of estimating the parameters of a stochastic process that is observed discretely in time. The overdamped Brownian motion of a particle confined in an optical trap is generally modelled by the Ornstein-Uhlenbeck process and can be observed directly in experiment. Here we present Bayesian methods for inferring the parameters of this process, the trap stiffness and the particle diffusion coefficient, that use exact likelihoods and sufficient statistics to arrive at simple expressions for the maximum a posteriori estimates. This obviates the need for Monte Carlo sampling and yields methods that are both fast and accurate. We apply these to experimental data and demonstrate their advantage over commonly used non-Bayesian fitting methods.

RECENT SCHOLAR PUBLICATIONS

  • 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 81 (1), 43 2024

  • 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

  • Experimental verification of arcsine laws in mesoscopic nonequilibrium systems
    R Dey, A Kundu, B Das, A Banerjee
    Physical Review E 106 (5), 054113 2022

  • 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

  • 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

  • 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

  • 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

  • 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

  • Experimental verification of Arcsine laws in mesoscopic non-equilibrium and active systems
    R Dey, A Kundu, B Das, A Banerjee
    arXiv preprint arXiv:2104.00127 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

  • 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

  • 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

  • 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

  • Measurement of Van der Waals force using oscillating optical tweezers
    A Kundu, S Paul, S Banerjee, A Banerjee
    Applied Physics Letters 115 (12) 2019

  • 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

  • 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

  • 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

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
    Citations: 46

  • 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
    Citations: 34

  • Measurement of Van der Waals force using oscillating optical tweezers
    A Kundu, S Paul, S Banerjee, A Banerjee
    Applied Physics Letters 115 (12) 2019
    Citations: 22

  • 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
    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
    Citations: 15

  • 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
    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
    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
    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
    Citations: 6

  • 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 81 (1), 43 2024
    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
    Citations: 3