Sreekanth Kizhakkumpurath Manikandan

All Publications

• Adaptive nonequilibrium design of actin-based metamaterials: Fundamental and practical limits of control. Proceedings of the National Academy of Sciences of the United States of America Chennakesavalu, S., Manikandan, S. K., Hu, F., Rotskoff, G. M. 2024; 121 (8): e2310238121

  Abstract

  The adaptive and surprising emergent properties of biological materials self-assembled in far-from-equilibrium environments serve as an inspiration for efforts to design nanomaterials. In particular, controlling the conditions of self-assembly can modulate material properties, but there is no systematic understanding of either how to parameterize external control or how controllable a given material can be. Here, we demonstrate that branched actin networks can be encoded with metamaterial properties by dynamically controlling the applied force under which they grow and that the protocols can be selected using multi-task reinforcement learning. These actin networks have tunable responses over a large dynamic range depending on the chosen external protocol, providing a pathway to encoding "memory" within these structures. Interestingly, we obtain a bound that relates the dissipation rate and the rate of "encoding" that gives insight into the constraints on control-both physical and information theoretical. Taken together, these results emphasize the utility and necessity of nonequilibrium control for designing self-assembled nanostructures.

  View details for DOI 10.1073/pnas.2310238121

  View details for PubMedID 38359294

• Mechano-regulation by clathrin pit-formation and passive cholesterol-dependent tubules during de-adhesion. Cellular and molecular life sciences : CMLS Mandal, T., Biswas, A., Ghosh, T., Manikandan, S., Kundu, A., Banerjee, A., Mitra, D., Sinha, B. 2024; 81 (1): 43

  Abstract

  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.

  View details for DOI 10.1007/s00018-023-05072-4

  View details for PubMedID 38217571

  View details for PubMedCentralID PMC10787898

• Enhanced directionality of active processes in a viscoelastic bath NEW JOURNAL OF PHYSICS Das, B., Paul, S., Manikandan, S. K., Banerjee, A. 2023; 25 (9)

  View details for DOI 10.1088/1367-2630/acfb31

  View details for Web of Science ID 001119301200001

• Inferring entropy production in anharmonic Brownian gyrators PHYSICAL REVIEW RESEARCH Das, B., Manikandan, S. K., Banerjee, A. 2022; 4 (4)

  View details for DOI 10.1103/PhysRevResearch.4.043080

  View details for Web of Science ID 000887229500001

• Nonmonotonic skewness of currents in nonequilibrium steady states PHYSICAL REVIEW RESEARCH Manikandan, S. K., Das, B., Kundu, A., Dey, R., Banerjee, A., Krishnamurthy, S. 2022; 4 (4)

  View details for DOI 10.1103/PhysRevResearch.4.043067

  View details for Web of Science ID 001081841500002

• Estimating time-dependent entropy production from non-equilibrium trajectories COMMUNICATIONS PHYSICS Otsubo, S., Manikandan, S. K., Sagawa, T., Krishnamurthy, S. 2022; 5 (1)

  View details for DOI 10.1038/s42005-021-00787-x

  View details for Web of Science ID 000741035900005

• Quantitative analysis of non-equilibrium systems from short-time experimental data COMMUNICATIONS PHYSICS Manikandan, S. K., Ghosh, S., Kundu, A., Das, B., Agrawal, V., Mitra, D., Banerjee, A., Krishnamurthy, S. 2021; 4 (1)

  View details for DOI 10.1038/s42005-021-00766-2

  View details for Web of Science ID 000725535500005

• Equidistant quenches in few-level quantum systems PHYSICAL REVIEW RESEARCH Manikandan, S. K. 2021; 3 (4)

  View details for DOI 10.1103/PhysRevResearch.3.043108

  View details for Web of Science ID 000719809400006

• Inferring Entropy Production from Short Experiments. Physical review letters Manikandan, S. K., Gupta, D., Krishnamurthy, S. 2020; 124 (12): 120603

  Abstract

  We provide a strategy for the exact inference of the average as well as the fluctuations of the entropy production in nonequilibrium systems in the steady state, from the measurements of arbitrary current fluctuations. Our results are built upon the finite-time generalization of the thermodynamic uncertainty relation, and require only very short time series data from experiments. We illustrate our results with exact and numerical solutions for two colloidal heat engines.

  View details for DOI 10.1103/PhysRevLett.124.120603

  View details for PubMedID 32281844

• Efficiency Fluctuations in Microscopic Machines. Physical review letters Manikandan, S. K., Dabelow, L., Eichhorn, R., Krishnamurthy, S. 2019; 122 (14): 140601

  Abstract

  Nanoscale machines are strongly influenced by thermal fluctuations, contrary to their macroscopic counterparts. As a consequence, even the efficiency of such microscopic machines becomes a fluctuating random variable. Using geometric properties and the fluctuation theorem for the total entropy production, a "universal theory of efficiency fluctuations" at long times, for machines with a finite state space, was developed by Verley et al. [Nat. Commun. 5, 4721 (2014)NCAOBW2041-172310.1038/ncomms5721; Phys. Rev. E 90, 052145 (2014)PRESCM1539-375510.1103/PhysRevE.90.052145]. We extend this theory to machines with an arbitrary state space. Thereby, we work out more detailed prerequisites for the "universal features" and explain under which circumstances deviations can occur. We also illustrate our findings with exact results for two nontrivial models of colloidal engines.

  View details for DOI 10.1103/PhysRevLett.122.140601

  View details for PubMedID 31050471

• Asymptotics of work distributions in a stochastically driven system (vol 90, 258, 2018) EUROPEAN PHYSICAL JOURNAL B Manikandan, S. K., Krishnamurthy, S. 2018; 91 (3)

  View details for DOI 10.1140/epjb/e2018-90024-x

  View details for Web of Science ID 000428953500005

• Exact results for the finite time thermodynamic uncertainty relation JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL Manikandan, S. K., Krishnamurthy, S. 2018; 51 (11)

  View details for DOI 10.1088/1751-8121/aaaa54

  View details for Web of Science ID 000425341100001

• Asymptotics of work distributions in a stochastically driven system EUROPEAN PHYSICAL JOURNAL B Manikandan, S. K., Krishnamurthy, S. 2017; 90 (12)

  View details for DOI 10.1140/epjb/e2017-80432-9

  View details for Web of Science ID 000418431900002