Seminar by S. K. Manikandan at the Department of Applied Physics, University of Tokyo, 8 September 2026

EquiNET uses a graph neural network to infer entropy production from non-equilibrium molecular trajectories and uses this information to estimate equilibrium free-energy differences. (Image by S. K. Manikandan.)
Nonequilibrium Fluctuations as Probes of Thermodynamics
Date: 8 September 2026
Time: 10:30
Place: Department of Applied Physics, University of Tokyo

The first and second laws of thermodynamics provide the basic principles for describing energy transformations and the emergence of the arrow of time in physical systems. Heat dissipation and entropy production, central quantities in these laws, are often difficult to quantify precisely in experiments because the associated energy exchanges are distributed over a vast number of typically inaccessible degrees of freedom in the environment. This is especially true at microscopic scales, where the relevant energy scales are often of the order of kB T, comparable to thermal fluctuations in the environment, and can lie several orders of magnitude below the sensitivity limits of state-of-the-art room-temperature calorimetry.

Recent advances in nonequilibrium statistical physics and data-driven inference provide new approaches for addressing these challenges. In this talk, I will first introduce recent theoretical results showing how nonequilibrium fluctuations can be exploited to quantify energy dissipation at scales inaccessible to conventional calorimetry. I will then demonstrate the practical applicability of these results by quantifying energy dissipation from experimental data in real physical systems, as well as estimating free-energy differences from nonequilibrium measurements in highly dissipative regimes where conventional fluctuation-theorem-based methods fail. I will conclude by discussing the remaining challenges and open questions.

Invited talk by S. K. Manikandan at the Yukawa Institute of Theoretical Physics, Kyoto, 2 September 2026

EquiNET uses a graph neural network to infer entropy production from non-equilibrium molecular trajectories and uses this information to estimate equilibrium free-energy differences. (Image by S. K. Manikandan.)
Nonequilibrium Fluctuations as Probes of Thermodynamics
Date: 2 September 2026
Time: 16:00
Place: Seminar Room K202, Main Building, Yukawa Institute, Kyoto U.

The first and second laws of thermodynamics provide the basic principles for describing energy transformations and the emergence of the arrow of time in physical systems. Heat dissipation and entropy production, central quantities in these laws, are often difficult to quantify precisely in experiments because the associated energy exchanges are distributed over a vast number of typically inaccessible degrees of freedom in the environment. This is especially true at microscopic scales, where the relevant energy scales are often of the order of kB T, comparable to thermal fluctuations in the environment, and can lie several orders of magnitude below the sensitivity limits of state-of-the-art room-temperature calorimetry.

Recent advances in nonequilibrium statistical physics and data-driven inference provide new approaches for addressing these challenges. In this talk, I will first introduce recent theoretical results showing how nonequilibrium fluctuations can be exploited to quantify energy dissipation at scales inaccessible to conventional calorimetry. I will then demonstrate the practical applicability of these results by quantifying energy dissipation from experimental data in real physical systems, as well as estimating free-energy differences from nonequilibrium measurements in highly dissipative regimes where conventional fluctuation-theorem-based methods fail. I will conclude by discussing the remaining challenges and open questions.

EquiNET: A new technique for estimating Equilibrium free-energy differences from Non-Equilibrium Trajectories on arXiv

EquiNET uses a graph neural network to infer entropy production from non-equilibrium molecular trajectories and uses this information to estimate equilibrium free-energy differences. (Image by S. K. Manikandan.)
Free-Energy Differences from Nonequilibrium Fluctuations in High Dissipation
Sreekanth K Manikandan and Giovanni Volpe
arXiv: 2608.23394

Equilibrium free-energy differences can be measured from nonequilibrium work fluctuations using fluctuation theorems, such as the Jarzynski equality and the Crooks fluctuation theorem. However, these approaches become statistically inefficient in high-dissipation regimes because their convergence requires trajectories with negative entropy production, events that occur exponentially rarely. Here, we demonstrate that repeated measurements of trajectory fluctuations are sufficient to determine entropy production without relying on such rare events, or to determine a lower bound on it when only partial measurements are available. This information then yields exact estimates of free-energy differences, or rigorous bounds. We validate this approach, named EquiNET, with numerical simulations, including one of biomolecular folding and unfolding, showing that it recovers accurate free-energy estimates even in regimes where conventional approaches fail.

Protein Dynamics Beyond Structure Prediction on ArXiv

Computational advances in protein folding studies. Current approaches address multiple levels of resolution and methodological frameworks, however, none of the existing methods provides quantitative and dynamic information of the relationship between protein sequence and folding mechanism at all-atom resolution and at scale. (Graphics by J. Sacquegno.)
Protein Dynamics Beyond Structure Prediction
Juliette Griffié, Sviatlana Shashkova, Antonio Ciarlo, Sreekanth K. Manikandan, Claes Andréasson, Malin Bäckström, Tristan Bereau, Hjalmar Brismar, Carlos Bustamante, Marta Carroni, Roberto Covino, Andreas Dahlin, Sebastian Deindl, Lucie Delemotte, Arne Elofsson, John Eriksson, Giovanna Fragneto, Anders Gunnarsson, Per Hammarström, Caroline Ingre, Christian Kaiser, Petronella Kettunen, Mark C. Leake, Benjamin Loos, Anna Månberg, Antonia S. J. S. Mey, Richard Neutze, Thomas Nyström, Karl Palmås, Charley Schaefer, Markus J. Tamás, Nicola Ticozzi, Tomás S. Pilvelic, Jacopo Sacquegno, B.M. (Betty)Tijms, Gunnar von Heijne, Björn Wallner, Vitali Zhaunerchyk, Simon Olsson, Joana B. Pereira, Julia Fernandez-Rodriguez, Fredrik Westerlund, Giovanni Volpe
arXiv: 2606.08647

How microorganisms respond to and interact with their environment can vary significantly from individual to individual, which can have important microbiological and ecological implications. However, most microscopy techniques can only observe motile microorganisms for short times because of their limited fields of view. Using Lagrangian tracking, a single microorganism can be followed in 3D, potentially indefinitely, allowing to decipher individual phenotypical traits. Current Lagrangian tracking methods use the fluorescence signal emitted by the microorganism as feedback to keep it in focus. However, over long times, epifluorescent imaging can induce photobleaching and photodamage, and importantly, not all microorganisms can easily be made fluorescent. Additionally, traditional algorithms used in feedback loops to determine microorganism position are prone to errors, especially in optically complex media. Here, we present a faster, more reliable, and versatile Lagrangian tracking method that uses deep learning to determine the 3D position of the microorganism. This new method demonstrates enhanced accuracy and speed in tracking fluorescent bacteria with fluorescence microscopy also in optically complex media. Furthermore, we track bacteria with other microscopy modalities, such as brightfield microscopy — for example, this enables us to track magnetotactic bacteria, which cannot be made fluorescent without degrading their magnetotactic properties. These novel capabilities allow to extract previously inaccessible quantitative information, significantly advancing the study of microorganism behavior — and thus opening new avenues for research in complex biological and ecological systems.

Poster by Sreekanth K Manikandan at the Protein Folding in Real Time conference, Stockholm, 11 March 2026

Recent advances in nonequilibrium physics allow extracting thermodynamic quantities, such as entropy production, directly from dynamical information in microscopic movies. (Figure by S. Manikandan, adapted from Manikandan et al., Phys. Rev. Research 6, 023310 (2024).)
Probing the Non-equilibrium Dynamics of Living Matter
Sreekanth K Manikandan
Date: 11 March 2026
Time: 18.00-20.00
Place: Aula Medica, Stockholm Sweden
Conference Protein Folding in Real Time, 11-13 March 2026, Stockholm, Sweden

Identifying whether a process is in equilibrium, quantifying its distance from equilibrium, and constructing optimal reduced descriptions of non-equilibrium dynamics remain central challenges in the study of living matter. Here, we discuss how data-driven approaches grounded in stochastic thermodynamics enable these features to be inferred directly from experimental data. In particular, we show how entropy production can be localized in space and time, and how maximally dissipative coordinates emerge as effective low-dimensional descriptions of non-equilibrium processes. We highlight applications to experimental biophysical systems and discuss key challenges and limitations.

Invited talk by S. K. Manikandan at The 15th Nordic Workshop on Statistical Physics, Nordita, 26 Feb 2026

Recent advances in nonequilibrium physics allow extracting thermodynamic quantities, such as entropy production, directly from dynamical information in microscopic movies. (Figure by S. Manikandan, adapted from Manikandan et al., Phys. Rev. Research 6, 023310 (2024).)
Localising Entropy Production and Maximally Dissipative Coordinates from Experimental Data
Sreekanth Manikandan
Date: 26th February 2026
Time: 14.15
Place: NORDITA, Stockholm, Sweden
The 15th Nordic Workshop on Statistical Physics: Biological, Complex and Non-equilibrium Systems

Identifying whether a process is in equilibrium, quantifying how far it lies from equilibrium, and determining optimal reduced descriptions of non-equilibrium processes remain challenging open problems. Here, we discuss how novel data-driven techniques grounded in stochastic thermodynamics can be used to efficiently learn these features directly from experimental data. In particular, we show how entropy production can be localized in space and time, and how maximally dissipative coordinates can be consistently inferred as effective low-dimensional descriptions of non-equilibrium processes. We further discuss applications to experimental biophysical systems and outline key challenges and limitations.

Photos

Sreekanth, presenting. (Photo by A. Ciarlo)

Invited lecture by A. Callegari, A. Ciarlo, and S. K. Manikandan at the Winter school on Geometry of nonequilibrium critical phenomena, Chalmers, 22-27 Feb 2026

Active Matter: Model Systems and Experimental Tests
Agnese Callegari, Antonio Ciarlo, Sreekanth Manikandan
Dates and times:
23 Feb 14:00-15:00 (Agnese)
24 Feb 11:30-12:30 (Antonio)
24 Feb 14:00-15:00 (Sreekanth)
Place: PJ
Winter school on Geometry of nonequilibrium critical phenomena

Active matter is a broad class of systems that operate intrinsically out of equilibrium. It spans multiple length scales—from macroscopic to micro- and nanoscopic—and includes both biological and artificial realizations, often displaying rich and emerging collective behaviors. The study of active matter aims to explain and interpret these phenomena using concepts and tools from physics. As such, understanding active and non-equilibrium systems requires a combination of theoretical, computational, and experimental approaches.

In the first part of the lecture, we introduce the concept of an active particle and demonstrate how it can be embodied in a macroscopic, self-propelled toy robot (a Hexbug). Despite their simplicity, such systems reproduce characteristic—and sometimes counterintuitive—features of microscopic active matter. These experiments have a strong pedagogical value and are designed to help bridge a gap in traditional physics curricula at the primary and secondary education levels.

The second part of the lecture focuses on active matter and non-equilibrium phenomena at the microscopic scale, where advanced experimental tools are essential. Optical tweezers provide precise control over microscopic systems and access to key physical observables. We introduce their operating principles and illustrate how they can be used to construct a minimal, well-controlled experimental model for studying non-equilibrium dynamics at the single-particle level.

In the final part of the lecture, we turn to the theoretical and computational tools required to analyze active matter systems. We discuss how non-equilibrium dynamics can be quantitatively characterized directly from experimental data in a model-independent framework. This naturally leads to an introduction to machine-learning–based inference techniques, which extract dynamical and thermodynamic information from data without relying on a priori assumptions about the underlying physical model.

References:
[1] A. Barona Balda, A. Argun, A. Callegari, G. Volpe. Playing with Active Matter, Am. J. Phys. 92, 847–858 (2024). https://doi.org/10.1119/5.0125111
[2] Martins, T.T., Malavazi, A.H.A., Kamizaki, L.P. et al. Fluctuation theorems with optical tweezers: theory and practice. Eur. Phys. J. Plus 141, 71 (2026). https://doi.org/10.1140/epjp/s13360-025-07181-4
[3] Manikandan, Sreekanth K. and Ghosh, T. and Mandal, T. and Biswas, A. and Sinha, B. and Mitra, D. Estimate of entropy production rate can spatiotemporally resolve the active nature of cell flickering. Phys. Rev. Res. 6, 023310 (2024). https://doi.org/10.1103/PhysRevResearch.6.023310

Photos

Antonio, presenting. (Photo by M. Orsino)
Sreekanth, presenting. (Photo by A. Ciarlo)

Presentation by S. K. Manikandan at The Arctic Meeting for Adaptive Mechanisms in Biological Systems, Abisko, Sweden, January 21, 2026

Recent advances in nonequilibrium physics allow extracting thermodynamic quantities, such as entropy production, directly from dynamical information in microscopic movies. (Figure by S. Manikandan, adapted from Manikandan et al., Phys. Rev. Research 6, 023310 (2024).)
Localizing entropy production in cellular processes
Sreekanth Manikandan
Date: 21 Jan 2026
Time: 10:00 CEST
Place: STF Abisko, Sweden
The Arctic Meeting for Adaptive Mechanisms in Biological Systems

Quantifying the spatiotemporal forces, affinities, and dissipative costs of cellular-scale non-equilibrium processes from experimental data and localizing it in space and time remain a significant open challenge. Here, I explore how principles from stochastic thermodynamics, combined with machine learning techniques, offer a promising approach to addressing this issue. I will present preliminary results from experiments on fluctuating cell membranes and simulations of non-equilibrium systems in stationary and time-dependently driven states. These studies reveal potential strategies for localizing entropy production in experimental biophysical contexts while also highlighting key challenges and limitations that must be addressed.

Invited talk by Sreekanth K. Manikandan at the online Workshop on Stochastic Thermodynamics (WOST), 14th May 2025

Recent advances in nonequilibrium physics allow extracting thermodynamic quantities, such as entropy production, directly from dynamical information in microscopic movies. (Image by S. Manikandan.)
Localizing entropy production in cellular processes
Sreekanth Manikandan
Date: 14 Mar 2025
Time: 17:30 CEST
Place: Online
Part of the Workshop on Stochastic Thermodynamics

Quantifying the spatiotemporal forces, affinities, and dissipative costs of cellular-scale non-equilibrium processes from experimental data and localizing it in space and time remain a significant open challenge. Here, I explore how principles from stochastic thermodynamics, combined with machine learning techniques, offer a promising approach to addressing this issue. I will present preliminary results from experiments on fluctuating cell membranes and simulations of non-equilibrium systems in stationary and time-dependently driven states. These studies reveal potential strategies for localizing entropy production in experimental biophysical contexts while also highlighting key challenges and limitations that must be addressed.

Invited talk by S. Manikandan at the 14th Nordic Workshop on Statistical Physics, Nordita, 5 March 2025

Recent advances in nonequilibrium physics allow extracting thermodynamic quantities, such as entropy production, directly from dynamical information in microscopic movies. (Image by S. Manikandan.)
Localizing entropy production in non-equilibrium processes
Sreekanth Manikandan
Date: 5 Mar 2025
Time: 14:45
Place: Nordita
Part of the 14th Nordic Workshop on Statistical Physics

Quantifying the spatiotemporal forces, affinities, and dissipative costs of cellular-scale non-equilibrium processes from experimental data and localizing it in space and time remain a significant open challenge. Here, I explore how principles from stochastic thermodynamics, combined with machine learning techniques, offer a promising approach to addressing this issue. I will present preliminary results from experiments on fluctuating cell membranes and simulations of non-equilibrium systems in stationary and time-dependently driven states. These studies reveal potential strategies for localizing entropy production in experimental biophysical contexts while also highlighting key challenges and limitations that must be addressed.