13th Nordic Workshop on Statistical Physics: Biological, Complex and Non-Equilibrium Systems

13 Mar 2024, 09:00 → 15 Mar 2024, 19:00 Europe/Stockholm

Albano Building 3

Alberto Imparato (Department of Physics and Astronomy University of Aarhus), Ralf Eichhorn (Stockholm University, Nordita)

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Venue

Nordita, Stockholm, Sweden

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Scope

This workshop series provides a “forum” where scientists in the Nordic countries working in the area of Statistical Physics can meet regularly. The meeting brings together experts interested in the broad spectrum of timely problems in Statistical Physics, ranging from fundamental aspects in the theory of non-equilibrium processes to modern applications in biophysics. Topics covered include diffusion problems, non-equilibrium transport, work relations and fluctuation theorems, microscopic heat engines, soft condensed matter (colloids, liquid crystals etc.), turbulence, pattern formation, self-assembly, population dynamics, physics of DNA and bio-molecules, single-molecule kinetics, dynamics and structure of networks, neuronal networks, quantum thermodynamics and many more.

The workshop will start on Wednesday morning at around 9.00 with registration and coffee/cake. It will end on Friday (early) afternoon. There will be a conference dinner on Thursday evening.

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Invited speakers

Dick Bedeaux (Norwegian University of Science and Technology)	Namiko Mitarai (Niels Bohr Institute)
Francesco Coghi (Nordita)	Karel Proesmans (Niels Bohr Academy)
Kristian Gustavsson (Gothenburg University)	Joakim Stenhammar (Lund University)
Mogens Hogh Jensen (Niels Bohr Institute)	Yu Tian (Nordita)
Signe Kjelstrup (Norwegian University of Science and Technology)	Giovanni Volpe (Gothenburg University)
Supriya Krishnamurthy (Stockholm University)	Astrid de Wijn (Norwegian University of Science and Technology)
Sreenath Manikandan (Nordita)	Niccolo Zagli (Nordita)

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Special Guest

Edgar Roldán (ICTP Trieste)

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Registration

If you want to participate in the workshop, please fill in the registration form (registration opening date to be announced).

Registration deadline: Feb 29, 2024

There is no registration fee.

There is a (very) limited number of travel grants available for PhD students and young Postdoc fellows from the Nordic countries. If you are interested in such a grant, please contact the organizers via email, and provide a rough estimate of your expenses (travel and/or accommodation).

For administrative reasons you have to register before February 10, if you want to apply for such a travel grant.

Depending on interest and time constraints we might set up a session dedicated to short talks by junior researchers (PhD students, young Postdocs). During registration you have the possibility to indicate if you are interested in contributing such a short talk (likely around 5-10 min).

 

Please be aware that scammers sometimes approach participants claiming to be able to provide accommodation and asking for credit card details. Do not give this information to them! If you are in any doubt about the legitimacy of an approach, please get in contact with the organizers.

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Sponsored by:

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Wednesday, 13 March

09:00 Registration and breakfast

1 Opening

Speakers: Alberto Imparato (Department of Physics and Astronomy University of Aarhus), Ralf Eichhorn (Stockholm University, Nordita)

2 Finite-Time Lyapunov Exponents of Deep Neural Networks

Deep neural networks have recently led to breakthroughs in various fields, ranging from image recognition and natural language processing to autonomous driving and medical diagnosis. Despite these achievements, a comprehensive understanding of their learning process is still lacking. We use parallels with dynamical systems to investigate how small perturbations to the input affect the output of deep neural networks. The growth or decay of the perturbations are characterized by finite-time Lyapunov exponents. We show that the maximal exponent forms geometrical structures in input space, akin to coherent structures in dynamical systems. These ridges visualize the geometry that deep networks construct in input space, shedding light on the fundamental mechanisms underlying their learning process.

Speaker: Kristian Gustavsson (Gothenburg University)

3 Quantifying resilience and modes of variability of chaotic systems through operator theory

Complex chaotic systems exhibit a non trivial internal variability with a power spectrum typically characterised by resonant broad peaks standing out on a continuous background of frequencies. These resonances correspond to nonlinear excitable modes of the evolution of the system that can be generally attributed to long lasting persistent events, weakly damped instabilities or to critical settings where the chaotic attractor is approaching a crisis. Such nonlinear oscillations manifest themselves as a decaying oscillatory behaviour in correlation functions of suitable observables of the system.

Ergodic theory provides a link between these nonlinear modes of the system and the spectral properties of operators underlying the evolution of statistical properties of the system. In this talk, I will show that data-driven techniques developed to investigate the properties of the Koopman operator describing the evolution in time of observables of the systems allow to capture such resonances from data. The resonances are evaluated as the eigenvalues of the Koopman operator whereas the nonlinear modes are represented by their relative eigenfunction.

I will provide numerical evidence that the dynamical evolution of the statistical properties of the system can be interpreted as a superposition of such modes. In particular, by employing a projection of observables onto the set of nonlinear modes (i.e. Koopman eigenfunctions), we show that we are able to reconstruct not only correlation functions but also the response of virtually any observable of interest. Even though so far restricted to low dimensional systems, this analysis highlights the importance of such nonlinear modes in shaping the variability and response of chaotic systems and provides a way to (a) interpret the relevance of observables as a proxy to investigating dynamical properties of the system and (b) explain the difference between intrinsic variability of observables and their response to perturbations.

Speaker: Niccolò Zagli (Stockholm University, Nordita)

4 Characterising dynamical phase transitions via large deviations

I will describe dynamical phase transitions as transitions occurring within the temporal fluctuations of time-additive observables in stochastic systems. These transitions manifest when a critical time scale within the system diverges, resulting in non-analytical behaviour in the large deviation function, akin to the role of free energy, of the specific observable studied. This critical time scale is pivotal in observing the system's relaxation towards stationarity and showcases the ergodicity of the system at criticality. Additionally, in cases where the dynamical phase transition is of the first order, I will show, particularly with random walks on graphs, that the critical behaviour of the system oscillates intermittently between phases, with the waiting time to transition from one phase to another serving as the key diverging time scale.

Speaker: Francesco Coghi (Stockholm University, Nordita)

12:30 Lunch

5 Thermodynamics at small scales

It is well established that fluids under confinement have thermodynamic properties that differ from those in their bulk phase. We may therefore ask; Does normal thermodynamic equations apply at small scales? Much effort has been devoted to answer this question; and extensions of Gibbs surface theories are popular. A more systematic extension of classical thermodynamics to deal with small systems exists, however. It was first proposed by Hill 60 years ago. This theory can deal with shape and size-as variables, and systems down to a few particles!

In this lecture, I will argue that Hill’s theory deserves more attention; it opens up a wide range of applications. This is important because the shape and size dependence is everywhere in porous media. To be able to connect small system properties with properties of systems in their thermodynamic limit is essential, for instance in the description of solutions. Some first successes in this context can be reported, e.g. in the determination of Kirkwood-Buff integrals. These integrals are central in solution theory.

Precise simulations of thermodynamic factors, activity coefficients, are now being explored for use in porous media. Recently, we used Hill’s theory to define the porous-medium pressure, a concept lacking consensus in the literature. By introducing the so-called integral pressure from the grand potential, we may deal with two-phase transport in pores, without needing the laws of Young and Young- Laplace. Local equilibrium can then be defined for a representative volume element without exploding the number of variables. The entropy production can be constructed, and Darcy’s law can be given a thermodynamic basis.

Recent achievements in small system thermodynamics may open up new
routes to understand confinement and microfluidics.

Acknowledgements
The author is grateful to the Research Council of Norway Center of Excellence Funding Sche for project no 262644 PoreLab.

Speaker: Signe Kjelstrup (Norwegian University of Science and Technology)

6 On how to measure the Subdivision Potential in Nanothermodynamics

We discuss a central concept of nanothermdynamics; the subdivision potential. We explain how it can be measured or calculated for some typical ensembles, as this has been disputed in the literature. We proceed to discuss its meaning for particular systems, and predict scaling laws for three ensembles. The laws depend on the small system geometry in a predictable way for an ideal gas model with surface adsorption. We provide new equations which relate the subdivision potential to experimental investigations, and give expressions for grand canonical ensembles of spheres, cylinders, slit pores and fluids confined in porous media. The subdivision potential is not compatible with the popular Hadwiger theorem in geometry, and can therefore not be described by a Minkowski set of variables. It is equivalent to Gibbs descriptions when shape- and size variables are defined.

Speaker: Dick Bedeaux (Norwegian University of Science and Technology)

15:30 Coffee break

7 Inferring entropy production of time-dependent systems

In this talk, I will discuss a method to infer entropy production of systems with time-dependent driving. In particular, we derive a lower bound on the entropy production entirely in terms of its first two time-dependent moments. We test the bound on experimental bit erasure and show that it works remarkably well, even with a very low amount of data.

Speaker: Karel Proesmans (Niels Bohr Academy)

8 Thermodynamic costs for resetting processes

Stochastic systems that undergo random restarts to their initial state have been widely investigated in recent years, both theoretically and in experiments. But the thermodynamic costs for implementing such resets has been less well studied. In this talk I will present some of the work done on this topic including our own recent results on the thermodynamic costs that a resetting entails for some variations of the resetting process, one of which has also been recently investigated in experiments.

Speaker: Supriya Krishnamurthy (Stockholm University)

Thursday, 14 March

9 Nanoscale friction and surfaces of polymers

Nanoscale structure and mechanisms of viscoelastic deformation and plasticity in polymers are complex, and have significant impact on their mechanical properties in the bulk, but also on surfaces. We use molecular-dynamics simulations to study the relation between viscoelasticity, plasticity, and surface mechanical properties and tribology of a semi-crystalline polymer, polyvinyl alcohol (PVA).

We subject a simulated PVA surface to external forces, including an Atomic Force Microscope tip, with and without a graphene sheet, and bi-axial compression. We investigate the plastic and elastic deformation during sliding, and how they relate to the structure and temperature. We also study the nanoscale mechanisms of formation of surface roughness in polymers.

Nanoscale Simulations of Wear and Viscoelasticity of a Semi-Crystalline Polymer,
R. Vacher and Astrid S. de Wijn
Tribology Letters 69, 1-12 (2021).

Nanoscale friction and wear of a polymer coated with graphene
Robin Vacher and Astrid S. de Wijn
Beilstein J. Nanotechnol. 2022, 13, 63–73. doi:10.3762/bjnano.13.4.

Molecular-Dynamics Simulations of the Emergence of Surface Roughness in a Polymer under Compression
Robin Vacher and Astrid S. de Wijn
Materials 2021, 14(23), 7327.

Speaker: Astrid de Wijn (Norwegian University of Science and Technology)

10 Osmotic stability and thermal fluctuations of unilamellar vesicles

The bending energy of the lipid membrane is central to all biological processes involving lipid vesicles, such as endocytosis and exocytosis. Since most biological systems sustain significant concentration gradients, osmotic pressure differences are potentially key players in biological membrane remodeling processes. In a recent paper [Liu et al., J. Phys. Chem. Lett., 13, 498], we demonstrated using single-component giant unilamellar vesicles (GUVs) that the bending energy stored in a GUV can sustain significant external osmotic stresses coming from concentration imbalances between the regions interior and exterior to the vesicle. For sufficient osmotic gradients (>0.15 atm) the vesicles globally deform into a prolate shape, and upon osmotic reversal the collapsed vesicles release the bending energy by forming monodisperse “daughter vesicles” through an endocytosis-like process. The observed deformation is in qualitative accordance with the traditional theoretical picture based on a continuum elasticity description of the membrane. However, the measured osmotic pressure needed for destabilization of the spherical vesicle is about 6 orders of magnitude higher than predicted by theory. In this talk, I will discuss the possible theoretical causes and practical implications of this large discrepancy, and present recent theoretical efforts in describing the effect of thermal vesicle fluctuations on the shape and stability of GUVs. I will also discuss the implications of a coupling between membrane bending and stretching for the stability of small unilamellar vesicles (SUVs) and its implications for “curvature sensing” in biological systems.

Speaker: Joakim Stenhammar (Lund University)

11 Condensate Phase Transitions, DNA Repair and Genetic Resonance in Cell Dynamics

When cells are damaged or stressed they respond by oscillating protein densities as have been observed for two famous proteins/transcription factors p53 and NF-kB [1]. The oscillations have a period of 3-5 hours and appear in both healthy and sick cells. p53 is a cancer gene while NF-kB plays a role in diabetes. For p53 we show that phase transitions lead to condensates of repair proteins around damage sites which occur in an oscillating fashion thus preventing Oswald ripening. The period of oscillations provides an optimal time scale for the repair mechanism [2]. By applying an external periodic protein signal, the internal oscillation can lock to the external signal and thus controls the genes. The locking occurs when the ratio between the two frequencies is a rational number leading to Arnold tongues [1]. If tongues overlap, chaotic dynamics appear which strongly influence gene production. When oscillations are not sustained we can excite oscillations at a certain frequency leading to genetic resonance. Our findings are in good agreement with experimental data from our collaborative groups at Harvard Medical, Beijing and Taiwan.

[1] M.L. Heltberg, S. Krishna, L.P. Kadanoff and M.H. Jensen, "A tale of two rhythms: Locked clocks and chaos in biology (Review)", Cell Systems, 12, 291-303 (2021).
[2] M.S. Heltberg, A. Lucchetti, F.-S. Hsieh, D.P.M. Nguyen, S.-h.Chen and Mogens H. Jensen, "Enhanced DNA repair through droplet formation and p53 oscillations", Cell 185, 4394–4408 (2022).

Speaker: Mogens Høgh Jensen (Niels Bohr Institute)

12:00 Lunch

12 Martingales for physicists

The theory of martingales played a key role in the development of probability theory and stochastic processes. For instance, it allowed to prove convergence theorems generalizing the central limit theorems, that are central also in physics. Furthermore, martingales played a key role in quantitative finance, setting the fundamental theorems of finance that rationalize Black-Scholes model for financial markets. In nonequilibrium statistical physics, the usage of martingales is quite recent yet insightful to establish new universal thermodynamic principles. In this talk, I will review pioneering efforts in developing a "martingale thermodynamics theory" to tackle nonequilibrium fluctuations of small systems. In particular, I will explain how this theory is fruitful in providing extreme-value and stopping-time statistics for entropy production, and sketch some experimental verifications. I will also overview how can one use clever stopping (e.g. first passage) strategies to overcome classical limits such as Carnot efficiency at the expense of efficient, yet still unorthodox, information processing schemes.

[1] Martingales for physicists: A treatise on stochastic thermodynamics and beyond, E Roldan, I Neri, R Chetrite, S Gupta, S Pigolotti, F Jülicher, K Sekimoto, arXiv:2210.09983 (2022) ; Advances in Physics - in press (2024)

Speaker: Edgar Roldán (ICTP Trieste)

14:30 Coffee break

13 Universality in annihilation reactions with constrained dynamics

Speaker: Enrique Rozas Garcia (Gothenburg University)

14 Emergent counter-current swimming of zooplankton

Speaker: Navid Mousavi (Gothenburg University)

15 Effect of Cysteine Oxidation in SARS-CoV‑2 Receptor-Binding domain on its function

Speaker: Maryam Ghasemitarei (Aalto University)

16 Active Reorganisation in Tissues

Speaker: Harish Pruthviraj Jain (University of Oslo)

17 Nonergodic Brownian oscillator: Nonequilibrium stationary state and quasi-resonance response

Speaker: Alexander Plyukhin (Saint Anselm College)

16:15 Coffee break

18 Selecting and sustaining oligomer sequences through phase separation

Speaker: Ivar Haugerud (Universität Augsburg)

19 Effect of salt on polyelectrolyte interactions and electrophoretic mobility

Speaker: Hossein Vahid Dastjerdi (Aalto University)

20 Challenges in the first order phase transitions kinetics

Speaker: Viktor Kurasov (Stockholm University)

21 Synthetic DNA Barcodes by Optical DNA Mapping

Speaker: Dibyajyoti Mohanta (Lund University)

19:00 Conference Dinner

Friday, 15 March

22 Microbial competition in an expanding colony

When a bacterial population expands by growth, access to new territory and nutrients at the expanding front becomes the determinant of the competition. In (quasi) two-dimensional (2D) range expansion, bacterial populations spread across flat surfaces. When fluorescently labelled bacteria of different colours are inoculated, random fluctuations lead to the formation of distinct sectors even without differences in their fitnesses, and the sectors at the front coarsen as the population expands [1]. This range expansion setup provides a flexible framework to test the microbial competition in a structured environment.

We present how a mixture of bacteria E. coli and temperate phage λ form a pattern [2]. When λ phages infect an E. coli cell, it can choose either the lytic cycle to kill the cell and produce several progeny phages or the lysogeny, where the lambda phage integrates its genome to E. coli genome, provide immunity to further infection by λ phage and replicate its genome as E. coli replicates. We use a lattice model to study what is necessary to produce the experimentally observed pattern and how the infection can keep up with the expanding front. Especially we find that mechanical pushing due to growing cells inside the colony is a necessary factor to consider.

We then briefly present our recent work, demonstrating that elongated cells always take over the range expansion when competing against round cells, even if they start as a minority [3]. Numerical simulation and single-cell observation show that the collective nematic ordering of elongated cells by mechanical interaction is the key to the takeover mechanism: Groups of locally aligned bacteria form "nematic arms", bridging the central region of the colony to the expanding front. Once at the front, bacteria align parallel to it and block shorter bacteria from accessing nutrients and space. Overall, our results illustrate the importance of mechanical interactions in microbial competition in expanding colonies.

[1] O. Hallatschek, P. Hersen, S. Ramanathan, DR Nelson. Genetic drift at expanding frontiers promotes gene segregation. Proc. Nat. Acad. Sci. 2007, 104(50):19926-30.

[2] Stephenson, G., Nadig, A., Parmar, T., Krishnamurthy, V., Mitarai, N., Krishna, S. and Thutupalli, S., 2022. Co-existence and extinction due to surfing viral infections in a spatially expanding bacterial colony. In APS March Meeting Abstracts (Vol. 2022, pp. T05-007).

[3] N. van den Berg, K. Thijssen, T. T. Nguyen, A. Sarlet, M. Cordero, A. G. Vázquez, N. Mitarai, A. Doostmohammadi, L. Jauffred. Emergent collective alignment gives competitive advantage to longer cells during range expansion. BioRxiv: 2024.01.26.577059; doi: https://doi.org/10.1101/2024.01.26.577059

Speaker: Namiko Mitarai (Niels Bohr Institute)

23 More than Positive Weights: Structural Balance and Random Walks

Two competing types of interactions often play an important part in shaping system behaviour, such as activatory or inhibitory functions in biological systems. Hence, signed networks, where each connection can be either positive or negative, have become popular models over recent years. However, the primary focus of the literature is on the unweighted and structurally balanced ones, where all cycles have an even number of negative edges. Hence here, we first introduce a classification of signed networks into balanced, antibalanced or strictly balanced ones, and illustrate the shared spectral properties within each type. We then apply the results to characterise the dynamics of random walks on signed networks, where local consensus can be achieved asymptotically when the graph is structurally balanced, while global consensus will be obtained when it is strictly unbalanced. Finally, we will show that the results can be generalised to networks with complex-valued weights.

Speaker: Yu Tian (Stockholm University, Nordita)

11:00 Coffee break

24 The 2nd Anomalous Diffusion Challenge

The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the particle trajectories. Despite the existence of multiple approaches to carry out this type of analysis, no objective assessment of these methods has been performed so far. Here, we have designed a competition to characterize and rank the performance of these methods when analyzing the dynamic behavior of single molecules. To run this competition (accepted in principle in Nature Communications, https://springernature.figshare.com/articles/journal_contribution/Quantitative_evaluation_of_methods_to_analyze_motion_changes_in_single-particle_experiments_Registered_Report_Stage_1_Protocol_/24771687 ), we have implemented a software library to simulate realistic data corresponding to widespread diffusion and interaction models, both in the form of trajectories and videos obtained in typical experimental conditions. The competition will constitute the first assessment of these methods, provide insights into the current limits of the field, foster the development of new approaches, and guide researchers to identify optimal tools for analyzing their experiments.

Speaker: Giovanni Volpe (Gothenburg University)

25 Continuous quantum measurements: from fundamentals to time-keeping, cooling, and quantum sensing applications

Quantum measurement is an inherently probabilistic process. Given this stochastic nature of quantum measurements, principles of stochastic thermodynamics can greatly help to understand and characterize the dynamics of a quantum system subject to continuous quantum measurements. I will discuss methods to characterize the irreversibility of quantum measurements from a thermodynamic perspective, by associating a statistical arrow of time for individual realizations of the quantum measurement process. I will show that continuous quantum measurements are absolutely irreversible---similar to the free expansion of a single gas molecule in a box---and I will discuss a cold atom experiment which demonstrates this. I will conclude the talk by presenting some of our recent results: (1) a quantum clock realization where quantum spin and fluorescence measurements are used to fuel the ticks of an autonomous quantum clock, (2) simultaneous measurements of position and momentum of a mechanical oscillator are used for optimal quantum parametric feedback cooling, and (3) time-continuous energy measurements of massive acoustic bar resonators are used for table-top tests of gravity in the quantum regime.

Speaker: Sreenath Kizhakkumpurath Manikandan (Stockholm University, Nordita)

13:00 Lunch

26 Self-orgnized discussions/Closing