12th Nordic Workshop on Statistical Physics: Biological, Complex and Non-Equilibrium Systems

15 Mar 2023, 09:00 → 17 Mar 2023, 19:00 Europe/Stockholm

Albano Building 3

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

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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 (* to be confirmed)

Cristobal Arratia (Nordita) Luiza Angheluta-Bauer (University of Oslo) Amin Doostmohammadi (Niels Bohr Institute) Heiner Linke (Lund University) Michael A Lomholt (University of Southern Denmark) Sreenath Manikandan (Nordita) Bernhard Mehlig (Gothenburg University) Namiko Mitarai (Niels Bohr Institute)

Kristian Stølevik Olsen (Nordita) Jukka Pekola (Aalto University) Karel Proesmans (Niels Bohr International Academy) Maria Sammalkorpi (Aalto University) Francesca Serra (University of Southern Denmark) Joakim Stenhammar (Lund University) Giovanni Volpe (Gothenburg University) Astrid de Wijn (Norwegian University of Science and Technology)

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Special Guest

Bart Cleuren (Hasselt Universiy)

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Registration

If you want to participate in the workshop, please fill in the registration form.

Registration deadline: 28 February, 2023

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.

 

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 15 March

09:00 Registration with Coffee/Tea and Cake

1 Welcome

Speaker: Niels Obers (Niels Bohr Institute)

2 Opening

Speaker: Ralf Eichhorn (Nordita)

3 Fundamental energy cost of finite-time, parallel computing

The fundamental energy cost of irreversible computing is given by the Landauer bound of kTln2/bit. However, this limit is only achievable for infinite-time processes. We here determine the fundamental energy cost of finite-time parallelizable computing within the framework of nonequilibrium thermodynamics. We apply these results to quantify the energetic advantage of parallel computing over serial computing. We find that the energy cost per operation of a parallel computer can be kept close to the Landauer limit even for large problem sizes, whereas that of a serial computer fundamentally diverges. We further discuss their implications in the context of current technology, including massively parallel, network-based biocomputers. Our findings provide a physical basis for the design of energy-efficient computers.

Konopik, M., Korten, T., Lutz, E. et al. Fundamental energy cost of finite-time parallelizable computing. Nat Commun 14, 447 (2023). 
https://doi.org/10.1038/s41467-023-36020-2

Speaker: Heiner Linke (Lund University)

4 The thermodynamic cost of controlling non-equilibrium systems

In this talk, I will introduce a general framework to determine optimal protocols to drive non-equilibrium systems. Utilizing non-equilibrium fluctuation-response relationships, I will demonstrate how to design protocols that transition systems from an initial to a final state with minimal dissipated work. The focus will be on two specific cases: active particle systems experiencing motility-induced phase separation and chemical reaction networks undergoing non-equilibrium phase transitions.

Speaker: Karel Proesmans (Niels Bohr International Academy)

5 Stochastic resetting to a distribution: non-equilibrium steady-states and entropy production

Stochastic resetting, whereby a system is reset to its initial state at random times, has been shown to be of relevance to wide range of natural or man-made systems. One of the key features of systems with resetting is the emergence of non-equilibrium steady states (NESS), which originate in the intermittent interruption of the relaxation process of the underlying dynamics. Here we characterize the NESS of Brownian particles moving in external potentials with resetting to a position drawn from a distribution. Being out of equilibrium, the system continuously produces entropy. Using methods from stochastic thermodynamics we calculate the first few moments of the entropy production and discuss associated optimization problems.

Speaker: Kristian Olsen (Stockholm University)

12:30 Lunch

6 An Anomalous Competition: Assessment of methods for anomalous diffusion through a community effort

Deviations from the law of Brownian motion, typically referred to as anomalous diffusion, are ubiquitous in science and associated with non-equilibrium phenomena, flows of energy and information, and transport in living systems. In the last years, the booming of machine learning has boosted the development of new methods to detect and characterize anomalous diffusion from individual trajectories, going beyond classical calculations based on the mean squared displacement. We thus designed the AnDi challenge, an open community effort to objectively assess the performance of conventional and novel methods. We developed a python library for generating simulated datasets according to the most popular theoretical models of diffusion. We evaluated 16 methods over 3 different tasks and 3 different dimensions, involving anomalous exponent inference, model classification, and trajectory segmentation. Our analysis provides the first assessment of methods for anomalous diffusion in a variety of realistic conditions of trajectory length and noise. Furthermore, we compared the prediction provided by these methods for several experimental datasets. The results of this study further highlight the role that anomalous diffusion has in defining the biological function while revealing insight into the current state of the field and providing a benchmark for future developers.

Speaker: Giovanni Volpe (Gothenburg University)

7 Bayesian inference and single particle tracking inference competitions

Recently, a competition (the AnDi challenge) was held where different research groups competed about analysing synthetic single particle tracking data from anomalous diffusion models, with the aim of inferring the model and anomalous exponent which was used to generate the data. In this talk, I will argue how this task is in principle solved optimally by Bayesian inference, but with the downside being computational efficiency for models with hidden variables.

Speaker: Michael A Lomholt (University of Southern Denmark)

15:30 Coffee break

8 Living cells as liquid crystals and the role of topological defects

Many types of cells are elongated, spindle-like objects and tend to align with their neighbors. This behavior resembles that of nematic liquid crystals, complex fluids with long-range orientational order. Cells also tend to form disordered regions similar to liquid crystal topological defects. There is increasing evidence that defects in living systems have a biological role, being related to morphogenesis and cell extrusion. In our lab, we aim to induce and control defects and their topological charge by growing cells on micro-patterned ridges. Our findings indicate that fibroblast cells accumulate near defects with +1 topological charge and deplete near defects with -1 topological charge. We try and explain this behavior in terms of collective motion, cell shape and division rate.

Speaker: Francesca Serra (University of Southern Denmark)

9 Flow patterns and dynamics of topological defects in active fluids

In the realm of biological systems, active fluids are instantiated across scales from mixtures of cytoskeletal filaments and motor proteins to bacterial suspensions and migrating epithelial cell tissues. Local alignment interactions and anisotropic shapes of active constitutes induce large-scale structural order which is locally teared by active stress forming topological defects. Topological defects are localised sources of spontaneous flow which distort the order, and this feedback between structural distortions and spontaneous flows sustains active turbulence and large-scale properties of active fluids.

In this talk, I will present theoretical considerations on the spontaneous flow patterns and kinematics of topological defects across representative two-dimensional active fluids with discrete rotational symmetries, e.g. active nematics,  active polar systems and confluent cell tissues. For the hydrodynamics of polar and/or nematic fluids, we derive the kinematics of the topological defects and show how defects can acquire self-propulsion due to activity through dipolar or polar forces as well as activity gradients. Flow incompressibility plays an important role in guiding the motion of defects. For confluent tissues, the T1 transitions, i.e local topological rearrangements of adjacent cell neighbors, are sources of local flow propagating to the tissue scale through chaining of T1 transitions.

Speaker: Luiza Angheluta-Bauer (University of Oslo)

Thursday 16 March

10 Stochastic thermodynamics of measurement driven quantum systems: engines and refrigerators

Quantum measurements are inherently probabilistic, with the fluctuations associated to quantum information acquisition in the measurement problem. The measurement induced fluctuations, however, can be rectified to produce non-zero work even at zero temperature, in contrast to their classical counter part. In this talk, I will first present a fluctuation theorem which characterizes the measurement process in simple quantum systems. The fluctuation theorem demonstrates that quantum measurement is an absolutely irreversible process (analogous to the free expansion of a single gas particle in a box), where the degree of absolute irreversibility is deeply connected to the many-to-one mapping aspect of the quantum measurement problem. I will conclude by presenting some recent examples of quantum measurement fueled engines and refrigerators, and discussing the fundamental limits quantum measurement added noise impose on the parametric feedback cooling of a quantum oscillator.

Manikandan, Sreenath K., Cyril Elouard, Kater W. Murch, Alexia Auffèves, and Andrew N. Jordan. "Efficiently fueling a quantum engine with incompatible measurements." Physical Review E 105, no. 4 (2022): 044137.
Manikandan, Sreenath K., and Sofia Qvarfort. "Cooling through parametric modulations and phase-preserving quantum measurements." arXiv preprint arXiv:2204.00476 (2022).
Manikandan, Sreenath K., Cyril Elouard, and Andrew N. Jordan. "Fluctuation theorems for continuous quantum measurements and absolute irreversibility." Physical Review A 99, no. 2 (2019): 022117.
Jayaseelan, Maitreyi, Sreenath K Manikandan, Andrew N. Jordan, and Nicholas P. Bigelow. "Quantum measurement arrow of time and fluctuation relations for measuring spin of ultracold atoms." Nature communications 12, no. 1 (2021): 1-7.
Yanik, Kagan, Bibek Bhandari, Sreenath K. Manikandan, and Andrew N. Jordan. "Thermodynamics of quantum measurement and Maxwell's demon's arrow of time." Physical Review A 106, no. 4 (2022): 042221.

Speaker: Sreenath Kizhakkumpurath Manikandan (Stockholm University)

11 Calorimetric measurements in superconducting quantum circuits

I present some recent experiments of detecting either extremely small heat currents or single quanta in the microwave regime using a nanocalorimeter. In these experiments systems are, in the first case in non-equilibrium steady state, and in the second case subject to stochastic time-local heat pulses. I will discuss the theoretical background of these experiments, their ultimate resolution, and the grand challenges in future work.

Speaker: Jukka Pekola (Aalto University)

12 A quantum thermodynamics approach to optimization in classical complex systems

An optimization problem can be translated into physics language as the quest for the energy minimum of a classical complex system with a Hamiltonian that encodes the problem itself. Stretching the analogy further, the optimization problem can be seen as the controlled cooling of such a complex system so as it lands in a minimum of its energy landscape corresponding to the optimal solution of the given problem.

I will discuss how an energy minimization problem can be efficiently tackled by employing a non-Markovian quantum bath prepared in a low energy state.  The energy minimization problem is thus turned into a thermodynamic cooling protocol where we repeatedly put the system of interest in contact with a colder auxiliary system.

Speaker: Alberto Imparato (Department of Physics and Astronomy University of Aarhus)

12:30 Lunch

13 Stresses around topological defects

Speaker: Lasse Bonn (NBI)

14 Active nematic vs polar unjamming

Speaker: Varun Venkatesh (NBI)

15 Experimental mechanobiology meets morphogenesis

Speaker: Nigar Abbasova (University of Oslo)

16 Passive and active Phase-Field-Crystal Models for colloidal mixtures

Speaker: Max Holl (Aalto University)

17 Estimating entropy production from moments

Speaker: Prashant Singh (NBI)

18 Wrinkling of soft composite sheets

Speaker: Anthony Bonfils (Stockholm University)

15:00 Coffee break

19 Who sleeps and when? Bacterial growth, dormancy, and persistence

Some bacteria can divide as fast as every 20 minutes in a good condition, while when the condition becomes too severe, the cells can enter dormancy where the division stops. The cells may tolerate the non-growing condition for days, and restart the growth when the environment improves again. Interestingly, very often, even if the environment allows the growth of the cells, a subpopulation of them may stay/become dormant. A dormant sub-population appears useless at the first sight, but those cells are often more tolerant to stresses lethal to growing cells, such as antibiotics. In this talk, we discuss a mathematical model to describe bacterial dormancy and analyze the optimal strategy for the bacteria population under the feast-famine cycle with a stochastic application of antibiotics.

Speaker: Namiko Mitarai (Niels Bohr Institute)

20 An overview of instability and transition to turbulence in plane shear flows

Explaining transition to turbulence in shear flows is a long-standing challenge that can be traced back to classical experiments by Reynolds in 1883. The most common and challenging case occurs in the absence of linear instabilities, for which there is no obvious way to build a perturbative approach to describe the initial departure from the laminar profile. In this talk, we will provide an overview of insights developed on this problem during the last few decades through a variety of methodological approaches. These range from the study of the linearized dynamics in small periodic domains, to the characterization and modelling of the interaction between distinct regions of laminar and turbulent flow in extended domains.

Speaker: Cristobal Arratia (Stockholm University)

21 Droplet evaporation at the cloud edge

The distribution of liquid water in ice-free clouds determines their radiative properties, a significant source of uncertainty in weather and climate models. Evaporation and turbulent mixing cause a cloud to display large variations in droplet-number density, but quite small variations in droplet size [Beals et al. (2015)]. Yet direct numerical simulations of the joint effect of evaporation and mixing near the cloud edge predict quite different behaviors, and it remains an open question how to reconcile these results with the experimental findings. To infer the history of mixing and evaporation from observational snapshots of droplets in clouds is challenging because clouds are transient systems. We formulated a statistical model that provides a reliable description of the evaporation-mixing process as seen in direct numerical simulations, and allows to infer important aspects of the history of observed droplet populations, highlighting the key mechanisms at work, and explaining the differences between observations and simulations.

Speaker: Bernhard Mehlig (University of Gothenburg)

20:30 Conference dinner

Friday 17 March

22 Active Matter: Flow, Topology, and Control

The spontaneous emergence of collective flows is a generic property of active fluids and often leads to chaotic flow patterns characterized by swirls, jets, and topological disclinations in their orientation field [1]. I will first discuss two examples of these collective features helping us understand biological processes: (i) to explain the tortoise & hare story in bacterial competition: how motility of Pseudomonas aeruginosa bacteria leads to a slower invasion of bacteria colonies, which are individually faster [2], and (ii) how self-propelled defects lead to finding an unanticipated mechanism for cell death [3,4].
I will then discuss various strategies to tame, otherwise chaotic, active flows, showing how hydrodynamic screening of active flows can act as a robust way of controlling and guiding active particles into dynamically ordered coherent structures [5]. I will also explain how combining hydrodynamics with topological constraints can lead to further control of exotic morphologies of active shells [6].

[1] A. Amiri, R. Mueller, and A. Doostmohammadi, J. Phys. A. (2021).
[2] O. J. Meacock et al., Nat. Phys. (2021).
[3] T. N. Saw et al., Nature. (2017).
[4] R. Mueller, J. M. Yeomans, and A. Doostmohammadi, Phys. Rev. Lett. (2019).
[5] A. Doostmohammadi et al., Nat. Comm. (2018).
[6] L. Metselaar, J. M. Yeomans, and A. Doostmohammadi, Phys. Rev. Lett. (2019).

Speaker: Amin Doostmohammadi (Niels Bohr Institute)

23 Collective (hydro)dynamics of bacterial suspensions

Due to their nonequilibrium character, the collective dynamics of swimming microorganisms systems is often dictated by long-ranged hydrodynamic interactions. One example is the collective motion of swimming, rear-actuated (“pusher”) bacteria that interact through their long-ranged dipolar flow fields to create a state of so-called “active turbulence” with chaotic, collective swimming with long-ranged correlations. This behaviour is in contrast to the behaviour of front-actuated (“puller”) organisms such as certain algae, that do not exhibit any collective motion in 3 dimensions. In this talk, I will summarize theoretical and computational results that provide new information about the transition to active turbulence in both unbounded and confined systems. Our results reveal a qualitatively different behaviour of microswimmers in quasi-2D confinement compared to the unbounded case, where the long-ranged instability leading to active turbulence in 3D is instead rendered short-ranged. Additionally, we find a previously uncharted density instability of confined puller microswimmers, which has no counterpart in unbounded systems. Our results thus highlight that the details of the experimental geometry is crucial for collective phenomena in active matter dominated by hydrodynamic interactions.

Speaker: Joakim Stenhammar (Lund University)

11:00 Coffee break

24 Lessons learned from modelling reverse micelles, emulsions, and surfactant adsorption from oils

In contrast to aqueous solutions, the self-assembly of amphiphilic surfactants in organic, apolar solvents remains relatively poorly understood. For example, the nature of critical micellization concentration (CMC), or whether small amounts of apolar solvent, such as water, are needed for assembly, remain under debate. Even more curious is the response of surfactant aggregates in oils in electric field: reverse micelles carry charge, but mechanisms remain open. Regardless, oil-based colloidal systems self-assembly and non-equilibrium dynamics are crucial in many pharmaceutical formulations, treatment of bio-oils, but also in designing advanced materials with emergent structure formation. In this talk, I bring together what we have learned studying surfactant aggregation in apolar solvents based on diverse modelling approaches in biosurfactant – apolar solvent systems. The modelling approaches range from atomistic detail to particle-based mesoscale modelling approaches and thermodynamic modelling.

[1] M. Vuorte, S. Kuitunen, P. R. Van Tassel, M. Sammalkorpi, J. Colloid Interface Sci. 630, 783 (2023).
[2] M. Vuorte, S. Kuitunen, M. Sammalkorpi, Phys. Chem. Chem. Phys. 571, 21840 (2021).
[3] M. Vuorte, S. Vierros, S. Kuitunen, M. Sammalkorpi, J. Colloid Interface Sci. 571, 55 (2020).
[4] S. Vierros and M. Sammalkorpi, ACS omega 4 (13), 15581 (2019).
[5] S. Vierros, M. Österberg, and M. Sammalkorpi, Phys. Chem. Chem. Phys. 20 (42), 27192 (2018).

Speaker: Maria Sammalkorpi (Aalto University)

25 Stretching, breaking, and dissolution of polymeric nanofibres

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

13:00 Lunch

26 Free discussion