Name: 6th Nordic Workshop on Statistical Physics: Biological, Complex and Non-Equilibrium Systems
Start: 2015-02-25T09:00:00+01:00
End: 2015-02-27T15:00:00+01:00
Location: Nordita, Stockholm

6th Nordic Workshop on Statistical Physics: Biological, Complex and Non-Equilibrium Systems

from Wednesday, 25 February 2015 (09:00) to Friday, 27 February 2015 (15:00)

Monday, 23 February 2015
Tuesday, 24 February 2015
Wednesday, 25 February 2015

09:00 Registration
Registration
09:00 - 10:15
Room: 132:028
10:15 Opening - Alberto Imparato (Aarhus University) Ralf Eichhorn (Nordita)
Opening
- Alberto Imparato (Aarhus University)
- Ralf Eichhorn (Nordita)
10:15 - 10:30
Room: 132:028
10:30 Logarithmic time evolution in hitchhiker dynamics and interacting many-body systems - Tobias Ambjörnsson (Lund University)
Logarithmic time evolution in hitchhiker dynamics and interacting many-body systems
- Tobias Ambjörnsson (Lund University)
10:30 - 11:15
Room: 132:028 There exists compelling experimental evidence in numerous systems for logarithmically slow time evolution, yet its full theoretical understanding remains elusive. In this talk two examples of systems displaying logarithmic time evolutions will be discussed. First, we consider, pictorially, a hitchhiker traveling through a series of towns [1]. In each town, traffic starts in the morning, and friendly drivers (persons willing to pick up our hitchhiker) appear at random intervals governed by a waiting time density, psi(tau). The hitchhiker typically arrives to a new town in between two friendly drivers showing up, and the delay time, i.e., the time the hitchhiker actually has to wait until the next ride, is non-trivially related to the interarrival times of friendly drivers. For heavy-tailed psi(tau) we show that the expected number of towns visited increase logarithmically with time, t. Also for medium-tailed psi(tau) we find interesting behaviour. Second, we study a labelled particle in a generic system of identical particles with hard-core interactions in a strongly disordered environment [2]. The disorder is manifested through intermittent motion with scale-free sticking times at the single particle level, i.e. a continuous time random walk with a power-law exponent between 0 and 1. We demonstrate that the combination of the disordered environment with the many-body interactions leads to an ultraslow, logarithmic dynamics -- the tracer particle's mean square displacement increase as the square root of the logarithm of time. [1] Michael A. Lomholt, Ludvig Lizana, Ralf Metzler, and Tobias Ambjörnsson, Phys. Rev. Lett. 110, 208301 (2013). [2] Lloyd P Sanders, Michael A Lomholt, Ludvig Lizana, Karl Fogelmark, Ralf Metzler and Tobias Ambjörnsson, New J. Phys. 16, 113050 (2014).
11:15 Transcription and Translation Initiation in Bacteria - Namiko Mitarai (Niels Bohr Institute)
Transcription and Translation Initiation in Bacteria
- Namiko Mitarai (Niels Bohr Institute)
11:15 - 12:00
Room: 132:028 Transcription and translation are fundamental processes in gene expression. In this talk, we first introduce the dynamics of bacterial transcription initiation and its effect on the cellular heterogeneity in the number of mRNAs, with and without transcriptional regulation [1,2], highlighting the importance of the intermediate steps in transcription initiation [3]. A formalism parallel to this can be applied to the ribosome initiation [4], while the difference in the reaction rates making the occlusion time much important for the latter. We then discuss recent experimental results [5,6] about how the ribosome binding and initiation can affect protein synthesis in various ways using a stochastic model. [1]Mitarai, N., Dodd, I. B., Crooks, M. T., & Sneppen, K. (2008). The generation of promoter-mediated transcriptional noise in bacteria. PLoS computational biology, 4(7), e1000109. [2]Nakanishi, H., Mitarai, N., & Sneppen, K. (2008). Dynamical analysis on gene activity in the presence of repressors and an interfering promoter. Biophysical journal, 95(9), 4228-4240. [3]McClure, W. R. (1980). Rate-limiting steps in RNA chain initiation. Proceedings of the National Academy of Sciences, 77(10), 5634-5638. [4] Ringquist, S., Shinedling, S., Barrick, D., Green, L., Binkley, J., Stormo, G. D., & Gold, L. (1992). Translation initiation in Escherichia coli: sequences within the ribosome‐binding site. Molecular microbiology, 6(9), 1219-1229. [5] Eriksen, M., Mitarai, N., Sneppen, K., & Pedersen, S. (2015). submitted. [6] Terkelsen, T. B, Madsen, J. E.,Eriksen, M., Mitarai, N, Runge, C., Pedersen, M., Sneppen, K., and Pedersen S. (2015) submitted.
12:00 Lunch
Lunch
12:00 - 14:00
Room: Restaurant Entré
14:00 The dark side of the network: mean-field, belief-propagation and replicas for learning a kinetic Ising model with hidden nodes - Yasser Roudi (Nordita)
The dark side of the network: mean-field, belief-propagation and replicas for learning a kinetic Ising model with hidden nodes
- Yasser Roudi (Nordita)
14:00 - 14:45
Room: 132:028 Our observations from complex systems e.g. financial, neuronal or gene regulatory networks are always done in the presence of hidden nodes. This means that, we only see a part of the network at any given time: we can record from only a fraction of neurons in a cortical network, or have access to data from only a part of the market. This raises the question of what we can say about this hidden nodes, and if their presence can be included on modeling the high-throughput data collected from these complex systems. Focusing on the kinetic Ising model as a prototypical problem for learning and inference in kinetic models, in this talk, I will describe how approximations based on mean-field theory, belief propagation and replicas can be used to recovering connections from partial observations in this network. This work is based on Dunn and Roudi, PRE 2013 Battistin, Hertz, Tyrcha and Roudi 2014 arXiv 1412.1727
14:45 Anisotropy of nanoscale friction - Astrid de Wijn (SU Fysikum/Kemisk Fysik)
Anisotropy of nanoscale friction
- Astrid de Wijn (SU Fysikum/Kemisk Fysik)
14:45 - 15:30
Room: 132:028 Mechanical properties of crystalline materials are ultimately determined by their atomic structure. A direct consequence of the symmetry of the atomic surface structure is anisotropy of friction and wear. We investigate the anisotropy of friction theoretically, as well as experimentally on graphitic surfaces. We find that the anisotropy does not depend on the geometry of the sliding object, only on that of the substrate. Friction vectors can deviate significantly from the pulling directions. For graphitic substrates, the strongest deviations are found for pulling directions which lie almost along one zigzag direction of the honeycomb structure, the preferred sliding directions. Numerical simulation and further theory reveal the role of temperature and of the two-dimensional character of the surface potential for the friction anisotropy. The friction is determined by atomic stick-slip events along and across molecular rows determine direction and magnitude of friction. (Collaboration with Balakrishna S. G. and R. Bennewitz, INM - Leibniz Institute for New Materials, Germany) [1] Preferential sliding directions on graphite, Balakrishna S.G., Astrid S. de Wijn, and Roland Bennewitz, Phys. Rev. B 89, 245440 (2014).
15:30 Coffee break
Coffee break
15:30 - 16:00
Room: 132:028
16:00 A model for gyrotactic pattern formation of motile micro-organisms in turbulence - Bernhard Mehlig (University of Gothenburg)
A model for gyrotactic pattern formation of motile micro-organisms in turbulence
- Bernhard Mehlig (University of Gothenburg)
16:00 - 16:45
Room: 132:028 Recent studies show that spherical motile micro-organisms in turbulence subject to gravitational torques gather in down-welling regions of the turbulent flow. By analysing a statistical model we analytically compute how shape affects this preferential sampling and small-scale spatial clustering (determining local encounter rates). By recursively refining approximations for the paths the organisms take through the flow we determine how preferential sampling and small-scale clustering in the model depend upon the dimensionless parameters of the problem. We show that singularities ("caustics") affect the dynamics of motile micro-organisms. Joint work with K. Gustavsson, F. Berglund, and P.R. Jonsson.
16:45 Field-induced assembly of colloidal ellipsoids into well-defined microtubules - Per Linse (Lund University)
Field-induced assembly of colloidal ellipsoids into well-defined microtubules
- Per Linse (Lund University)
16:45 - 17:30
Room: 132:028 Current theoretical attempts to understand the reversible formation of stable microtubules and virus shells are generally based on shape-specific building blocks or monomers, where the local curvature of the resulting structure is explicitly built-in via the monomer geometry. Here we demonstrate that even simple ellipsoidal colloids can reversibly self-assemble into regular tubular structures when subjected to an alternating electric field. Supported by model calculations and simulations, we discuss the combined effects of anisotropic shape and fieldinduced dipolar interactions on the reversible formation of self-assembled structures. Our observations show that the formation of tubular structures through self-assembly requires much less geometrical and interaction specificity than previously thought, and advance our current understanding of the minimal requirements for self-assembly into regular virus-like structures.
Thursday, 26 February 2015
09:00 Mechanics of shape formation and controlled actuation in thin sheets of liquid-crystal elastomers - Marcelo Dias (Aalto University and Nordita)
Mechanics of shape formation and controlled actuation in thin sheets of liquid-crystal elastomers
- Marcelo Dias (Aalto University and Nordita)
09:00 - 09:45
Room: 132:028 Stimulus-induced shape change of soft materials opens the door to a wide range of engineering applications from soft robotics to artificial muscles. A particularly challenging problem is concerned with manipulating the shape of these materials so as to affect and control their response to external stimuli. Heretofore, efforts in this direction have been mainly devoted to obtaining three-dimensional structures from the imposition of a two-dimensional pattern on an isotropic material. Liquid-crystal elastomers (LCE) are an even more promising class of soft materials for actuation since they provide two forms of exploitable shape transformation: prescriptions of the cross-link density to control differential swelling, and an orientational order of rod-like molecules that respond to internal and external stimuli. In this talk I will present a phenomenological model of strain-order coupling for shape formation in thin elastic sheets of LCEs and show how the presence of the nematic degree-of-freedom induces buckling instabilities in these materials.
09:45 Avalanches in Wood (Compression) - Mikko Alava (Aalto University, Espoo, Finland)
Avalanches in Wood (Compression)
- Mikko Alava (Aalto University, Espoo, Finland)
09:45 - 10:30
Room: 132:028 Wood is a multi-scale material and exhibits a complex mechanical response. We study the avalanches in small wood samples in compression. Acoustic emission or crackling noise in the deformation is similar to what is seen in rocks and laboratory tests of porous, brittle materials. Both the distribution of events energy and the waiting (silent) time distribution follow power-laws. The stress-compressive strain response exhibits the typical characteristics of wood and other porous materials with clear signatures of the localization of the compression deformation to "weak spots" of, here, softwood layers. This can be directly identified using Digital Image Correlation. Even though material structure-dependent localization takes place, it does not change the act that avalanche behavior is scalefree and merely modifies the event rate of avalanches.
10:30 Coffee break
Coffee break
10:30 - 11:00
Room: 132:028
11:00 Reversible operation of a hot carrier solar cell - Heiner Linke (Lund University)
Reversible operation of a hot carrier solar cell
- Heiner Linke (Lund University)
11:00 - 11:45
Room: 132:028 Hot carrier solar cells are envisioned to utilize electron and hole energy filtering in order to extract power from photo-generated carriers before they thermalize with the lattice, and thus offer the potential to increase power conversion efficiency above that of conventional single-junction solar cells. Here we establish that strategies previously developed for ideal thermoelectric devices such as quantum-dot heat engines [1, 2] are also applicable to hot-carrier solar cells. Specifically, we establish the condition under which hot-carrier solar cells can be operated reversibly, namely when charge carriers are exchanged under conditions of energy-specific equilibrium. We find that the maximum efficiency of a hot-carrier solar cell is actually larger than the Carnot efficiency corresponding to the involved spatial differential in charge carrier temperature, because of the additional non-equilibrium represented by the quasi-Fermi level splitting. We identify separate contributions to the open-circuit voltage of the hot carrier solar cell from thermoelectric effects and from electron-hole pair generation, and quantify its reduction away from the reversible operation point at points in current-voltage curve space where carrier extraction takes place under non-equilibrium conditions. [1] T.E. Humphrey, R. Newbury, R.P. Taylor, H. Linke, Phys. Rev. Lett., 89 (2002) 116801. [2] T.E. Humphrey, H. Linke, Phys. Rev. Lett., 94 (2005) 096601.
11:45 Heat fluctuations in classical model systems - Hans Fogedby (Aarhus University and NBI)
Heat fluctuations in classical model systems
- Hans Fogedby (Aarhus University and NBI)
11:45 - 12:30
Room: 132:028 We review recent and not so recent work done in collaboration with Alberto Imparato (Aarhus) on heat fluctuations and fluctuation theorems in classical model systems. i) As a starter we consider a single particle driven by two heat reservoirs. We discuss heat fluctuations, the large deviations function, and associated fluctuation theorem. ii) Next we consider a linear harmonic chain driven by heat reservoirs. We again address heat fluctuations and fluctuation theorems. iii) Finally, we round off the presentation with a discussion of recent work on a chain with quenched mass and coupling constant disorder. Here we discuss the influence of disorder on Fourier’s law, heat fluctuations, and fluctuation theorems.
12:30 Lunch
Lunch
12:30 - 14:00
Room: Restaurant Entré
14:00 Towards a Maxwell’s Demon realization – unified model for Brownian ratcheting and power stroke - Jonas Johansson (Lund University)
Towards a Maxwell’s Demon realization – unified model for Brownian ratcheting and power stroke
- Jonas Johansson (Lund University)
14:00 - 14:45
Room: 132:028 In two letters and in his book “Theory of Heat”, Maxwell mentioned a thought experiment about “a being whose faculties are so sharpened that he can follow every molecule”. The being was later referred to as a demon. In this presentation I will give a brief historical introduction to Maxwell’s Demon and discuss some of the attempts to resolve the paradox of Maxwell’s Demon. The accepted solution is known as “Landauer’s erasure principle” and it is based on the observation that the demon needs to store information and it is the erasure of this information that compensates for the entropy decrease – the second law is saved. During the last few years, spurred by the developments in stochastic thermodynamics, a few realizations of devices that transform information to energy, that is, Maxwell’s Demons, have been demonstrated. I will describe some of these and continue with our own ideas for the implementation of a Maxwell’s Demon, which is based on a microbead in a feedback controlled, linear optical trap. So far, we have theoretically analyzed a general and idealized version of our set up. The demon can operate as a feedback controlled Brownian ratchet, or as a power stroke motor, or as a mixture of both. The main result of our modeling is that the efficiency has a maximum when the two modes of operation are at work simultaneously. In the context of biological molecular motors, there is a general discussion whether such motors are mainly operating as Brownian ratchets or utilizing power stroke. Our modeling results suggest the possibility that the highest efficiency and robustness of biological molecular motors can be reached when both mechanisms are simultaneously active.
15:15 A thermodynamic route to the quantum-to-classical transition - Mauro Paternostro (Queen’s University Belfast)
A thermodynamic route to the quantum-to-classical transition
- Mauro Paternostro (Queen’s University Belfast)
15:15 - 16:15
Room: Oskar Klein Auditorium Microscopic systems (such as electrons, atoms, or faint light fields) can be prepared, according to the principles of quantum mechanics, in physical configurations with no classical counterpart. Such a possibility appears to be precluded when the degree of 'complexity' of the system at hand (intended as its size, mass or the number of its elementary constituents) grows towards the macroscopic domain. Indeed, our daily observations do not readily give us any evidence of non-classical behaviour of the macroscopic world around us. Is there any reason preventing the establishment of quantum features at the macroscopic scale? And how is quantumness lost as we abandon the microscopic domain? These questions address the phenomenon known as quantum-to-classical transition, i.e. the process through which quantum features are lost in favour of a fully classical description of a physical system. The characterization of the QtC transition is one of the most interesting and challenging goals of modern research in quantum mechanics. In this Colloquium I will discuss how fundamental progress can be made towards a better grasp of the quantum-to-classical crossover by adopting a novel methodological approach based on the non-equilibrium thermodynamics of quantum evolutions. Harnessing the fundamental interplay between complexity and quantumness will underpin the development of more resilient architectures for quantum information processing.
16:15 Coffee break
Coffee break
16:15 - 16:30
Room: 132:028
16:30 Rheology of inertial suspensions: Effects of confinement - Dhrubaditya Mitra
Rheology of inertial suspensions: Effects of confinement
- Dhrubaditya Mitra
16:30 - 16:45
Room: 132:028
16:45 The Josephson effect in systems out of thermal equilibrium - Simone Borlenghi Garoia (Uppsala University)
The Josephson effect in systems out of thermal equilibrium
- Simone Borlenghi Garoia (Uppsala University)
16:45 - 17:00
Room: 132:028
17:00 Iso-flux tension propagation theory of driven polymer translocation through a nano-pore - Jalal Sarabadani (Aalto University)
Iso-flux tension propagation theory of driven polymer translocation through a nano-pore
- Jalal Sarabadani (Aalto University)
17:00 - 17:15
Room: 132:028
17:15 Dragged colloid hydrodynamically coupled to a heat bath - Vaibhav Thakore (Aalto University)
Dragged colloid hydrodynamically coupled to a heat bath
- Vaibhav Thakore (Aalto University)
17:15 - 17:30
Room: 132:028
17:30 Stochastic thermodynamics of nearly adiabatically driven open quantum systems - Samu Suomela (Aalto University)
Stochastic thermodynamics of nearly adiabatically driven open quantum systems
- Samu Suomela (Aalto University)
17:30 - 17:45
Room: 132:028
19:00 Conference dinner
Conference dinner
19:00 - 22:00
Room: Gotland Grill
Friday, 27 February 2015
09:15 Calorimetry for quantum thermodynamics experiments - Jukka Pekola (Aalto University, Helsinki)
Calorimetry for quantum thermodynamics experiments
- Jukka Pekola (Aalto University, Helsinki)
09:15 - 10:00
Room: 132:028 I discuss the concept, theoretical analysis and experiments on calorimetric measurement of work and heat in a quantum system. The experimental realization is based on a superconducting quantum circuit with a calorimeter approaching single micro-wave photon resolution.
10:00 Coffee break
Coffee break
10:00 - 10:30
Room: 132:028
10:30 Thermodynamics of work in open quantum systems - Tapio Ala-Nissilä (Aalto University)
Thermodynamics of work in open quantum systems
- Tapio Ala-Nissilä (Aalto University)
10:30 - 11:15
Room: 132:028 Fluctuation relations provide a powerful way to study the stochastic nature of fluctuating thermodynamic variables, such as (free) energy, entropy, heat and work in small systems driven beyond the linear response regime [1]. In driven classical systems, the fluctuating work and its distribution play an important role in the relevant fluctuation relations. However, attempts to generalize the concept of work to open quantum systems have met with some difficulties. The main problem in quantum mechanics is that there is no unique work operator, since for irreversible processes work depends both on the state of the system as well as the path taken. I will discuss some recent progress in defining work and its moments for quantum systems within the two-measurement protocol (TMP) approach, which for isolated systems coincides with the classical definition of work in the appropriate limit. In particular, I will show that using the TMP within the Linblad master equation formalism allows one to derive (i) a general integral fluctuation relation and (ii) moments of work for weakly or nearly adiabatically driven, open quantum systems [2,3]. 1. M. Esposito, U. Harbola, and S. Mukamel, Rev. Mod. Phys. vol. 81, 1665 (2009). 2. S. Suomela, J. Salmilehto, I.G. Savenko, T. Ala-Nissila, and M. Möttönen, Phys. Rev. E vol. 91, 022126 (2015). 3. S. Suomela, P. Solinas, J.P. Pekola, J. Ankerhold, and T. Ala-Nissila, Phys. Rev. B vol. 90, 094304 (2014).
11:15 The change in the von Neumann entropy of a bath interacting with a driven quantum system - Erik Aurell (KTH)
The change in the von Neumann entropy of a bath interacting with a driven quantum system
- Erik Aurell (KTH)
11:15 - 12:00
Room: 132:028 We compute the change of the von Neumann entropy of a bath coupled to an externally driven quantum system by adapting the formalism of Feynman and Vernon (1963). This quantity has been proposed as a possible extension of classical entropy production in the environment to the quantum domain (Esposito, Lindenberg, Van den Broeck 2010; Pucci, Esposito, Peliti 2013). In general we find that this entropy change is the (quantum) expectation value of three functionals over the forward and reversed paths in the Feynman-Vernon formalism. The classical limit of these functionals partly reproduces the well-known classical entropy production in the environment of a Kramers-Langevin process, and partly gives rise to new terms which have no analogous in stochastic thermodynamics. We do not at this time have a clear understanding of the physical meaning of these terms. This is joint work with Ralf Eichhorn, available as arXiv:1412.7029.
12:00 Lunch
Lunch
12:00 - 13:45
Room: Restaurant Entré

13:45 Free discussion/Closing
Free discussion/Closing
13:45 - 15:45
Room: 132:028