5th Nordic Workshop on Statistical Physics: Biological, Complex and Non-Equilibrium Systems

26 Mar 2014, 09:00 → 28 Mar 2014, 15:00 Europe/Stockholm

132:028 (Nordita, Stockholm)

Alberto Imparato (University of Aarhus), Ralf Eichhorn (Nordita)

Venue

Nordita, Stockholm, Sweden

Scope

This workshop series provides a “forum” where scientists in the Nordic countries working in the area of Statistical Physics can meet regularly. It brings together experts interested in the broad spectrum of timely problems in (classical) Statistical Physics, ranging from fundamental aspects in the theory of non-equilibrium processes to modern applications in biophysics.

Topics covered include diffusion problems, physics of DNA and bio-molecules, population dynamics, pattern formation, non-equilibrium transport, bacterial motility, single-molecule kinetics, dynamics and structure of networks, statistical inference, Monte-Carlo simulation techniques, self-assembly, soft condensed matter (colloids, liquid crystals etc.), work relations and fluctuation theorems, and many more.

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[Timetable - available from start of the program]

Special Guest

Stefan Klumpp (MPI Golm-Potsdam, Germany)

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Invited Speakers

Tapio Ala-Nissilä (Aalto University) Erik Aurell (KTH, Stockholm) Dick Bedeaux (Norwegian University of Science and Technology) Jeppe Dyre (Roskilde Universitet) Måns Ehrenberg (Uppsala University) Hans Fogedby (Aarhus University) Natalia Golubeva (Aarhus University) Mogens Høgh Jensen (Niels Bohr Institute, Copenhagen)

Heiner Linke (Lund University) Bernhard Mehlig (Göteborg University) Namiko Mitarai (Niels Bohr Institute, Copenhagen) Cecilia Rorai (Nordita) Kim Sneppen (Niels Bohr Institute, Copenhagen) Mats Wallin (KTH, Stockholm) Astrid de Wijn (Stockholm University)

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

Registration deadline: 3 March 2014

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.

Sponsored by:

Wednesday 26 March

09:00 Registration

1 Opening

2 Clustering of particles falling in a turbulent aerosol

Spatial clustering of identical particles falling through a turbulent aerosol enhances the collision rate between the falling particles, an important problem in aerosol science. We analyse this problem using perturbation theory in a dimensionless parameter, the so-called Kubo number. This allows us to derive an analytical theory quantifying the spatial clustering. We find that clustering of small particles in incompressible random velocity fields may be reduced or enhanced by the effect of gravity, depending on the Stokes number of the particles and the Froude number of the flow. This work was performed in collaboration with K. Gustavsson (University of Gothenburg).

Speaker: Bernhard Mehlig (University of Gothenburg)

3 Modeling the motion of cells in microfluidic devices

Living cells are usually immersed in fluids they interact with. The nature of the interaction is complex and involves biochemical and biophysical mechanisms. Even when the problem is simplified to account for the hydrodynamical aspects only, it turns out that cells cannot be regarded as "passive". The fluid flow and the motion of the cell are mutually and nonlinearly coupled due to the deformability of the cell membrane. This leads to a multiplicity of hardly predictable dynamical behaviors exploited by nature in biological systems and by humans in microfluidic devices for medical diagnostic. The problem is strongly dependent on the flow geometry and the deformability of the membrane. We have numerically studied flow geometries that allow for cell alignment and sorting. We present and discuss some preliminary results and we propose a microfluidic device able to sort cells, modeled as elastic capsules, by deformability.

Speaker: Cecilia Rorai (Nordita)

12:00 Lunch

4 Vorticity Patterns in Tissues induced by Cell Divisions

In healthy blood vessels with a laminar blood flow, the endothelial cell division rate is low, only sufficient to replace apoptotic cells. The division rate significantly increases during embryonic development and under halted or turbulent flow. We study the long-range dynamics induced by cell division in an endothelial monolayer under non-flow conditions, mimicking the conditions during vessel formation or around blood clots [1]. Cell divisions induce long-range, well-ordered vortex patterns extending several cell diameters away from the division site, in spite of the system's low Reynolds number. We model these observations by a hydrodynamic continuum model simulating division as a local pressure increase in a non-nematic, meso-scale turbulent state [1]. In order to describe the injected energy by cell motion in the tissue we assume a negative local viscosity stabilized by a higher order term. We find a vorticity pattern very similar to the experimental observations with a similar order and periodicity of the patterns. [1] N.S. Rossen, J.M. Tarp, J. Mathiesen, M.H. Jensen and L.B. Oddershede, Nature Physics, under review (2014)

Speaker: Mogens Hogh Jensen (The Niels Bohr Institute, University of Copenhagen)

5 Curvature dependence of the heat and mass transfer resistances of the surface of nano bubbles and droplets

We analyze the curvature dependence of the heat and mass transfer resistances of the surface of nano bubbles and droplets. For this we use an extension [1-7] of the so-called square gradient model introduced by van der Waals to describe the density profile in a one-component fluid, and by Kahn and Hilliard for mixtures, to time dependent problems. This enables us to calculate equilibrium and non-equilibrium density profiles for the two phase state. Together with earlier derived integral relations [8] we are then able to calculate these resistances. It is found that the resistances change considerably in the nanoscale range. This agrees with molecular dynamics results [9]. In earlier work we studied the stability of nanoscale droplets and bubbles [10,11]. [1] D. Bedeaux, E. Johannessen and A. Røsjorde, The Nonequilibrium van der Waals Square Gradient Model I: The Model and its Numerical Solution, Physica A 330 (2003) 329-353. [2] E. Johannessen and D. Bedeaux, The Nonequilibrium van der Waals Square Gradient Model II: Local Equilibrium of the Gibbs Surface, Physica A 330 (2003) 354-372. [3] E. Johannessen and D. Bedeaux, The Nonequilibrium van der Waals Square Gradient Model III: Heat and Mass Transfer Coefficients, Physica A 336 (2004) 252-270. [4] K.S. Glavatskiy and D. Bedeaux, Non-equilibrium properties of a two-dimensional isotropic interface in a two-phase mixture as described by the square gradient model, Phys. Rev. E 77 (2008) 061101-17. [5] K.S. Glavatskiy and D. Bedeaux, Numerical solution and verification of local equilibrium for the flat interface in the two-phase binary mixture, Phys. Rev. E 79 (2009) 031608, 1-19. [6] K. S. Glavatskiy and D. Bedeaux, Transport of heat and mass in a two-phase mixture. From a continuous to a discontinuous description, J. Chem. Phys. 133 (2010) 144709-17. [7] K. S. Glavatskiy and D. Bedeaux, Resistances for heat and mass transfer through a liquid-vapor interface in a binary mixture, J. Chem. Phys. 133 (2010) 234501. [8] E. Johannessen and D. Bedeaux, Integral Relations for the Heat and Mass Transfer Resistivities of the Liquid-Vapor Interface, Physica A 370 (2006) 258-274. [9] A. Lervik, F. Bresme, S. Kjelstrup, D. Bedeaux and J.M. Rubi, Heat transfer in Protein-water interfaces, Phys. Chem. Chem. Phys. 12 (2010) 1610-1617. [10] K. S. Glavatskiy, D. Reguera, and D. Bedeaux, Effect of compressibility in bubble formation in closed systems, J. Chem. Phys. 138 (2013) 204708-6. [11] Ø. Wihelmsen, D. Bedeaux, S. Kjelstrup, D. Reguera, Thermodynamic stability of nanosized multicomponent bubbles/droplets: The square gradient theory and the capillary approach, J. Chem. Phys. 140 (2014) 024704-9.

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

15:30 Coffee break

6 Hidden scale invariance in condensed matter

Liquids and solids with (primarily) van der Waals bonds or metallic bonds - or weak Coulomb forces - have "isomorphs" in their thermodynamic phase diagram, whereas covalently bonded systems or systems with hydrogen-bonds do not. An isomorph is a configurational adiabat along which structure and dynamics are invariant in reduced units. We summarize the evidence for this novel picture of condensed matter and demonstrate how it all follows in a quite straightforward way from the former systems' "hidden scale invariance", as shown recently [1]. [1] J. C. Dyre, Phys. Rev. E 88, 042139 (2013).

Speaker: Jeppe Dyre (DNRF centre "Glass and Time", Roskilde University)

7 Stochastic Loewner Evolution: Fractal shapes and curves in two dimensions

The most exciting concepts in theoretical physics are those that relate algebraic properties to geometrical ones. Of course, the outstanding example of this is the geometric meaning of the equations of general relativity, and their realization in the shapes of possible universes and in black holes. Other examples abound including the patterns of the paths of Brownian motion, the forms of percolating clusters, the shapes of snowflakes and the phase boundaries, and the beautiful fingers of interpenetrating fluids and of dendrites. An approach called Schramm-Loewner evolution (SLE) provides a new method for dealing with a wide variety of scale-invariant problems in two dimensions. This approach is based upon an older method called Loewner Evolution (LE), which connects analytical and geometrical constructions in the complex plane.

Speaker: Hans Fogedby (Aarhus University)

Thursday 27 March

8 Predicting and triggering long jumps and sticks in molecular diffusion

Diffusion can be strongly affected by the appearance of ballistic flights (long jumps) as well as long-lived sticking trajectories (long sticks). Using statistical inference techniques, we investigate the appearance of long jumps and sticks in molecular-dynamics simulations of diffusion in a prototype system, a benzene molecule on a graphite substrate. These techniques are usually reserved for prediction of large rare events, such as earth quakes and strong wind gusts. We find that specific fluctuations in certain, but not all, internal degrees of freedom of the molecule can be linked to the occurrence of either long jumps or sticks. Furthermore, we show that by changing the prevalence of these predictors with an outside influence, the diffusion of the molecule can be controlled. The approach presented is very generic, and can be applied to larger and more complex molecules. Additionally, the predictor variables can be chosen in a general way so as to be accessible in experiments, making the method feasible for control of diffusion in applications. Our results also demonstrate that data-mining techniques can be used to investigate the phase-space structure of high-dimensional nonlinear dynamical systems.

Speaker: Dr Astrid de Wijn (SU Fysikum/Kemisk Fysik)

9 Entropy production and fluctuation relations in non-Markovian systems

Fluctuation relations provide a powerful formalism 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. Most of the work done to date in this field has been done within the context of the Markovian approximation, where the system has no memory of its previous states. However, it is easy to argue that in reality many interacting systems become non-Markovian when driven out of equilibrium. I will present some new results for the fluctuation relations, and entropy, heat and work production in a system of driven single-electron transitions (the "single-electron box"), which becomes non-Markovian due to excess heat dissipation [1], or which can be driven to a steady-state non-equilibrium state [2]. I will also discuss the relationship between different sources of entropy generation in non-Markovian systems using the driven SEB as a benchmark [3]. [1] J.P. Pekola, A. Kutvonen, and T. A-N., JSTAT P02033 (2013). [2] J.V. Koski, T. Sagawa, O-P. Saira, Y. Yoon, A. Kutvonen, P. Solinas, M. Möttönen, T.A-N., and J.P. Pekola, Nat. Phys. 9, 644 (2013). [3] A. Kutvonen, J.P. Pekola, and T. A-N., unpublished (2014).

Speaker: Tapio Ala-Nissilä (Aalto University School of Science)

10:30 Coffee break

10 Efficiency at maximum power of interacting biological and artificial nanomachines

We investigate the efficiency at maximum power (EMP) of systems of autonomous molecular machines operating under constant load and interacting through hard-core exclusion. For biological machines we show in the case of kinesin motors moving on a single filament that mutual interactions enhance the EMP, as compared to the non-interacting case, due to a change in the characteristic response of the system to external load [1-2]. Remarkably, the EMP enhancement occurs in a limited region of the system parameter space, compatible with the biologically relevant range. By considering exclusion processes on networks for generic tightly and loosely coupled motors we show that interaction induced EMP enhancement can also be observed for more general cooperative systems [3]. Furthermore, we identify parameter regimes for which the loss in the maximum output power due to exclusion is compensated by the corresponding EMP boost, thereby providing design strategies for efficient artificial nanomotors operating at maximum power. [1] N. Golubeva and A. Imparato, Phys.Rev.Lett 109, 190692 (2012) [2] N. Golubeva and A. Imparato, Phys.Rev.E 88, 012114 (2013) [3] N. Golubeva and A. Imparato, arXiv:1402.0713

Speaker: Natalia Golubeva (Aarhus University)

11 Engineering with molecular motors

In so-called motility assays, a surface is coated with functional motor proteins (such as myosin or kinesin) and filaments (such as actin or microtubules) are propelled along the surface, powered by ATP. In close collaboration with Alf Månsson at the Linné University in Kalmar, we are exploring the development of functional, nanostructured devices based on such assays. For example, motors can be used to actively concentrate analyte for enhanced detection in diagnostics [1] , and we demonstrated the use of motor proteins to characterize light-guiding in nanowires that leads to a novel concept for enhanced, optical biosensing [2]. I will also report on an ongoing project to use molecular motors for massively parallel biocomputation, a project for which we are developing functional elements such as gates [3] and tunnels [4], allowing the crossing of nanochannels guiding motor proteins in a lab-on-a-chip application. [1] Lard, M. et al. Ultrafast molecular motor driven nanoseparation and biosensing. Biosens. Bioelectron. 48, 145-152 (2013). [2] ten Siethoff, L., Lard, M., Generosi, J., Andersson, H. S., Linke, H., Månsson, A. Molecular motor propelled filaments reveal light-guiding efficiency in nanowire arrays for enhanced biosensing. Nano Lett. 14(2), 737-742 (2013) doi: 10.1021/nl404032k. [3] Schroeder, V., Korten, T., Linke, H., Diez, S., & Maximov, I. (2013). Dynamic Guiding of Motor-Driven Microtubules on Electrically Heated, Smart Polymer Tracks. Nano Letters, 13(7), 3434–3438 (2013). doi:10.1021/nl402004s [4] Lard, M., ten Siethoff, L., Generosi, J., Månsson, A., Linke, H. Molecular motor transport through hollow nanowires. Submitted (2014).

Speaker: Heiner Linke (Nanometer Structure Consortium, Lund University)

12:30 Lunch

12 Accuracy of genetic code translation by transfer RNAs: ancient dreams and recent validations

Speaker: Måns Ehrenberg (Uppsala University)

13 Cellular economy of molecular machines

The central dogma of molecular biology states that genetic information flows unidirectionally, from DNA to RNA to protein. The steps in processing the genetic information are carried out by specifically dedicated molecular machines (RNA and DNA polymerases, ribosomes) that themselves are either proteins or (in the case of ribosomes) RNA-protein complexes. Thus, the seemingly unidirectional flow of genetic information involves feedback loops for the required machinery. In the talk, I will explore some interesting consequences of these feedbacks. I will address both mechanistic aspects and aspects of the cellular economy of these machines (how many of the machines are found in a cell, how is that number adjusted to growth conditions etc.). Specific topics to be discussed are physical constraints on the maximal rates of RNA synthesis (transcription), the effect of dense RNA polymerase traffic on transcription accuracy, the growth rate dependence of the cellular abundance of these machines and the role of molecular crowding in protein synthesis (translation).

Speaker: Stefan Klumpp (MPI Golm-Potsdam)

16:30 Coffee break

14 The Primary and Processed Bacterial Transcriptome of the Human Pathogen Enterococcus Faecalis

Modern high-throughput DNA sequencing enables many experimental approaches that address other questions than to find the nucleotide sequences in a genome. Here I report on one such application where we combine RNA sequencing (or "transcriptomics") with selective tagging of RNA sequences to map out many transcription start sites on a bacterial genome. This is of interest as RNA molecules are typically degraded in the living cell, and sequencing all RNA therefore gives a mixture of the primary and the processed fraction, and thus a mixture of transcription start sites and processing sites. The method also gives access to other information such as about one hundred new non-coding genes (that do not code for a protein), and one case where one can separate transcriptional and post-transcriptional regulation.

Speaker: Erik Aurell (KTH)

18:30 Conference dinner

Friday 28 March

15 Bacterial colony dynamics

I will discuss recent experiments and theory for the growth of bacterial colonies. The growth dynamics may depend on a many different parameters like choice of substrate, access to nutrients, age and size of the colony, etc. I will focus on some experimental observations about pattern formation and discuss model approaches to analyze colony growth.

Speaker: Mats Wallin (Theoretical Physics KTH)

10:15 Coffee break

16 Diversity of Bacteriophage Phage strategies

The talk will discuss the lysis-lysogeny choice from a game theoretical viewpoint, suggesting that the optimal frequency of lysogeny is close to the likelihood that the environment of the phage collapses. Subsequently I will discuss possible ways to understand sustainability of virulent phages, including limits for the diversity of virulent phage species in a given environment.

Speaker: Kim Sneppen (The Niels Bohr Institute)

17 Conditional Cooperativity in Toxin-Antitoxin Battle in Bacteria

Many toxin-antitoxin operons are regulated by the toxin/antitoxin ratio by mechanisms collectively coined ”conditional cooperativity”. Toxin and antitoxin form heteromers with different stoichiometric ratios, and the complex with the intermediate ratio works best as a transcription repressor. This allows transcription at low toxin level, strong repression at intermediate toxinlevel, and then again transcription at high toxin level ([1] and references therein). Such regulation has two interesting features; firstly, it provides a non-monotonous response to the concentration of one of the proteins, and secondly, it opens for ultra-sensitivity mediated by the sequestration of the functioning heteromers. We explore possible functions of conditional regulation in simple feedback motifs, and show that it can provide bistability for wide a range of parameters [2]. We demonstrate that the conditional cooperativity in toxin-antitoxin systems combined with the growth-inhibition activity of free toxin can mediate bistability between a growing state and a dormant state. Conditional cooperativity also secures that the antitoxin dominated state has a substantial amount of toxins present, which helps the transition to the toxin dominated state under stress. These features may be relevant for understanding persister formation in E. coli. [1] I. Cataudella, A.Trusina, K. Sneppen, K. Gerdes, and N. Mitarai, Nucl. Acids Res. (2012) 40, 6424-6434. [2] I. Cataudella, K. Sneppen, K. Gerdes, and N. Mitarai, Plos. Comput. Biol. (2013) 8, e1003174.

Speaker: Namiko Mitarai (The Niels Bohr Institute)

12:15 Lunch

18 Discussion/Closing