Name: 7th Nordic Workshop on Statistical Physics: Biological, Complex and Non-Equilibrium Systems
Start: 2016-03-16T09:00:00+01:00
End: 2016-03-18T16:00:00+01:00
Location: Nordita, Stockholm

7th Nordic Workshop on Statistical Physics: Biological, Complex and Non-Equilibrium Systems

from Wednesday, 16 March 2016 (09:00) to Friday, 18 March 2016 (16:00)

Monday, 14 March 2016
Tuesday, 15 March 2016
Wednesday, 16 March 2016

09:00 Registration with Coffee & Cake
Registration with Coffee & Cake
09:00 - 10:15
Room: 122:026

10:15 Opening
Opening
10:15 - 10:30
Room: 122:026
10:30 Noisy finite time singularities, power laws, and stretched exponentials - Hans Fogedby (Aarhus University)
Noisy finite time singularities, power laws, and stretched exponentials
- Hans Fogedby (Aarhus University)
10:30 - 11:15
Room: 122:026 Finite time singularities are encountered in stellar structures, black holes, turbulent flow, bacterial growth, Euler flow, free surface flows, rupture, earthquakes, econophysics, DNA “breathing”, and neurophysics. We discuss the influence of white noise on a generic dynamical finite-time-singularity model for a single degree of freedom. We find that the noise effectively resolves the finite-time-singularity and replaces it by a first-passage-time or absorbing state distribution with a peak at the singularity and a long time tail exhibiting power law or stretched exponential behavior.
11:15 Zero-crossing statistics of discrete stationary Gaussian processes - Ludvig Lizana (Umeå University)
Zero-crossing statistics of discrete stationary Gaussian processes
- Ludvig Lizana (Umeå University)
11:15 - 12:00
Room: 122:026 In many applications one wishes to know not only when a stochastic variable crosses a boundary for the first time, but also how many times it is crossed in a specific time interval. While we know the average number of crossings <m> for discrete stationary Gaussian processes through the well established Rice formula, we do not know the fluctuations <m^2> or the distribution of crossing events. We calculate those quantities analytically from a generalisation of the so-called Independent Interval approximation, a method where we assume that the length of time intervals between successive zero-crossings are uncorrelated. We apply our results to a discrete version of the Ornstein–Uhlenbeck process, the autoregressive process, but the Independent Interval approximation has a much wider applicability. For example continuous non-stationary Gaussian processes.
12:00 Lunch
Lunch
12:00 - 14:00
Room: 122:026
14:00 Improving sampling by using a thermodynamic metric - Jack Lidmar (KTH Royal Institute of Technology)
Improving sampling by using a thermodynamic metric
- Jack Lidmar (KTH Royal Institute of Technology)
14:00 - 14:45
Room: 122:026 In computer simulations, using molecular dynamics or Monte Carlo, it is often the case that it is harder to converge the simulation for certain parameters than other. We discuss how the notion of distance in a parameter space of probability distributions can help deciding and optimizing how samples should be distributed in the parameter space. In particular, we show how a properly defined metric may be used to guide extended ensemble simulations over bottleneck configurations in the parameter space, and how this may improve, e.g., biomolecular simulations.
14:45 Stochastic analysis of nucleation rates - Jonas Johansson (Lund University)
Stochastic analysis of nucleation rates
- Jonas Johansson (Lund University)
14:45 - 15:30
Room: 122:026 Nucleation is the first step in the formation of a new thermodynamic phase, either during a spontaneously occurring phase transition or under more controlled circumstances, such as in crystal growth processes. In this presentation, I start by introducing the Becker-Döring rate equations and classical nucleation theory. I show an alternative way to approximate the Becker-Döring equations underlying the nucleation process using a Fokker-Planck equation, based on stochastic calculus. The derivation proceeds via a Langevin equation with multiplicative noise. Because of the Ito-Stratonovich dilemma this leads to a family of possible Fokker-Planck equations. The purpose of this investigation is to find out which of the Fokker-Planck equations gives the best approximation to the nucleation rate. For a simple and general set of attachment and detachment rates, I compare the equilibrium cluster sizes and the nucleation rates resulting from the various interpretations of the noise term (Ito, Stratonovich, and anti-Ito) with the exact nucleation rate. I find that the Ito choice provides the best approximations and the Fokker-Planck equation corresponding to this choice coincides with the Fokker-Planck equation resulting from the common way to Taylor expand the original set of rate equations.
15:30 Coffee break
Coffee break
15:30 - 16:00
Room: 122:026
16:00 Synchronisation and coupled transport in networks of nonlinear oscillators - Simone Borlenghi (Uppsala University)
Synchronisation and coupled transport in networks of nonlinear oscillators
- Simone Borlenghi (Uppsala University)
16:00 - 16:45
Room: 122:026 I will present an overview on recent research on the off-equilbrium discrete nonlinear Schrödinger equation. The latter is a general semi-classical model that describes networks of nonlinear oscillators, and has application in several branches of Physics, including Bose-Einstein condensates, spin systems, lasers, mechanical oscillators and photosynthetic reactions. When some oscillators of the network are coupled to stochastic bath at different temperatures, the system reaches a non-equilibrium steady states where coupled currents propagate. The essential condition for current propagation is the phase-synchronisation of the oscillators, indicating a deep relation between irreversibility an phase-coherence, that can be expressed by means of a general fluctuation theorem. I will present several examples of realistic spin devices, where transport can be enhanced or suppressed by controlling the phase synchronisation between the spin-oscillators, giving rises to interesting phenomena, such as thermal/spin rectification. References: S. Iubini et al.,Phys. Rev. E 86, 011108 (2012). S. Borlenghi et al., Phys. Rev. Lett 112, 047203 (2014). S. Borlenghi et al., Phys. Rev E 92, 012116 (2015). S. Borlenghi, Phys. Rev. E 93, 012133 (2016).
16:45 Population dynamics of signaling phenotypes - Sorin Tanase Nicola (Uppsala University)
Population dynamics of signaling phenotypes
- Sorin Tanase Nicola (Uppsala University)
16:45 - 17:30
Room: 122:026
Thursday, 17 March 2016
09:00 Coarse-graining in Mechanics - Theoretical, Numerical and Experimental studies - Ken Sekimoto (University Paris Diderot and ESPCI)
Coarse-graining in Mechanics - Theoretical, Numerical and Experimental studies
- Ken Sekimoto (University Paris Diderot and ESPCI)
09:00 - 10:00
Room: 122:026 The first part of the talk deals with a method of coarse-graining based on mechanical viewpoint. We study the overdamped dynamics, either in equilibrium or non-equilibrium, of dense medium consisting of mesoscopic elements. Essentially based only on the momentum-conservation, we found that the Irving-Kirkwood type formula are the generic expressions for the macroscopic momentum and angular momentum fluxes with whatsoever the mesoscopic structures and dynamics, In the second part we discuss the well-known Newton's cradle but with a modified repulsive interaction. This system realizes the separation of timescales of dynamics and, as a result, the cluster of particles behaves as a single rigid body. We show our numerical findings*, experimental realizations, and the coarse-grained mechanical model. Analogy is evoked to Mossbauer effects as quantum counterpart. *PRL 104, 2010. The theoretical works have been done in collaboration with Dr. Antoine Fruleux, and the experiments are conducted by three students, Karim Alloubia, Romain Arteil and Mehdi Benane.
10:00 Coffee break
Coffee break
10:00 - 10:30
Room: 122:026
10:30 Unified description of liquid and solid phases of matter - Tapio Ala-Nissilä (Dept. of Applied Physics, Aalto SCI, Espoo, Finland)
Unified description of liquid and solid phases of matter
- Tapio Ala-Nissilä (Dept. of Applied Physics, Aalto SCI, Espoo, Finland)
10:30 - 11:15
Room: 122:026
11:15 Direct tests of single-parameter aging - Jeppe Dyre (Roskilde University)
Direct tests of single-parameter aging
- Jeppe Dyre (Roskilde University)
11:15 - 12:00
Room: 122:026 The talk first gives an overview of “physical aging”, the highly non-linear very slow changes of material properties observed, e.g., just below the glass transition. During the last 50 years material scientists have obtained a good understanding of physical aging, and a useful phenomenological theory for describing aging exists, the 1971 Narayanaswamy theory. It is based on the physically appealing concept of a so-called material time, which may be thought of as the time measured on a clock with rate that itself ages. The paper goes on to present data for the physical aging of organic glasses just below the glass transition probed by monitoring the following quantities after temperature up and down jumps: the shear-mechanical resonance frequency (∼360 kHz), the dielectric loss at 1 Hz, the real part of the dielectric constant at 10 kHz, and the loss-peak frequency of the dielectric beta process (∼10 kHz). The setup used allows for keeping temperature constant within 100 μK and for thermal equilibration within a few seconds after a temperature jump (both of which are unprecedented). The data conform to a new simplified version of the classical Tool-Narayanaswamy aging formalism, which makes it possible to calculate one relaxation curve directly from another without any fitting to analytical functions. If time permits, we derive the new equations.
12:00 Lunch
Lunch
12:00 - 14:00
Room: 122:026
14:00 Nanoscopic friction under electrochemical control - Astrid de Wijn (Trondheim University)
Nanoscopic friction under electrochemical control
- Astrid de Wijn (Trondheim University)
14:00 - 14:45
Room: 122:026 A unique path to control and ultimately manipulate forces between material surfaces is through an applied electric field. Several experimental and theoretical studies of electro chemical interfaces demonstrated that the orientation of polar molecules adsorbed at electrode surfaces is potential dependent. We propose a theoretical model for friction under electrochemical conditions focusing on the interaction of a force microscope tip with adsorbed polar molecules of which the orientation depends on the applied electric field. The dependence of friction force on the electric field is shown to be determined by the interplay of two channels of energy dissipation: (i) the rotation of dipoles and (ii) slips of the tip over potential barriers. The molecule geometry and oscillating fields are investigated as well. [1] Nanoscopic friction under electrochemical control, A. S. de Wijn, A. Fasolino, A. Filippov, M. Urbakh, Phys. Rev. Lett. 112, 055502 (2014). [2] Effects of molecule anchoring and dispersion on nanoscopic friction under electrochemical control, A. S. de Wijn, A. Fasolino, A. E. Filippov, and M. Urbakh, J. Phys.: Condens. Matter 28, 105001 (2016).
14:45 Silent avalanches and Omori's law - Mikko Alava (Aalto)
Silent avalanches and Omori's law
- Mikko Alava (Aalto)
14:45 - 15:30
Room: 122:026 Systems exhibiting so-called crackling noise - intermittent response to slow driving - most often surprise by the fact that the crackling noise events are separated by waiting times which follow fairly clean power-law distributions. As the normal expectation would be instead Poissonian statistics this indicates correlations and leaves us with the question why. Here I present some results that explain this by our inability to follow properly avalanches experimentally (and in theory!): the waiting time behaviour is due to detecting sub-avalanches that all belong to the same correlated event. Experimental data from a slow (in-plane) crack propagation experiment and studies of a coarse-grained depinning model are presented to this effect.
15:30 Coffee break
Coffee break
15:30 - 16:00
Room: 122:026
16:00 Dynamics of cells and within cells - Lene Oddershede (Niels Bohr Institute)
Dynamics of cells and within cells
- Lene Oddershede (Niels Bohr Institute)
16:00 - 16:45
Room: 122:026 Cells making up biological tissue are connected and their motility highly correlated. The focus of this talk is on a physical description of the complex dynamics of and within cells comprising different tissue types. Endothelial cells line the blood vessels. In healthy 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. Under non-flow conditions, mimicking the condition around a blood clot, we show that a cell division in endothelial tissue causes the emergence of long-range well-ordered vortex patterns, in spite of the system’s low Reynolds number [1]. Our experimental results are reproduced by a hydrodynamic continuum model simulating division as a local pressure increase. We also experimentally mimic the conditions of a closing wound and investigate how endothelial cells migrate into empty space, and how this migration depends on flow conditions. Another system studied is cancerous tissue, here, we correlate the aggressiveness of cancer cells to their dynamics, with the goal of achieving a deeper understanding of how dynamics is related to cancer invasiveness. The last part of the talk focuses on the dynamics of organelles inside living stem cells, and how these tracers can be used as a mean to characterize the mechanical properties of stem cells; we found that the mechanical properties of embryonic stem cells is highly correlated to their differentiation and that the presence of actin might serve as a check-point for differentiation control. [1] Rossen, Tarp, Mathiesen, Jensen, Oddershede, Nature Communications vol 5 p. 5720 (2014)
16:45 Engineering sensorial delay, nonadditivity of critical Casimir forces, and control of active matter systems - Giovanni Volpe (Bilkent University, Ankara)
Engineering sensorial delay, nonadditivity of critical Casimir forces, and control of active matter systems
- Giovanni Volpe (Bilkent University, Ankara)
16:45 - 17:30
Room: 122:026 In this talk I will present three projects we have recently completed: 1) Engineering sensorial delay to control the behaviour of a group of robots. Ensembles of autonomous agents, such as swarms of insects, human crowds and groups of robots, exhibit collective behaviors independent of each agent's specific motion. In this work, we have shown that time delays between signal sensing and processing affect the individual and collective long-term behaviors. Sensorial delay can therefore be used as a novel parameter to control these behaviors [1]. 2) Experimental measurement of the nonadditivity of critical Casimir forces. Critical Casimir forces are potentially a powerful tool to control the self-assembly and complex behavior of micro- and nanoparticles. In order to fully exploit their potential, it is crucial to understand whether and to what extent many-body forces are in action. Despite having been predicted theoretically, their experimental demonstration has been lacking. Employing holographic optical tweezers, we provided the first experimental demonstration of the nonadditivity of critical Casimir forces [3]. 3) Controlling active matter in disordered potentials. Many living systems, such as bacterial colonies, exhibit collective and dynamic behaviors that are sensitive to changes in environmental conditions. Our results show that a colloidal active matter system switches between gathering and dispersal of individuals in response to the roughness of an attractive potential generated by extended light fields [3]. [1] M Mijalkov, A. McDaniel, J. Wehr & G Volpe, “Engineering Sensorial Delay to Control Phototaxis and Emergent Collective Behaviors,” Phys. Rev. X 6, 011008 (2016). [2] S Paladugu, A Callegari, Y Tuna, L Barth, S Dietrich, A Gambassi & G Volpe, “Nonadditivity of Critical Casimir Forces,” Arxiv, 1511.02613 (2015). [3] E Pince, SKP Velu, A Callegari, P Elahi, S Gigan, G Volpe & G Volpe, “Disorder-mediated crowd control in an active matter system,” Nature Commun. 7, in press (2016).
19:00 Conference dinner
Conference dinner
19:00 - 21:30
Room: 122:026
Friday, 18 March 2016
09:00 Anisotropic sensing of membrane curvature - Martin Lindén (Dept. och Cell and Molecular Biology, Uppsala University)
Anisotropic sensing of membrane curvature
- Martin Lindén (Dept. och Cell and Molecular Biology, Uppsala University)
09:00 - 09:45
Room: 122:026 Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodeling cell membranes. However, the molecular driving forces behind these processes are not well understood. I will describe a new approach to study curvature sensing, by simulating the direction-dependent interactions of single molecules with a buckled lipid bilayer. In particular, I will describe results for three antimicrobial peptides, a class of membrane-associated molecules that specifically target and destabilize bacterial membranes, where we find surprisingly different sensing characteristics that would be difficult to resolve with other methods. These results challenge existing continuum theories of curvature sensing by hydrophobic insertion, and prompts the developments of more detailed curvature sensing models. Time permitting, I will also describe ongoing work to improve the computational efficiency of the method, generalize the theory to describe the role of structural symmetry for curvature sensing, and implications for improved experimental approaches.
09:45 Thermodynamic bounds to information harvesting in sensory systems - Stefano Bo (Nordita)
Thermodynamic bounds to information harvesting in sensory systems
- Stefano Bo (Nordita)
09:45 - 10:30
Room: 122:026 To be able to survive and prosper, cells need to acquire, exchange and process information under noisy conditions. Recording multiple measurements is an effective way of reducing the noise. It is known in general that handling information has a thermodynamic cost. Inspired by this biological problem and in view of the relation between information and thermodynamics we investigate how much information about an external protocol can be stored in the memory of a stochastic measurement device given an energy budget. We consider a layered system with a memory component storing information about the external environment by monitoring the history of a sensory part coupled to the environment. We derive an integral fluctuation theorem for the entropy production and a measure of the information accumulated in the memory device. Its most immediate consequence is that the amount of information is bounded by the average thermodynamic entropy produced by the process. At equilibrium no entropy is produced and therefore the memory device cannot add any information and is superfluous. Such a device can be used to model the sensing process of a cell measuring the external concentration of a chemical compound and encoding the measurement in the amount of phosphorylated cytoplasmic proteins.
10:30 Coffee break
Coffee break
10:30 - 11:00
Room: 122:026
11:00 The effect of particle and fluid inertia on the dynamics of particles in flows - Bernhard Mehlig (Gothenburg University)
The effect of particle and fluid inertia on the dynamics of particles in flows
- Bernhard Mehlig (Gothenburg University)
11:00 - 11:45
Room: 122:026 The dynamics of a very small particle suspended in a fluid flow is simple: the centre-of-mass is advected by the fluid velocity, and the angular dynamics is determined by the sequence of fluid-velocity gradients that the particle experiences. For larger particles inertial effects may become important. Particle inertia is relatively straightforward to treat and there has recently been substantial progress in understanding its effect upon the dynamics of particles in flows [1]. The effect of fluid inertia, by contrast, is more difficult to describe. In this talk I will review what is known about the effect of weak fluid inertia upon the translational and angular motion of particles in flows. I will describe new results on the effects of weak fluid inertia on the rotation of neutrally buoyant spheroidal particles in a simple shear flow [2,3] [1] K. Gustavsson and B. Mehlig, Statistical models for spatial patterns of heavy particles in turbulence, submitted to Adv. Phys. (2016) [2] J. Einarsson, F. Candelier, F. Lundell, J.R. Angilella, and B. Mehlig, Rotation of a spheroid in a simple shear at small Reynolds number, Phys. Fluids 27, 063301 (2015) [3] T. Rosen, J. Einarsson, A. Nordmark, C. K. Aidun, F. Lundell, and B. Mehlig, Numerical analysis of the angular motion of a neutrally buoyant spheroid in shear flow at small Reynolds numbers, Phys. Rev. E 92, 063022 (2015)
11:45 Cell Dynamics and Arnold Tongues - Mogens Hogh Jensen (Niels Bohr Institute, University of Copenhagen)
Cell Dynamics and Arnold Tongues
- Mogens Hogh Jensen (Niels Bohr Institute, University of Copenhagen)
11:45 - 12:30
Room: 122:026 Oscillating genetic patterns have been observed in networks related to the transcription factors NFkB, p53 and Hes1. We have identified the central feed-back loops leading to oscillations. By applying an external periodic signal, it is possible to lock the internal oscillation to the external signal. For the NF-kB systems in single cells we have observed that the two signals lock when the ration between the two frequencies is close to basic rational numbers. The resulting response of the cell can be mapped out as Arnold tongues. When the tongues start to overlap we may observe a chaotic dynamics of the concentration in NF-kB. The group of Savas Tay (ETH, Zurich) has in single cell dynamics of the NF-kB system observed transitions from one tongue to the other when they overlap. We investigate this effect by Gillespie simulations and find interesting time correlation for the transitions probabilities when switching from one tongue to the other.
12:30 Lunch
Lunch
12:30 - 14:00
Room: 122:026

14:00 Free discussion
Free discussion
14:00 - 17:00
Room: 122:026