Opening Room: 132:028

Statistical mechanics of unknown unknowns

• Yasser Roudi (NTNU, Kavli Institute for Systems Neuroscience)

Room: 132:028 Our understanding of complex systems is typically limited by the fact that we only see a fraction of the variables describing these systems: we only see parts of a financial market, we typically only see and analyze subparts of a protein protein interaction network, and we can only record from the activity of few cells in the brain; a potentially large number of variables in these systems are not directly observed and measured. In addition to the existence of unknown (hidden) variables, we face the problem that we cannot even monitor the known (observed) variables for a very long time, that is, we may have under-sampled data. In many cases we may not even know that other variables beyond what we see exist and influence our system, that is we may be dealing with "unknown unknowns". What is the effect of this incomplete data? This question can be posed as a problem of inference in the presence of latent variable, something that people in machine learning are very interested in. In this talk, I will describe some results on how not knowing the relevant variables influences our effort in modeling complex systems. I will describe recent advances in statistical modeling of data in which by using techniques from non-equilibrium statistical physics we can build efficient approaches to take into account the influence of hidden variable. References. B. Dunn, Y. Roudi (2013) in press, arXiv:1301.7275v1 M. Marsili, I. Mastromatteo, Y. Roudi (2013) arxiv 2013 arXiv:1301.3622v2 J. Tyrcha, J. Hertz (2013) arXiv:1301.7274v1

Mean field theory and Bayesian inference in single molecule biophysics

• Martin Linden (Stockholm University, DBB/CBR)

Room: 132:028 Single molecule experiments opens new windows to molecular biology and biophysics, by allowing us to follow individual proteins at work in real time. However, instrumental artifacts and the inherent randomness of Brownian motion and low copy number chemistry often makes for noisy data that can be challenging to interpret. A very common problem is to analyze noisy time series with abrupt changes, reflecting for example binding events, or conformational changes in a protein complex. I will describe an approach to tackle such problems using physical modeling and a Bayesian version of mean field theory, and show results for two techniques that use diffusive motion as a reporter on the underlying chemical or conformational state: single particle tracking of fluorescent proteins in vivo, and DNA looping experiments using tethered particle motion in vitro.

Resilience of social-ecological systems

• Steven Lade (Stockholm Resilience Center)

Room: 132:028 ‘Resilience’ is emerging as a key concept that researchers and organisations (including the United Nations and the World Bank) use to understand and deal with many of the problems facing contemporary environment and society. In this talk I provide an overview of research on the resilience of social-ecological systems and how physicists could contribute to its future development. I illustrate this theme with some recent results from my own work. Local stability concepts of nonlinear dynamics are closely linked to the original, resistance to shock conception of resilience. Studies based on nonlinear dynamical approaches can still provide insights into the dynamics of social-ecological systems. This is particularly true with respect to regime shifts, a type of sudden change in a social-ecological system that is closely related to fold bifurcations. I summarise one recent work in which I used the recently developed nonlinear dynamical tool of generalised modelling to better understand regime shifts of a social-ecological system. Rather than analyse bifurcations for a specific model, generic modelling can identify bifurcations in a model class. The social-ecological system that we modelled consisted of a community of harvesters that could each choose whether to harvest a common pool resource at a community-efficient level or at a higher, self-interested level that led to overharvesting of the resource. The co-operators encourage the defectors to co-operate through a social ostracism mechanism. Among other results, we show that a nonlinear social-ecological coupling can lead to a regime shift even if there were none in the isolated social and ecological subsystems. Resilience concepts are often used in a qualitative or heuristic manner to inspire particular research questions or management approaches. One recent line of research where resilience has become more quantitative is in the study of early warning signals for regime shifts. Here, generic early warning signals for regime shifts are calculated from time series observations. For example, an increasing variance can indicate a loss of stability and impending regime shift. Using the generalised modelling approach introduced above, I developed a generalised modelling-based early warning signal that can incorporate system-specific information into a generic early warning signal approach. More recently, however, the understanding of resilience has expanded beyond local stability to include the ability of a system to adapt and transform in response to threats and challenges. So far modelling studies have generally not kept pace with these conceptual developments, but as I will outline network perspectives show potential to do so. Brainstorming on other modelling approaches that may meet modern challenges of resilience research will also be most welcome.

Instability patterns in thin nematic & smectic films

• Oksana Manyuhina (Nordita)

Room: 132:028 The formation of spatially periodic patterns is a well-known phenomenon in physics of liquid crystals. Nevertheless, new experiments often pose questions which cannot be answered by the existing theories. For example, the experiments in the group of Anne-Marie Cazabat in Paris, demonstrated that thin nematic films, spread on liquid substrates, exhibit a long-wavelength periodically deformed stripe state up to the thickness of 20 nm. The formation of this instability pattern can be attributed to the response of the system to the antagonistic boundary conditions. To get a theoretical insight on the experimental findings, we (re)consider the onset of stripe instability and (re)examine the role of surface-like terms. Another experiments, performed by Giorgia Tordini and Peter Christianen in Nijmegen, suggest the formation of a finger-like pattern, when smectic order, characterised by equally spaced layers, is imposed on the bent nematic structure. I propose a simple geometric approach of constructing the space-filling energy minimising structure, which accounts for the bending of smectic layers and yields two distinct wavelengths, compatible with experimental data.

Strongly correlating liquids and their isomorphs: With applications to confined and non-equilibrium liquids

• Trond Ingebrigtsen (Roskilde University)

Room: 132:028 In a series of articles [1–5] a new class of liquids was identified, namely the class of strongly correlating liquids. These liquids are characterized by having isomorphs to a good approximation. Isomorphs [4] are curves in a liquid’s phase diagram along which structure and dynamics are invariant in reduced units, as well as some thermodynamic quantities. We present here an overview of strongly correlating liquids, their isomorphs and some of the consequences of isomorphs in a liquid’s phase diagram. For instance, it has recently been shown that strongly correlating liquids have a simple thermodynamics [6] as well as simple liquid-state physics [7] . Examples of the isomorph theory are taken from: 1) Spatially confined liquids showing stratification and position-dependent relaxation processes when confined to the nano-scale. 2) Non-equilibrium liquids simulated via the SLLOD equations of motion for Couette shear flow [8]. [1] N. P. Bailey, U. R. Pedersen, N. Gnan, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 129, 184507 (2008). [2] N. P. Bailey, U. R. Pedersen, N. Gnan, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 129, 184508 (2008). [3] T. B. Schrøder, N. P. Bailey, U. R. Pedersen, N. Gnan, and J. C. Dyre, J. Chem. Phys. 131, 234503 (2009). [4] N. Gnan, T. B. Schrøder, U. R. Pedersen, N. P. Bailey, and J. C. Dyre, J. Chem. Phys. 131, 234504 (2009). [5] T. B. Schrøder, N. Gnan, U. R. Pedersen, N. P. Bailey, and J. C. Dyre, J. Chem. Phys. 134, 164505 (2011). [6] T. S. Ingebrigtsen, L. Bøhling, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 136, 061102 (2012). [7] T. S. Ingebrigtsen, T. B. Schrøder, and J. C. Dyre, Phys. Rev. X 2, 011011 (2012). [8] L. Separdar, N. P. Bailey, T. B. Schrøder, S. Davatolhagh, and J. C. Dyre, arXiv 1, 1212.4480v1 (2012).

Incorporation of the charge structure of water into electrostatics at the nanoscale

• Sahin Buyukdagli (Aalto University School of Science)

Room: 132:028 Water mediated electrostatic interactions between charged macromolecules and ions are omnipresent in various nanoscale systems. From the charge selectivity of ionic channels in cells and artificial nanofiltration membranes to the energy storage ability of supercapacitors, these interactions are at the heart of many biological and industrial processes. An accurate formulation of electrostatics is thus necessary to understand the functioning of these systems, and also for the conception of new generation nanoscale devices with optimized efficiency. However, for several decades, the theoretical understanding of electrostatic interactions has been limited to dielectric continuum models such as the Poisson-Boltzmann (PB) formalism that bypass the charge structure of the water solvent. The talk will focus on newly developed theoretical approaches that aims at overcoming this limitation by incorporating the charge structure of solvent molecules into the current formulation of electrostatics. In the first part of the talk, I will introduce the key electrostatic forces that are in play in nanoscale systems, and explain the modeling of these forces within the classical formulation of electrostatics. Then, I will outline the main drawbacks of the classical PB approach and present a more general dipolar PB (DPB) approach that considers the solvent molecules on the same footing as the ions [1,2]. Being a MF theory that models the solvent molecules as point dipoles, this extended approach neglects both electrostatic correlation effects and the non-local dielectric response of water. The remaining part of the talk will focus on improved formulations that overcome these two limitations. The second part of the talk will be devoted to an extended DPB (EDPB) formalism, still based on the point dipole approximation, but able to account for electrostatic correlations beyond the MF level of approximation [3]. This new approach is particularly adequate for predicting the energy storage ability of carbon based supercapacitors, which are efficient nanoscale devices where electrostatic interactions bring the most important contribution to the structure of the double layer in the neighborhood of the electrode surface. I will show that unlike the PB and DPB approaches that largely overestimate the experimental differential capacitance data, the EDPB formalism that can account for the surface polarization effects driven by electrostatic correlations exhibits a good agreement with experimental capacitance data of carbon based materials, thus correcting the predictions of the previous MF theories by one order of magnitude. I will present in the third part of the talk a microscopic reformulation of non-local electrostatics that goes beyond the point-dipole approximation. By explicitly accounting for the discrete charge composition of solvent molecules, the microscopic polar liquid model embodies for the first time non-local electrostatic interactions at the molecular level of precision. I will show that unlike the previous DPB and EDPB formalisms that yields a local picture of solvent partition at charged surfaces, the new formalism is able to reproduce several characteristics of the interfacial non-local dielectric response behavior of water solvent revealed in Molecular Dynamics simulations [4] and Atomic Force experiments [5]. Within the same theoretical framework, I will discuss the hydration induced modification of the bare ionic polarizability, which is believed to be the most important ion specific effect on the interfacial behavior of inhomogeneous electroltyes. I will conclude by presenting a brief summary of open questions in the theoretical modeling of polar liquids. [1] Rob D. Coalson, A. Duncan and N. B. Tal, J. Phys. Chem. 100, 2612 (1996). [2] A. Abrashkin, D. Andelman, and H. Orland, Phys. Rev. Lett. 99, 077801 (2007). [3] S. Buyukdagli and T. Ala-Nissila, Europhys. Lett. 98, 60003 (2012). [4] O. Teschke, G. Ceotto, and E. F. de Souza, Phys. Rev. E 64, 011605 (2001). [5] V. Ballenegger and J.-P. Hansen, J. Chem. Phys. 122, 114711 (2005).

The search mechanisms of the restriction enzyme EcoRV

• Michael Anderson Lomholt (University of Southern Denmark)

Room: 132:028 The restriction enzyme EcoRV searches for its specific target on DNA via facilitated diffusion exploiting a combination of 1D sliding along DNA and 3D bulk diffusion. This has been demonstrated in several experiments. However, in vitro measurements of the overall search time of EcoRV give results that are much smaller than the predictions of standard models for facilitated diffusion. The discrepancy can be explained by EcoRV having an inactive state. But this seems to introduce a paradox, since the survival of E. coli bacteria depends on the efficiency of the EcoRV target search. In this talk I will explain how this paradox can be resolved under in vivo conditions, and how the inactive state turns out to be an advantage under conditions leading to subdiffusion.

Mesoscopic non-equilibrium thermodynamic analysis of molecular motors

• Signe Kjelstrup (Norwegian University of Science and Technology)

Room: 132:028 We show that the kinetics of a molecular motor fuelled by ATP and operating betweeen a deactivated and activated state, can be derived from the principles of non-equilibrium thermodynamics for the mesoscopic domain [1, 2]. As example we study muscle contraction. The activation by ATP, the possible slip of the motor, as well as the forward stepping carrying a load, are viewed as slow diffusion along a reaction coordinate. Local equilibrium is assumed in the reaction coordinate spaces, making it possible to derive the non-equilibrium thermodynamic description. Using this scheme, we find non-linear expressions for the velocity of the motor, in terms of the driving force along the spacial coordinate, and in terms of the chemical potentials of the reactants and products which maintain the cycle. The second law efficiency is defined, and the velocity corresponding to maximum power is obtained. Experimental results taken from the literature [3], support the description, and give a maximum efficiency near 0.6 at a muscle filament velocity of 5Å/ms. The formalism proposed can be applied to other non-equilibrium activated processes, say of protein binding or DNA stretching. It opens the possibility for detailed molecular models, which may be needed to explain experiments. References [1] S. Kjelstrup, J.M. Rubi, D. Bedeaux, Phys. Chem. Chem. Phys. 2005, 7, 4009. [2] A. Lervik, D. Bedeaux, and S. Kjelstrup, Eur. Biophys. J. 2012, 41, 437 [3] T. Førland, Biophys. J. 1985, 47, 665.

Magnetic-field symmetry of thermoelectric transport

• Heiner Linke (Nanometer Structure Consortium, Lund University)

Room: 132:028 Symmetry relationships such as the Onsager relations, which are based on the principle of microreversibility, are cornerstones of physics. In the context of mesoscopic physics, symmetries of the conductance in two-terminal and multiterminal devices have been explored in great detail [1,2,3]. Here, we extend these studies to the case where combined thermal and electric (thermoelectric) biases are present. Also for this case, symmetry relations have been predicted, but it has also been predicted that these relations break down at the transition from quantum to classical behavior. An experimental test is therefore necessary. We have experimentally investigated the magnetic field dependence of thermoelectric transport properties in a four-terminal micro-junction, with heat and voltage reservoirs attached to each terminal [4,5]. The linear response thermoelectric coefficients are found to be symmetric under a simultaneous reversal of magnetic field and exchange of injection and emission terminals, confirming the generality of the magnetic-field symmetries. In the non-linear thermal bias regime we find signatures of a break-down of the symmetries, raising new fundamental questions about the mechanism of this breakdown. References [1] Büttiker, M., Symmetry of electrical conduction. IBM J. Res. Developm., 32(3), 317 (1988). [2] Löfgren, A., Marlow, C., Shorubalko, I., Taylor, R., Omling, P., Samuelson, L., & Linke, H., Symmetry of two-terminal nonlinear electric conduction. Physical Review Letters, 92(4), 046803 (2004). [3] Marlow, C., Taylor, R., Fairbanks, M., Shorubalko, I., & Linke, H., Experimental investigation of the breakdown of the Onsager-Casimir relations. Physical Review Letters, 96(11), 116801 (2006). [4] Matthews, J., Sánchez, D., Larsson, M., & Linke, H., Thermally driven ballistic rectifier. Physical Review B, 85(20), 205309 (2012) [5] J. Matthews et al., to be submitted (2013).

Energy Fluctuations and Maxwell’s Demon in Nano-electronic Circuits

• Jukka Pekola (Aalto University School of Science)

Room: 132:028 In nanostructures fluctuations of energy play an important role, and the second law of thermodynamics, for example, applies only on the average. The distribution of entropy production and the work performed under non-equilibrium conditions are then governed by so-called fluctuation relations [1-3]. I apply these concepts to a simple single-electron box [4,5], and present an experimental demonstration of basic fluctuation relations in them [6,7]. Single-electron circuits provide furthermore a basic example of a Maxwell’s Demon, where information can be converted into energy [8]; here the information is collected by a detector with single-electron sensitivity. Finally I discuss the subtle issues of work and heat in open quantum systems. I use superconducting qubits as examples of driven systems in this context [9,10]. [1] C. Jarzynski, Nonequilibrium equality for free energy differences, Phys. Rev. Lett. 78, 2690 (1997). [2] G. E. Crooks, Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences, Phys. Rev. E 60, 2721 (1999). [3] U. Seifert, Entropy Production along a Stochastic Trajectory and an Integral Fluctuation Theorem, Phys. Rev. Lett. 95, 040602 (2005). [4] D.V. Averin and J.P. Pekola, Statistics of the dissipated energy in driven single-electron transitions, EPL 96, 67004 (2011). [5] J. P. Pekola and O.-P. Saira, Work, Free Energy and Dissipation in Voltage Driven Single-Electron Transitions, J. Low Temp. Phys. 169, 70 (2012). [6] O.-P. Saira, Y. Yoon, T. Tanttu, M. Möttönen, D. V. Averin, and J. P. Pekola, Test of Jarzynski and Crooks fluctuation relations in an electronic system, Phys. Rev. Lett. 109, 180601 (2012). [7] J. V. Koski et al., Distribution of entropy production in nonequilibrium single-electron tunneling, in preparation (2013). [8] D. V. Averin, M. Möttönen, and J. P. Pekola, Maxwell's demon based on a single-electron pump, Phys. Rev. B 84, 245448 (2011). [9] P. Solinas, D. V. Averin, and J. P. Pekola, Work and its fluctuations in a driven quantum system, arXiv:1206.5699 (2012). [10] J. P. Pekola, P. Solinas, A. Shnirman, and D. V. Averin, Calorimetric measurement of quantum work, arXiv:1212.5808 (2012).

Weak Noise in Non Equilibrium

• Hans Fogedby (University of Aarhus)

Room: 132:028 We develop a weak noise scheme addressing problems in non equilibrium statistical physics. The evaluation of transition probabilities is expressed in terms of a classical action in a Hamiltonian framework. We consider as examples: 1) free brownian particle, 2) over damped particle in harmonic potential, 3) noisy finite singularity, and 4) the Kardar-Parisi-Zhang equation for a growing interface.

The Maxwell Demon: A Personal View

• Juan Parrondo (Universidad Complutense de Madrid)

Room: Oskar Klein Auditorium Information can be used to extract energy from a single thermal bath, in apparent contradiction with the Second Law of Thermodynamics. This observation was first pointed out by Maxwell in 1867 with the introduction of his celebrated demon. Since then, the demon has inspired much research on the relationship between information and entropy, most of it focused on the thermodynamic cost of the acquisition and processing of information. In the last years, new tools for the study of the energetics of small fluctuating systems –the so-called fluctuation theorems- have provided a better understanding of the thermodynamics of information. In this seminar, I will review part of the history of the Maxwell demon, with special emphasis on these recent results, trying to give some clues to the fundamental question: what is information?

Criticality in Dynamic Arrest: Correspondence between Glasses and Traffic

• Astrid de Wijn (Stockholm University)

Room: 132:028 Dynamic arrest is a general phenomenon across a wide range of dynamic systems including glasses, traffic flow, and dynamics in cells, but the universality of dynamic arrest phenomena remains unclear. We connect the emergence of traffic jams in a simple traffic flow model directly to the dynamic slowing down in kinetically constrained models for glasses. In kinetically constrained models, the formation of glass becomes a true (singular) phase transition in the limit $T\rightarrow 0$. Similarly, using the Nagel-Schreckenberg model to simulate traffic flow, we show that the emergence of jammed traffic acquires the signature of a sharp transition in the deterministic limit $p\rightarrow 1$, corresponding to overcautious driving. We identify a true dynamic critical point marking the onset of coexistence between free flowing and jammed traffic, and demonstrate its analogy to the kinetically constrained glass models. We find diverging correlations analogous to those at a critical point of thermodynamic phase transitions.

Long-range ordered vorticity patterns induced by cell division

• Lene Oddershede (Niels Bohr Institute)

Room: 132:028 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 is significantly increased during embryonic development and in unhealthy endothelium with halted or turbulent blood flows. Cells in a tissue are connected and their motility highly correlated. Here, we investigate the long-range dynamics induced by cell division in an endothelial monolayer under non-flow conditions, mimicking the conditions during vessel formation or healing around blood clots. We demonstrate that a cell division induces a long-range ordered pattern of vortices in the monolayer. Two pairs of primary vortices arise adjacent to the dividing cell, and eight pairs of secondary and tertiary vortices appear several cell diameters away. The occurrence of ordered vortices is surprising considering the system's low Reynolds number and may be crucial for embryonic development and healing of endothelial tissue.

Fluid dynamics of liquid-granule mixture

• Namiko Mitarai (Niels Bohr Institute)

Room: 132:028 Wet granular materials shows behavior very different from that of dry granular materials, and the behavior depends strongly on the amount of the liquid. When grains are partially wet, the liquid bridges and clusters exert the cohesive force among grains [1]. For larger amount of liquid, the pores among grains are filled and the system becomes dense slurry, where both grain-liquid interaction and grain-grain interaction play important roles [2-4]. In this talk, we introduce simple models to describe the behavior of wet granular materials [1-3]. We especially focus on a model for a dense mixture of granules and liquid, that shows a severe shear thickening and is called a dilatant fluid. We construct a fluid dynamics model for the dilatant fluid by introducing a phenomenological state variable for a local state of dispersed particles [2,3]. We demonstrate that the model can describe basic features of the dilatant fluid, and predicts an instability in a shear flow for some regime to exhibit the shear thickening oscillation, i.e., the oscillatory shear flow alternating between the thickened and the relaxed states [2,3]. We also report the first experimental observation of the shear thickening oscillation with starch-water mixture in the Tayler-Couette flow geometry [4]. REFERENCES [1] N. Mitarai and H. Nakanishi, "Simple model for wet granular materials with liquid clusters", Eur. Phys. Lett. 88 64001 (2009). [2] H. Nakanishi and N. Mitarai, “Shear Thickening Oscillation in a Dilatant Fluid”, J. Phys. Soc. Jpn, 80, 033801 (2011). [3] H. Nakanishi, S. Nagahiro, and N. Mitarai, “Fluid dynamics of dilatant fluids”, Phys. Rev. E, 85, 011401 (2012). [4] S. Nagahiro, H. Nakanishi, and N. Mitarai, “Experimental observation of shear thickening oscillation”, arXiv:1211.2886 (2012).

Tumbling rates in turbulent and random flows

• Bernhard Mehlig (University of Gothenburg)

Room: 132:028 The dynamics of turbulent aerosols (suspensions of particles in turbulent flows) is important for the understanding of key processes in the Natural Sciences and Technology (turbulent rain clouds, planet formation in circumstellar accretion disks, and fibre suspensions, to name but a few). In recent years our understanding of the dynamics of turbulent aerosols has increased substantially, by means of direct numerical simulations, and by model calculations - often based on idealised models of the underlying flow and of the interactions between the flow and the particles. The analysis of models of spherical particles moving subject to Stokes force in random flows (with the appropriate statistics) has contributed to our understanding of the fundamental mechanisms giving rise to spatial clustering and collisions between spherical point particles suspended in such flows. Less is known about the dynamics of asymmetrical, non-spherical particles, despite the fact that non-spherical particles are of interest in a wide range of contexts. For example, tumbling ice particles in turbulent clouds may play an important role in cloud-particle interactions. Dust grains in circumstellar accretion disks are not spherically symmetric and the relative orientation at which such grains collide may have important consequences for the outcome of the collision process. The competition between tumbling and rotational diffusion of non-spherical particles determines the rheology of fibrous suspensions. Singularities in the orientation field of non-spherical particles determine the orientational patterns of rheoscopic suspensions. Recently, the tumbling rate of small particles in turbulent flows was investigated experimentally and by means of direct numerical simulations. It was found that disks tumble, on average, at a much higher rate than rods, and this fact was related to the observation that rods tend to preferentially align with the vorticity of the flow. We have analysed the tumbling of small non-spherical particles in random flows with finite correlation length and time. We compute the orientational dynamics systematically in terms of a perturbation expansion in the Kubo number. This makes it possible to address the following questions. First, how and when do disks and rods tumble differently? How does the nature of the Lagrangian flow statistics influence the tumbling? What is the effect of inertia on the orientational dynamics of small particles? We compare the results to those of recent experimental and numerical studies of non-spherical particles tumbling in turbulent flows.

Discussions/Closing Room: 132:028