Opening Room: FB42

Modeling nucleosome mediated epigenetics

• Kim Sneppen (NBI)

Room: FB42 In the talk I will discuss how localized part of an eucaryotic genome can be bistable. Bistable systems open for epigentics, a central theme in regulation of living cells. It is demonstrated that both copperativity and non-local interactions along the DNA are needed to obtain bistability. Further various localization mechanisms are discussed, with aim of explaining how the system maintain boundaries between silenced and active regions along the chromosome.

Non-Equilibrium Phase Transitions in Biomolecular Signal Transduction

• Supriya Krishnamurthy (KTH and Stockholm University)

Room: FB42 We study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. <br>We find that multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration. Bistability occurs as either a first-order or second-order non-equilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. We also find that the number of substrate molecules is a key parameter controlling the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory using functional integral methods from reaction-diffusion theory.

Growth efficiency as a cellular objective in Eschericia coli

• Olli Yli-Harja (Tampere University of Technology)

Room: FB52 Tommi Aho (1), Juha Kesseli (1), Olli Yli-Harja (1), Stuart A. Kauffman (2) <br>(1) Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 1, 33720 Tampere, Finland <br>(2) Complex Systems Center, University of Vermont, U.S.A <br>The shortage of nutrients is one of the most common challenges that organisms confront. Thus, nature has developed various highly efficient systems for processing nutrients, e.g. enzymes that efficiently transform substrates to products. Here, we study transformation efficiency in another level, namely in bacterial metabolism. We use a metabolic model of Eschericia coli to examine growth efficiency, i.e. the transformation efficiency of substrates to new biomass. We find that under the common assumption of maximal growth, the growth efficiency remains sub-optimal. We find that in the E. coli model the maximal growth efficiency is obtained at a finite nutrient uptake rate. We examine whether the growth efficiency could serve as the cellular objective in metabolic modeling, and find that cellular growth can be predicted reasonably well under this assumption. <br>Maximal growth efficiency is a plausible candidate as the cellular objective under the examined cultivation conditions in E. coli. Transformation efficiency in general could be studied as a functional design principle of cellular systems.

Bacterial motility and pilus dynamics

• Mats Wallin (KTH)

Room: FB52 Certain bacteria can crawl on moist surfaces using a mechanism that involves extension and retraction of extracellular pilus filaments. The mechanism and cell motion has been studied in various experiments on cell level and on single molecule level, for example, live cell imaging of pilus dynamics. This talk presents modeling approaches of the dynamics and some results that characterize the mechanism of cell motility.

Intracellular diffusion and kinetics at the level of single molecules

• Johan Elf (Uppsala University)

Room: FB52 I will present our resent advancements in tracking individual freely diffusing fluorescent proteins molecules at in the cytoplasm of bacterial cells. High speed tracking of individual mEos2 molecules reveals how the physical nature of the bacterial cytoplasm is perceived by a protein molecule. In vivo tracking of individual fusion proteins further makes it possible to study intracellular kinetics high time resolution without synchronizing the population of molecules. For example by monitoring the ribosome binding kinetics of the key regulatory enzyme RelA, we have developed a single molecule assay to study stress response and amino acid starvation at the level of individual bacteria.

Hierarchical organization of large integrated systems

• Martin Rosvall (Umeå University)

Room: FB52 Ever since Aristotle, organization and classification have been cornerstones of science. In network science, categorization of nodes into modules with community-detection algorithms has proven indispensable to comprehending the structure of large integrated systems. But in real-world networks, the organization rarely is limited to two levels, and modular descriptions can only provide cross sections of much richer structures. For example, both biological and social systems are often characterized by hierarchical organization with submodules in modules over multiple scales. In many real-world networks, directed and weighted links represent the constraints that the structure of a network places on dynamical processes taking place on this network. Networks thus often represent literal or metaphorical flows: people surfing the web, passengers traveling between airports, ideas spreading between scientists, funds passing between banks, and so on. This flow through a system makes its components interdependent to varying extents. In my talk, I will present our information-theoretic approach to reveal the multiple levels of interdependences between the nodes of a network.

Temporal network structure of human contact patterns and its implication for disease dynamics and control

• Petter Holme (Umeå University)

Room: FB52 Contacts between individuals form the infrastructure over which diseases spread. Such contact patterns are far from randomÑthere are correlations both in the network of who has been in contact with whom, and when these contacts happen. These structures affect the dynamics of disease spreading but can also be exploited in preventive action such as vaccination campaigns. In this talk, I will use datasets from the proximity of patients in hospitals, online dating services and Internet-mediated prostitution to discuss some methods to analyze such temporal network structures and evaluate their effects on disease spreading. I will also discuss targeted immunization protocols utilizing such structures.

Inferring network structure using dynamical mean-field theory

• Yasser Roudi (Norwegian University of Science and Technology)

Room: FB42 I will describe how interactions in a non-equilibrium Ising model can be inferred from observing state samples. We will start by a short review of how this could be done for equilibrium systems and then study how Dynamical Mean-Field (naive mean field and TAP) theory can be developed for a nonequilibrium Sherrington-Kirkpatrick model and exploited for inferring the network connectivity. We will also quantify the error in inferring the connectivity in the high temperature regime.

Statistical physics of DNA melting in nanochannels

• Tobias Ambjörnsson (Lund University)

Room: FB42 The new melting map approach developed in our collaborator Jonas Tegenfeldt's lab at Gothenburg University constitutes a promising ultra-fast alternative to previous DNA sequencing techniques. Fluorescently stained DNA is stretched in nanochannels and subsequently heated. The resulting local melting will reduce the quantum yield of an intercalating fluorescent dye such that black spots will occur along the DNA. Since AT and GC basepairs have different melting propensities the result is essentially a "barcode" that is a function of the sequence of the DNA and that can thus be used to identify the DNA from different organisms. <br>In this talk issues related to theoretical DNA melting calculations will be discussed. The Poland-Scheraga (PS) model of DNA melting has been proven to well reproduce (macroscopic) melting data. The PS model is an Ising model with a long-range term, expressed in terms of a critical random walk exponent c, due to the entropy associated with the melted single-stranded regions. The solution to two new problems in the DNA melting field will be addressed in the talk: <br>1) The numerical solution of the PS model is computationally prohibitive for bacterial genomes with 10⁷ basepairs of interest in experiments. We therefore recently developed a coarse-grained approximate scheme for performing DNA melting calculations for heterogeneous DNA sequences, as a function of local fraction of AT and GC basepairs. <br>2) The problem of DNA melting for infinite homogeneous DNA sequences has been solved previously. In the talk finite-size effects in homoDNA melting will be discussed.

In silico studies of protein misfolding and aggregation

• Anders Irbäck (Lund University)

Room: FB42 The aggregation of misfolded proteins into oligomers and fibrils has been linked to a variety of disorders such as Alzheimer's and Parkinson's diseases. The conformational mechanisms involved in the aggregation process remain incompletely understood. Here I present results from a Monte Carlo study of monomers and dimers of the 42-residue Abeta42 protein, associated with Alzheimer's disease. A comparison of results obtained for wild type Abeta42 and three mutants hints at specific conformational properties that might play a key role in aggregation. I also present results from an on-going study of protofibril formation for a 6-residue fragment of protein tau, based on simulations with up to 500 chains.

Coarse-graining polymers with the MARTINI approach

• Giulia Rossi (Aalto University School of Science)

Room: FB42 G. Rossi (1), L. Monticelli (2), S. R. Puisto (3), N. Rostedt (3), I. Vattulainen (4) and T. Ala-Nissilä (1) <br>(1) Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, 00076 Aalto, Espoo, Finland <br>(2) INSERM, UMR-S 665, DSIMB, 6 rue Alexander Cabanel, 75015 Paris, France <br>(3) MatOx Pembroke House, 36-37 Pembroke Street, Oxford OX1 1BP, United Kingdom <br>(4) Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland <br>Optimization of polymer properties in industrial applications is generally achieved by controlling the fine details of their chemical composition, often through expensive and time-consuming trial-and-error procedures. Computer modelling can speed up these procedures by predicting changes in material properties as a function of chemical composition. Unfortunately, the classical simulations of polymer melts from atomistic detail are subject to stringent limitations to the time and length scales of the phenomena that can be observed. <br>Coarse-graining strategies can help to overcome these limitations. Coarse-graining involves grouping clusters of atoms into super-atoms, or beads. Coarse-grained (CG) models are computationally faster than atomistic ones thanks to a reduction in the number of degrees of freedom and the use of smoother interaction potentials, allowing for longer time step in molecular dynamics (MD) simulations. We introduce a new hybrid thermodynamic-structural approach to the coarse- graining of polymers. The new model is developed within the framework of the MARTINI force-field [Marrink et al., J. Phys. Chem. B, 2007, 111, 7812], which uses mainly thermodynamic properties as targets in the parameterization. Density and structural properties of the polymer melt can be used to refine the force-field parameterization. We test our procedure on polystyrene [G. Rossi et al., Soft Matter, DOI:10.1039/C0SM00481B], a standard benchmark for coarse-grained polymer force-fields. Structural properties in the melt are well reproduced, and their scaling with chain length agrees with available experimental data. The CG force-field shows reasonable transferability between 350 and 600 K. The model is computationally efficient and polymer melts and solutions can be simulated by MD over length scales of tens of nanometers and time scales of tens of microseconds. <br>Two applications of polymer models developed within the MARTINI framework are shown. The first concerns the dynamics of polystyrene-C60 nanocomposites, a system that has been shown to have unusual rheological and mechanical properties. The second application concerns a polyester resin, whose mechanical properties are investigated by means of non-equilibrium molecular dynamics simulations.

Non-equilibrium behavior in materials

• Mikko Alava (Helsinki University of Technology)

Room: FB42 The irreversible yielding in materials has usually been described in the terms of rheology, but recent advances in from glasses to plasticity mediated by topological defects are starting to show this century-old picture to be wrong. In this talk I will discuss three issues: what happens during the deformation of crystalline solids, which is related to collective dislocation dynamics, how such phenomena are indeed more universal and easy to see during creep deformation, and thirdly some ongoing work on the internal dynamics of complex suspension flows. These are often thixotropic, and exhibit aging.

ALBANOVA COLLOQUIUM: Anomalous Diffusion and Ergodicity Breaking

• Ralf Metzler (TU München)

Room: FR4 In 1905 Einstein formulated the laws of diffusion, and in 1908 Perrin published his Nobel-prize winning studies determining Avogadro's number from diffusion measurements. With similar, more refined techniques the diffusion behaviour in complex systems such as the motion of tracer particles in living biological cells is nowadays measured with high precision. Often the diffusion turns out to deviate from Einstein's laws. This talk will discuss the basic mechanisms leading to such anomalous diffusion as well as point out its consequences. In particular the unconventional behaviour of non-ergodic, ageing systems will be discussed. Indeed, non-ergodic diffusion in living cells has recently been demonstrated experimentally.

Universality and non-universality of motion in heterogenous single-files

• Michael&nbsp;A. Lomholt (University of Southern Denmark)

Room: FB42 A single-file of identical particles diffusing along a line without being able to overtake each other is one of the better studied non-equilibrium systems in physics. It has been known for almost half a century that the mean square displacement of a single particle in the file will grow subdiffusively with an exponent 1/2. In this talk I will discuss heterogenous single files of particles with random friction constants. It will be shown that for distributions of frictions with a finite average the single-file will behave universally for long times in the same way as the identical case. For heavy tailed power-law distributions of frictions it is found that no self-averaging occurs even at long times and the behavior thus becomes non-universal.

Kinetic description of a homogeneous Bose fluid with condensate

• Jani Lukkarinen (University of Helsinki)

Room: FB53 In a joint work with Jogia Bandyopadhyay and Antti Kupiainen, we consider the kinetics of a three-dimensional fluid of weakly interacting bosons with supercritical densities. More precisely, we consider the postulated nonlinear Boltzmann-Nordheim equations for this system, in a spatially homogeneous state which has an isotropic momentum distribution. The resulting evolution equations have a surprisingly rich mathematical structure, where proper definitions play an important role. Elaborating on previous results, we propose a definition of the coupled equations for which the thermal equilibrium states are stationary. To test the validity of the equations, we study the global existence and uniqueness of solutions, as a problem about return to equilibrium from a perturbation of a thermal state with a condensate. The lessons learned from this enterprise ough

Pattern forming ground states in spin systems and self-assembling systems

• Martin Nilsson Jacobi (Chalmers University of Technology)

Room: FB53 Many natural systems display striped morphologies and many different models have been proposed to explain this phenomenon. I will discuss a universal explanation for why stripes occur at low temperatures in systems with isotropic interactions. Further I show that similar arguments can be used to explain the patterns that can occur as ground states for many particle systems interacting with pairwise central forces.

Aging dynamics in ant societies

• Paolo Sibani (University of Southern Denmark)

Room: FB53 In recent experiments (Richardson et al. (2010), PLoS ONE 5(3): e9621. doi:10.1371/journal.pone.0009621) ant motion out of the nest is shown to be a non-stationary process intriguingly similar to the so called <i>aging</i> dynamics, of physical glassy systems. Under different conditions, (Nouvellet et al.(2010), Journal of Theoretical Biology 266, 573) the same exit process is well described by a Poisson process. To investigate possible mechanisms producing both types of behavior, a model is introduced where interacting agents, e.g. ants, move from one site to a neighbor site on a finite 2D lattice. The probability of each move is determined by the ensuing changes of a utility function conventionally dubbed 'energy'. The latter is a sum of pairwise interactions between agents, weighted by distance. Depending on how the interactions are defined and on a control parameter dubbed `temperature', the dynamics either quickly converges to a stationary state, where movements are a standard Poisson process, or may enter a non-stationary aging regime, where exits can be described in the way suggested by Richardson et al., i.e. as a Poisson process in logarithmic time, for short a log-Poisson process.

Ecosystems with mutually exclusive interactions

• Namiko Mitarai (NBI)

Room: FB53 Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual de- pendencies. The minimum requirements to maintain a large species diversity on long time scales are in general unknown. Using lichen communities as an example, we propose a model for the evolution of mutually excluding organisms that compete for space.

Population genetics in compressible flows

• Simone Pigolotti (Niels Bohr Institute)

Room: FB53 Population genetics studies how mutant forms of genes spread in space and can eventually take over a population. The physical mechanisms underlying this process can be very different in the ocean, where flows can radically alter the chances of genes being fixated. I will present a new model that generalizes basic models of population genetics in the presence of a fluid flow. I will show that even the presence of a weak compressible flow has a dramatic effect on the fixation times and probabilities. I will then discuss the possible consequences of these findings for understanding the behavior of plankton populations in the oceans.

Discussion/Closing Room: FB53