Opening

• Alberto Imparato (Aarhus University)
• Ralf Eichhorn (Nordita)

Room: 122:026

Solving moment hierarchies for chemical reaction networks

• Supriya Krishnamurti (SU)

Room: 122:026 The study of Chemical Reaction Networks (CRN's) is a very active field. Earlier well-known results [1,2] identify a topological quantity called deficiency, for any CRN, which, when exactly equal to zero, leads to a factorized steady-state for these networks. No results exist however for the steady states of non-zero-deficiency networks. Here we show how to write the full moment-hierarchy for any non-zero-deficiency CRN obeying mass-action kinetics, in terms of equations for the factorial moments (FM). Using these, we can recursively predict values for lower moments from higher moments, reversing the procedure usually used to solve moment hierarchies. We show, for non-trivial examples, that in this manner we can predict to high accuracy, any moment of interest, for CRN's with non-zero deficiency and non-factorizable steady states. 1. M. Feinberg, Chemical reaction network structure and the stability of complex isothermal reactors -- I. The deficiency zero and deficiency one theorems, Chem. Enc. Sci., 42, 2229, (1987) 2. D. F. Anderson, G. Craciun, and T. G. Kurtz, Product-form stationary distributions for deficiency zero chemical reaction networks, Bull. Math. Bio., 72, 1947 (2010)

Re-examine the Existence of Dynamic Disorder in Single Molecule Enzymatic Kinetics

• Chun-Biu Li (SU)

Room: 122:026 Using single-molecule fluorescence approaches, the time series of catalytic events of an enzymatic reaction can be monitored, yielding a sequence of fluorescent “on”- and “off”-states. An accurate on/off-assignment is complicated by the intrinsic and extrinsic noise in every single-molecule fluorescence experiment. Using simulated data, the performance of the most widely employed binning and thresholding approach was systematically compared to change point analysis. It is shown that the underlying on- and off-histograms as well as the off-autocorrelation are not necessarily extracted from the “signal'' buried in noise. The shapes of the on- and off-histograms are affected by artifacts introduced by the analysis procedure and depend on the signal-to-noise ratio and the overall fluorescence intensity. When using change point analysis for data of the enzyme α-chymotrypsin, no characteristics of dynamic disorder was found. In light of these results, dynamic disorder might not be a general sign of enzymatic reactions.

Bayesian analysis of DNA unfolding in nanochannels

• Michael A Lomholt (University of Southern Denmark)

Room: 122:026 When a piece of circular DNA breaks in a nanochannel it slowly unfolds to a linear conformation. I present a simple model for the process, where the unfolding is driven by an entropic force and opposed by hydrodynamic friction with the channel walls. The model is compared with experimental data using Bayesian inference. It is demonstrated that this provides a conceptually simple way of extracting numerical values for the force and friction from the experimental data.

One-parameter theory for DNA extension in nanochannels

• Bernhard Mehlig (Gothenburg University)

Room: 122:026 The extension of DNA during confinement in a nanochannel has attracted substantial attention for next-generation genomics and as a fundamental problem in polymer physics. But recent experiments measuring DNA extension in nanonchannels are at odds with even the most basic predictions of current scaling theories for the conformations of confined semiflexible polymers like DNA. We posit that this discrepancy arises because the experimental systems do not satisfy the strong inequalities underlying the existing scaling theory. We develop a new theory, based on the properties of a weakly self-avoiding, one-dimensional random walk. Both recent experimental results and new simulation data reported here collapse onto one master curve as a function of a single parameter that varies continuously throughout the experimentally relevant region of the parameter space. In special cases previous scaling theories are recovered.

Aspects of an autonomous symmetric Brownian motor

• Hans Fogedby (Aarhus University)

Room: 122:026 This study, done in collaboration with Alberto Imparato (organiser), concerns the symmetric Brownian motor proposed by Gomez-Marin and Sancho.The model is an autonomous heat engine with two coupled degrees of freedom moving in periodic potentials driven by two temperature biased heat reservoirs. For phase shifted sinusoidal potentials and a temperature bias the model exhibits a finite propagation velocity. We extend the model to general periodic potentials and present analytic expressions in the strong coupling limit. We show that the model is related to the Buetikker-Landauer “Blow Torch” model and to the model of a single degree of freedom in a titled periodic potential. We, moreover, analyse the model numerically both within a Langevin and a Fokker-Planck formulation for general coupling strength and determine the dependence of the velocity on coupling strength, temperature bias, and phase shift. We find that the optimal velocity is obtained already at moderate coupling strength. We finally evaluate and discuss the efficiency of the model.

The physics of high-density crowds: mode analysis sheds light on crowd disasters

• Arianna Bottinelli (Nordita)

Room: 122:026 When people gather in large groups like those found at Black Friday sales events, pilgrimages, heavy metal concerts, and parades, crowd density often becomes exceptionally high. In these situations, social norms and global coordination happen sometimes to break down, giving rise to unusual and occasionally tragic collective motions known as “crowd turbulence”. While active particle simulations can reproduce most phenomenology of human collective motion, the mechanisms underlying the emergence of such collective motions from purely physical interactions between contacting bodies are poorly understood. Here, we take inspiration from techniques developed in the context of jammed granular materials to study an active matter model inspired by situations when large groups of people gather at a point of common interest. Our analysis identifies Goldstone modes, soft spots, and stochastic resonance as structurally-driven mechanisms for potentially dangerous emergent collective motions.

Exact symmetries in the velocity fluctuations of a hot Brownian swimmer

• Klaus Kroy (University of Leipzig)

Room: 122:026 Symmetries constrain dynamics. We test this fundamental physical principle, experimentally and by molecular dynamics simulations, for a hot Janus swimmer operating far from thermal equilibrium. Our results establish scalar and vectorial steady-state fluctuation theorems and a thermodynamic uncertainty relation that link the fluctuating particle current to its virtual entropy production at an effective temperature. A Markovian minimal model elucidates the underlying non-equilibrium physics. Gianmaria Falasco, Richard Pfaller, Andreas P. Bregulla, Frank Cichos, and Klaus Kroy, Exact symmetries in the velocity fluctuations of a hot Brownian swimmer, Phys. Rev. E 94, 030602(R)

Collective behaviours in dry and wet active matter

• Joakim Stenhammar (Lund University)

Room: 122:026 "Active matter" is usually defined as materials that are driven out of thermodynamic equilibrium at the microscopic scale, usually by the persistent conversion of chemical fuel into motion. Such materials are often characterized as either "dry", dominated by frictional damping, or "wet", dominated by interactions mediated by a momentum-conserving solvent. Because of their strong deviation from equilibrium, these two classes of active matter exhibit very different, although equally intriguing, collective behaviours. In this talk, I will analyze two such classes of collective behaviours occuring in simple model systems of active matter, namely 1) "motility-induced phase separation", whereby active particles that interact solely through excluded volume interactions undergo a separation into dense and dilute phases, and 2) "bacterial turbulence", the hydrodynamically mediated transition into a coherently flowing state observed in dipolar microswimmers such as swimming bacteria.

Current Perspectives on Active Matter

• Giovanni Volpe (Gothenburg University)

Room: 122:026 Active Brownian particles, also referred to as microswimmers and nanoswimmers, are biological or manmade microscopic and nanoscopic particles that can self-propel. Because of their activity, their behavior can only be explained and understood within the framework of nonequilibrium physics. In the biological realm, many cells perform active motion, for example, when moving away from toxins or towards nutrients. Inspired by these motilemicroorganisms, researchers have been developing artificial active particles that feature similar swimming behaviors based on different mechanisms; these manmade micro- and nanomachines hold a great potential as autonomous agents for healthcare, sustainability, and security applications. With a focus on the basic physical features of the interactions of active particles with a crowded and complex environment, this seminar will provide a guided tour through the basic principles of active matter, the development of artificial self-propelling micro- and nanoparticles, and their application to the study of nonequilibrium phenomena, as well as the open challenges that the field is currently facing.

Multiscale Modelling of Graphene from Nano to Micron Scales

• Tapio Ala-Nissilä (Dept. of Applied Physics, Aalto SCI, Espoo, Finland)

Room: 122:026 Over the last few years novel two-dimensional materials and nanoscopically thin heteroepitaxial overlayers have attracted intense attention due to their unusual properties and important technological applications. Many physical properties of these systems such as thermal conductivity and electrical transport are intimately coupled to the large scale mechanical and structural properties of the materials. However, modeling such properties is a formidable challenge due to a wide span of length and time scales involved. In this talk, I will review recent significant progress in structural multi-scale modeling of two dimensional materials and thin heteroepitaxial overlayers [1], and graphene in particular [2], based to a large extent on the Phase Field Crystal (PFC) model combined with standard microscopic modeling methods (classical Molecular Dynamics and quantum density functional theory). The PFC framework allows one to reach diffusive time scales for structural relaxation of the materials at the atomic scale, which facilitates quantitative characterisation of domain walls, dislocations, grain boundaries, and strain-driven self-organisation up to almost micron length scales. This allows one to study e.g. thermal conduction and electrical transport in realistic multi-grain systems [3]. References 1. K. R. Elder et al,. Phys. Rev. Lett. vol. 108, 226102 (2012); Phys. Rev. B vol. 88, 075423 (2013); J. Chem. Phys. 144, 174703 (2016). 2. P. Hirvonen et al., Phys. Rev. B 94, 035414 (2016). 3. Z. Fan et al., to be published.

How square ice helps lubrication

• Astrid de Wijn (Trondheim University)

Room: 122:026 The combination of water with graphite or graphene is under active investigation in several fields for a number of reasons. In the field of tribology, it is of interest due to the action of graphite powder as a solid lubricant, which is far more effective under humid conditions than in vacuum or dry air. This is opposite to the case for other solid lubricants, such as WS2 and MoS2 [1]. Moreover, water alone is a poor lubricant, due to its low viscosity-pressure co-efficient. While suggestions have been made as to the reason behind water's beneficial effects on graphite as a lubricant [2], this effect is not yet understood. We use atomistic molecular-dynamics simulations to investigate equilibration of water confined between graphene sheets over a wide range of pressures. We demonstrate that, under the right sliding conditions, square ice can form in an asperity, and that it is similar to cubic ice VII and ice X. We find that thermal equilibration of the confined water is hindered at high pressures. We simulate sliding of the square ice on atomically at graphite and find extremely low friction due to structural superlubricity. The conditions needed for this equilibration correspond to low sliding speeds, and we suggest that the ice observed in experiments of friction on wet graphite [3, 4] is of this type. [1] C. Donnet and A. Erdemir, Tribol. Lett. 17, 389 (2004). [2] A. S. de Wijn, A. Fasolino, A. E. Filippov, and M. Urbakh, Europhysics Lett. 95, 66002 (2011). [3] K. B. Jinesh and J. W. M. Frenken, Phys. Rev. Lett. 96, 166103 (2006). [4] K. B. Jinesh and J. W. M. Frenken, Phys. Rev. Lett. 101, 036101 (2008).

A new formulation of the Isomorph Theory - and beyond

• Thomas Schrøder (Dept. of Sciences, Roskilde University, Roskilde, Denmark)

Room: 122:026 The original formulation of the Isomorph Theory [1] predicts that some liquids have "isomorphs", i,e,, lines of invariant dynamics, structure and excess entropy in parts of their phase diagram, Here we present a new - and more elegant - version of the theory, which from a single assumption regarding the scaling properties of the high-dimensional potential energy surface predicts the existence of isomorphs [2]. Furthermore, the new version of the theory solves some of the (few) problems of the original version, e.g., the variance of heat capacity along an isomorph is now accurately predicted. Finally, we will discuss the extension to "pseudoisomorphs" in liquids with intramolecular vibrational degrees of freedom [3]. [1] N. Gnan, T.B. Schrøder, U.R. Pedersen, N.P. Bailey, and J.C. Dyre, "Pressure-energy correlations in liquids. IV. 'Isomorphs' in liquid state diagrams", Journal of Chemical Physics v131, p234504 (2009) [2] T.B. Schrøder and J.C. Dyre, "Simplicity of condensed matter at its core: Generic definition of a Roskilde-simple system", Journal of Chemical Physics, v141, p204502 (2014). [3] A.E. Olsen, J.C. Dyre, and T.B. Schrøder, "Communication: Pseudoisomorphs in liquids with intramolecular degrees of freedom", Journal of Chemical Physics, v145, p241103 (2016).

Criticality and fluctuations in discrete dislocation dynamics

• Mikko Alava (Aalto University)

Room: 122:026 The character of the crackling noise and intermittent response of dislocation systems remains a partly unresolved problem. Partly this has been charted by the use of extensive Discrete Dislocation Dynamics (DDD) simulations. 2D studies [1,2,3,4] show that these systems exhibit glassy response and extensive criticality even at zero stresses, while introducing impurities such as solutes on changes the phase diagram and leads to additional phases and complexity [2,4]. In 3D, the phenomenology seems similar to 2D [5], in that an extended critical phase down to zero applied stress is found. One of the research directions is to consider the impact of "disorder" such as precipitates [6] and prismatic loops on plasticity in these systems [7].

Synchronizing the Markov chain at microscopic times

• Rogelio Díaz-Méndez (KTH)

Room: 122:026 The lack of an equation of motion for classical discrete-variable models is supplemented with the introduction of a master equation (ME), governing the probabilities for a system to be in any particular state. Thus, the information describing the dynamical evolution of the local variables in a Markov process can be obtained from the ME through analytical and numerical techniques. Available numerical methods capable of simulate ME stochastic trajectories, however, fail to reproduce the Markov chain dynamics for very small timescales, i.e. at times of the order of the elementary relaxation. We overcome this shortcoming by introducing the Event-Driven Monte Carlo algorithm (ED), whose scheme allows for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels [1]. Unlike existing methods, the ED does not assume any particular statistical distribution to perform moves or to advance the time, and thus is a unique tool for the numerical exploration of fast and ultra-fast dynamical regimes. As a prime example of ED applications we will discuss preliminary results on the effects of self-induced fields in the dynamics of the 2D Ising model. While the cumulative effect of Eddy currents is wellknown to affect the distribution of avalanches in Barkhausen noise [2], its numerical study in Ising-like systems requires access to the short-time spin dynamics. Using the ED scheme, we couple the diffusion equation of the induced field to the real-time evolution of the local magnetization and observe an interesting phenomenology. [1] A. Mendoza-Coto, R. Díaz-Méndez and G. Pupillo, Event-driven Monte Carlo: Exact dynamics at all time scales for discrete-variable models, Europhysics Letters 114, 5, 2016. [2] F. Colaiori, G. Durin and S. Zapperi, Eddy current damping of a moving domain wall: Beyond the quasistatic approximation, Phys. Rev. B 76, 224416, 2007.

Percolation on random planar maps

• Sigurdur Örn Stefansson (University of Iceland)

Room: 122:026 Random planar quadrangulations (and, more generally, random planar maps) belong to an active field of research in theoretical physics, probability and combinatorics. In recent years there has been an enormous progress on understanding probabilistic aspects of large random planar maps themselves. The next big step is to add matter to them, that is, to study models from statistical physics on large random planar maps. In this talk we consider one such model, more specifically site percolation on uniform quadrangulations of the half-plane. In a recent work with Jakob Björnberg we obtained a sharp estimate on the critical percolation probability. Building on the work of O. Angel, we use the so called peeling process to explore the map and the percolation cluster simultaneously. I will explain the general method, how it allows us to get the bounds for quadrangulations and why it is not the correct approach to the problem.

Invasion and Extinction Dynamics in Foodwebs

• Namiko Mitarai (NBI)

Room: 122:026 Foodwebs represents the species interactions in a local habitat. When a new species invade a local habitat, their competitive interaction with resident species may result in cascade of extinction of resident species, but the condition for extinction and the evolution of foodweb under such invasion events are not well understood. We here present a study on the dynamics of invasion and extinction using the generalized Lotka-Volterra equations. When the foodweb has a tree-structure, we prove that there is a unique, globally stable solution that determine the species that will extinct and the species that coexist stably. Using this, we propose a protocol that describes the repetition of invasion and extinction events in a foodweb, and analyze the dynamics and the resulting foodweb structure. We further simplify the process to the Invasion Extinction Model, which gives a power low distribution of the species life time, consistent with the simulated invasion extinction dynamics. Reference: J. O. Haeter, N. Mitarai, and K. Sneppen, Plos Comp. Biol. 12 (2016): e1004727; J. O. Haeter, N. Mitarai, and K. Sneppen doi: https://doi.org/10.1101/097907; J. O. Haeter, N. Mitarai, and K. Sneppen, under review.

Free discussion / Closing Room: 122:026