1st Nordic Workshop on Statistical Physics: Biological, Complex and Non-equilibrium Systems

Contribution List

250. Opening

3/17/10, 10:00 AM

251. DNA Analysis in Nanostructured Devices

Jonas Tegenfeldt

3/17/10, 10:15 AM

We use standard staining protocols and epifluorescence microscopy to gain information on the local AT/GC ratio along large DNA molecules stretched in nanoscale channels[1]. Our development opens up a novel route to mapping of large-scale genomic variations as well as fast identification of rare or single cells. With rising temperature, dark patches appear along the DNA corresponding...

252. Polymer Escape from Metastable Kramers Potential: Path Integral Hyperdynamics Study

Timo Ikonen

3/17/10, 11:30 AM

We study the dynamics of flexible, semiflexible and self-avoiding polymer chains under the Kramers metastable potential. Due to thermal noise the polymers, initially in the metastable well, can cross the potential barrier, but these events are rare at low temperatures. To speed up the slow rate processes in computer simulations we employ the hyperdynamics method using the...

253. A Stochastic Model of Anomalous Heat Transport

Carlos Mejia-Monasterio

3/17/10, 12:15 PM

Abstract: We investigate the non-equilibrium dynamics of a chain of harmonic oscillators in contact with two stochastic Langevin heat baths at different temperatures and undergoing random collisions between neighbours that exchange their momenta with a constant rate $\gamma$. By means of an appropriate continuum limit, we solve the equations for the covariance matrix to leading order in...

254. Interacting Random Walkers in One-Dimansional Systems

Tobias Ambjörnsson

3/17/10, 2:30 PM

The problem of a single random walker has received a lot of attention in the science community during the last century. There is now an increasing amount of interest in the problem of INTERACTING random walkers (due to the strong connection of this problem to the fields of, for instance, biophysics, nanofluidics, and cell biology). In particular, much attention has been on the behavior...

255. Lipid-Protein Membranes out of Equilibrium

Michael Lomholt

3/17/10, 3:15 PM

Biological membranes are typically not in thermal equilibrium. Experiments on lipid-protein model membranes have revealed that protein activity influences the mechanical properties of the membrane. A possible explanation for this alteration is given by a theoretical model in which the active proteins act as force-dipoles on the surrounding medium. A prediction of this model is that the...

256. Aging Dynamics is Trivial in Logarithmic Time

Paolo Sibani

3/17/10, 4:30 PM

The dynamics of complex systems collectively known as glassy shares important phenomenological traits. I.e., a transition is generally observed from a time-homogeneous dynamical regime to an aging regime where physical changes occur intermittently and, on average, at a decreasing rate. It has been suggested that a global change of the independent time variable to its logarithm may render...

257. Aggregation of Variables in Linear Systems

Martin N. Jacobi

3/17/10, 5:15 PM

I will present some new ideas for how to coarse grain linear dynamical systems through aggregation of variables. Both spectral methods and a very recent technique based on identification of ground states in a corresponding Potts glass model will be discussed. The methods are demonstrated by application to coarse graining of cellular automata and identification of the genetic code and...

259. Lipids in Membranes Speak the Language of Curvature

Ole Mouritsen

3/18/10, 9:00 AM

The physical properties of the lamellar lipid-bilayer component of biological membranes is controlled by a host of thermodynamic forces leading to overall tensionless bilayers with a conspicuous lateral pressure profile and build-in curvature-stress instabilities that may be released locally or globally in terms morphological changes. In particular, the average molecular shape and the...

260. Complex Dynamics in Lipid Membranes

Erik Brandt, Olle Edholm

3/18/10, 9:45 AM

A biological lipid membrane may be viewed as a two dimensional (liquid crystal) fluid that is immersed in a three dimensional water solution. The system is further complicated by that the membrane is non flat, undergo time dependent undulations and have a thickness that fluctuates in time and space. This gives rise to complicated correlation functions in time and space. Experimentally...

261. Diffusion Within Living Cells

Lene Oddershede

3/18/10, 11:00 AM

Using optical tweezers combined with image analysis we investigate motility of single proteins in membranes and of organelles inside living cellular organisms, one key issue being that the organisms are kept alive and healthy. Studies of two different biological systems will be presented: By specifically attaching a bead to a single protein, the lambda-receptor, which is a porin in the...

262. Diffusion Controlled Reactions and Living Cell Biochemistry

Zoran Konkoli

3/18/10, 11:45 AM

The talk will discuss how Statistical Physics tools can be used to understand biochemistry of the living cell. Structures found in the living cell are rather special and to achieve such task techniques used in the field of Statistical Physics need to be slightly modified. A critical reflection is needed on which techniques to use and for what purpose. As an example the theory of...

270. Genetic Regulation in Time and Space

Mogens Høgh Jensen

3/18/10, 2:00 PM

Genetic circuits have been studied quite intensively in recent years. In particular, we have focussed on oscillatory patterns related to negative feed-back loops inside single cells in eucaryotic systems [1,2]. In many cases, however, it is of interest to study how cells communicate with each other when cells are arranged in certain spatial structures, like biofilms and tissues. We have...

264. ALBANOVA COLLOQUIUM - Stochastic Thermodynamics: Theory and Experiments

Udo Seifert

3/18/10, 3:15 PM

Stochastic thermodynamics provides a framework for describing small systems embedded in a heat bath and externally driven to non-equilibrium. Examples are colloidal particles in time-dependent optical traps, single biomolecules manipulated by optical tweezers or AFM tips, and motor proteins driven by ATP excess. A first-law like energy balance allows to identify applied work...

265. Fluctuation Theorems and Single Molecule Experiments

Alessandro Mossa

3/18/10, 5:00 PM

The manipulation of individual macromolecules made possible by experimental techniques such as optical tweezers or atomic force microscopy gives a unique insight into the non-equilibrum thermodynamics of small systems. Besides a general introduction about the theoretical and experimental framework, this talk is focused on two topics: the proper way of measuring the work applied to the...

266. Equilibrium and Non-Equilibrium Physics of Nucleosome Positioning

Ulrich Gerland

3/19/10, 9:00 AM

267. Dynamics, Clustering and Collisions of Inertial Particles in Mixing Flows

Bernhard Mehlig

3/19/10, 9:45 AM

We study the dynamics of small particles suspended in mixing flows (e.g. microscopic water droplets in turbulent rain clouds). We describe how the particles move, cluster together, and collide. Our results enable us, for example, to address the question of how long it takes to rain from a vigorously turbulent rain cloud. The talk is based on the manuscripts appended below. Mehlig &...

263. Mesoscopic Non-Equilibrium Thermodynamics

Dick Bedeaux

3/19/10, 11:00 AM

Classical thermodynamics is a theory for a collection of molecules in equilibrium. What happens if the number of molecules in the system becomes smaller and smaller, and the system boundaries reflect conditions further and further away from equilibrium? Can we still use thermodynamics? This lecture aims to explain that the field of non-equilibrium thermodynamics can be extended to...

268. Metabolic Networks, Information, Null Model, and Evolution

Petter Minnhagen

3/19/10, 11:45 AM

The metabolism in an organism is reduced to a network of substances. The resulting degree-distribution is power law like with an exponent about 2.2. In order to understand this, we use information theory to obtain a null-model defined by assigning equal probabilities to what is assumed to be the fundamental network possibilities. A stochastic variant of variational calculus is used to...

271. The Inverse Ising Problem: A Survey and some Empirical Results

Prof. Erik Aurell (KTH)

3/19/10, 2:00 PM

The "Inverse Ising Problem" refers to finding the parameters (the J_ij's and the h_i's) in an Ising model given the first and second moments (the magnitizations m_i and the correclation functions c_ij). This is of great interest in machine learning and data analysis whenever the data set and the number of variables is large, but the values taken by the variables can be taken to be...

272. The Inverse Ising Model: Why and How

John Hertz (Nordita)

3/19/10, 2:45 PM

Ising models form a natural framework for modeling the distribution of multi-neuron spike patterns: Of all models that correctly describe the firing rates and pairwise firing correlations, the Ising model is the one of maximum entropy. The problem at hand here is an inverse one to that we usually encounter. Normally, one has a model with given couplings (Jij) and the task is to...

273. Discussion and Closing

3/19/10, 3:30 PM