Seminar on the Theory of Complex Systems  Winter Term 2017-18

To be confirmed:

• Mario Nicodemi, University of Nepals and Max Dellbruck Center Berlin

Confirmed:

• Thu 09.11.17   at 14 c.t.
  Martin Hasenbusch   Humboldt Universität Berlin
  Interfaces in the three-dimensional Ising model: Monte Carlo simulations
  

  We define the model and discuss how interfaces can be forced into the system. We discuss basic properties of interfaces such as the interface tension, the interface profile and the interface width. We recall how these quantities scale in the neighbourhood of the critical point. Theoretical results based on effective interface models are reviewed. Note that interfaces are related by duality with strings in gauge theories. Recently there had been considerable theoretical progress in understanding the the predictive power of effective string or interface models. We discuss Monte Carlo algorithms that are used to determine interfacial properties, focussing on the interface free energy. Finally we present our numerical results and compare them with theoretical predictions. Accurate results are obtained for the universal amplitude ratios. For example $R_{2nd,+} = f_{2nd,+}^2 \simga_0 = 0.3863(6)$, where $f_{2nd,+}$ and $\simga_0$ are the amplitudes of the second moment correlation length in the high temperature phase and the interface tension, respectively.

• Thu 16.11.17   at 14 c.t.
  Modelling reaction-triggered diffusional activation of retroviral infectivity
  S. Kashif Sadiq Heidelberg Institute for Theoretical Studies, HITS
  

  Retrovirus particle (virion) maturation is a remarkable example of macromolecular assembly coupled to chemical reactions. Infectivity usually requires clustering of multiple transmembrane envelope proteins (Env3) on the virion exterior, yet is only triggered by protease-dependent degradation of a membrane-bound Gag polyprotein lattice on the virion interior through a mechanism that is unclear. High-resolution cryo-electron microscopy has revealed the architecture of the outer shell of the immature virion, but alone does not explain maturation pathways. Modeling could provide insight but current approaches are unable to account simultaneously for both assembly and reactions at this scale. Recently, interaction particle-based reaction diffusion (iPRD) approaches have emerged. These combine space-excluded particle- based isotropic Brownian diffusion with state-changing phenomenological chemical reactions, including the assignment of inter-particle and particle-geometry interaction potentials and make a range of reaction-coupled clustering problems accessible at the required spatiotemporal scale. Here, I develop an approach (1) that integrates cryo-EM and crystallographic data with iPRD models to provide insight into the onset of HIV-1 infectivity from an immature virion. The model implements an ultra-coarse-graining (UCG) scheme based on the structural dimensions of each molecule to treat entire proteins at near-single particle resolution. It includes binding stoichiometry and lattice symmetries and can follow transmembrane Env3 diffusion in the presence of a monotopic truncated Gag lattice composed of membrane-bound matrix (MA) proteins linked to capsid (CA) subunits and freely diffusing protease (PR) enzymes. Simulations suggest that initial immobility of Env3 is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by PR vertically decouples the matrix and capsid layers, induces both MA and Env3 diffusion, and permits Env3 clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and suggests how infectivity can be achieved. Finally, I will outline how such a model could both be extended to orientation-specific assembly problems and then coupled to atomistic MD and BD simulations and physical geometry models within a multiscale framework that would then more completely handle the complexity of such phenomena.

  1. 1. Sadiq, S.K. (2016) Phil Trans R Soc A. Reaction-diffusion basis of retroviral infectivity 374:20160148.

• Thu 11.01.18   at 14 c.t.
  Design of metamaterials: form follows function
  Carsten Rockstuhl KIT
  

  The design of novel optical metamaterials very often starts by considering individual scatterers that have a complicated shape, that are made out of different materials, and that are potentially an assembly from different sub-structures. Controlling the way such scatterers interact with an external field is the key to discover novel artificial optical materials with unprecedented properties. Here, we summarize our efforts first from a methodological perspective to study the scattering properties of complex objects and detail afterwards multiple materials with various emerging properties. Particularly, we study novel non-scattering materials, self-assembled metamaterials with a strong magnetic response, and, as a last example, maximal electromagnetic chiral materials, i.e. materials that interact with light of only one helicity while being transparent to the opposite. [Such materials find application in helicity filtering glasses in stereoscopic cinema projection systems or for a twofold resonantly enhanced and background-free circular dichroism measurement setup that can be use in pharmaceutical production lines.]