Program Talks:

 ENTROPY, INFORMATION AND ORDER IN SOFT MATTER PROGRAM TALKS 11:00 AM - 12:30 PM - Talk and Discussions Monday, 3 September 2018 Mukund Thattai NCBS, Bengaluru Title: Algorithmic biosynthesis of branched carbohydrates in eukaryotes. Abstract: An algorithm converts inputs to corresponding unique outputs through a sequence of actions. Algorithms are used as metaphors for complex biological processes such as organismal development. Here we make this metaphor rigorous for glycan biosynthesis. Glycans are branched carbohydrate oligomers that are attached to cell-surface proteins and convey cellular identity. Eukaryotic glycans are synthesized by collections of enzymes in Golgi compartments. A compartment can stochastically convert a single input oligomer to a heterogeneous set of possible output oligomers; yet a given type of protein is invariably associated with a narrow and reproducible glycan oligomer profile. Here we resolve this paradox by borrowing from the theory of algorithmic self-assembly. We rigorously enumerate the sources of glycan microheterogeneity: incomplete oligomers via early exit from the reaction compartment; tandem repeat oligomers via runaway reactions; and competing oligomer fates via divergent reactions. We demonstrate how to diagnose and eliminate each of these, thereby obtaining algorithmic compartments" that convert inputs to corresponding unique outputs. Given an input and a target output we either prove that the output cannot be algorithmically synthesized from the input, or explicitly construct a succession of algorithmic compartments that achieves this synthesis. Our theoretical analysis allows us to infer the causes of non-algorithmic microheterogeneity and species-specific diversity in real glycan datasets. Tuesday, 4 September 2018 Anupam Kundu ICTS , Bengaluru Title: Dynamics in a Gas-Piston system Abstract : Consider a single particle gas confined in one dimension between a heavy piston and a Maxwell thermal reservoir. When the piston is held fixed the particle is expected to reach an equilibrium state after a long time. In the first part I will talk about how does the particle relax to equilibrium. When the piston is released with a force applied on it, it will start moving. But the motion will soon become stochastic due to the collisions with the particle. Is it possible to have an effective Langevin equation description of the piston motion? In the second part, I will talk about our attempt to answer this question. Wednesday, 5 September 2018 Mark Miller Durham University, UK Title: Encoding Building-Blocks for Programmable Self-Assembly Abstract: The self-assembly of discrete objects can take place via many schemes, ranging from the elegant efficiency of certain virus capsids (which assemble from multiple copies of just one protein) to the latest developments in addressable assembly (where every building block is unique). Programmable assembly refers to the ambition of controlling every individual site in a target structure as well as the pathways by which it forms. In this talk I will test different strategies for controlling and optimising the self-assembly of discrete targets using an idealised model of particles with patterned interactions. In particular, I will examine the special challenges that come into play in the case of addressable assembly. In this limit, each building block must be encoded with enough information to find its unique location in the target structure. Furthermore, independently growing structures must avoid becoming mutually incompatible, which would lead to frustration in the assembly process. Along the way, I will describe some new tools for design, simulation and analysis in the context of colloidal self-assembly Thursday, 6 September 2018 Santosh Ansumali JNCASR, Bengaluru Title: Second law in Discrete Time kinetic theory Abstract: The entropic lattice Boltzmann model (ELBM) aims to construct a simplified kinetic picture on a lattice designed to capture the physics of macroscopic flow through simple local micro-scale operations.   The method is unique in the sense that it enforces the numerical stability of a hydrodynamic solved by insisting on adherence to the thermodynamics at the discrete time level.   This compliance with the H theorem is typically enforced by searching for the maximal discrete path length corresponding to the zero dissipation state by iteratively solving a nonlinear equation. We demonstrate that an exact solution for the path length can be obtained by assuming a natural criterion of negative entropy change, thereby reducing the problem of solving an inequality.     Such a discrete space-time map can also be thought as geometric discretization of the dissipative Boltzmann dynamics.  Finally, I will discuss the possibility that such an implicit modeling of unresolved scales of the flow, via the thermodynamic route, may provide a new insight into subgrid modeling of turbulence. Friday, 7 September 2018 Oleksiy Tkachenko Brookhaven National Laboratory, US Title: How to Build a Diamond? Abstract: Self-assembly is a key phenomenon in living matter, and at the same time, a booming field of modern material science and engineering. In my talk I will review emerging trends and ideas in this field, and give theorist's perspective on its conceptual challenges. I will discuss the strategy of programmable self-assembly that uses molecular recognition properties of DNA to build nano- and micro-scale building blocks with designed pairwise interactions. This approach opens an entirely new class of theoretical problems in statistical physics. Instead of studying phenomenology of a large system of particles with given properties, we must solve the inverse problem: finding the interactions that would result in a self-assembly of a desired macroscopic or mesoscopic morphology. I will start with a discussion of self-assembly in a very simple binary system of spherical particles, and gradually move towards a greater complexity of both the building blocks and the resulting structures. One structure that is notoriously challenging for self-assembly, and often viewed as a Holy Grail of the field, is a diamond lattice. I will therefore use diamond as a model system to illustrate general principles and specific approaches to programmable self-assembly. Some of those approaches are already implemented in experiments, while others are just theoretical prescriptions. VENUE: MADHAVA LECTURE HALL 11:00 AM - 12:30 PM - Talk and Discussions Monday, 10 September 2018 Mark Miller Durham University, UK Title: Curved Surfaces and Percolation of Nanorods Abstract: In this talk I will present highlights from two independent projects. Apart from the fact that they both deal with soft matter systems, the only (tenuous) link is that they both involve the use of non-standard Monte Carlo techniques that are specialised to the respective tasks. The first case concerns phase transitions in curved two-dimensional spaces, such as colloidosomes, where colloidal spheres are confined to the surface of a spherical droplet. The curvature, finite extent and thermodynamic ensemble all have pronounced effects on the nucleation process. More exotic toroidal surfaces give rise to some entirely new considerations. The second case is the percolation transition in composite materials containing carbon nanotubes, where the emergence of a system-spanning network of nanotubes confers electrical conductivity on the material. We have investigated the interplay of length polydispersity and external aligning fields on the percolation threshold of these highly elongated particles, leading to some important general conclusions for optimising the formulation of such materials. Tuesday, 11 September 2018 Prabal Maiti Department of Physics, Indian Institute of Science, Bangalore, 560012 Title: Understanding DNA based nanostructures Abstract: DNA and its crossover motifs are integral components for designing DNA based nanostructure and nanomechanical devices. In this talk I will discuss simulation methodologies to study various DNA based nanostructures. I report MD simulations results on cross-over DNA molecules to obtain a comprehensive understanding of relationship between structure, topology, and stability of various Paranemic crossover (PX/JX) DNA molecules. We present atomistic model of various DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nano technological and biological applications. In particular, we introduce a computational design to create atomistic model of 8-helix DNT (8HB) and 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically with two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). The measured persistence lengths of these nanotubes are ~10 μm, which is 2 orders of magnitude larger than that of dsDNA. We have also examined the interaction of DNA nanotubes embedded in the lipid bilayer membranes. The Ohmic conductance measured from I-V characteristics of the ions channel varies from 4.3 to 20.6 nS with ionic strength. Finally, I present atomistic model of DNA icosahedron, and study the structure and dynamics of DNA icosahedrons. Our simulations on cargo loaded DNA icosahedra provide insight on the dynamics of the DNA scaffold that gives information not only on polyhedra-cargo interactions, but also interaction of a tag-displaying, cargo-loaded icosahedron with its biological target. Wednesday, 12 September 2018 Rama Govindarajan ICTS, Bengaluru Title: Droplet and vortex interactions in the context of clouds Abstract: In this talk I will discuss the dynamics of droplets in the vicinity of vortices. The dynamics is described by simple parameter-free equation which have a boundary layer structure. Droplets within a critical distance from the vortex centre can participate in caustics events, and seed rapid droplet growth by collisions and coalescence. Our simulations provide evidence for this in three dimensions. I will then discuss how small droplets falling under gravity are affected by the Basset history force, a force which is normally extremely cumbersome to compute, but which we solve by an efficient method. Finally I will discuss how turbulence is affected by condensation on droplets. I will discuss some of these in the context of clouds. Friday, 14 September 2018 Atsushi Ikeda University of Tokyo Title: Viscosity divergence and dynamical slowing down at the jamming transition Abstract: Jamming transition of athermal particles is characterized by the divergence of the viscosity. This transition looks very similar to the glass transition, but there are several key differences. One of the differences is that the dynamical slowing down is apparently absent in the jamming transition. In this talk, I will report our recent study on the dynamics near the jamming transition. We especially focus on the dynamics in the simplest setting. i.e. relaxation from the random configuration of soft particles without shear. I show that the relaxation exhibits remarkable slowing down. I also show that this relaxation is dominated by a non trivial anomalous mode and is quantitatively related to the viscosity divergence.