- Current Week (Please note the change in timings)
|ENTROPY, INFORMATION AND ORDER IN SOFT MATTER|
|11:00 AM - 12:30 PM - Talk and Discussions|
|Monday, 3 September 2018|
|Title: Algorithmic biosynthesis of branched carbohydrates in eukaryotes.|
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|
ICTS , Bengaluru
|Title: Dynamics in a Gas-Piston system|
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|
Durham University, UK
|Title: Encoding Building-Blocks for Programmable Self-Assembly|
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|
|Title: Second law in Discrete Time kinetic theory|
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|
Brookhaven National Laboratory, US
|Title: How to Build a Diamond?|
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|
Durham University, UK
|Title: Curved Surfaces and Percolation of Nanorods|
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|
Department of Physics, Indian Institute of Science, Bangalore, 560012
|Title: Understanding DNA based nanostructures|
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|
|Title: Droplet and vortex interactions in the context of clouds|
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|
University of Tokyo
|Title: Viscosity divergence and dynamical slowing down at the jamming transition|
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.
|11:10 AM - 12:30 PM - Talk and Discussions|
|Monday, 8 October 2018|
|Samriddhi Sankar Ray
|Title: Turbulent Transport: Beyond Spherical Particles|
|Abstract : We present recent results on non-spherical particles and elastic fibers in a turbulent flow. In particular, we discuss the issue of preferential sampling of flows by such "particles" with internal degrees of freedom and compare them with the more standard spherical particle approach. If time permits, we will present recent results on the emergence of collective motion for active rods and disks in fully developed turbulence.|
|Tuesday, 9 October 2018|
University of Bonn, Germany
|Title: AQS-automata, state transition graphs, return-point memory and random maps|
|Abstract: AQS-automata arise naturally in the description of the athermal dynamics of a disordered system -- such as spin glasses -- when a slowly changing uniform driving force is applied. The response of such systems is characterized by abrupt transitions between quasi-static configurations which are generally irreversible, giving thus rise to hysteresis. The dynamical response of such systems can be described in terms of a pair of random, directed and acyclic graphs, capturing the transitions triggered by force increases and decreases, respectively. Properties such as return-point memory emerge then as features of these graphs. In this talk I will develop the graph-theoretic description of AQS-automata and then present recent work with T. Witten on modelling the AQS dynamics by random maps.|
|Wednesday, 10 October 2018|
Procter & Gamble, Singapore
|Title: The Physics of Beauty – A hairy story|
|Abstract: The perception of beauty is strongly linked to order and symmetry. These perceptions engraved into our evolutionary psychology as we survive by being the fittest. However, quantifying these perceptions, and the technical truth underlying them has many challenges, some of which will be shared in the context of hair. Two specific problems are (1) the dynamics of the tangling/detangling of hair, and (2) the movement of hair. Getting stronger analytical insights on the impact of microscale material parameters against macroscopic variations in the amount of structural disorder or momentum distributions would help design products for consumers.|
|Thursday, 11 October 2018|
|Title: Extreme Active Matter at High Densities|
Extreme active matter, comprising self-propelled particles characterised by large persistence time \tau_p and high Péclet number, exhibits remarkable behaviour at high densities. As \tau_p → 0, the material undergoes a conventional fluid-to-glass transition via density relaxation, as one reduces the active propulsion force f . In the other limit, \tau_p → ∞, the fluid jams at a critical point on lowering f to f^∗ (∞), with stresses concentrated along force-chains. In between these limits, the approach to dynamical arrest at low f , goes through a phase characterised by intermittency in the kinetic and potential energy. This intermittency is a consequence of long periods of jamming followed by bursts of plastic yielding associated with Eshelby deformations, akin to the response of dense amorphous solids to an externally imposed shear. In the vicinity of the intermittency-fluid phase boundary, correlated plastic events result in large scale vorticity and turbulence. Dense extreme active matter brings together the physics of glass, jamming, plasticity and turbulence, in a new state of driven classical matter.
|Friday, 12 October 2018|
|Monday, 15 October 2018 15:00 to 16:00
VENUE: Emmy Noether Seminar Room, ICTS Campus, Bangalore
(TIFR Centre for Interdisciplinary Sciences, Hyderabad)
|Title: Solid rigidity: A thermodynamic origin story|
Abstract: School textbooks tell us that the main difference between a solid and a liquid is the ability of the former to retain its shape. Any attempt at changing the shape of a solid is resisted by an internal elastic stress unless the deformation crosses a limiting value; at which point the solid fails. This naive viewpoint, although of great practical value, is, however, fundamentally incorrect. For example, one can argue that given enough time, atoms in the solid can always rearrange to eliminate stress no matter how much, or how little, the solid is deformed. Resolution of this paradoxical result lies at the core of our understanding of the behavior of solids under deformation. Adapting ideas which were introduced recently to study glasses, we find that rigidity arises a result of a hidden first-order phase transition between phases which differ in the way they respond to changes of shape . When deformed by any amount, howsoever small, the rigid solid goes into a meta-stable state analogous to superheated water. Eventually, this meta-stable state always decays by nucleating bubbles of the stable, stress-free, solid by a process very similar to how bubbles of steam appear in a kettle of boiling water. This fresh conceptual viewpoint curiously allows us to study failure of perfect crystalline solids in quantitative detail without invoking specifics of many-body, defect–defect interactions, raising hope of a more unified description of materials in the future.
 Nath et al. PNAS 115 E4322-E4329 (2018)
|VENUE: MADHAVA LECTURE HALL, ICTS|
|DATE AND TIME: Monday, 15 October 2018 16:30 to 17:30|
|DATE AND TIME: Tuesday, 16 October 2018 11:10 to 12:00|
YITP, Kyoto University
|Title: The characterization of dense jammed matter: mutual relationships among the shear-jammed, fragile states and the discontinuous shear thickening|
|Abstract: The mechanical response of two-dimensional frictional granular materials under an oscillatory shear in a constant volume are numerically investigated. It is confirmed that the shear storage modulus G′ depends on the initial amplitude of the oscillation to prepare the system before the measurement. For sufficiently large initial strain amplitude, the shear jammed state satisfying G′ > 0 is observed even if the packing fraction is below the jamming point. The fragile state is also identified as a long lived metastable state where G′ depends on the phase of the oscillatory shear. The dynamic viscosity evaluated from the shear loss modulus G′′ exhibits a sudden jump similar to the discontinuous shear thickening in the fragile state. In this talk we also show some preliminary results of hydrodynamic simulation for colloidal suspensions to discuss shear jamming and DST as well as the behavior of dry granular particles under the pressure control protocol.|
|DATE AND TIME: Wednesday, 17 October 2018 11:10 to 12:00|
|Title : Yielding in amorphous solids|
|Abstract : The loss of rigidity in amorphous solids when subjected to external stress has been investigated actively in recent years. I will describe recent results regarding the nature of the yielding transition, including strain localisation in the yielded solid, annealing effects below and above the yielding threshold, obtained by computational investigations of amorphous solids subjected to oscillatory deformation.|
|VENUE : MADHAVA LECTURE HALL|
|11:10 AM - 12:30 PM - Talk and Discussions|
|Monday, 22 October 2018|
|Title : Diversity in Dynamics of Phase Transitions: Recent findings from studies of simple model systems|
|Abstract : Following a general discussion on universalities related to various structural and dynamical aspects of phase transitions, I will concentrate on nonequilibrium phenomena. In this domain a set of problems will be described with the objective of highlighting how various aspects of coarsening phenomena depend upon space dimension, morphology, etc. Finally, I will present results from two problems of my current interest. One is related to kinetics of vapor-solid transitions and the other deals with the ordering in popular Ising ferromagnet. The aim will be to project the breadth of diversity even in simple situations.|
|Tuesday, 23 October 2018|
|Title: Butterfly effect in classical spin systems.|
|Abstract: Connections between many-body chaos and ergodicity form the basis of statistical mechanics. Starting with an overview of recent interests in this area, I shall discuss our numerical results characterising spatio-temporal signatures of chaos in spin systems and point out their possible quantitative connection to measures of transport such as diffusion coefficients. I shall discuss how the physics of frustration in classical spin systems help retain the signatures of chaos even at low temperatures.|
|Wednesday, 24 October 2018|
|Title: Growth of Order and its role in the Dynamics of Supercooled Liquids|
Abstract: Existence and growth of amorphous and other structural order in supercooled liquids approaching glass transition is a subject of intense research. Even after decades of work, there is still no clear consensus on the molecular mechanisms that lead to a rapid slowing down of liquid dynamics approaching this putative transition. The existence of a correlation length associated with amorphous order has recently been postulated and also been estimated using multi-point correlation functions which cannot be calculated easily in experiments. Thus the study of growing amorphous order remains mostly restricted to systems like colloidal glasses and simulations of model glass-forming liquids. We proposed an experimentally realizable yet simple correlation function to study the growth of amorphous order. We then demonstrate the validity of this approach for a few well-studied model supercooled liquids and obtain results, which are consistent with other conventional methods. Finally I will discuss role of the static length-scale associated with this amorphous order in dynamics of glassy systems with medium range crystalline order. We tried to understand the molecular mechanisms for glass transition in liquids with and without medium range crystalline order. The issue is important to answer because if the liquid eventually starts to form crystalline domains while approaching the glass transition then the complexity of the problem may simplify and may just be governed by the physics of the growing crystalline order. If not then there exists a new class of glass forming materials whose molecular mechanism for slowing down of dynamics will probably be easier to understand in terms of the dynamics of the growing medium range crystalline order. We found evidence that dynamics of glasses with medium range crystalline order are generically different from other glass forming liquids with no predominant local order.
1. R Das, S Chakrabarty and S Karmakar, Soft Matter 13, 6929 (2017).
2. S Chakrabarty, I Tah, S Karmakar and C Dasgupta, PRL 119, 205502 (2017).
3. I Tah, S Sengupta, S Sastry, C Dasgupta and S Karmakar, PRL 121, 085703 (2018).
4. BP Bhowmik, I Tah and S Karmakar, PRE, 98, 022122 (2018).
|Thursday, 25 October 2018|
|Title: Response of glassy systems to quenched disorder|
|Abstract: Understanding how quenched disorder affects the glassy behaviour of materials has been of interest, for quite some time, for example, in the context of type-II superconductors, metallic alloys etc. More recently, specific constructions in the form of pinned particles, have been used to investigate the onset of slow dynamics and exploring the ideal glass transition scenario. In this context, using numerical studies, we will discuss two different situations : (a) the interplay of a simple glass forming liquid with a spatially-varying external potential, motivated by recent optical realisations & (b) yielding dynamics of a glass embedded with impurities.|
|Friday, 26 October 2018|
|Title: Mutual information for protein structure and dynamics|
|Abstract: Though the physical laws at the atomic level interactions of amino acids in proteins are well defined and simple, understanding how proteins work is non-trivial. Protein sequence -> structure -> dynamics is believed to be the key to the hierarchy of their functional organization. There are several gaps in this perspective which are being filled with informatic methods these days. For example, using large scale evolutionary data of sequences to predict the structure or to derive relationship with dynamics. One of the commonly used tools for this purpose is mutual information. The lecture will cover the basics of this informatic method as well as its implications to the understanding of proteins.|