ICTS

Finite element methods or particle-based simulations have become a common investigative approach in Physics. They offer a way to fine-tune and test what ingredients of a model give rise to particular observed behaviour. In these two lectures, I will introduce you to the molecular dynamics simulator, LAMMPS (lammps.org) using the example of a granular materials simulation.

We will present the various fundamental concepts behind the dynamics of charged macromolecular systems. Phenomenology on both synthetic and biological systems will be presented, along with modern explanations. Potential future directions will be mentioned.

Colloids are one of the basic building blocks of soft and biological matter. Driving them out of equilibrium leads to dynamic assemblies that have interesting structure and function. Optical potentials in the form of laser traps and tweezers have emerged as interesting reconfigurable substrates to study out-of-equilibrium soft-systems. We have been using structured optical traps (such as optical vortex traps, holographic laser traps and thermo-plasmonic traps) to create reconfigurable optical and optothermal potentials to study hot Brownian motion and evolutionary dynamics of colloidal systems including dielectric and plasmonic nano-colloids [1]. We will present of our recent work on plasmon-assisted directed pulling [2] and trapping [3] of Brownian colloids, and dynamic assembly of thermally-active colloids in a defocused laser trap [4]. Specifically, we discuss the challenges and opportunities of structured optical tweezers in manipulating colloidal nano-(bio)matter.

[1] Plasmofluidic Single-Molecule Surface Enhanced Raman Scattering from Dynamic Assembly of Plasmonic Nanoparticles; P. P. Patra, R. Chikkaraddy, R. P.N. Tripathi, A. Dasgupta, G.V. Pavan Kumar;
Nature Communications, 5, 4357 (2014) 

[2]Optothermal pulling, trapping, and assembly of colloids using nanowire plasmons; V Sharma, S Tiwari, D Paul, R Sahu, V Chikkadi, and G V Pavan Kumar ; Soft Matter, 17, 10903-10909, (2021) 

[3]Single Molecule Surface Enhanced Raman Scattering in a Single Gold Nanoparticle-Driven Thermoplasmonic Tweezer; S. Tiwari, U. Khandelwal, V. Sharma and G V Pavan Kumar; Journal of Physical Chemistry Letters, 12, 11910–11918, (2021)

[4]Optothermal evolution of active colloidal matter in a defocused laser trap; D Paul, R Chand, G. V. Pavan Kumar;  ACS Photonics, 9, 10, 3440–3449  (2022)

The world of insects includes a large set of patterned cuticles with bumps, pits, bands, pixels or spots and a diversity of iridescent colors. These patterns result from the chiral liquid crystal organization of chitin fibrils [1]. Recent review papers, however, have reported that current biomimetic materials rarely mimic the range of physical complexity found in natural materials [2]. I will discuss the challenges of biomimicry, and the benefits when using synthetic liquid crystalline materials, a strategy that is skimmed over in scientists' toolkits. I will give examples of biomimetic and bioinspired materials taking as models striped (bicolor) and uniformly-colored cuticles of scarab beetles from the genus Chrysina. Glassy samples possess a high level of photonic and structural characteristics for Chrysina gloriosa [3]. Cryptography applications [3], chiral micromirrors with wavelength-selective focusing [4], and time temperature indicators [5] will be discussed. 

[1] M. Mitov, Soft Matter, 13, 4176 (2017).
[2] U. G. K. Wegst et al., Nature Mater., 14, 23 (2015). M. Kolle and S. Lee, Adv. Mater. 30, 1702669 (2018). Y. Yang et al., Adv. Mater., 30, 1706539 (2018).
[3] A. Scarangella, V. Soldan and M. Mitov, Nature Comm., 11, 4108 (2020).
[4] A. Jullien, M. Neradovskiy, A. Scarangella and M. Mitov, J. Roy. Soc. Interface, 17, 20200239 (2020).
[5] C. Boyon, M. Mitov and V. Soldan, ACS Applied Mat. & Interfaces, 13, 30118 (2021).

Deoxyribonucleic acid (DNA) is a negatively charged bio-macromolecule that helps in the transmission of genetic information for the growth and functioning of a living organism. Therefore, it is considered as a potential tool in gene therapeutics. Packing or condensing of this macromolecule is difficult because of the intra and inter molecular repulsive electrostatic and entropic interactions. Even though there are reports of condensing the molecule using inorganic salts in bulk aqueous medium, the assembly at the air-water interface is rarely reported. Here, we report the assembly of the DNA molecule at the interface induced by an imidazolium based ionic liquid (IL) 1,3 didecyl-2-methylimidazolium chloride. The surface pressure-area isotherm ensures the presence of the molecule at the interface with a high mean molecular area. Interfacial rheology measurements quantify the elastic nature of the molecular film. The storage and loss modulus of the film is found to strongly depend on the in-plane pressure. Advanced in-situ synchrotron X-ray scattering study relates these physical properties of the film with its structure. The electron density profile of the film across the interface manifests the compact nature of the film in presence of the IL. This work suggests an easy way of immobilizing the DNA macromolecule at the air-water interface. The work has been extended to bulk aqueous solution of DNA and the results are found to be in consistent with the interfacial one.

There are many natural settings in which we encounter solid objects at a fluid interface, such as a raindrop on a window pane, or a leaf floating on the surface of a pond.  We’ll start with examples such as these to build up the basic vocabulary of fluid-solid contact, but the main focus of these three lectures will be situations where the solid object can deform significantly due to the presence of a liquid.  These phenomena fall into two broad classes:  one where the solid is intrinsically soft, and the other where the flexibility of the solid has a geometric origin i.e. where it is a filament or a sheet.  We will discuss relevant ideas on the capillarity of liquid interfaces and the elasticity of solids such as surface energy and tension, surface stresses, bending, and stretching; these are elementary concepts but can still cause confusion in these new contexts.  These ideas will lead us to recently-studied elastocapillary phenomena such as wrapping and encapsulation by sheets, clumping of fibres, pattern formation in floating objects, rigidity of solid-fluid composites, and control of droplet motion.

Insects in the wild develop a variety of navigation strategies to achieve a desired goal within their environmental niche. Social insects such as ants use stigmergy and follow trails of pheromone laid out by successful foragers. However the trajectory that the collective treads often is not stationary and has to adapt to changes in the environmental condition. In this talk we will probe the question of how collectives can innovate and adapt their trails in a prototypical setting of agents following a semi-circular trail. Using the environment as the memory, we will see that agents with simple behavioural rules can innovate to find novel trajectories. To theoretically understand the process of innovation, we borrow ideas from non-equilibrium statistical mechanics and reinforcement-learning.

Single celled microalga Chlamydomonas reinhardtii exhibit directed motion towards blue light, a phenomenon called phototaxis. Phototaxis is well understood at the level of single cells. However, how a collection of cells respond to light remains unknown. We show that both phototaxis efficiency and response time of algal cells becomes cell concentration dependent. We identify the physical mechanism behind this collective behavior to be the changes in cell speed with change in concentration.

We summarize in this series of lectures the experiments which have been performed to test the theoretical findings in stochastic thermodynamics such as fluctuation theorem, Jarzynski equality, stochastic entropy, out-of-equilibrium fluctuation dissipation theorem, and the generalized first and second laws. We briefly describe experiments on mechanical oscillators, colloids, biological systems, and electric circuits in which the statistical properties of out-of-equilibrium fluctuations have been measured and characterized using the above-mentioned tools. We discuss the main findings and drawbacks. Special emphasis is given to the connection between information and thermodynamics. The perspectives
and followup of stochastic thermodynamics in future experiments and in practical applications are also discussed.

[1] S. Ciliberto, R. Solano, A. Petrossyan, J. Stat. Mech. P12003 (2010)
[2] S. Ciliberto, PHYSICAL REVIEW X 7, 021051 (2017)

Under the influence of oscillatory shear, a monolayer of frictional granular disks exhibits two dynamical phase transitions: a transition from an initially disordered state to an ordered crystalline state and a dynamic active-absorbing phase transition. Although there is no reason a priori for these to be at the same critical point, they are. The transitions may also be characterized by the disk trajectories, which are nontrivial loops breaking time-reversal invariance

Polymers dissolved in a turbulent flow experience intermittent fluctuating strain-rates and thereby stretch and recoil repeatedly. The consequent elastic feedback dramatically modifies the flow, resulting in a reduction of turbulent drag by as much as 80%. However, this stretching also leads to the mechanical scission or breakup of polymers, due to which the benefits of drag reduction are gradually lost. Now, while drag reduction has been successfully reproduced, albeit qualitatively, by continuum simulations of viscoelastic fluids, its loss by scission cannot be predicted unless we consider individual polymer molecules. In fact, scission is just one example of how molecular-scale polymer dynamics impacts the macro-scale flow. With this broad motivation, I will examine the Lagrangian dynamics of polymers advected by a turbulent flow. Using a hierarchy of models for the polymer and the flow—from dumbbells in a random velocity field to chains in a turbulent DNS—I will elucidate several intriguing aspects of the stretching statistics of polymers, including the coil-stretch transition, the emergence of self-similar distributions of extension, and the influence of intermittent turbulent straining. I will then turn to the problem of scission, where the Lagrangian approach allows us to track polymers as they break and form a distribution of daughter fragments. Our analytical and numerical predictions agree with, and help explain, past experimental results as well as engineering rules-of-thumb.

We summarize in this series of lectures the experiments which have been performed to test the theoretical findings in stochastic thermodynamics such as fluctuation theorem, Jarzynski equality, stochastic entropy, out-of-equilibrium fluctuation dissipation theorem, and the generalized first and second laws. We briefly describe experiments on mechanical oscillators, colloids, biological systems, and electric circuits in which the statistical properties of out-of-equilibrium fluctuations have been measured and characterized using the above-mentioned tools. We discuss the main findings and drawbacks. Special emphasis is given to the connection between information and thermodynamics. The perspectives
and followup of stochastic thermodynamics in future experiments and in practical applications are also discussed.

[1] S. Ciliberto, R. Solano, A. Petrossyan, J. Stat. Mech. P12003 (2010)
[2] S. Ciliberto, PHYSICAL REVIEW X 7, 021051 (2017)

In particulate flows, caustics form when inertial particle trajectories cross each other. IN these regions we cannot describe particle dynamics by a field. Caustics are interesting because they are singular features, and also they contribute enormously to particle collisions and coalescence. We shall discuss this phenomenon in the context of flow near a vortex, for both inertial and active particles. Collaborators: Rajarshi Chattopadhyay, Rahul Chajwa, Sriram Ramaswamy

Understanding deformations of macroscopic thin plates and shells has a long and rich history, culminating with the Foeppl-von Karman equations in 1904, a precursor of general relativity characterized by a dimensionless coupling constant (the "Foeppl-von Karman number") that can easily reach vK = 10^7 in an ordinary sheet of writing paper. However, thermal fluctuations in thin elastic membranes fundamentally alter the long wavelength physics, as exemplified by experiments that twist and bend individual atomically-thin free-standing graphene sheets (with vK = 10^13!) With thermalized graphene sheets, it may be possible to study the quantum mechanics of two dimensional Dirac massless fermions in a fluctuating curved space whose dynamics resembles a simplified form of general relativity. We then move on to analyze the physics of sheets mutilated with puckers and stitches. Puckers and stitches lead to Ising-like phase transitions that strongly affect the physics of the fluctuating sheet. Thin shells with a background curvature that couples in-plane stretching modes with the out-of-plane undulation modes, lead to qualitative differences between thermalized spherical shells compared to flat membranes.

Living fluids, arising from a complex organization of matter driven at the scale of its constituent agents, are confounding, and can exhibit "active turbulence". Analogies with high Reynolds number, inertial (Kolmogorov) turbulence, however, have not survived beyond the qualitative. Using a continuum hydrodynamic model for dense bacterial suspensions, we investigate the Lagrangian and Eulerian features distinguishing active from inertial turbulence. We find a flow transition to universality beyond a critical activity, which is accompanied by intermittency and maximal chaos. Interestingly, this asymptotic flow state manifests superdiffusion via Lévy walks, and consequently other Lagrangian anomalies, which we trace back to oscillatory streaks emerging in the Eulerian flow field - features that set living flows distinctly apart from inertial turbulence limited to classical diffusion. All of this makes the phenomenology of living matter rich and riddled with surprising nuances, which at times bridge the analogy with inertial turbulence, and at others break them. Broad-brushed parallels, therefore, obfuscate what may be biologically relevant strategies for survival and growth.

In order for artificial neural networks to learn a task, one must solve an inverse design problem. What are all the node weights for a network that will give the desired output? I will demonstrate how approaches developed by computer scientists can be harnessed to solve inverse design problems in soft matter. Specifically, we design mechanical and flow networks to perform functions inspired by biology. But artificial neural networks are constrained by their top-down approach to learning, which requires global minimization of a cost function. I will discuss our recent work pioneering a new approach, bottom-up learning, by which physical systems can learn on their own.

In this talk I will present a comparative study of  the  structure-dynamics correlation for systems interacting via attractive Lennard- Jones and its repulsive counterpart, the WCA potentials. The structural order parameter (SOP) is the curvature of the microscopic mean-field caging potential, termed the softness parameter. When calculated at a particle level, the SOP shows a distribution with particles having different degrees of softness. Although the two systems have similar structures, their average SOP is different. However, this difference is insufficient to explain the well known slowing down of the dynamics in LJ system at low temperatures. The slowing down of the dynamics can be explained in terms of a stronger coupling between the SOP and the dynamics. To understand the origin of this system specific coupling, we study the difference in the microscopic structure between the hard and soft particles by dividing the whole system into two communities. We find that compared to the WCA system for the LJ system, the communities’ structural differences are more significant and have a much stronger temperature dependence. Thus the study suggests that attractive interaction creates more structurally different communities. Even for the similar value of the average SOP, the difference in the local structure of the two communities is more comprehensive for the LJ system. Our study suggests that this broader difference in the structural communities is probably responsible for stronger coupling between the structure and dynamics. Thus the system specific structure-dynamics correlation, which also leads to a faster slowing down in the dynamics, appears to have a structural origin.

In this talk, my main focus will be on describing the model to explain embryo elongation and somitogenesis. First, I will describe the agent-based model that is able to mimic the presomitic mesoderm and embryo elongation. I will extend this model to mimic somitogenesis. Based on the results from the agent-based model I will develop a macroscopic continuum model. The content of this talk is mainly from the following two manuscripts and some unpublished results. 
1>  Rectified random cell motility as a mechanism for embryo elongation, Development (2022) 149, dev199423
2> Activity-driven extracellular volume expansion drives vertebrate axis elongation
https://doi.org/10.1101/2022.06.27.497799

Static and dynamic properties of confluent epithelial monolayers are crucial for several biological processes, such as wound healing, embryogenesis, cancer progression, etc. The importance of these processes calls for a detailed quantitative understanding of these properties. Recent experiments suggest a remarkable nearly-universal cell shape variability in such systems. Moreover, the average cell shape shows a strong correlation with cellular dynamics. In this talk, I will discuss a mean-field theory explaining the nearly universal cell shape variability and its consequences. I will further discuss the unusual glassy properties of such systems and show that the static and dynamic properties are strongly correlated. The results have crucial implications for various theories of glassy dynamics.

Motor proteins participate in intracellular transport and can generate mechanical forces on cytoskeletal filaments. In the first part of the talk, we will consider cargo transport by a kinesin-3 motor protein (MP) in touch receptor neurons of C. elegans. Analyzing experimental data, we find signatures of cooperative cargo binding and modifications of transport properties in the MPs under alteration of ubiquitination. In the second part, we will consider deformations of biopolymers and membranes under the active drive of motor proteins. We use analytic theory and numerical simulations for this purpose. Semiflexible filaments undergo re-entrant morphological transitions from open chain to spiral conformations in a gliding assay. On the other hand, a spherical cell membrane coupled to curvature-inducing activator proteins and active forces from polymerizing actin and myosin pull shows instabilities towards pattern formation and localized/running pulsations.

I will present our work on the preparation of colloidal assemblies in the form of chains, sheets and porous monoliths. These systems represent interesting models with Brownian colloidal particles connected through flexible polymer linkers. This results in unusual properties for the 3D monoliths, that are able to sustain large compressive deformations and recover elastically. 1D assemblies represent interesting model systems to understand the behaviour of flexibly connected chains. We have prepared colloidal chains that are thermoresponsive. For a critical range of chain rigidity, these chains form helical strands on heating. More recently, we have prepared 2D sheets of colloids, with independent control over their size, local order, flexibility and with the ability to make holes in these sheets.