Monday, 07 August 2023
We will present the various fundamental concepts behind the structure of charged macromolecular systems. Phenomenology on both synthetic and biological systems will be presented, along with modern explanations. Potential future directions will be mentioned.
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.
This lecture will narrate the space-time odyssey of a carrot, beginning in 1888 at the German University of Prague in the Czech Republic and completing in 1968 on the ground floor of Rockefeller Center in New York–USA. RCA revealed there a breakthrough in the field of liquid crystal research to sixty reporters and displayed prototypes of flat screens for pictures and moving images. Thus began the worldwide information-display industry's change. A cast of scientists took part in the debate, and they will come to testify during this lecture: the path that led to the recognition of new states of matter was long and painful. Finally, liquid crystals changed our perception of matter by shattering the ""three-state"" paradigm.
References:
M. Mitov, ChemPhysChem, 15, 1245 (2014); Sensitive Matter, Harvard Univ. Press (2012).
D. Dunmur and T. Sluckin, Soap, Science, & Flat-Screen TVs, Oxford Univ. Press (2011).
P. M. Knoll and H. Kelker, Otto Lehmann, Books on Demand GmbH, Norderstedt (2010).
J. A. Castellano, Liquid Gold, World Scientific (2005).
T. J. Sluckin et al., Crystals That Flow, Taylor and Francis (2004).
H. Kelker, Mol. Cryst. Liq. Cryst., 165, 1 (1988); 21, 1 (1973).
The idea of tiny vessels roaming around in human blood vessels working as surgical nanorobots was first proposed by Richard Feynman, a vision that has triggered the imagination of scientists and non-scientists alike. With current advances in nanotechnology, there have been several strategies to realize this dream of a "nano voyager," which is of both fundamental and technological interest. We will discuss an approach to realizing the voyager based on helical propulsion. We will describe how this system can have applications in multiple areas, ranging from microfluidic manipulation to intra- and extracellular biophysical measurements. Finally, we will describe our efforts to render this system self-propelled, which has resulted in a unique medical intervention that affects millions of people and share our progress in commercializing this technology.
Tuesday, 08 August 2023
The twisted, cholesteric liquid crystal structure is a recurring design in animal and plant kingdoms. Cholesteric patterns are found in the iridescent chitin-containing cuticles of many insects. They may exhibit spatial variation in the helical pitch and in the orientation of the helix axis, as in the two-band, green and silver cuticle of the scarab beetle, Chrysina gloriosa. The silver bands are pattern-free, whereas the green bands exhibit an array of microcells. Each microcell behaves as a wavelength-selective mirror. By hyperspectral microscopy with 6 nm spectral resolution in the range of 400 nm-1000 nm, the topography of twisted structures under various orientations of the helical axis is investigated, from an orientation close to the normal to the cuticle surface in the silver bands to a spatially varying orientation in the microcells. The spatial distribution of the spectral center of mass portrays the geometrical shape of the hexagonal microcells.
Several biological purposes, such as conspecific or intra-species visual communication, thermoregulation and camouflage can be postulated.
References:
A. Jullien, M. Neradovskiy and M. Mitov, APL Photon. 5, 096102 (2020).
M. Mitov, V. Soldan and S. Balor, Arthropod Struct. & Dev. 47, 622 (2018).
G. Agez, C. Bayon and M. Mitov, Acta Biomaterialia, 48, 357 (2017).
M. Mitov, Soft Matter, 13, 4176 (2017).
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.
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 behavior. In these two lectures, I will introduce you to the molecular dynamics simulator, LAMMPS (lammps.org) using the example of a granular materials simulation.
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)
Wednesday, 09 August 2023
We will describe how fast fracture takes place by describing both the structure of the classical theory of fracture as well as recent experiments in which the theory is validated. These experiments describe fast fracture in slow motion. By studying dynamic fracture of brittle gels , we will be able to approach the putatively singular near-tip region. This first lecture would kind of give an introduction to dynamic fracture mechanics and show how linear elastic fracture mechanics can be generalized to include nonlinear elasticity. These results set the stage for the next lecture in which we will talk about when cracks ‘don’t follow the classical rules’.
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).
We will present the various fundamental concepts behind self assembly and phase behaviors of charged macromolecular systems. Phenomenology on both synthetic and biological systems will be presented, along with modern explanations. Potential future directions will be mentioned.
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.
Thursday, 10 August 2023
This second talk will include things that are not included in classical fracture mechanics. These include a description of waves that propagate along a crack front together with very new results showing the physics within dynamic crack fronts - and some new work that suggests a new view of crack instabilities.
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.
Friday, 11 August 2023
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.
This third talk will introduce relatively new work about how we can view classical friction as a "classical" shear fracture problem - basically suggesting a fundamental new paradigm for friction - with some new results that show what it is good for. We will then relate these results to a new picture of the fundamentals of earthquake dynamics.
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.
Monday, 14 August 2023
Active learning
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)
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.
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
Tuesday, 15 August 2023
We present a universal characterization of stress correlations in athermal systems, across crystalline to amorphous packings. Via numerical analysis of static configurations of particles interacting through harmonic as well as Lennard-Jones potentials, for a variety of preparation protocols and ranges of microscopic disorder, we show that the properties of the stress correlations at large lengthscales are surprisingly universal across all situations, independent of structural correlations, or the correlations in orientational order. In the near-crystalline limit, we present exact results for the stress correlations for both models, which work surprisingly well at large lengthscales, even in the amorphous phase. Finally, we study the differences in stress fluctuations across the amorphization transition, where stress correlations reveal the loss of periodicity in the structure at short lengthscales
with increasing disorder.
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.
Wednesday, 16 August 2023
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)
Examples: Bandits and Sequential Probability Ratio Test
Thursday, 17 August 2023
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
Friday, 18 August 2023
Introduction to Reinforcement Learning: MDP, POMDP, Q-Learning
We will discuss coarse-grained models of liquid crystals with two important classes of inclusions: magnetic particles and active matter. These two systems are respectively termed "ferronematics" and "living liquid crystals" in the experimental literature. We will present detailed results from theoretical studies of these systems.
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.
Monday, 21 August 2023
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.
Liquid Crystals I-Fundamental Aspects
Liquid crystals (LC) are well known because of the displays used in most gadgets. The gadgets use thermotropic nematic LCs with an apolar orientational order, made of rod-like organic molecules. The weak curvature elasticity of this medium, which is a hall mark of soft condensed matter, leads to low operating voltages needed in portable devices. The order also leads to complex flow properties. Chiral rod-like molecules give rise to a spontaneous helical twisting of the director (n, the direction of average orientational order) along one or two directions, giving rise to new structures. The rod-like molecules can also form liquid layers, which can in turn have a periodic stacking. The director can be along the layer-normal (smectic A) or tilted (smectic C). Smectic to nematic transition has a formal analogy with the superconductor-normal metal transition, giving rise to structures analogous to the Abrikosov lattice in chiral materials. Chiral smectic C can also exhibit polarization in the layer-plane, leading to ferroelectric, antiferroelectric and ferrielectric structures. Disc-like molecules exhibit liquid columnar structures, which in turn form different types of two-dimensional lattices. I will briefly describe these liquid crystals, and touch upon the relevant theoretical background.
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.
Tuesday, 22 August 2023
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.
Liquid Crystals II-Recent Developments
Organic molecules with a variety of shapes can be synthesised, and those with bent cores (BC) were discovered in the late 1990s to exhibit LC phases with novel structures. Usually, they form smectic LCs with tilted molecules, with a polar order in the layer plane. The layer polarization can have a spontaneous splay deformation, leading to two-dimensional structures, which have interesting properties. The nematic phase exhibited by some of the compounds consist of small molecular clusters, giving rise to strong responses to external stimuli. I will describe these developments, along with a glimpse of the theories proposed for the occurrence of the structures.
The most recent development is the discovery of the ferroelectric nematic phase in compounds made of small highly polar rod-like molecules. Though such a phase was predicted by Max Born in 1906, the polar molecules usually exhibit antiparallel near neighbour orientation, favored by electrostatic interaction and the medium has only an apolar long range order. This in turn gives rise to a couple of interesting phenomena like smectic polymorphism and reentrant phases. The surprising discovery of the ferroelectric nematic with a polarization ~ a few C/cm2 in some compounds synthesized in 2017 has led to a flurry of activity, and I will outline the development, and a model to understand the ferroelectric order.
Wednesday, 23 August 2023
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.
Enormous enhancement in the viscosity of a liquid near its glass transition is generally connected to growing many-body static correlations near the transition, often coined as ‘amorphous ordering’. Estimating the length scales of such correlations in different glass-forming liquids is very important to unravel the physics of glass formation. Experiments on molecular glass-forming liquids become pivotal in this scenario as the viscosity grows several folds ( ~1014 ), simulations or colloidal glass experiments fail to access these required long-time scales. Here we design an experiment to extract the static length scales in molecular liquids using dilute amounts of another large molecule as a pinning site. Results from dielectric relaxation experiments on supercooled glycerol with different pinning concentrations of Sorbitol and Glucose, as well as the simulations on a few models glass-forming liquids with pinning sites indicate the versatility of the proposed method, opening a plethora of opportunity to study the physics of glass transition in other molecular liquids.
REFERENCES
1. Soft-pinning: experimental validation of static correlations in supercooled molecular glass-forming liquids - R Das, BP Bhowmik, AB Puthirath, TN Narayanan, Smarajit Karmakar, PNAS Nexus 2023 (in press).
Thursday, 24 August 2023
The universal mechanism of particle transport at finite temperature is diffusion. However, it is a slow process and is enhanced in various living systems with the help of active transport processes. The entities that can adapt to the active processes by consuming internal sources of energy are called active matter. The realm of active matter is very diverse as they are observed in biological as well as synthetic systems. One of the common mechanisms that active particles utilise for acquiring active force is the diffusiophoresis mechanism, which is the spontaneous motion of any dispersed particles in a fluid due to the concentration gradient of dissolved molecular substances in the fluid. The scope of this talk lies in active polymers that can change their shape and acquires activity by selfdiffusiophoretic mechanisms, wherein the perpetual conversion of chemical energy into mechanical energy is responsible for driving the system out-of-equilibrium. The two
classes of active polymers that we will target here are (i) linear polymers and (ii) ring polymers. The influence of activity on the overall conformational and dynamical properties of the single flexible linear and ring polymer using coarse-grained simulation approach will be discussed.
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
Active Brownian motion with intermittent direction reversals is common in a class of bacteria like Myxococcus xanthus and Pseudomonas putida. For such a motion in two dimensions, the presence of the two time scales set by the rotational diffusion constant and the reversal rate gives rise to four dynamical regimes showing distinct behaviors. We characterize these behaviors by analytically computing the position distribution and persistence exponents. I will also present results on the steady state of such a "direction reversing active Brownian particle" in a harmonic potential. In this case, due to the interplay between the rotational diffusion constant, the reversal rate, and the trap strength, the steady state distribution shows four different types of shapes. *References*: Phys. Rev. E 104, L012601 (2021); Soft Matter 17, 10108 (2021); J. Phys. A: Math. Theor. 55, 385002 (2022); J. Phys. A: Math. Theor. 55 414002 (2022).
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.
Friday, 25 August 2023
Epithelial cell monolayers expand on substrates by forming finger-like protrusions in the boundary created by leader cells. Information transmission and communication between individual entities in the cohesive collective lead to long-range order, vortical structures, and disorder-ordered phase transitions. We ask the following questions: what makes a leader? What is the role of followers in leader cell formation? We investigated the mechanisms underlying leader formation using MDCK cells that were initially patterned in circular shapes on glass substrates. Leader cells (n=35) have higher radial velocities, increased areas during migration, and actively propel (MSD = 1.47) outwards. Of these, 66% cells transitioned into surfer phase (MSD = 1.03) that moved azimuthally whereas 34% divided into daughter cells after 90 minutes. Of the surfer cells, 23% transitioned again to leaders. We used a particle-based model to simulate cell migrations on substrates of varied stiffness. The dynamics of cellular motion in the ensemble are governed by orientational Vicsek and inter-cellular interactions between neighboring particles. The model includes bending, curvature-based motility, acto-myosin contractile cable forces, density dependent noise, and proliferations. We show that border forces are essential in the leader cell formation and the overall areal expansions of epithelial monolayers on substrates. We demonstrate that regions of increased cell density occur behind the leader cell edge. Finally, we assessed the role of cell divisions and quantified tractions on 10 kPa substrates using monolayer stress microscopy. These results demonstrate the relationships between cell proliferations and density fluctuations in leader to surfer cell transitions during epithelial migrations.
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.
The Mpemba effect is a fingerprint of the anomalous relaxation phenomenon wherein an initially hotter system equilibrates faster than an initially colder system when both are quenched to the same low temperature. Experiments on a single colloidal particle trapped in a carefully shaped double well potential have demonstrated this effect recently. In a similar vein, we consider a piece-wise linear double well potential that allows us to demonstrate the Mpemba effect using an exact theoretical analysis and explore the parameter space. We elucidate the role of the metastable states in the energy landscape as well as the initial population statistics of the particles in showcasing the Mpemba effect. Crucially, our findings indicate that neither the metastability nor the asymmetry in the potential is a necessary or a sufficient condition for the Mpemba effect. These observations pose questions on the current qualitative understanding of this relaxation phenomenon.