Talk Abstracts
Abhishek Dhar
Title: Entropy growth during free expansion of an ideal gas
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Abstract:
To illustrate Boltzmann’s construction of an entropy function that is defined for a microstate of a macroscopic system, we present here the simple example of the free expansion of a one dimensional gas of non-interacting point particles. The construction requires one to define macrostates, corresponding to macroscopic variables and we will discuss two specific macrostate constructions. Our results illustrate that concepts such as that of ergodicity and chaos are not as relevant as sometimes claimed, for observing macroscopic irreversibility and entropy increase. Rather, the notions of initial conditions, typicality, large numbers and coarse-graining are the important factors.
A. V. Anil Kumar
Title: Dynamics of binary colloidal mixtures in an external potential barrier : Role of depletion interaction
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Abstract:
Binary colloidal mixtures of unequal sizes serve as a paradigm for entropic manipulation of structural as well as the dynamical properties of soft matter. The primary reason behind this is the attractive depletion interaction between the larger species in the mixture due to the presence of smaller components. In this talk, we look at the role of these depletion interactions when the binary mixture is subjected to an external potential barrier. The depletion interactions between the barrier and larger particles significantly alters the dynamics of both components in the mixture. The temperature dependence of the diffusion of larger particles deviates from normal Arrhenius law. At low densities, the temperature dependence of diffusion coefficient follow a sub-Arrhenius behaviour. This is in contrast to the suggestion that sub-Arrhenius diffusion is intimately related to the quantum tunnelling effect. As density increases, there is a cross over from sub-Arrhenius to super-Arrhenius diffusion. This crossover coincides with the formation of crystalline domain of larger components in the region of external potential barrier.
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Amitabha Nandi
Title: Kinesin-mediated axonal transport of vesicles
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Abstract:
Intracellular transport is a complex process that allows reliable delivery of material, thus allowing the proper functioning of a living cell. Vesicles inside cells are transported either actively by molecular motors along intracellular filaments or by diffusional transport. While diffusional transport helps the vesicles to probe the local environment, ballistic transport, on the other hand, is helpful for traversing large distances in a directed way. In this talk, we will discuss the mechanism of kinesin-mediated axonal transport of synaptic vesicles in C. elegans and the role of motor cooperativity during such transport.​
Apratim Chatterji
Title: Inducing organization in intrinsically disordered polymeric systems: lessons from bacterial chromosomes
Abstract:
In recent times, researchers are using statistical physics to understand the emergent dynamics and organization in living systems, such as organization of the DNA within the living cell.
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle [1,2,3]. Using principles of entropic repulsion between polymer loops confined in a cylinder, we use Monte carlo simulations to show that the segregation is spontaneously enhanced by the adoption of a certain DNA-polymer architecture as replication progresses. Secondly, the chosen polymer-topology ensures its self-organization along the cell axis while segregation is in progress, such that various chromosomal segments (loci) get spatially localized. The evolution of loci positions match the corresponding experimentally reported results. Additionally, the contact map generated using our bead-spring model reproduces the macro-domains of the experimental Hi-C maps.
Thus we have proposed a framework [4] which reconciles many spatial organizational aspects of E. coli chromosome as seen in-vivo, and provides a consistent mechanistic understanding of the process underlying segregation. Certain proteins are expected to contribute to change the DNA-polymer architecture. We also studied other polymer architecttures, and seen that the same mechanism can be used to explain the experimental data of the C.crescentus chromosome [5].
[1] Jay K. Fisher, A. Bourniquel, G. Witz, B. Weiner, M. Prentiss, and N. Kleckner.
Four-dimensional imaging of e. coli nucleoid organization and dynamics in living cells.
Journal Cell, 153(4):882–895, 2013.
[2] A. Japaridze, C. Gogou, J. W. J. Kerssemakers, H. M. Nguyen, and Cees Dekker. Direct observation of independently moving replisomes in Escherichia coli.
Journal : Nature Communications, 11(1), June 2020.
[3] Virginia S. Lioy, Ivan Junier, and Frédéric Boccard.
Multiscale dynamic structuring of bacterial chromosomes.
Journal : Annual Review of Microbiology, 75(1), August 2021.
[4] D.Mitra, S. Pande, Apratim Chatterji.
DNA-polymer architecture orchestrates the segregation and spatial organization of bacterial chromosomes during replication.
Journal : accepted in Soft Matter (2022)
[5] D.Mitra, S. Pande, Apratim Chatterji.
Modified topology of ring polymers in confinement leads to spatial organization
Journal: submitted
Balasubramanian Sundaram
Title: Conformations and configurations: Throwing everything including the kitchen sink at liquid ethylene glycol
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Abstract:
Ethylene glycol (EG) is a small molecule exhibiting a rich conformational landscape. In its gas and crystalline phases, the molecule's central dihedral is in gauche state. However, in its liquid state, although it was known through vibrational spectroscopy that a fraction of molecules are in the trans state, the same was not quantified. Following up a recent ab initio molecular dynamics simulation (AIMD), we confirm that neat liquid EG contains 21% molecules with their central dihedral in trans conformation. A non-polarizable force field which quantitatively reproduces several physical properties as well as reproduces the conformational distribution is developed. Aqueous EG solutions at various compositions modelled with this force field exhibit a fascinating reduction in the fraction of trans conformers upon dilution, due largely to the increase in the polarity of the solution. The talk will also cover interesting results of liquid-vapor interfaces of both the neat liquid EG and its aqueous solution.
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Kavita Jain
Title: Slow quench dynamics in classical systems
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Abstract:
The phase ordering dynamics of a system following an instantaneous quench have been well studied but such dynamics have been relatively less explored when the quench occurs at a finite rate. I will describe our analytical and numerical results on a kinetic Ising model and a zero-range process when the system is annealed slowly to the critical point. Starting from the time-evolution equations, we derive the Kibble-Zurek scaling laws for the defect density at the critical point and elucidate the role of critical coarsening in the approach to the critical point.
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Prabal K Maiti
Title: Activity induced phase separation and ordering in various model soft matter systems
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Abstract:
We report scalar activity induced phase separation and crystallization in a system of 3-d Lennard- Jones particles taken at state points spanning from gas to liquid regime using Molecular dynamics simulation (MD). Scalar activity was introduced by increasing the temperature of half of particles (labeled ‘hot’) while keeping the temperature of the other half constant at a lower value (labelled ‘cold’). The relative temperature difference between the two subsystems is considered as a measure of the activity. From our simulations we observe that the two species tend to phase separate at sufficiently high activity ratio. We observe similar activity induced phase separation in a mixture of active and passive dumbbells. We also study the order-disorder transition and phase separation in a mixture of hot and cold spherocylinder of different aspect ratio (L/D) interacting through Weeks-Chandler-Anderson (WCA) potential in three dimensions. Activity drives the cold particles through a phase transition to a more ordered liquid crystalline (LC) state and the hot particles to a state of less order compared to the initial equilibrium state. The cold components of a homogeneous isotropic (I) structure acquire nematic (N) and, at higher activity, crystalline (K) order. Similarly, the cold zone of a nematic initial state undergoes smectic (Sm) and crystal ordering above a critical value of activity while the hot component turns isotropic. Surprisingly, activity induces LC ordering for spherocylinder having aspect ratio below Onsager limit. We find that the hot particles occupy a larger volume and exert an extra kinetic pressure, confining, compressing and provoking an ordering transition of the cold-particle domains. Finally, we show similar activity induced phase separation in a chiral system.
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References:
1. Scalar activity induced phase separation and liquid–solid transition in a Lennard-Jones system, S. S. N. Chari, C. Dasgupta and P. K. Maiti, Soft Matter, 2019, 15, 7275–7285.
2. Heating leads to liquid-crystal and crystalline order in a two-temperature active fluid of rods, J. Chattopadhyay, S. S. P. Sivajothi, K. Varma, S. Ramaswamy, C. Dasgupta and P. K. Maiti, PRE, 104, 054610 (2021) arXiv preprint arXiv:2105.04571 (2021)
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3. Two temperature activity induces liquid crystal phase inaccessible in equilibrium, J. Chattopadhyay, S. S. P. Sivajothi, K. Varma, S. Ramaswamy, C. Dasgupta and P. K. Maiti, arXiv:2205.00667 (2022)
4. Phase behavior of active and passive dumbbells, Nayana V , Shiang-Tai Lin , Prabal K Maiti, arXiv preprint arXiv:2109.00415 (2021)
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Prabhat Jaiswal
Title: Kinetics of Wetting: Universal Fast Mode and Potential-dependent Regimes
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Abstract:
We present molecular dynamics (MD) simulation results of surface-directed spinodal decomposition (SDSD) in unstable symmetric binary mixtures at wetting surfaces. Our primary focus in this talk is to discuss the early-stage wetting kinetics for various surface fields. First, we consider the long-ranged power-law potential. In this case, the wetting-layer thickness R1(t) at very early times exhibits a potential-dependent power-law growth. It then crosses over to a universal fast-mode regime with the growth exponent ~ 3/2. In contrast, for the short-ranged surface potential, a logarithmic behavior in R1(t) is observed at initial times which further displays the similar rapid growth. Our MD results firmly establish the existence of universal fast-mode kinetics and settle the related controversy.
Rajesh Ganapathy
Title: Intermediate Range Order Governs Dynamics in Dense Colloidal Liquids
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Abstract:
Colloidal suspensions comprise of micrometer-sized particles that remain suspended in a fluid by Brownian motion. Their large size, typically a micron, allows for simultaneous manipulation and investigation of dynamics at the single-particle level using relatively simple tabletop experimental techniques. This feature combined with the tunability of particle shape and interactions makes them promising candidates to address a plethora of problems in statistical mechanics and condensed matter. In my talk, I will describe results from real-space imaging experiments of dense colloidal liquids that show that liquids have structural order at intermediate length scales that are not captured by conventional two-point density correlators. We will show that this intermediate range order is predictive of dynamics in liquids.
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References:
[1] Navneet Sing, Zhen Zhang, A K Sood, Walter Kob and Rajesh Ganapathy (manuscript in preparation 2022)
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Snigdha Thakur
(with Namita Jain)
Title: Collapse Dynamics of Flexible Active Polymer
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Abstract:
The active matter systems feature the perpetual conversion of chemical energy or other forms of energy into mechanical motion that drives the system out-of-equilibrium. In the biological context, the active matter system spans all the length scales of living organisms, from bacterial colonies , sperm cells, self-organising bio-polymers such as microtubles and actin to the school of fish, the flock of birds, human crowds etc., which ranges from microscopic length scale to macroscopic. There are many applications such as transportation of materials, targeted drug delivery, flagellar motion shown by cilia and flagella, collective behaviour, pattern formation during motion etc., where self-propulsion is essential. Microtubule filaments are an important active polymer where the motor protein (kinesin) make use of chemical energy derived from the hydrolysis of adenosine triphosphate (ATP) to induce the conformational changes, which then leads to its motion on microtuble. These examples help us to gain an understanding about the modelling of active matter (or self-propulsion) systems. In this work, we are interested in studying one particular branch of such active systems, that is the active polymer which exhibits various interesting dynamics like self-propulsion, swelling, shrinkage, loop formation, spontaneous oscillation, spiral formations, enhanced diffusion etc [1, 2, 3]. In our study, we investigate the structural and dynamical properties of a chemically active flexible polymer chain immersed in a solvent bath by using hybrid simulation techniques in a three-dimensional space [4]. The source of activity on the polymer is the self-generating, nonequilibrium solvent gradient caused by the chemical reaction at different sites on the polymer. The chemical gradient then leads to the generation of the local tangential force along the filament. Here we present the effect of activity on the configurational dynamics of a flexible chain emphasizing globulelike transformation at the higher activity. Particular attention is paid to how the radius of gyration (Rg) changes with the activity. We find that the polymer undergoes a coil-to-globule-like transition with increasing active force. Decreasing the Flory scaling exponent of Rg, the correlation of the end-to-end vector and radial distribution of the monomers around the filament quantifies this transition. We also analyze the motion of a polymer and its center of mass in terms of time-averaged mean-squared displacement (MSD). The superdiffusive motion of the active flexible polymer reverts to random walk at a long time scale with an enhanced diffusion, where the scaling of the diffusion coefficient is the same as the Zimm model.
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References:
[1] Kaiser, Andreas and Löwen, H. J. Chem. Phys. 2014, 141, 4.
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[2] Isele-Holder, R. E.; Elgeti, J.; Gompper, G. Soft Matter 2015, 36, 11.
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[3] Bianco, V.; Locatelli, E.; Malgaretti, P. Phys. Rev. Lett. 2018, 121, 217802.
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[4] Jain, N.; Thakur, S. Macromolecules 2022 55, 7.
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Srikanth Sastry
(with Himangsu Bhaumik and Giuseppe Foffi)
Title: Avalanches and clusters in sheared glasses
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Abstract:
Avalanches are collective, often large scale, reorganizations that take place in a variety of systems that exhibit intermittent behaviour. They have been studied extensively in amorphous solids, to understand the nature of plasticity prior to and beyond the yielding transition. Avalanches can be composed of spatially disconnected clusters, and the relationship between the statistics of avalanches and clusters, not investigated in detail till recently, reveal interesting and unexpected dependence on the details of interparticle interactions and local geometry. Results from investigations of avalanches, clusters and local geometry in the case of silica, in comparison with other model glasses, will be presented.
Sutapa Roy
Title: Droplet Coalescence Dynamics during Phase Separation
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Abstract:
When two droplets come in contact with each other, they form a liquid bridge which evolves with time until a final product drop is formed. An important topic in this direction is the relative positioning of the final drop with respect to the parents — a phenomenon known as “coalescence preference (CP) dynamics”. In this talk, results from computer simulations will be presented on the spatial and temporal properties of CP and compared with analytical predictions.
Tejas Dhamecha
(with Subir K. Das )
Title: Finite-size Scaling in Dynamics of Error Reduction in Neural Network Training
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Abstract:
With the objective of understanding the evolution of accuracy during neural network (NN) training, we present results from the analyses of a database that contains images. For a data set of a given size, we investigate how, as a function of time, i.e. the number of iterations in the NN algorithm that employs a gradient descent method, the accuracy in the identification of the images improves. As expected, the asymptotic value, in the long time limit, depends upon the size of a data set, being higher for a larger set. We demonstrate how this behavior resembles the growth phenomena during phase transitions in finite systems. Inspired by the similarity, we performed analyses via a finite-size scaling (FSS) technique that, in recent times, found applications in non-conventional problems, beyond the domain of phase transformation, like the dynamics of spread of communicable diseases. It is shown that the outputs from the NN training, for various set sizes, nicely follow a FSS behavior. From our analyses it transpires that with the increase of time the decay in error, from its maximum value, occurs in a power-law fashion, in the finite-size unaffected regions, the exponent for which we have estimated accurately. We also discuss an accurate mathematical expression for the overall FSS function. In addition to being of fundamental nature, the study is important with respect to optimal planning for arriving at a desired predictive accuracy, within a given time, in the general area of machine learning.
Subir K. Das
Title: Mpemba effect in magnetic transitions
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Abstract:
Should a hotter system equilibrate faster than a colder one, when quenched to a common final lower temperature? An affirmative answer to this question is counter intuitive. Nevertheless, it is observed and is related to the, by now well known, Mpemba effect, who rediscovered this forgotten fact, concerning cooling of water, in the last century. Recently, there have been efforts to investigate it in other systems. In this talk, I will discuss results from the studies of para- to ferromagnetic transitions in the q-state Potts model.