Rajsekhar Das

The University of Texas at Austin

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Xin Li

The University of Texas at Austin

T. R. Kirkpatrick

University of Maryland, College Park

Sumit Sinha

The University of Texas at Austin

Smarajit Karmakar

Tata Institute of Fundamental Research

D. Thirumalai

The University of Texas at Austin

D. Thirumalai

The University of Texas at Austin

Chandan Dasgupta

Indian Institute of Science Bangalore

Saurish Chakrabarty

Nanyang Technological University

Bhanu Prasad Bhowmik

University of Edinburgh

Anand B. Puthirath

Rice University

Cooperative Institutions

The University of Texas at Austin

Tata Institute of Fundamental Research

University of Maryland, College Park

TIFR Centre for Interdisciplinary Sciences

Indian Institute of Science Bangalore

International Centre for Theoretical Sciences

Academy of Scientific and Innovative Research

Rice University

University of Hyderabad

University of Campania "Luigi Vanvitelli"

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Author Response: Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis

Rajsekhar Das Sumit Sinha Xin Li T. R. Kirkpatrick D. Thirumalai

10.7554/elife.87966.3.sa2

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Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis

eLife (2023)

Rajsekhar Das Sumit Sinha Xin Li T. R. Kirkpatrick D. Thirumalai

A recent experiment on zebrafish blastoderm morphogenesis showed that the viscosity ( η ) of a non-confluent embryonic tissue grows sharply until a critical cell packing fraction ( ϕ S ). The increase in η up to ϕ S is similar to the behavior observed in several glass-forming materials, which suggests that the cell dynamics is sluggish or glass-like. Surprisingly, η is a constant above ϕ S . To determine the mechanism of this unusual dependence of η on ϕ , we performed extensive simulations using an agent-based model of a dense non-confluent two-dimensional tissue. We show that polydispersity in the cell size, and the propensity of the cells to deform, results in the saturation of the available free area per cell beyond a critical packing fraction. Saturation in the free space not only explains the viscosity plateau above ϕ S but also provides a relationship between equilibrium geometrical packing to the dramatic increase in the relaxation dynamics.

Volume fraction

Blastoderm

Saturation (graph theory)

10.7554/elife.87966

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Soft pinning: Experimental validation of static correlations in supercooled molecular glass-forming liquids

PNAS Nexus (2023)

Rajsekhar Das Bhanu Prasad Bhowmik Anand B. Puthirath Tharangattu N. Narayanan Smarajit Karmakar

Enormous enhancement in the viscosity of a liquid near its glass transition is a hallmark of glass transition. Within a class of theoretical frameworks, it is connected to growing many-body static correlations near the transition, often called "amorphous ordering." At the same time, some theories do not invoke the existence of such a static length scale in the problem. Thus, proving the existence and possible estimation of the static length scales of amorphous order in different glass-forming liquids is very important to validate or falsify the predictions of these theories and unravel the true physics of glass formation. Experiments on molecular glass-forming liquids become pivotal in this scenario as the viscosity grows several folds (∼1014), and 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 model glass-forming liquids with pinning sites, indicate the versatility of the proposed method, opening possible new avenues to study the physics of glass transition in other molecular liquids.

Supercooling

10.1093/pnasnexus/pgad277

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Citations (7)

Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis

Rajsekhar Das Sumit Sinha Xin Li T. R. Kirkpatrick D. Thirumalai

A recent experiment on zebrafish blastoderm morphogenesis showed that the viscosity ( η ) of a non-confluent embryonic tissue grows sharply until a critical cell packing fraction ( ϕ S ). The increase in η up to ϕ S is similar to the behavior observed in several glass forming materials, which suggests that the cell dynamics is sluggish or glass-like. Surprisingly, η is a constant above ϕ S . To determine the mechanism of this unusual dependence of η on ϕ , we performed extensive simulations using an agent-based model of a dense non-confluent two-dimensional tissue. We show that polydispersity in the cell size, and the propensity of the cells to deform, results in the saturation of the available free area per cell beyond a critical packing fraction. Saturation in the free space not only explains the viscosity plateau above ϕ S but also provides a relationship between equilibrium geometrical packing to the dramatic increase in the relaxation dynamics.

10.7554/elife.87966.2

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Author response: Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis

Rajsekhar Das Sumit Sinha Xin Li T. R. Kirkpatrick D. Thirumalai

A recent experiment on zebrafish blastoderm morphogenesis showed that the viscosity (η) of a non-confluent embryonic tissue grows sharply until a critical cell packing fraction (ϕS). The increase in η up to ϕS is similar to the behavior observed in several glass forming materials, which suggests that the cell dynamics is sluggish or glass-like. Surprisingly, η is a constant above ϕS. To determine the mechanism of this unusual dependence of η on ϕ, we performed extensive simulations using an agent-based model of a dense non-confluent two-dimensional tissue. We show that polydispersity in the cell size, and the propensity of the cells to deform, results in the saturation of the available free area per cell beyond a critical packing fraction. Saturation in the free space not only explains the viscosity plateau above ϕS but also provides a relationship between equilibrium geometrical packing to the dramatic increase in the relaxation dynamics.

Volume fraction

Saturation (graph theory)

Blastoderm

10.7554/elife.87966.2.sa4

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Mechanical feedback controls the emergence of dynamical memory in growing tissue monolayers

bioRxiv (Cold Spring Harbor Laboratory) (2022)

Sumit Sinha Xin Li Rajsekhar Das D. Thirumalai

The growth of a tissue, which depends on cell-cell interactions and biologically relevant process such as cell division and apoptosis, is regulated by a mechanical feedback mechanism. We account for these effects in a minimal two-dimensional model in order to investigate the consequences of mechanical feedback, which is controlled by a critical pressure, p c . A cell can only grow and divide if the pressure it experiences, due to interaction with its neighbors, is less than p c . Because temperature is an irrelevant variable in the model, the cell dynamics is driven by self-generated active forces (SGAFs) that are created by cell division. It is shown that even in the absence of intercellular interactions , cells undergo diffusive behavior. The SGAF-driven diffusion is indistinguishable from the well-known dynamics of a free Brownian particle at a fixed finite temperature. When intercellular interactions are taken into account, we find persistent temporal correlations in the force-force autocorrelation function ( FAF ) that extends over timescale of several cell division times. The time-dependence of the FAF reveals memory effects, which increases as p c increases. The observed non-Markovian effects emerge due to the interplay of cell division and mechanical feedback, and is inherently a non-equilibrium phenomenon.

Negative feedback

Dynamics

Positive feedback

Brownian dynamics

10.1101/2022.02.09.479806

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Citations (1)

Soft-Pinning: Experimental Validation of Static Correlations in Supercooled Molecular Glass-forming Liquids

arXiv (Cornell University) (2021)

Rajsekhar Das Bhanu Prasad Bhowmik Anand B. Puthirath Tharangattu N. Narayanan Smarajit Karmakar

Enormous enhancement in the viscosity of a liquid near its glass transition is generally connected to the 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 highly 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 ($\sim 10^{14}$), simulations or colloidal glass experiments fail to access the long-time scales required. 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 the simulations on a few model glass-forming liquids with pinning sites indicate the robustness of the proposed method, opening a plethora of opportunity to study the physics of other glass-forming liquids.

Supercooling

10.48550/arxiv.2106.06325

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Citations (4)

Mechanical feedback controls the emergence of dynamical memory in growing tissue monolayers

The Journal of Chemical Physics (2022)

Sumit Sinha Xin Li Rajsekhar Das D. Thirumalai

The growth of a tissue, which depends on cell-cell interactions and biologically relevant processes such as cell division and apoptosis, is regulated by a mechanical feedback mechanism. We account for these effects in a minimal two-dimensional model in order to investigate the consequences of mechanical feedback, which is controlled by a critical pressure, pc. A cell can only grow and divide if its pressure, due to interaction with its neighbors, is less than pc. Because temperature is not a relevant variable, the cell dynamics is driven by self-generated active forces (SGAFs) that arise due to cell division. We show that even in the absence of intercellular interactions, cells undergo diffusive behavior. The SGAF-driven diffusion is indistinguishable from the well-known dynamics of a free Brownian particle at a fixed finite temperature. When intercellular interactions are taken into account, we find persistent temporal correlations in the force-force autocorrelation function (FAF) that extends over a timescale of several cell division times. The time-dependence of the FAF reveals memory effects, which increases as pc increases. The observed non-Markovian effects emerge due to the interplay of cell division and mechanical feedback and are inherently a non-equilibrium phenomenon.

Dynamics

Brownian dynamics

Negative feedback

Positive feedback

10.1063/5.0087815

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Citations (16)

Understanding the dynamics of glass-forming liquids with random pinning within the random first order transition theory

The Journal of Chemical Physics (2016)

Saurish Chakrabarty Rajsekhar Das Smarajit Karmakar Chandan Dasgupta

Extensive computer simulations are performed for a few model glass-forming liquids in both two and three dimensions to study their dynamics when a randomly chosen fraction of particles are frozen in their equilibrium positions. For all the studied systems, we find that the temperature-dependence of the $\alpha$ relaxation time extracted from an overlap function related to the self part of the density autocorrelation function can be explained within the framework of the Random First Order Transition (RFOT) theory of the glass transition. We propose a scaling description to rationalize the simulation results and show that our data for the $\alpha$ relaxation time for all temperatures and pin concentrations are consistent with this description. We find that the fragility parameter obtained from fits of the temperature dependence of the $\alpha$ relaxation time to the Vogel-Fulcher-Tammann (VFT) form decreases by almost an order of magnitude as the pin concentration is increased from zero. Our scaling description relates the fragility parameter to the static length scale of RFOT and thus provides a physical understanding of fragility within the framework of the RFOT theory. Implications of these findings for the values of the exponents appearing in the RFOT theory are discussed.

10.1063/1.4958632

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Citations (16)

Collective dynamic length increases monotonically in pinned and unpinned glass forming systems

The Journal of Chemical Physics (2025)

Rajsekhar Das T. R. Kirkpatrick D. Thirumalai

The Random First-Order Transition (RFOT) theory predicts that transport proceeds by the cooperative movement of particles in domains, whose sizes increase as a liquid is compressed above a characteristic volume fraction, ϕd. The rounded dynamical transition around ϕd, which signals a crossover to activated transport, is accompanied by a growing correlation length that is predicted to diverge at the thermodynamic glass transition density (>ϕd). Simulations and imaging experiments probed the single particle dynamics of mobile particles in response to pinning all the particles in a semi-infinite space or randomly pinning (RP) a fraction of particles in a liquid at equilibrium. The extracted dynamic length increases non-monotonically with a peak around ϕd, which not only depends on the pinning method but is also different from ϕd of the actual liquid. This finding is at variance with the results obtained using the small wavelength limit of a four-point structure factor for unpinned systems. To obtain a consistent picture of the growth of the dynamic length, one that is impervious to the use of RP, we introduce a multiparticle structure factor, Smpc(q,t), that probes collective dynamics. The collective dynamical length, calculated from the small wave vector limit of Smpc(q,t), increases monotonically as a function of the volume fraction in a glass-forming binary mixture of charged colloidal particles in both unpinned and pinned systems. This prediction, which also holds in the presence of added monovalent salt, may be validated using imaging experiments.

Volume fraction

Structure factor

10.1063/5.0241501

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