Wednesday, 01 February 2023
Macromolecular crowding modulates the conformation of plasmids and even condenses them by osmotic pressure and excluded volume effect after a threshold concentration. The laser light scattering (dynamic and static) experiments were performed to explore the role of dextran (size (d): 2.6, 6.9, and 17.0 nm) in compacting the plasmids (pBS: 2.9 kbps; pCMV-Tag2B: 4.3 kbps; and pET28a: 5.3 kbps) in vitro in the volume fraction (ϕ) range 0.01 to 0.15. Two compaction regimes were observed in terms of the radius of gyration (Rg) for plasmid−dextran combinations, wherein the plasmid diffusivity is governed by normal diffusion and subdiffusion, respectively. Generalized scaling, Rg ∼ ϕ−1/(1+x), where x represents the conformational geometry of plasmids, is reported. The plasmid conformation depends on the crowder’s size, with larger conformational changes observed in the presence of smaller crowders. The second virial coefficients and translational diffusion coefficients are estimated to understand the effects of interplasmid repulsive interactions and diffusivity on plasmid conformation,
Fragility is the inability of a material to elas2cally support some infinite simal loads. In the linear elas2c response, the fragile regimes lie at the thresholds of material rigidity where certain combina2ons of the elas2c moduli vanish. While over the past decades, many sta2c realiza2ons of fragile elas2city have appeared in the field of mechanical metamaterials, in this talk, we discuss how the cytoskeleton of the living cell offers a unique dynamic realiza2on of fragile, ac2ve, renewable maBer. Ac2ve myosin motors undergoing turnover, in a strain dependent manner, on an overdamped ac2n nemato-elastomer dynamically renormalize its elas2c moduli. In this self-organiza2on process, fragile bulk and surface
modes may dynamically appear or disappear. The material, further, endogenously generates ac2ve nonlineari2es to stabilize the linear fragile response. In addi2on to this unconven2onal elas2city, the material displays ac2ve segrega2on and excitability, while ‘odd’ contribu2ons to the ac2ve stress may give rise to propaga2ng ‘odd’ waves.
Biomolecular and physical cues of the extracellular matrix environment regulates collective cell dynamics and tissue patterning. Nonetheless, how the viscoelastic properties of the matrix regulate collective cell spatial and temporal organization is not fully understood. Here we show that the passive viscoelastic properties of the matrix that encapsulate a spheroidal tissue of breast epithelial cells guide tissue proliferation in space and in time. Matrix viscoelasticity prompts symmetry breaking of the spheroid, leading to the formation of invading finger-like protrusions, YAP nuclear translocation and epithelial to mesenchymal transition both in vitro and in vivo in a Arp2/3 complex dependent manner. Computational modelling of these observations allow us to establish a phase diagram relating morphological stability with matrix viscoelasticity, tissue viscosity, cell motility and cell division rate, which is experimentally validated by biochemical assays
and in vitro experiments with an intestinal organoid. Altogether, this work highlights the role of stress relaxation mechanisms in tissue growth dynamics, a fundamental process in morphogenesis and oncogenesis.
In this talk, I will mainly focus on developing the computational model and its agreement with experimental observations. How the change in the mechanical properties of the passive viscoelastic matrix leads to morphological stability/instability of the spheroids and organoids. How the computational models can be helpful to guide the experiments in the right direction.
Reference: Matrix viscoelasticity controls spatio-temporal tissue organization, Alberto Elosegui-Artola, Anupam Gupta, Alexander J. Najibi, Bo Ri Seo, Ryan Garry, Christina M
Tringides, Irene de Lázaro, Max Darnell, Wei Gu, Qiao Zhou, David A. Weitz, L. Mahadevan, David J. Mooney. bioRxiv:10.1101/2022.01.19.476771
The coupling of the active actin-myosin cortex and the cell membrane allows the cell to deform, move, and undergo division. We consider deformations of spherical membranes under the active drive of motor proteins. Using numerical calculations complemented by analytical theory, we show the emergence of several morphological phases and phase transitions. A spherical cell membrane coupled to curvature-inducing activator proteins and active forces from polymerizing actin and myosin show instabilities towards pattern formation, localized pulsation, and pole-to-pole running pulsations.
Although many phenotypic traits are determined by a large number of genetic variants, how a polygenic trait adapts in response to a change in the environment is not completely understood. I will describe our recent results for
the adaptation dynamics of a large but finite population evolving under stabilizing selection; in particular, I will focus on how van Kampen’s system size expansion can be utilized to get some insight into these dynamics.
Experiments performed using micro-patterned 1 dimensional collision assays has allowed for precise quantitative analysis of the collective manifestation of the phenomenon of contact inhibition locomotion (CIL) wherein, individual migrating cells reorient their direction of movement when they come in contact with other cells. Inspired by these set of experiments, we present a discrete minimal 1D driven lattice gas model which mimics the CIL interaction between cells and active movement of the cell in 1-d channel. We analyze the emergent collective behaviour of migrating cells in such confined geometry.
The thermodynamics of a charged polymer system is characterized by the interaction potentials, conformational entropy of the polymer chains and entropy of free counterions and salt ions. We review a few theories which investigate the comparative roles of entropy to enthalpy in several charged polymer systems. From a single polyelctrolyte (PE) chain to PE networks it is seen that the ideal gas entropy of free counterions and the configurational entropy of polymers play important roles in determining the equilibrium structure of the PEs. The pressure due to confined counterions is important in dictating the kinetics of conformational changes in a single PE chain. In PE gels, the free
ion entropy is accounted for by the mixing entropy to characterize its swollen state in solution. A system of two oppositely charged polyelectrolytes displays the critical role played by the entropy of free counterions in complex formation, and shows its strengths comparative to Coulomb energy and dependence on the ambient conditions, like temperature, dielectricity and salt concentration. Although the Coulomb energy is an important entity in charged polymer systems, the complexation between two oppositely charged PE chains shows a large release of counterions from the respective chains, resulting in a large entropy gain which drives the process. The concept can be generalized to asymmetric and
partially ionized polymers, and also to intrinsically disordered proteins (IDP).
Keywords: polyelectrolytes, entropy, free energy, complexation, kinetics
We consider the collective dynamics of self-propelling particles in two dimensions. They can align themselves according to the direction of propulsion of their neighbours, together with small rotational fluctuations. They also interact with each
other via soft, isotropic, repulsive potentials. The particles are confined in a circular trap. The steepness of the trap is tuneable. When the trap is steep, particles flock along its boundary. They form a polar cluster that spreads over the boundary. The cluster is not spatially ordered. When the steepness is decreased beyond a threshold value, the cluster becomes round, compact and eventually spatial order (hexagonal) emerges in addition to the pre-established polar order. First we
investigate the kinetics of such ordering with varying steepness. Next we investigate the information flow within the ordered cluster while colliding with the boundary of the trap.
We employ grand canonical Monte-Carlo and molecular dynamics simulations to investigate the phase behavior and viscoelastic properties of a simple liquid asymmetrically confined by two structureless walls. Confinement asymmetry drives a rich phase behavior and a two-regime viscoelastic response which is found to be universal for strongly confined fluids. The fluid exhibits a gel-like mechanical response vicinity of the ordering transition, before elastic behavior becomes dominant.
Amorphous materials display seemingly random behavior at short-length scales, with elasticity emerging at larger length scales. On the other hand, crystals, with a periodic spatial profile, also display similar elastic behavior at large length scales. Gradually introducing disorder into athermal crystalline packings can therefore be used to build a relation between the well-established physics of crystals and that of amorphous solids. We present a universal characterization of stress correlations in athermal systems, across crystalline as well as amorphous packings. We present exact results for the stress correlations in energy-minimized configurations of near-crystalline packings. We present numerical as well as theoretical results for the correlations in the components of the stress tensor across a wide variety of situations, including crystalline, as well as fully amorphous packings. We find that properties of the stress correlations at large lengthscales are display universal behaviour and are independent of the underlying structure.
In this talk, we will discuss novel features that arise in an active particle model due to the interplay between multiple timescales.
Active matter refers to systems driven out of equilibrium through the uptake and dissipation of energy at the level of individual constituents. As a result, they display anomalous features that closely resemble numerous biological and natural phenomena, such as flocking animals and collective cell migration. Yet, a detailed understanding of these systems remains an open challenge. Over the past few decades, experimentalists have developed various systems to explore the physical
principles governing active matter. However, these systems are often very different from each other, thus, limiting the scope of drawing systematic comparisons between them. In this talk, I will present a novel robotic active matter system developed in our lab. It consists of a collection of centimeters-long programmable self-propelled robots to mimic various active matter systems. The robots have hardware components like IR sensors and light intensity sensors that enable them to detect obstacles and react to external optical signals. As an initial step, at a single robot level, we have successfully programmed it to exhibit various scalar active particle models with an excellent agreement with theoretical models. In addition to revealing rich physics, these experiments offer potential applications for bio-inspired and nature-inspired robotics.
Motor proteins work in teams to carry the cellular cargo transport. Lipid rafts on membranous cargos reorganize, causing the motors present in these areas to physically cluster. Unregulated clustering of motors leads to diseases such as Leishmaniasis, Newmann-Pick disease, etc. Various in-vitro and computational studies have reported improved cargo velocity and travel distance of a fluid cargo as compared to a rigid cargo. However, only cargo velocity increases with increase in membrane fluidity of a fluid cargo. Thermal and motor forces acting tangentially on a cargo generate random torque and motor torque respectively, leading to cargo rotation and motor tail sliding on cargo surface. However, it is unknown which of these forces/torques play a crucial role in improving the transport properties. Here, we use computational models that incorporate random torque, motor torque, and combination of both random and motor torques to understand how they influence the clustering of Kinesin motors on cargo surface due to drift and diffusion of their tails.
Soft amorphous materials are diversely used in many applications and hence understanding their mechanical properties from a microscopic perspective is essential, specially in the context of sustaining against failures that
would occur while under use. Recently, the failure via spontaneous cavitation during expansion processes has gained a lot of interest, even for soft glassy materials. The initial microcavities that form can eventually lead
to catastropic failure via large scale fractures. From a thermodynamic perspective, cavitation is understood to happen in cohesive glass-forming systems, when the solidgas coexistence is accessed during the material’s expansion. Understanding this phenomenon via the lens of the potential energy landscape framework has turned out to be an interesting exercise. Using extensive numerical simulations, we study the failure of model soft amorphous solids while undergoing
athermal quasi-static expansion, starting from a highdensity state where the material is spatially homogeneous. We observe that plastic instabilities occur while the solid is under expansion, and these events get expressed as sudden jumps in macroscopic pressure and energy. As the pressure starts building up inside the material, it eventually yields via cavitation. Subsequently, cavities merge, if the expansion is continued, and this leads to the final fracture, i.e. disintegration of the solid.Thus, cavitation acts as a precursor to fracture. We show that all plastic events, be it before yielding or afterwards, are characterized by saddle-node bifurcation, during which the smallest non-zero eigenvalue of the Hessian matrix vanishes via a square-root singularity. We also find that in the post-yielding regime, the statistics of pressure or energy jumps corresponding to the plastic events show sub-extensive system-size scaling, similar to the case of simple shear but with different exponents Thus, overall, this study reveals universal features in the transformation within the potential energy landscape, during mechanical failure in amorphous solids under any quasi-static deformation protocol. More recently, we have extended the scope of our investigations to other expansion related protocols to further probe the stability of the amorphous solid to diverse kinds of mechanical deformations.
We have studied Integrable-to-Chao5c transi5ons in some quantum spin models with intrinsic disorder and/or coupled to an inhomogeneous random magne5c field [1-2] using the inves5ga5on of both short-range spectral (eigenvalue) correla5ons (Nearest Neighbour Spacings Distribu5on - NNSD, Ra5o Distribu5on - RD, etc.) within the Random Matrix Theory (RMT) framework [1-2], and also a detailed analysis of corresponding wavefunc5ons across the full spectral range via a study of the Number of Principal Components (NPC), as well as that of the Generalized Shannon Entropies (or Mul5fractal Dimensions) [3]. Based on the extent of the Localiza5on or Delocaliza5on of the eigenstates in the many-body basis of the models, we are able to classify these as Ergodic, Localized, Fractal or Mul5fractal. Our studies suggest that the spectrum of eigenstates of disordered spin models can show a complex mul5fractal character which depends sensi5vely on the posi5on of the eigenstate in the eigenspectrum and can deviate significantly from the predic5ons of standard RMT ensembles [3].
It is a central question in the amorphous world whether structural inhomogeneities in the initial undeformed glassy samples determine the location of a shear band nucleation or whether the formation of a shear band is linked to stochasticity and the details of the shear protocol. We numerically investigate this by studying the detailed failure pathway in glasses with spatial inhomogeneity, generated using two different protocols. The first protocol uses a temperature gradient pulse [1] to introduce a spatial inhomogeneity dominated by density and potential energy, while the second protocol uses inhomogeneous annealing to generate glasses with inhomogeneities dominated by potential energy. Subsequently, we study the shear response of such inhomogeneous glassy samples over a range of shear-rates. We observe, the emergence of non-equilibrium steady states and the formation of shear-bands in the transient regime strongly depends on the level of spatial heterogeneity in glassy samples. Further, we show, stochasticity in the location of shearband nucleation is important if inhomogeneity is relatively small [2].
[1]V. Vaibhav, J. Horbach, and P. Chaudhuri, Response of glassy liquids to thermal gradients, Physical Review E 101, 022605 (2020).
[2]V. Vaibhav, J. Horbach, and P. Chaudhuri, Controlling the mechanical failure in glasses by designed spatial inhomogeneity, under review (2023).
Many dense particulate suspensions show a stress-induced transformation from a liquid-like state to a solid-like shear jammed (SJ) state. However, the underlying particle-scale dynamics leading to such a striking, reversible transition of the bulk remains unknown. Here, we study the transient stress relaxation behaviour of SJ states formed by a well-characterized dense suspension under a step strain perturbation. We observe a strongly non-exponential relaxation that develops a sharp discontinuous stress drop at a short time for high enough peak-stress values. High-resolution boundary imaging and normal stress measurements confirm that such stress discontinuity originates from the localized plastic events, whereas, the system spanning dilation controls the slower relaxation process. We also find an intriguing correlation between the nature of transient relaxation and the steady state shear jamming phase diagram obtained from the Wyart-Cates Model.
While the mechanical disruption of microscopic structures in complex fluids by large shear flows has been studied extensively, the effects of applied strains on the dielectric properties of macromolecular aggregates have received far less attention. Simultaneous rheology and dielectric experiments can be employed to study the dynamics of sheared colloidal suspensions over spatiotemporal scales spanning several decades. Using a precision impedance analyzer, we
study the dielectric behavior of strongly sheared aqueous suspensions of thermoreversible microgel poly(N-isopropylacrylamide) (PNIPAM) particles at different temperatures. We also perform stress relaxation experiments to uncover the influence of large deformations on the bulk mechanical moduli of these suspensions. While we note a counter-intuitive slowdown of the dielectric relaxation dynamics, our bulk rheology experiments, performed under identical
conditions, reveal shear-thinning dynamics with increasing strain amplitudes. We propose the shear-induced rupture of fragile clusters of swollen PNIPAM particles to explain our observations. Our work illustrates that rheo-dielectric studies have enormous potential for providing deep insights into the length scale-dependent dynamical properties of complex systems such as dense suspensions and soft glasses.
In presence of a strong field/coupling, a closed (not attached to bath) quantum many-body system tends to exhibit an emergent stability against chaos and thermalization. We will briefly discuss the scenario.
A many-body interacting system of classical kicked rotor serves as a prototypical model for stldying Floqlet heating dynamics. Having established the fact that this system exhibits a long-lived prethermal phase with a qlasiconserved average Hamiltonian before entering into the chaotic heating regime, we lse spatiotemporal flctlation correlation of kinetic energy as a two-point observable to probe the above dynamic phases. We remarkably fnd the diflsive transport of flctlation in the prethermal regime slggesting an lnderlying hydrodynamic pictlre in a generalized Gibbs ensemble with a defnite temperatlre that depends on the driving parameter and the initial conditions. On the other hand, the heating regime is characterized by a diflsive growth of kinetic energy where the correlation is sharply localized arolnd the flctlation center for all time. Conseqlently, we attriblte nondiflsive and nonlocalized strlctlre of correlation to the crossover regime, connecting the prethermal phase to the heating phase, where the kinetic energy displays a complicated growth strlctlre. We lnderstand these nlmerical fndings lsing the notion of relative phase matching where the prethermal phase (heating regime) refers to an
efectively colpled (isolated) natlre of the rotors. We exploit the statistical lncorrelated natlre of the angles of the rotors in the heating regime to fnd the analytical form of the correlator that mimics olr nlmerical resllts in a convincing way.
We have obtained quantum cluster expansion of the grand free energy in a closed form for an ideal Bose or Fermi gas in both the 3-D box geometry and the harmonically trapped geometry. We have analytically obtained 1-particle density matrices for the same system in the restricted geometries. We have proposed a theorem (with a proof) about the generic form of the quantum cluster integral [1].
Our Theorem: The generic form of the quantum cluster integral for a cluster of size ν of any system of ideal indistinguishable bosons (upper sign) or fermions (lower sign) in thermodynamic equilibrium would be (±1)^(ν-1) times the canonical partition function of a single composite particle composed of ν bosons or fermions in the cluster. Our results are exact for the entire range of temperature, and are directly useful for understanding finite-size effects on a quantum gas. Our results would be relevant in the context of experimental study of spatial correlations in ultra-cold systems of dilute Bose and Fermi gases of alkali atoms.
References:
[1] S. Dey, P. Manchala, S. Basu, D. Banerjee, and S. Biswas, Finite-size effects on the cluster expansions for quantum gases in restricted geometries, Phys. Scr. 95, 075003 (2020)
We explore the persistence properties of a class of worm algorithms in the vicinity of equilibrium critical points, finding evidence for universal behavior characterized by a nontrivial Hurst exponent.
(with Sabyasachi Choudhuri [TIFR] and Anoop Raj [IITB])
In this talk, I will show that kinetic constraints can drive a 'dynamical phase transition\'92 in an otherwise chaotic spin system, separating a delocalised phase, where the classical OTOC propagates ballistically, from a localised phase, where the OTOC does not propagate at all and the entire system freezes. This is unexpected given that all spins configurations are dynamically connected to each other. We show that localisation arises due to the dynamical formation of frozen islands, contiguous segments of spins immobile due to the constraints, dominating over the melting of such islands. In the second part of the talk, I will discuss how this problem can be mapped onto a directed percolation (DP) problem and show that the constraint-induced phase transition indeed lies in the DP universality class in both one and two spatial dimensions.
Thursday, 02 February 2023
We start with a microscopic derivation of the generalized Langevin equation for a passive Brownian particle interacting with active particle suspension. This leads to non-trivial active noise-noise correlations and friction memory kernel. We then study a Stirling like engine of a harmonically confined passive Brownian particle interacting with a suspension of selfpropelling Active Brownian Particles (ABP) in a viscous solvent. The engine operation consists of time periodic variation of the trap strength, and self-propulsion speed of the ABPs under isothermal conditions. In the quasi-static limit, completely analytical expressions for heat, work and efficiency are derived. We show that the engine can produce finite work
out put. We then discuss the behavior of the engine in different parameter regimes pertaining to the interplay of different time scales involved. Finally, we discuss the reasons for reduction or enhancement in the efficiency of the engine when compared to the passive counterpart.
Reference:
1) A Brownian cyclic engine operating in a viscoelastic active suspension, Carlos Antonio Guevara-Valadez, Rahul Marathe, Juan Ruben Gomez-Solano, Physica A, 609, 128342 (2023).
Recent experiments show that periodic drives on dipolar systems lead to long-lived prethermal states. These systems are weakly coupled to the environment and reach prethermal states in a timescale much shorter than the timescale for thermalization. Such nearly-closed systems have previously been analyzed using Floquet formalism, which shows the emergence of a prethermal plateau. We use a fluctuation-regulated quantum master equation (FRQME) to describe these
systems. In addition to the system-environment coupling, FRQME successfully captures the dissipative effect from the various local interactions in the system. Our investigation reveals a cascaded journey of the system to a final steady state. The cascade involves a set of prethermal or arrested states characterized by a set of quasi-conserved quantities. We show that these prethermal states emerge in a timescale much shorter than the relaxation timescale. We also find and report the
existence of a critical limit beyond which the prethermal plateau ceases to exist.
In this work, we focus on the study of one and two-qubit finite-time Otto engines interacting with squeezed thermal reservoirs, and discuss their important distinctions as well as the advantages of using the two-qubit engine. In particular, the two-qubit engine offers an interesting study of the interplay between the degree of squeezing and of the coherence between the two qubits. We find that the two-qubit engine generally yields higher power than the one-qubit
engine. Additional effects due to the change in the inter-qubit separation have been studied.
Stochastic resetting is a strategy for boosting speed of target-searching process. After proposed a decade ago, most studies have been carried out under the assumption that resetting takes place instantaneously. However, as thermodynamic cost must be incurred for resetting process due to its irreversible nature, instantaneous resetting is not physically allowed unless infinite cost is provided. Here, we take into full consideration on both cost and first passage time (FPT) for stochastic resetting process, where reset is implemented by using a trapping potential during a finite time. Introducing iterative generating function method and counting functional, we calculate average work and FPT in this process. From this result, we obtain the explicit form of the time-cost trade- off relation, which gives the lower bound of mean FPT for a given work, when the trapping potential is linear in position. This trade-off relation clearly shows that instantaneous resetting is achievable only when infinite amount of work is provided. More surprisingly, this trade-off relation calculated from the linear potential seems to be valid for wide range of trapping potentials.
Hydrodynamic interaction strongly influences the collective behavior of microswimmers. With this work, we study the behavior of two hydrodynamically interacting self-propelled chiral swimmers in the low Reynolds number regime, considering both the near and far-field interactions. We use the chiral squirmer model, a spherically shaped body with non-axisymmetric surface slip velocity, which generalizes the well-known squirmer model. We calculate the lubrication force and torque between the swimmers when they are close to each other. By varying the slip coefficients and the initial configuration of the swimmers, we investigate their hydrodynamic behavior. In the presence of lubrication force, the swimmers either repel each other or exhibit bounded motion where the distance between the swimmers alters periodically. The influence of external chemical gradients in the hydrodynamic behavior of chiral swimmers is also investigated. Interestingly, the lubrication and chemical gradient favor the bounded motion in some parameter regimes. This study helps in understanding the collective behavior of dense suspension of self-propelled swimmers.
Keywords: Active Matter, Swimming of Microorganisms, Lubrication effects
References:
1. P. S. Burada, R . Maity and F. Julicher, Hydrodynamics of chiral squirmers, Phy. Rev. E 105, 024603 (2022).
2. R . Maity and P. S. Burada, Near and far-field hydrodynamic interaction of two chiral squirmers, Phy. Rev. E 106,
054613 (2022).
3. R . Maity and P. S. Burada, Unsteady chiral swimmer and its response to a chemical gradient. J. Fluid Mech., 940,
A13 (2022).
4. R . Maity and P. S. Burada, External chemical gradient leads to efficient swimming of chiral swimmers, Phy. Fluids
(under review)
An extensively addressed question in the context of driven dilute inelastic systems is regarding the non-Maxwellian form of their velocity statistics. Experiments, numerical studies and phenomenological models have looked at the problem, yet not been able to provide a consistent answer. In this talk, I will present our results on a microscopic model of the system illustrating an exact universal form for their statistics, along with some recent developments
In this talk we’ll ask whether a cloud needs to be in high Reynolds number turbulence for rain to occur, and if so, whether there is a lower limit on the Reynolds number.
Active matter is a special kind of condensed matter system, that is inherently driven far away from equilibrium. The constituent of such systems are capable of self propeling by their own, by consuming energy from the environment, hence termed as active particles. These particles are different from the passive Brownian particle and expected to exhibit some interesting features in the dynamics. In this talk I will mainly focus on the dynamics of an inertial active Ornstein-Uhlenbeck particle and discuss some interesting features in the dynamical beahaviour of such particle in various circumstances.
A large fraction of active particles, such as motile microorganisms and phoretic microswimmers, are suspended in ambient fluid media. Self-propulsion of the individual particles drives these systems arbitrarily far from thermal equilibrium and sets up nontrivial active flows, resulting in a wide range of rich and complex suspension dynamics. By now it is well understood that the background fluid flows and fluid mediated interactions play important roles in the dynamics. However, analyzing them in detail is non-trivial and challenging, and have so far been done mostly in simple unconfined systems in the dilute regime. In this talk I will present our current approaches to study the hydrodynamics of self-propelling objects in a few particularly challenging situations - namely in dense suspensions, under confinements and in complex media. We will discuss how deformations lead to modified self-propulsion dynamics, cell-cell interactions and collective
dynamics and how near-field hydrodynamics lead to new understanding under confinements and obstacles.
The catalytic action of invertase generates bilayer asymmetry that stabilises membrane curvature. The driving mechanism for the generation of membrane curvature by invertase is investigated using giant unilamellar vesicles
(GUVs). The invertase cleaves the sucrose in the exterior compartment, thereby creating a sugar asymmetry across the bilayer mem-brane that is measured for GUV membranes consisting of the lipid dioleoylphosphatidylcholine (DOPC). Finally, the advantage of this method to control membrane curvature and to stabilize multisphere morphologies is demonstrated. The GUV system in the presence of invertase is beneficial as a tool to generate multiple on-demand compartments with more extended stability after the enzymatic activity has established the asymmetry.
Reference: ChemSystemsChem, https://doi.org/10.1002/syst.202200027
We study a two-channel Feshbach-coupled model of resonant ultracold Bose gas, consisting of both atomic and molecular Bose-Einstein condensates (BEC). The system shows Josephson oscillations, and the Feshbach-assisted transition from atomic BEC to molecular BEC plays the role of the tunneling. Depending on the values of the Feshbach detuning, the system shows (i) a particle localization crossover, and (ii) a transition from the oscillatory phase mode to running phase mode dynamics.
FIG. 1. Oscillatory dynamics of fractional population imbalance corresponding to variable detuning (for a fixed set of other parameters). Panel (c) corresponds to a particle localization crossover. Panel (f) corresponds to the transition from oscillatory phase mode to running phase mode.
Next we consider stochastic dynamics, assuming both the Feshbach coupling and the Feshbach detuning have Gaussian white noise components. Considering small deviations from the fixed points, we study the relaxation dynamics, and calculate the longituidinal and transverse relaxation times.
Reference : [1]Avinaba Mukherjee and Raka Dasgupta, Stochastic Josephson Oscillation Dynamics of a Feshbach-coupled Atomic-Molecular Bose-Einstein Condensate, manuscript under preparation Email: rdphy@caluniv.ac.in
TBA
Periodically driven quantum spin chains are an important class of models in manybody quantum physics, which generically (with noteworthy exceptions like manybody localization or integrable points) exhibit many-body quantum chaos, ergodicity and fast equilibration to a stroboscopic ensemble. Here, we investigate a class of systems where a driven, disordered spin chain is opened by the addition of a periodic projection at one end of the chain, in analogy with chaotic classical or quantum maps with escape. The evolution operator over one period then becomes subunitary with a complex spectrum inside the unit circle. This class of systems exhibits several interesting properties, which we demonstrate by studying its level statistics, entanglement dynamics and spectral features like exceptional points which are unique to non-normal matrices. This class of systems may also be experimentally realized in a set-up where certain configurations of the spin chain can be post-selected after a measurement.
We study a spin-1 Hamiltonian with Heisenberg (JH) and biquadratic (JB) exchanges supplemented further by a Q2-term made out of biquadratic terms. For JH = 0, this is equivalent to a SU(3)-symmetric Hamiltonian where deconfined critical behaviour has been found earlier by Lou et al [1] as JB/JQ2 is tuned. When Heisenberg exchange is turned on, the symmetry is now reduced to that of SU(2) and we are interested in understanding the nature of Antiferromagnetic-Valence Bond solid transition in the reduced symmetry case of SU(2), S = 1. A previous study [2] with JH/JQ2 as the tuning parameter had found a (weakly) first-order transition. Our results in the absence of JH perturbation shows a continuous transition with critical values (Q2/J = 0.169, νON = 0.64, ηON = 0.37) for the order parameter, ON) in agreement with the SU(3) study of Lou et al [1]. When a finite JH = 0.1 is present, we find the following exponents (ν = 0.44, η = 0.19) suggesting a different universality class than SU(3).
[1] J. Lou, A. W. Sandvik, and N. Kawashima, Antiferromagnetic to valence-bond-solid transitions in two-dimensional SU(n) heisenberg models with multispin interactions, Phys. Rev. B 80, 180414 (2009).
[2] J. Wildeboer, N. Desai, J. D’Emidio, and R. K. Kaul, First-order n´eel to columnar valence bond solid transition in a model square-lattice s = 1 antiferromagnet, Phys. Rev. B 101, 045111 (2020).
Chaotic-to-non-chaotic transitions play a prominent role in our understanding of the dynamical phase diagram of both quantum and classical systems. In quantum many-body systems, a certain kind of chaotic-non-chaotic transitions, dubbed as ‘measurement-induced phase transitions’ (MIPT) have led to a new paradigm for dynamical phase transitions in recent years. On the other hand, prominent examples of transition in chaos in classical dynamical systems are the stochastic synchronization transitions (ST). In this case, classical trajectories starting from different initial conditions synchronize when subjected to sufficiently strong common random stochastic noise. In this talk, I will establish a direct link between MIPT and ST by considering models of interacting particles, whose positions are measured continuously, albeit weakly. In the semiclassical limit, the dynamics of the system is described by a stochastic Langevin equation where the noise and the dissipation terms are both controlled by the small quantum parameter and measurement strength. I will show the existence of a chaotic-to-non-chaotic transition in the Langevin evolution as a function of either interaction or noise/dissipation strength.
I will present a class of star-shaped networks, composed of identical spin-1/2 chains coupled to a central spin, that have two properties: (1) They reduce to free-fermion hopping on the graph, and (2) Incoherently driving the centre generates strong multipartite entanglement across the network. In particular, measuring the global parities of a subset of legs projects the outermost qubits onto a maximally-entangled W state. The manifold of W states can be controlled by one or more auxiliary qubits that mediate the coupling to the centre. This construction works for any number of legs and may be realisable in superconducting circuits.
Several physical systems show spectral properties intermediate between integrable (Poisson) and chaotic (Wigner) dynamics. Matrix ensembles exhibiting such intermediate statistics are important in understanding the physics of manybody localization (MBL) and the β-ensemble is a simple such realization. We show that a non-ergodic extended regime exists between an ergodic transition point and a localization transition point. We identify the dynamical timescales of the β-ensemble and discuss the differences with the Rosenzweig-Porter ensemble.
The elliptic type of bursting in a neuronal system is a recurrent alternation between large amplitude oscillations and quiescent phases with small amplitude oscillations. This kind of rhythmic pattern can be found in many neuronal systems. This talk reviews the synchronization behaviour of two and three Bautin-type elliptic bursters with linear direct coupling schemes, and it can be extended to various network topologies. We will reveal various kinds of synchronization behaviour of connected neural burster networks and their importance, possibly effective information processing, transmission mechanisms, and neurobiological science for studying complex systems.
1. M. E. Izhikevich, ``Synchronization of Elliptic Bursters’’ SIAM Review 43, 315 – 44 (2001).
2. Abdul Kalam Azad, Peter Aswin, ``Within-Burst Synchrony Changes for Coupled Elliptic Bursters’’ SIAM Journal on Applied Dynamical Systems 10, 261-281 10, 2010.
Proteins are vital for almost all biochemical and cellular processes. Although there is an enormous growth in the protein sequence data, the statistical characterization, structure, and function of many of these sequences are still
unknown. The statistical and spectral analysis of the Pearson correlation matrices between positions based on physiochemical properties of amino acids of seven protein families is performed and compared with the random
Wishart matrix model results. A detailed analysis shows that the protein families significantly diverge from the Marcenko-Pastur distribution with many eigenvalues (outliers) outside the Wishart lower and upper bound. It is shown
that level spacing distribution of protein families is similar to the Gaussian orthogonal ensemble. Further, the number variance varies as log of the system size indicating the presence of long range correlations within the
protein families. Some results on the network analysis on these families will also be presented.
The passage of different liquids or electrical currents through different media in the light of percolation is a much studied topic in recent years. This can as well be applied to electrical movement in neurons inside the heart and brain tissues, which can usually be called Semi Directed Percolation (SDP). In this work we study a 2D square grid of $nxn$ cells which can model forest fire and heart-like cellular automata models. Here initially the cells may be in two states, "Waiting" and "Inactive". We chose the system so that the cells are "Waiting" with probability $p$. We initiate an Action Potential through the system from one end. An "Waiting" cell can be activated with an action potential and then the cell will be an "Active" one. A Waiting cell transforms to an Active one in the next step, if one or more of its "nearest cell neighbors" was Active. A cell follows the transformation as Waiting $\rightarrow$ Active $\rightarrow$ Inactive. We introduced three probabilities $p_{act}$ (probability of an Waiting cell to become Active), $p_{switch}$ (probability of an Inactive cell to become a Waiting one), $p_{inact}$ (probability of an Active cell to become Inactive). With variation of probabilities the percolation threshold, tortuosity, cluster size distribution and other relevant quantities have been studied. The system is also observed with NNN type activation of Waiting cells. The number of arrivals is increased with increased NNN type activation. Several other interesting features have been observed. The simple system is seen to explain the actions of heart/brain like systems very well.
Cooperation is widely thought to be promoted in graphs with a strong heterogeneity of connections, scale-free networks being the most studied example. We demonstrate that this is not necessarily true and a wide variety of behaviour is possible.
We also explore how payoffs -- even when weakly dependent on the underlying network topology -- can alter the dynamics and indeed the very nature of the game.
Friday, 03 February 2023
Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Detailed models of these networks are known to suffer from over-parameterization. We will describe recent work formalizing an alternative approach first presented by Waddington, which likens differentiation of different cell types to flow through a landscape in which valleys represent alternative fates. This allows the construction of minimally parameterized models consistent with cell behaviour. We will describe how this construction leads to intuitive models that are well adapted to biological data. Using the mouse blastocyst as an example, we will show how differences in geometry can lead to concrete differences in experimental predictions for the system's response to perturbations.
Glassy dynamics are crucial for several critical biological processes, such as wound healing, cancer progressions, embryogenesis, cytoplasmic transportation, Etc. As biological systems are inherently out of equilibrium, how activity affects the glassy dynamics becomes fundamentally important. It also extends the scope and extent of the as-yet mysterious physics of glass transition. Theories of equilibrium glassy dynamics have been extended for the active glasses where the constituent particles have a self-propulsion force, f0, and a persistence time, τp, of their motion. f0 always drives the system away from the glassy regime, but effects of τp is more complex and depends on the details of activity. The relaxation dynamics of active glassy systems seem qualitatively similar to that in an equilibrium system at an effective temperature. However, activity has nontrivial complex effects on the dynamical heterogeneity. In this talk, I will discuss some of these effects and show that mode-coupling theory, extended for active systems, can surprisingly capture both these aspects of activity.
Rapid technological advances are now allowing measurements of various biological parameters at the single cell level. While such univariate distributions provide interesting insights into cell-to-cell variability and heterogeneity in cell states, much less explored and understood are the implications of correlations amongst single cells. Particularly in cellular populations that are growing and dividing, there is increasing realization that lineage correlations can provide key biological insights that cannot be gleaned simply from single-cell distributions alone. In this talk, I will present two such cases where lineage correlations in (a) cell-fate after drug treatment and (b) in cell-cycle times, allow inference of underlying cellfate control mechanisms in cancer cells. I will first demonstrate how the ubiquitous exponential growth model (and generalizations such as age-structured models), fail to predict population growth rates of drug-treated cancer cells from single cell measurements. I will argue that the key to resolving this paradox lies in accounting for cell-fate correlations, which indicate that fate decisions occur well before addition of the drug. Next, I will show how in the same cellular population, surprising correlation structures in cell-division times imply control of the cell cycle by the circadian clock. Using stochastic simulations of the underlying molecular networks, I will show that circadian control of the cell cycle can indeed produce the observed correlations, suggesting a novel, reporter-free approach to investigating "gating" of cell divisions by the clock.
After application of a step stimulus the receptor activity and tumbling bias of an E.coli cell changes sharply to reach an extremal value and the cell is far from adaptation at this time. Surprisingly, our simulations show that the extremal activity is related to the free energy via Boltzmann distribution, which is expected only for adapted states. We perform exact calculation to explain this striking effect. We also make experimentally verifiable prediction that there is an optimum size of the step stimulus at which the extremal response is reached in the shortest possible time.
The holy grail of modern molecular biology and biophysics is to identify and understand how macroscopic biological behaviors emerge from the microscopic interactions of biomolecules. The key challenge to such an effort is that biological interactions occur over broad spatiotemporal scales. Traditional simulation or experimental techniques by themselves are inadequate to investigate these questions, because they were designed to explore events in narrow spatiotemporal scales. In this talk, I shall describe a novel theoretical technique, called the Green’s Function Reaction Dynamics that allows us to bridge the spatiotemporal scales between microscopic interactions and macroscopic behavior. Using this tool, I shall demonstrate how diffusion in 2D leads to nontrivial emergent reaction kinetics and shall discuss its repercussions.
Biological cells are apt in making accurate measurement of extracellular stimuli, despite the noisy environments they inhabit and their noisy intracellular information processing apparatus. In this talk we will illustrate examples highlighting the limitations and accuracies in cellular information processing of extracellular stimuli. We will see that Dictyostelium measures chemotatic gradients at an accuracy set by the physical limitations imposed on gradient measurements. We will next highlight the accuracy in measurement of glutamine concentration in the synaptic cleft by neuronal cells. We conclude by presenting our study on the limitations to positional measurements in calcium signal transduction.
Morphogenetic patterns in developing systems arise from a tight coupling between mechanochemical signals and dynamical geometry. Recent work has highlighted possible couplings between topological defects in the orientational patterns of intracellular/supracellular filamentous structures and the surface geometry of developing embryos. Motivated by these phenomena, we study a minimal model of a polar flock on a curved surface and show that it supports a rich variety of phases that arise from the non-trivial coupling between activity and surface curvature. Specifically, we show, by a combination of analytical and numerical techniques, that the competition between activity and orientational elasticity leads to the emergence of curvature-induced waves in non-flat geometries.
We consider an anharmonic chain which is driven periodically at one end and can dissipate energy at both ends. This models light transmission through an array of coupled qubits and was recently shown to exhibit an interesting parameter regime where energy is carried by breather modes. Analytic results on the the breather mode and the effect of thermal noise on it will be discussed.
I will provide a brief overview of the Cahn-Hilliard-Navier-Stokes (CHNS) framework for multiphase fluid flows. I will then present examples, from our recent work, of applications of this CHNS framework to a variety of challenging multi-fluid flows, in laminar, turbulent, and active-fluid systems, including antibubbles [1], self-propelling droplets [2], liquid-lens mergers [3], and elastic turbulence in droplet-laden flows [4].
References:
1. Ephemeral antibubbles: Spatiotemporal evolution from direct numerical simulations, N Pal, R Ramadugu, P Perlekar, and R Pandit, Physical Review Research 4 (4), 043128 (2022).
2. Activity-induced droplet propulsion and multifractality, NB Padhan and R Pandit, arXiv e-prints, arXiv: 2209.04864 (2022).
3. Viscous-to-Inertial Crossover in Liquid-Lens Coalescence from the Cahn-Hilliard-Navier-Stokes Equations, NB Padhan and R Pandit (in preparation).
4. Elastic turbulence in droplet-laden flows, NB Padhan, D. Vincenzi, and R Pandit (in preparation).
In this talk, we try to understand the dynamical stability of a coupled scalar field theory. By discretizing the field theory to a lattice, the Hamiltonian of the model becomes a combination of regular and inverted harmonic oscillators. Interestingly, we observed that the Out-of-Time-Order Correlator (OTOC) corresponding to this Hamiltonian is exponentially growing (in the inverted frequency regime) in time, which indicates the instabilities (chaotic nature) in the model. We also study the heat transport in the lattice model for both symmetric and asymmetric coupling with the baths. For symmetric coupling, we re-expressed the problem in terms of the normal modes to find an equivalence of this transport as a limiting case of a previously well-studied transport problem in ordered harmonic lattices. Moreover, we described the dynamics of the model in terms of a pseudo-hermitian matrix. Some of its properties coincide with Green's function's properties from the heat transport study.
Coarsening refers to a process in which order builds up in a system prepared in a disordered state. We studied the coarse-grained depth (CD) models that exhibit ‘fluctuation dominated phase ordering’ (FDPO), where both the order and fluctuations appear on macroscopic scales. We found that the total number of domain walls and the length of the largest cluster together quantify the unique characteristics of FDPO. While the fluctuations in the domain wall structure is broad and nontrivial, the largest cluster grows as a power law with significant multiplicative logarithms which involve both the time and system size. We further identify corrections to the leading power behaviour in the coarsening length scale, that significantly affects several quantities. Time permitting, I shall outline the different phases of a generalisation of the CD models and the occurence of FDPO at a mixed-order phase transition point.
I will present an extensive Monte Carlo investigation of the metastable lifetime through the reversal of the magnetization of spin-s Ising and Blume-Capel models, where s = {1/2, 1, 3/2, 2, 5/2, 3, 7/2}.
The mean metastable lifetime (or reversal time) is studied as a function of the applied magnetic field and for both models is found to obey the Becker-D ̈oring theory, as was initially developed for the case of s = 1/2 Ising
ferromagnet within the classical nucleation theory. Moreover, the decay of metastable volume fraction nicely follows the Avrami’s law for all values of s and for both models considered. The results are published in Phys. Rev. E,
104 (2021) 014107.
It is well known that systems approaching a critical point has diverging correlation length. As a result, the responses are scale free and therefore highly unequal (e.g., avalanche sizes in sandpiles). It is possible to quantify the inequality in such responses using measures some of which are used for over a century in quantifying economic inequality. These inequality measures show remarkably universal properties near the critical points. In this talk, we will discuss some of these properties, such as: (i) The system size independent behavior of Gini index of order parameter at the critical point, (ii) the critical scaling behavior formulated through Gini index, and (iii) the universal behavior of inequality indices near self-organized critical points.
References:
1. Critical scaling through Gini index, Soumyaditya Das, Soumyajyoti Biswas, arxiv:2211.01281 (2022).
2. Near universal values of social inequality indices in self-organized critical models, S. S. Manna, Soumyajyoti Biswas, Bikas K. Chakrabarti, Physica A 596, 127121 (2022).
3. Success of social inequality measures in predicting critical or failure points in some model physical systems, Asim Ghosh, Soumyajyoti Biswas, Bikas K. Chakrabarti, Front. Phys. 10, 990278 (2022).
4. Social inequality analysis of fiber bundle model statistics and predictions of materials failure, Soumyajyoti Biswas, Bikas K. Chakrabarti, Phys. Rev. E 104, 044308 (2021).
In modern era MOCVD, MBE, FLL and other investigational method, low dimensional structures having quantum confinement in one, two and three dimensions such as ultra-thin films, inversion layers, quantum wires and dots, have involved much consideration, not only for their probable in detection new phenomena in nanostructured electronics but also for their stimulating devices submission in heterostructure based numerous materials, that are being presently calculated because of the improvement of carrier mobility and such quantum confined systems find ex-digital networks, optical modulators and also in other devices. In this paper, an effort is made to study the Fermi-Dirac distribution function in degenerate semiconductors forming band tails ( ) on the basis of a newly formulated electron dispersion law ( is the well Fermi-Dirac function) and it is more interested in carrier degeneracy condition Fermi-Dirac distribution function the investigation is , since it is my support will degenerate semiconductors and the electronic device, the transport coefficient and electron dynamics change either .
The effective dynamics of a colloidal particle immersed in a complex medium is often described in terms of an overdamped linear Langevin equation for its velocity with a memory kernel which determines the effective (time-dependent) friction and the correlations of fluctuations. Recently, it has been shown in experiments and numerical simulations that this memory may depend on the possible optical confinement the particle is subject to, suggesting that this description does not
capture faithfully the actual dynamics of the colloid, even at equilibrium. Here, we propose a different approach in which we model the medium as a Gaussian field linearly coupled to the colloid. The resulting effective evolution equation of the colloidal particle features a non-linear memory term which extends previous models and which explains qualitatively the experimental and numerical evidence in the presence of confinement. This non-linear term is related to the
correlations of the effective noise via a novel fluctuation-dissipation relation which we derive.
We define a new disordered asymmetric simple exclusion process (ASEP) with two species of particles, first-class and second-class, on a two-dimensional toroidal lattice. The dynamics is controlled by first-class particles, which only move horizontally, with forward and backward hopping rates $p_i$ and $q_i$ respectively if the particle is on row $i$. The motion of second-class particles depends on the relative position of these with respect to the first-class ones, and can be both
horizontal and vertical. We show that the stationary weight of any configuration is proportional to a monomial in the $p_i$'s and $q_i$'s. Our process projects to the disordered ASEP on a ring, and so explains combinatorially the stationary distribution of the latter first derived by Evans (Europhysics Letters, 1996). We compute the partition function, as well as densities and currents of all particles in the steady state. We observe a novel mechanism we call the Scott Russell
phenomenon: the current of second class particles in the vertical direction is the same as that of first-class particles in the horizontal direction. This is joint work with P. Nadeau (European Journal of Combinatorics, 2022).
Trade-off relations involving the relative uncertainty of currents and the associated entropy production have been of enormous interest for the past few years in the field of non-equilibrium stochastic thermodynamics. It is now realized, for
example, that the optimization of heat engines should balance power, efficiency as well as power fluctuations. In this talk, I will talk about multi-affinity-driven continuous thermal machines and show that the relative fluctuations of individual
currents for thermal machines are not independent but follow strict bounds, giving rise to a new universal bound for the mean efficiency of thermal machines and is tighter than the well known Carnot bound as predicted by macroscopic
thermodynamics. I will also talk about the extension of this bound for time-reversal symmetry-breaking systems and also for discrete finite-time cycles.
References:
1. Universal bounds on fluctuations in continuous thermal machines, S. Saryal et alPhys. Rev. Lett, 127, 190603 (2021).
2. Bounds on fluctuations for finite-time quantum Otto cycle, S. Saryal and Bijay Agarwalla, Phys. Rev. E. Lett 103 L060103 (2021).
3. Universal bounds on fluctuations for machines with broken time-reversal symmetry, S. Saryal, S. Mohanta, and Bijay Agarwalla, Phys. Rev. E 105, 024129 (2022).
The physics of quantum Ising model (qIm) plays an important role in quantum many body system. We study and present the results of qIm and longer range quantum Ising model (lqIm) in presence of strong correlation. We
do the quantum field theoretical renormalization group (RG) calculation to study the behaviour of RG flow lines for different couplings for different region of parameter space. We show how the strong correlation effect enrich
the quantum physics of these two systems. We show explicitly that the ordered ferromagnetic (FM) phase to the disorder quantum paramagnet (dqpI) quantum phase transition occurs only in the strongly correlated regime for
qIm otherwise only dqpI phase appears for non-interacting and attractive regime. We show explicitly for lqIm that FM to dqpI transition occurs at the extremely correlated region and also the dqpI phase appears in correlated
regime. We show that short range FM coupling and longer range coupling are competiting with each other and also the effect of strong correlation in this competition. We also show the most interesting feature that the transverse field oppose the FM coupling of qIm but it is favour the longer range coupling of lqIm. We find the evidence of another disorder quantum paramagnetic (dqpII) phase due to the relevance of longer range coupling. We also present the existence of another quantum phase transition from dqpII phase to FM phase. We show explicitly that there is no phase transition from dqpI phase to dqpII phase rather they coexists. We also observe three different kind of coexistence phases depending on the correlated regime. This work provides a new perspective not only for the statistical physics of quantum Ising model but also for the quantum many body systems.
The asymmetric simple exclusion process (ASEP) is broadly regarded as a paradigmatic model for non-equilibrium transport processes. Motivated by a simplistic description of multi lane traffic flow, we present a multi species generalization of ASEP along with impurities. The impurities can activate flips between different species, imitating the lane change dynamics in multi lane traffic flow. The exact non-equilibrium steady state probability distribution is obtained using the technique of matrix product ansatz [1]. For special choices of the microscopic dynamics, the model exhibits (i) cluster formation as a result of counter-flow of different species [2], (ii) negative differential mobility where current can decrease with increasing bias [1].
References:
[1] A. K. Chatterjee and H. Hayakawa, arXiv:2205.03082 (2022).
[2] A. K. Chatterjee and H. Hayakawa, arXiv:2208.03297 (2022).
We study a system of equal-sized circular discs each with an asymmetrically placed pivot. The pivots form a regular triangular lattice, and the discs can rotate freely about the pivots, with the constraint that no discs can overlap with each other. We investigate a particular limit where the distance between the pivot point and the center of the plates is infinitesimal, which further simplifies the hamiltonian of the system. Our Monte Carlo simulations show that the probability distribution of the orientation of a randomly chosen disc shows multiple cusp-like singularities. We determine the positions and qualitative behavior of these singularities. We find that in addition to the expected geometrical singularities, the system shows an intervening Kosterlitz-Thouless phase between the phases with broken orientational symmetry and the disordered phase.