arXiv subjects

Shashi Thutupalli

Publications and source records attributed to Shashi Thutupalli.

At least 19 recordsLinked to original sources

arXiv2026

Conditions for Darwinian evolution in compartmentalized autocatalytic reaction networks

The first forms of life likely consisted of protocells endowed with metabolism, growth, and division. Such systems may have evolved due to variation and heredity in their chemical composition, even before the advent of genetics. However, whether compositional heredity is robust enough to sustain evolution by natural selection remains unknown, especially given that early compartmentalization cycles were likely imperfect, potentially disrupting stable inheritance across generations. Here, we show that multistable autocatalytic reaction networks can maintain heritable compositional states across a broad class of growth-division regimes, including continuous, serial, symmetric division, and multi-fragmentation cycles. We further identify parameter domains that preserve stable inheritance in the presence of stochastic variation, such that selection can operate efficiently. We finally demonstrate rudimentary forms of evolution by natural selection in populations of protocells with two heritable states, which we illustrate in an experimentally feasible setting. Our findings establish conditions for natural selection in compartmentalized autocatalytic systems and set the stage for understanding the minimal requirements for open-ended evolution.

physics.bio-ph↗

arXiv2026

Adaptation to extreme stress under the growth-survival fitness trade-off

Microbial adaptation to extreme stress, such as starvation, antimicrobial exposure, or freezing often reveals fundamental trade-offs between survival and proliferation. Understanding how populations navigate these trade-offs in fluctuating environments remains a central challenge. We develop a quantitative model to investigate the adaptation of populations of yeast (Saccharomyces cerevisiae) subjected to cycles of growth and extreme freeze-thaw stress, focusing on the role of quiescence as a mediator of survival. Our model links key life-history traits: growth rate, lag time, quiescence probability, and stress survival, to a single underlying phenotype, motivated by the role of intracellular trehalose in the adaptation of yeast to freeze-thaw stress. Through stochastic population simulations and analytical calculation of the long-term growth rate, we identify the evolutionary attractors of the system. We find that the strength of the growth-survival trade-off depends critically on environmental parameters, such as the duration of the growth phase. Crucially, our analysis reveals that populations optimized for growth-stress cycles can often maintain viability alongside growth-optimized populations even in the absence of stress. This demonstrates that underlying physiological trade-offs do not necessarily translate into fitness trade-offs at the population level, providing general insights into the complex interplay between environmental fluctuations, physiological constraints, and evolutionary dynamics.

q-bio.PE↗

arXiv2026

De novo emergence of metabolically active protocells

A continuous route from a disordered soup of simple chemical feedstocks to a functional protocell -- a compartment that metabolizes, grows, and propagates -- remains elusive. Here, we show that a homogeneous aqueous chemical mixture containing phosphorus, iron, molybdenum salts and formaldehyde spontaneously self-organizes into compartments that couple robust non-equilibrium chemical dynamics to their own growth. These structures mature to a sustained, dissipative steady state and support an organic synthetic engine, producing diverse molecular species including many core biomolecular classes. Internal spherules that are themselves growth-competent are produced within the protocells, establishing a rudimentary mode of self-perpetuation. The chemical dynamics we observe in controlled laboratory conditions also occur in reaction mixtures exposed to natural day-night cycles. Strikingly, the morphology and chemical composition of the protocells in our experiments closely resemble molybdenum-rich microspheres recently discovered in current oceanic environments. Our work establishes a robust, testable route to de novo protocell formation. The emergence of life-like spatiotemporal organization and chemical dynamics from minimal initial conditions is more facile than previously thought and could be a recurring natural phenomenon.

cond-mat.soft↗

arXiv2025

Explosive dispersal of non-motile microbes through metabolic buoyancy

For non-motile microorganisms, spatial expansion in quiescent fluids is presumed to be limited by diffusion. We report that microbial colonies can explosively circumvent this constraint through a self-amplifying physical process. As non-motile yeast and bacteria metabolize dense nutrients into lighter waste within their fluid environment, they generate buoyancy-driven Rayleigh-Bénard convection, an ubiquitous fluid-dynamical phenomenon that organizes material on scales from chemical reactors to planetary atmospheres. This robust, self-generated flow fragments and disperses cellular aggregates, which seed new growth sites, enhancing total metabolic activity and further strengthening the convective flow in an autocatalytic cycle. The resulting expansion follows accelerating power-law kinetics, quantitatively captured by a physical theory linking metabolic flux to flow velocity, and produces fractal patterns through a flow-focusing instability we term Circulation-Driven Aggregation, the hydrodynamic analogue of Diffusion-Limited Aggregation. This `metabolic fireworks' mechanism establishes a canonical instance of proliferating active matter, where cellular metabolic activity self-organizes a physical transport engine--a living Rayleigh-Bénard convection--providing a fundamental, physics-based dispersal strategy.

cond-mat.soft↗

arXiv2025

Temperature switchable self-propulsion activity of liquid crystalline microdroplets

We report on a switchable emulsion droplet microswimmer by utilizing a temperature-dependent transition of the droplet phase. The droplets, made from a liquid crystalline (LC) smectic phase material ($T =$ 25 $^{\circ}$C), self-propel only in their nematic and isotropic phases at elevated temperatures ($T\ge$ 33.5 $^{\circ}$C). This transition between motile and non-motile states is fully reversible - in the motile state, the droplets exhibit persistent motion and directional memory over multiple heating-cooling cycles. Further, we distinguish the state of rest from the state of motion by characterizing the chemical and hydrodynamic fields of the droplets. Next, we map the motility behaviour of the droplets across varying surfactant concentrations and temperatures, observing that swimming occurs only at sufficiently high surfactant concentrations above and temperatures above the smectic-nematic phase transition temperature $\textit{i.e.}$ $T\ge$ 33.5 $^{\circ}$C. Our work envisions the potential of LC emulsion droplets as switchable microswimmers.

cond-mat.soft↗

arXiv2024

Emergent dynamics due to chemo-hydrodynamic self-interactions in active polymers

The field of synthetic active matter has, thus far, been led by efforts to create point-like, isolated (yet interacting) self-propelled objects (\emph{e.g.} colloids, droplets, microrobots) and understanding their collective dynamics. The design of flexible, freely jointed active assemblies from autonomously powered components remains a challenge. Here, we report freely-jointed active polymers created using self-propelled droplets as monomeric units. Our experiments reveal that the self-shaping chemo-hydrodynamic interactions between the monomeric droplets give rise to an emergent rigidity (the acquisition of a stereotypical asymmetric C-shape) and associated ballistic propulsion of the active polymers. The rigidity and propulsion of the chains vary systematically with their lengths. Using simulations of a minimal model, we establish that the emergent polymer dynamics are a generic consequence of quasi two-dimensional confinement and auto-repulsive trail-mediated chemical interactions between the freely jointed active droplets. Finally, we tune the interplay between the chemical and hydrodynamic fields to experimentally demonstrate oscillatory dynamics of the rigid polymer propulsion. Altogether, our work highlights the possible first steps towards synthetic self-morphic active matter.

cond-mat.soft↗

arXiv2024

Rigid flocks, undulatory gaits, and chiral foldamers in a chemically active polymer

Active matter systems - such as a collection of active colloidal particles - operate far from equilibrium with complex inter-particle interactions that govern their collective dynamics. Predicting the collective dynamics of such systems may aid the design of self-shaping structures comprised of active colloidal units with a prescribed dynamical function. Here, using simulations and theory, we study the collective dynamics of a chain consisting of active Brownian particles with internal interactions via trail-mediated chemicals, connected by harmonic springs in two dimensions to obtain design principles for active colloidal molecules. We show that two-dimensional confinement and chemo-repulsive interactions between the freely-jointed particles lead to an emergent rigidity of the chain in the steady-state dynamics. In the chemo-attractive regime, the chain collapses into crystals that abruptly halt their motion. Further, in a chain consisting of a binary mixture of monomers, we show that non-reciprocal chemical affinities between distinct species give rise to novel phenomena, such as chiral molecules with tunable dynamics, sustained undulatory gaits and reversal of the direction of motion. Our results suggest a novel interpretation of the role of trail-mediated interactions, in addition to providing active self-assembly principles arising due to non-reciprocal interactions.

cond-mat.soft↗

arXiv2022

Dynamical phases in growing populations: understanding recovery from bottlenecks

Since steep declines in a population's size also typically alter its composition, population bottlenecks are considered highly important for evolution. However, despite such significance, the mechanisms governing the impact of a given population bottleneck remain poorly understood. In this context, we show that long-term post-bottleneck outcomes can depend crucially on the rate at which a diminished population grows whilst recovering. That is, two otherwise identical populations, each having undergone the same bottleneck, can fixate on dramatically different demographics due to different rates of post-bottleneck growth. This behaviour is moreover shown to change non-trivially with different levels of mutation. The underlying mechanism can be traced to intrinsic fluctuations whose standard deviation decreases in time with the inverse square root of the growing population size. Crucially, such decreasing fluctuations couple to the underlying dynamics and result in distinct regimes of (non-equilibrium) demographic behaviour, delimited by abrupt transitions at critical population sizes. Seen through this lens, growth and mutation alter evolutionary outcomes by changing the duration and character of dynamical phases; a feature that we speculate may be of generic importance across many systems.

q-bio.PE↗

arXiv2021

Active ploughing through a compressible viscoelastic fluid: Unjamming and emergent nonreciprocity

A dilute suspension of active Brownian particles in a dense compressible viscoelastic fluid, forms a natural setting to study the emergence of nonreciprocity during a dynamical phase transition. At these densities, the transport of active particles is strongly influenced by the passive medium and shows a dynamical jamming transition as a function of activity and medium density. In the process, the compressible medium is actively churned up -for low activity, the active particle gets self-trapped in a spherical cavity of its own making, while for large activity, the active particle ploughs through the medium, either accompanied by a moving anisotropic wake, or leaving a porous trail. A hydrodynamic approach makes it evident that the active particle generates a long range density wake which breaks fore-aft symmetry, consistent with the simulations. Accounting for the back reaction of the compressible medium leads to (i) dynamical jamming of the active particle, and (ii) a dynamical non-reciprocal attraction between two active particles moving along the same direction, with the trailing particle catching up with the leading one in finite time. We emphasize that these nonreciprocal effects appear only when the active particles are moving and so manifest in the vicinity of the jamming-unjamming transition.

cond-mat.soft↗

arXiv2021

Whirligig Beetles as Corralled Active Brownian Particles

We study the collective dynamics of groups of whirligig beetles Dineutus discolor (Coleoptera: Gyrinidae) swimming freely on the surface of water. We extract individual trajectories for each beetle, including positions and orientations, and use this to discover (i) a density dependent speed scaling like $v\simρ^{-ν}$ with $ν\approx0.4$ over two orders of magnitude in density (ii) an inertial delay for velocity alignment of $\sim 13$ ms and (iii) coexisting high and low density phases, consistent with motility induced phase separation (MIPS). We modify a standard active brownian particle (ABP) model to a Corralled ABP (CABP) model that functions in open space by incorporating a density-dependent reorientation of the beetles, towards the cluster. We use our new model to test our hypothesis that a MIPS (or a MIPS like effect) can explain the co-occurrence of high and low density phases we see in our data. The fitted model then successfully recovers a MIPS-like condensed phase for $N=200$ and the absence of such a phase for smaller group sizes $N=50,100$.

q-bio.QM↗

arXiv2021

Harnessing confinement and driving to tune active particle dynamics

A distinguishing feature of active particles is the nature of the non-equilibrium noise driving their dynamics. Control of these noise properties is, therefore, of both fundamental and applied interest. We demonstrate emergent tuning of the active noise of a granular self-propelled particle by confining it to a quasi one-dimensional channel. We find that this particle, moving like an active Brownian particle (ABP) in two-dimensions, displays run-and-tumble (RTP) characteristics in confinement. We show that the dynamics of the relative orientation co-ordinate of the particle maps to that of a Brownian particle in a periodic potential subject to a constant force, in analogy to the dynamics of a molecular motor. This mapping captures the essential statistical characteristics of the one-dimensional RTP motion. Specifically, our theoretical analysis is in agreement with the empirical distributions of the relative orientation co-ordinate and the run-times (tumble-rates) of the particle. Finally, we explicitly control these emergent run-and-tumble like noise parameters by external driving. Altogether, our work illustrates geometry-induced tuning of the active dynamics of self-propelled units thus suggesting an independent route to harness their internal dynamics.

cond-mat.soft↗

arXiv2019

A self-driven phase transition drives Myxococcus xanthus fruiting body formation

Combining high-resolution single cell tracking experiments with numerical simulations, we show that starvation-induced fruiting body (FB) formation in Myxococcus xanthus is a phase separation driven by cells that tune their motility over time. The phase separation can be understood in terms of cell density and a dimensionless Peclet number that captures cell motility through speed and reversal frequency. Our work suggests that M. xanthus take advantage of a self-driven non-equilibrium phase transition that can be controlled at the single cell level.

physics.bio-ph↗

arXiv2018

Flow-induced phase separation of active particles is controlled by boundary conditions

Active particles, including swimming microorganisms, autophoretic colloids and droplets, are known to self-organize into ordered structures at fluid-solid boundaries. The entrainment of particles in the attractive parts of their spontaneous flows has been postulated as a possible mechanism underlying this phenomenon. Here, combining experiments, theory and numerical simulations, we demonstrate the validity of this flow-induced ordering mechanism in a suspension of active emulsion droplets. We show that the mechanism can be controlled, with a variety of resultant ordered structures, by simply altering hydrodynamic boundary conditions. Thus, for flow in Hele-Shaw cells, metastable lines or stable traveling bands can be obtained by varying the cell height. Similarly, for flow bounded by a plane, dynamic crystallites are formed. At a no-slip wall the crystallites are characterised by a continuous out-of-plane flux of particles that circulate and re-enter at the crystallite edges, thereby stabilising them. At an interface where the tangential stress vanishes the crystallites are strictly two-dimensional, with no out-of-plane flux. We rationalize these experimental results by calculating, in each case, the slow viscous flow produced by the droplets and the dissipative, long-ranged, many-body active forces and torques between them. The results of numerical simulations of motion under the action of the active forces and torques are in excellent agreement with experiments. Our work elucidates the mechanism of flow-induced phase separation (FIPS) in active fluids, particularly active colloidal suspensions, and demonstrates its control by boundaries, suggesting new routes to geometric and topological phenomena in active matter.

cond-mat.soft↗

arXiv2015

Intermittent chaotic chimeras for coupled rotators

Two symmetrically coupled populations of N oscillators with inertia $m$ display chaotic solutions with broken symmetry similar to experimental observations with mechanical pendula. In particular, we report the first evidence of intermittent chaotic chimeras, where one population is synchronized and the other jumps erratically between laminar and turbulent phases. These states have finite life-times diverging as a power-law with N and m. Lyapunov analyses reveal chaotic properties in quantitative agreement with theoretical predictions for globally coupled dissipative systems.

nlin.CD↗

arXiv2014

Phase transitions during fruiting body formation in Myxococcus xanthus

The formation of a collectively moving group benefits individuals within a population in a variety of ways such as ultra-sensitivity to perturbation, collective modes of feeding, and protection from environmental stress. While some collective groups use a single organizing principle, others can dynamically shift the behavior of the group by modifying the interaction rules at the individual level. The surface-dwelling bacterium Myxococcus xanthus forms dynamic collective groups both to feed on prey and to aggregate during times of starvation. The latter behavior, termed fruiting-body formation, involves a complex, coordinated series of density changes that ultimately lead to three-dimensional aggregates comprising hundreds of thousands of cells and spores. This multi-step developmental process most likely involves several different single-celled behaviors as the population condenses from a loose, two-dimensional sheet to a three-dimensional mound. Here, we use high-resolution microscopy and computer vision software to spatiotemporally track the motion of thousands of individuals during the initial stages of fruiting body formation. We find that a combination of cell-contact-mediated alignment and internal timing mechanisms drive a phase transition from exploratory flocking, in which cell groups move rapidly and coherently over long distances, to a reversal-mediated localization into streams, which act as slow-spreading, quasi-one-dimensional nematic fluids. These observations lead us to an active liquid crystal description of the myxobacterial development cycle.

physics.bio-ph↗

arXiv2013

Mode Coupling of Phonons in a Dense One-Dimensional Microfluidic Crystal

Long-living coupled transverse and longitudinal phonon modes are explored in dense and regular arrangements of flat microfluidic droplets. The collective oscillations are driven by hydrodynamic interactions between the confined droplets and can be excited in a controlled way. Experimental results are quantitatively compared to simulation results obtained by multi-particle collision dynamics. The observed transverse modes are acoustic phonons and can be described by a linearized far-field theory, whereas the longitudinal modes arise from a non-linear mode coupling due to the lateral variation of the flow field under confinement.

cond-mat.soft↗

arXiv2013

Chimera States in Mechanical Oscillator Networks

The synchronization of coupled oscillators is a fascinating manifestation of self-organization that nature employs to orchestrate essential processes of life, such as the beating of the heart. Although it was long thought that synchrony or disorder were mutually exclusive steady states for a network of identical oscillators, numerous theoretical studies in recent years have revealed the intriguing possibility of `chimera states', in which the symmetry of the oscillator population is broken into a synchronous and an asynchronous part. However, a striking lack of empirical evidence raises the question of whether chimeras are indeed characteristic to natural systems. This calls for a palpable realization of chimera states without any fine-tuning, from which physical mechanisms underlying their emergence can be uncovered. Here, we devise a simple experiment with mechanical oscillators coupled in a hierarchical network to show that chimeras emerge naturally from a competition between two antagonistic synchronization patterns. We identify a wide spectrum of complex states, encompassing and extending the set of previously described chimeras. Our mathematical model shows that the self-organization observed in our experiments is controlled by elementary dynamical equations from mechanics that are ubiquitous in many natural and technological systems. The symmetry breaking mechanism revealed by our experiments may thus be prevalent in systems exhibiting collective behaviour, such as power grids, opto-mechanical crystals or cells communicating via quorum sensing in microbial populations.

nlin.AO↗

arXiv2012

Oscillation patterns in active emulsion networks

We study water-in-oil emulsion droplets, running the Belousov-Zhabotinsky reaction, that form a new type of active matter unit. These droplets, stabilised by surfactants dispersed in the oil medium, are capable of internal chemical oscillations and also self-propulsion due to dynamic interfacial instabilities that result from the chemical reactions. The chemical oscillations can couple via the exchange of activator and inhibitor type of reaction intermediates across the droplets under precise conditions of surfactant bilayer formation between the droplets. Here we present the synchronization behaviour of networks of such chemical oscillators and show that the resulting dynamics depend on the network topology. Further, we demonstrate that the motion of droplets can be synchronized with the chemical oscillations inside the droplets, leading to exciting possibilities in future studies of active matter.

cond-mat.soft↗