arXiv subjects

Anupam Sengupta

Publications and source records attributed to Anupam Sengupta.

At least 19 recordsLinked to original sources

arXiv2026

Engineering Collective Microbial Dynamics for Sustainable Thermal Management

The rapid growth of energy-intensive technologies, including artificial intelligence, large-scale computing, and thermal management systems, has intensified global energy demand amid accelerating climate change. Meeting these demands requires innovative, low-carbon thermal management strategies that improve energy efficiency while minimizing environmental impact. This review revisits the underexplored phenomenon of bioconvection, a self-organized fluid motion generated by motile microorganisms, as a bio-inspired approach to sustainable heat transfer. Drawing on studies from natural ecosystems and laboratory experiments, we synthesize current knowledge of microorganism-induced hydrodynamics, pattern formation, and thermofluidic transport to assess the feasibility of harnessing bioconvection for thermal management. We further support this assessment through quantitative analyses of the thermal performance of bioconvective systems and discuss this in the framework of relevant non-dimensional numbers. By generating spontaneous convective plumes through density stratification, motile microorganisms enhance heat and mass transfer without external mechanical forcing. These self-organized flows provide a promising route toward hybrid bio-engineered cooling systems that reduce pumping energy, disrupt thermal boundary layers, and improve heat transfer efficiency. We conclude the review with the key challenges on the way to practical implementation, including microbial stability, material compatibility, controllability, scalability, as well as integration with existing cooling technologies. Finally, we identify critical research directions spanning heat transfer, microbiology, and nonlinear fluid mechanics within the broad context of sustainability, positioning bioconvection as a promising strategy for environmentally responsible thermal management in an era of rapidly increasing energy demand.

physics.bio-ph↗

arXiv2026

Ecological memory of hydrodynamic cues shapes growth and migration of motile microorganisms

Microorganisms live in inherently dynamic environments where fluctuations in biotic and abiotic factors shape their behaviour, physiology, and fitness. The concept of ecological memory: the lasting imprint of prior environmental cues, suggests that past exposures can exert prolonged effects on microbial growth, resilience, and phenotypic expressions. For motile microbes in aquatic ecosystems, environmental variability is mediated by fluid motion, which may engender a form of hydrodynamic memory, whereby prior exposure to specific spatio-temporal cues influence future growth and migratory behaviour. Yet, the emergence of such flow-induced memory, or its long-term consequences for trait evolution and population dynamics, remain unexplored. We integrate millifluidic flow control, high-resolution cell tracking, and tunable hydrodynamic cues to quantify growth and migration of Heterosigma akashiwo, a model microbe, across growth stages. Using two complementary perturbation scenarios: standard (flow after static conditions) and reverse (flow before static growth), we test how the temporal structure of forcing shapes multigenerational responses. This combinatorial design disentangles exposure history from its duration, and reveals how prior flow modulates sensitivity, generating legacy effects. Compared with static controls, repeated hydrodynamic exposure alters doubling time, carrying capacity, gravitactic stability, and swimming speed distributions; shifting growth phase progression and tolerance to subsequent perturbations. These results establish a mechanistic framework for flow-induced memory in motile microbes, revealing how past fluidic cues shape future growth and migration. Our study advances predictive understanding of motile microbes in natural and engineered hydrodynamic systems experiencing increasing variability under global environmental changes.

physics.bio-ph↗

arXiv2025

Nascent biofilms on soft surfaces

Soft surfaces, spanning vastly different environmental and biomedical settings, are frequently colonised by surface-associated bacteria. Yet, how soft surfaces govern bacterial dynamics and their self-organisation into colonies remains poorly understood. Using experiments and agent-based modelling, we report the self-organisation of bacterial cells into nascent biofilms on soft substrates. By tuning the elastic modulus over two orders of magnitude, we show that the colony morphology, spreading dynamics and collective behaviour depend on the substrate stiffness, wherein softer surfaces promote slowly expanding, geometrically anisotropic, multilayered colonies, while harder substrates drive rapid, isotropic expansion of bacterial monolayers before multilayer structures emerge. Supported a cell mechanical model and two-dimensional agent-based simulations, our results identify that anisotropic drag forces on soft substrates, emerging due to local deformations, underpin colony anisotropy and swift verticalisation. In contrast, reduced drag on hard surfaces allows rapid expansion of monolayers, thus delaying the transition to a multilayer structure. Surface compliance, a key but overlooked determinant of early-stage biofilm development, could be harnessed to engineer biofilm structures and dynamics for nature-inspired and biomedical applications.

physics.bio-ph↗

arXiv2025

Substrate stiffness governs dynamics and self-organization of nascent biofilms

The evolutionary success of bacteria lies in their ability to form complex surface-associated communities in diverse biophysical settings. However, it remains poorly understood how compliance of soft surfaces, measured in terms of their elastic deformability, impacts the dynamics and self-organization of bacterial cells proliferating into colonies. Using experiments and biomechanical modelling, here we study the expansion and self-organization of bacterial cells into sessile colonies on soft substrates. The dynamics and spatiotemporal structures were captured by visualising growing bacterial colonies on nutrient-rich, soft agarose pads, with elastic modulus in the range ~0.3 kPA to ~100 kPA by varying the concentration of the agarose in the underlying substrate. Our results show that, at the scale of the colonies, significant differences emerge in the spreading dynamics and colony geometry as the substrate stiffness is altered: softer substrates promote distinct, multilayered colony structures, and as revealed by fractal analysis of the colony boundaries, they exhibit higher boundary roughness. In contrast, colonies growing on harder substrates first grow up to large monolayers, before undergoing the mono-to-multilayer transition (MTMT), showing nearly 300% increase in the overall colony area at MTMT. A simple biomechanical model captures the role of effective drag forces at different scales, acting on the colonies as they spread on substrates with different stiffness: higher drag in soft substrates drive early verticalisation of the colonies, while lower effective drag delays the MTMT, resulting in larger colony areas. Based on the results and biomechanical insights, a comprehensive data-backed numerical model is currently being developed. Our findings highlight the role of surface stiffness in determining the self-organization of bacterial cells into an expanding multi-scale colony.

cond-mat.soft↗

arXiv2024

Tipping points in fitness landscape of heterogeneous populations

Predicting fitness of biologically-active populations, communities or systems in fluctuating environments is a long-standing challenge. Phenotypic plasticity and bet-hedging strategy, two key evolutionary traits living systems harness to optimize fitness in dynamic environments, have been widely reported yet how interplays therein could mediate fitness landscapes of heterogeneous populations remain unknown. Leveraging the financial asset pricing model, here we provide a dynamical framework for fitness of heterogeneous populations, underpinned by the interrelations between sub-populations exhibiting phenotypic plasticity and bet-hedgeding. Our framework, independent of the definition of fitness, employs a nonlinear difference equation to present fitness dynamics, and capture the emergence of tipping points, marking the onset of critical state transitions which lead to catastrophic shifts. This study identifies limits on the selective advantage conferred by bet-hedging through reduction in the temporal variance of fitness, with far-reaching ramifications on our current understanding of hedging-mediated fitness enhancement of a population. The lower bound of the effective fitness variance is set by a maximum number of bet-hedgers, beyond which the fitness landscape approaches critical transition, as confirmed by critical slowing down in the vicinity of tipping points. We estimate the scaling law for the critical slowing down numerically and derive the characteristic recovery time for heterogeneous populations. Taken together, our work provides a generic theoretical framework to quantify fitness dynamics and predict critical transitions in heterogeneous populations. The results can be extended further to model fitness landscapes of natural and synthetic multi-species consortia exposed to environmental fluctuations mimicking climatic shifts and immunopathological settings.

q-bio.PE↗

arXiv2024

Substrate stiffness modulates bacterial adhesion and diversity of adherent phenotypes across growth stages

Surface-adhesion and stiffness of underlying substrates mediate geometry, mechanics and self-organization of bacterial colonies. Recent studies have qualitatively indicted that stiffness may impact bacterial attachment, yet the variation of cell-to-surface adhesion with substrate stiffness remains to be quantified. Here, by developing a cell-level Force Distance Spectroscopy (FDS) technique based on Atomic Force Microscopy (AFM), we simultaneously quantify the cell-surface adhesion alongside stiffness of the underlying substrates to reveal stiffness-dependent adhesion in phototrophic bacterium Chromatium okenii. As stiffness of the soft substrate, modelled via low-melting-point (LMP) agarose pad, was varied between 20 kPa and 120 kPa by changing agarose concentrations, we observe a progressive increase of the mean adhesion force by over an order of magnitude, from 0.21 (+/-0.10) nN to 2.42 (+/-1.16) nN. In contrast, passive polystyrene (PS) microparticles of comparable dimensions showed no perceptible change in their surface adhesion. Furthermore, for Escherichia coli, the cell-surface adhesion varied between 0.29 (+/-0.17) nN to 0.39 (+/-0.20) nN, showing a weak dependence on the substrate stiffness, thus suggesting that the stiffness-modulated adhesion is a species-specific trait. Finally, by quantifying the adhesion of C. okenii populations across growth stages, we report an emergent co-existence of weak and strongly adherent sub-populations, demonstrating a diversification of adherent phenotypes over time. Taken together, these findings suggest that bacteria, depending on the species and their physiological stage, actively modulate cell-to-surface adhesion in response to substrate stiffness, and leverage it as a functional trait to modulate initial attachment and colonization on soft substrates during early stages of biofilm development.

physics.bio-ph↗

arXiv2023

Role of Motility and Nutrient Availability in Drying Patterns of Algal Droplets

Sessile drying droplets in various bio-relevant systems, encompassing passive bio-colloids like DNA, proteins, and blood to active microbes, gain considerable attention due to intricate interplay among different convective flows, droplet pinning, mechanical stress, wettability, and the emergence of distinctive patterns. Chlamydomonas reinhardtii, or chlamys, is a versatile algal model employed in molecular biology research and spanning diverse biotechnological realms. While chlamys are harnessed at single-cell and population levels, their exploration in the context of drying sessile droplets remains limited. This paper illuminates the multifaceted potential of chlamys, delving into motility-nutrient interactions and their role in emergent morphological patterns. The interplay of two competing stressors -- localized nutrient scarcity and mechanical stress during drying -- is investigated. Irrespective of these stressors, the global mechanical stress fails to induce any cracks during the drying process. Interestingly, the reverse ``coffee-ring effect" is predominantly observed in the non-motile chlamys in the presence of local nutrients whereas the nutrient depletion prompts local stress in motile chlamys, culminating in cooperative aggregation and cluster formation. Furthermore, the quantitative image processing technique leverages textural statistics to classify the patterns into four classes, motile+with nutrients, motile+without nutrients, non-motile+with nutrients, and non-motile+without nutrients, with five distinct drying stages -- Droplet Deposition, Capillary Flow, Dynamic Droplet Phase, Aggregation Phase, and Dried Morphology.

cond-mat.soft↗

arXiv2023

Collective mechano-response dynamically tunes cell-size distributions in growing bacterial colonies

Mechanical stresses stemming from environmental factors are a key determinant of cellular behavior and physiology. Yet, the role of self-induced biomechanical stresses in growing bacterial colonies has remained largely unexplored. Here, we demonstrate how collective mechanical forcing plays an important role in the dynamics of the cell size of growing bacteria. We observe that the measured elongation rate of well-nourished \textit{Escherichia coli} cells decreases over time, depending on the free area around each individual, and associate this behavior with the response of the growing cells to mechanical stresses. Via a cell-resolved model accounting for the feedback of collective forces on individual cell growth, we quantify the effect of this mechano-response on the structure and composition of growing bacterial colonies, including the local environment of each cell. Finally, we predict that a mechano-cross-response between competing bacterial strains with distinct growth rates affects their size distributions.

cond-mat.soft↗

arXiv2023

Microbes in porous environments: From active interactions to emergent feedback

Microbes thrive in diverse porous environments -- from soil and riverbeds to human lungs and cancer tissues -- spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decade and a half. With a focus on bacteria, here we review recent advances in microbial self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback which mediate their survival and fitness. We conclude by discussing open questions and opportunities for leveraging integrative cross-disciplinary approaches to advance our understanding of the biophysical strategies that microbes employ -- at both species and community scales -- to make porous settings habitable. Active and responsive behaviour is key to microbial survival in porous environments, with far-reaching ramifications for developing strategies to mitigate anthropogenic impacts, innovate subsurface storage solutions, and predict future ecological scenarios imposed by current climatic changes.

physics.bio-ph↗

arXiv2023

Curvature-mediated Programming of Liquid Crystal Microflows

Using experiments and numerical simulations, we demonstrate that the curvature of microscale conduits allow programming of liquid crystal (LC) flows. Focusing on a nematic LC flowing through U- and L-shaped channels of rectangular cross-section, our results reveal that curved flow paths can trigger gradients of flow-induced director field in the transverse direction. The emergent director field feeds back into the flow field, ultimately leading to LC flows controlled by the channel curvature. This curvature-mediated flow control, identified by polarizing optical microscopy and supported by the nematofluidic solutions, offers novel concepts in LC-based microfluidic valves and throttles, wherein the throughput distribution is determined by the Ericksen number and the variations in the local curvature. Finally, this work highlights the role of deformation history on flow-induced director alignments, when the viscous and elastic effects comparable in strength.

cond-mat.soft↗

arXiv2023

Planktonic Active Matter

Planktonic active matter represents an emergent system spanning different scales: individual, population and community; and complexity arising from sub-cellular and cellular to collective and ecosystem scale dynamics. This cross-scale active matter system responds to a range of abiotic (temperature, fluid flow and light conditions) and biotic factors (nutrients, pH, secondary metabolites) characteristic to the relevant ecosystems they are part of. Active modulation of cell phenotypes, including morphology, motility, and intracellular organization enable planktonic microbes to dynamically interact with other individuals and species; and adapt - often rapidly - to the changes in their environment. In this chapter, I discuss both traditional and contemporary approaches to study the dynamics of this multi-scale active matter system from a mechanistic standpoint, with specific references to their local settings and their ability to actively tune the behaviour and physiology, and the emergent structures and functions they elicit under natural ecological constraints as well as due to the shifting climatic trends.

physics.bio-ph↗

arXiv2022

Drying of Bio-colloidal Sessile Droplets: Advances, Applications, and Perspectives

Drying of biologically-relevant sessile droplets, including passive systems (like DNA and proteins), as well as active microbial systems comprising bacteria and algae, have garnered considerable attention over the last decades. Distinct morphological patterns emerge when bio-colloids undergo drying, with significant potential in a range of biomedical applications, spanning bio-sensing, medical diagnostics, drug delivery, and antimicrobial resistance. This review presents a comprehensive overview of bio-colloidal droplets drying on solid substrates, focusing on the experimental progress during the last ten years. We provide a summary of the relevant properties of bio-colloids and link their composition (constituent particles, solvent, and concentrations) to the patterns emerging due to drying. We examined the drying patterns generated by passive bio-colloids (DNA, globular, fibrous, and composite proteins, plasma, serum, blood, urine, tears, saliva). This article highlights how morphological patterns are influenced by the nature of the biological entities and the solvent, micro- and global environmental conditions. Correlations between emergent patterns and the initial droplet compositions enable the detection of potential clinical abnormalities when compared with the patterns of drying droplets of healthy control samples, offering a diagnostic blueprint. Recent experimental investigations of pattern formation in the bio-mimetic and salivary drying droplets, relevant to COVID-19 are also presented. Finally, we summarize the role of biologically active agents in drying process, including bacteria and algae during the drying process. The review concludes with a perspective on the next generation of research and applications based on drying droplets, enabling potential innovations and tools to study this exciting interface of physics, biology, data sciences, and machine learning.

cond-mat.soft↗

arXiv2022

Spatio-temporal programming of lyotropic phase transition in nanoporous microfluidic confinements

Self-assembly of simple molecules into complex phases can be driven by physical constraints, for instance, due to selective molecular uptake by nanoporous surfaces. Despite the significance of surface-mediated assembly in evolution of life, physical routes to molecular enrichment and assembly have remained overlooked. Here, using a lyotropic chromonic liquid crystal as model biological material, confined within nanoporous microfluidic environments, we study molecular assembly driven by nanoporous substrates. We demonstrate that nanoporous polydimethylsiloxane (PDMS) surfaces, due to selective permeation of water molecules, drive transition of disordered isotropic phase to ordered nematic, and higher order columnar phases under isothermal conditions. Synergistically, by tailoring the wettability, the surface-to-volume ratio, and surface topography of the confinements, we program the lyotropic phase transitions with a high degree of spatial and temporal control. Using a combination of timelapse polarized imaging, quantitative image processing, and a simple mathematical model, we analyze the phase transitions, and construct a master diagram capturing the role of surface wettability and channel geometry on programmable lyotropic phase transitions. Intrinsic PDMS nanoporosity and confinement cross-section, together with the imposed wettability regulate the rate of the N-M phase transition; whereas the microfluidic geometry and embedded topography enable phase transition at targeted locations. We harness the emergent long-range order during N-M transition to actuate elasto-advective transport of embedded micro-cargo, demonstrating particle manipulation concepts governed by tunable phase transitions. Our results present a programmable physical route to material assembly, and offer a new paradigm for assembling genetic components, biological cargo, and minimal synthetic cells.

cond-mat.soft↗

arXiv2022

Steering self-organisation through confinement

Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement occurs through interactions with boundaries, and can function as either a catalyst or inhibitor of self-organisation. It can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework for future research, we examine the role of confinement in self-organisation and identify overarching scientific challenges across disciplines that need to be addressed to harness its full scientific and technological potential. This framework will not only accelerate the generation of a common deeper understanding of self-organisation but also trigger the development of innovative strategies to steer it through confinement, with impact, e.g., on the design of smarter materials, tissue engineering for biomedicine and crowd management.

nlin.AO↗

arXiv2021

Trade-offs in phenotypic noise synchronize emergent topology to actively enhance transport in microbial environments

Phenotypic noise underpins homeostasis and fitness of individual cells. Yet, the extent to which noise shapes cell-to-population properties in microbial active matter remains poorly understood. By quantifying variability in confluent \textit{E.coli} strains, we catalogue noise across different phenotypic traits. The noise, measured over different temperatures serving as proxy for cellular activity, spanned more than two orders of magnitude. The maximum noise was associated with the cell geometry and the critical colony area at the onset of mono-to-multilayer transition (MTMT), while the lower bound was set by the critical time of the MTMT. Our results, supported by a hydrodynamic model, suggest that a trade-off between the noise in the cell geometry and the growth rate can lead to the self-regulation of the MTMT timing. The MTMT cascades synchronous emergence of hydrodynamic fields, actively enhancing the micro-environmental transport. Our results highlight how interplay of phenotypic noise triggers emergent deterministic properties, and reveal the role of multifield topology--of the colony structure and hydrodynamics--to insulate confluent systems from the inherent noise associated with natural cell-environment settings.

physics.bio-ph↗

arXiv2021

Anchoring-dependent bifurcation in nematic microflows within cylindrical capillaries

Capillary microflows of liquid crystal phases are central to material, biological and bio-inspired systems. Despite their fundamental and applied significance, a detailed understanding of the stationary behaviour of nematic liquid crystals (NLC-s) in cylindrical capillaries is still lacking. Here, using numerical simulations based on the continuum theory of Leslie, Ericksen and Parodi, we investigate stationary NLC flows within cylindrical capillaries possessing homeotropic (normal) and uniform planar anchoring conditions. By considering the material parameters of the flow-aligning NLC, 5CB, we report that instead of the expected, unique director field monotonically approaching the alignment angle over corresponding Ericksen numbers (dimensionless number capturing viscous v/s elastic effects), a second solution emerges below a threshold flow rate (or applied pressure gradient). We demonstrate that the onset of the second solution, a nematodynamic bifurcation yielding energetically degenerate director tilts at the threshold pressure gradient, can be controlled by the surface anchoring and the flow driving mechanism (pressure-driven or volume-driven). For homeotropic surface anchoring, this alternate director field orients against the alignment angle in the vicinity of the capillary center; while in the uniform planar case, the alternate director field extends throughout the capillary volume, leading to reduction of the flow speed with increasing pressure gradients. While the practical realization and utilization of such nematodynamic bifurcations still await systematic exploration, signatures of the emergent rheology have been reported previously within microfluidic environments, under both homeotropic (Sengupta et al., Phys. Rev. Lett. 110, 048303, 2013) and planar anchoring conditions (Sengupta, Int. J. Mol. Sci. 14, 22826, 2013).

cond-mat.soft↗

arXiv2021

Mono-to-multilayer transition in growing bacterial colonies

The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. Using a combination of numerical simulations and analytical modeling, here we demonstrate that this transition originates from the competition between growth-induced in-plane active stresses and vertical restoring forces, due to the cell-substrate interactions. Using a simple chainlike colony of laterally confined cells, we show that the transition sets when individual cells become unstable to rotations, thus it is localized and mechanically deterministic. Asynchronous cell division renders the process stochastic, so that all the critical parameters that control the onset of the transition are continuously distributed random variables. Here we demonstrate that the occurrence of the first division in the colony can be approximated as a Poisson process in the limit of large cells numbers. This allows us to approximately calculate the probability distribution function of the position and time associated with the first extrusion. The rate of such a Poisson process can be identified as the order parameter of the transition, thus highlighting its mixed deterministic-stochastic nature.

cond-mat.soft↗

arXiv2020

Time dependent lyotropic chromonic textures in PDMS-based microfluidic confinements

Nematic and columnar phases of lyotropic chromonic liquid crystals (LCLCs) have been long studied for their fundamental and applied prospects in material science and medical diagnostics. LCLC phases represent different self-assembled states of disc-shaped molecules, held together by noncovalent interactions that lead to highly sensitive concentration and temperature dependent properties. Yet, microscale insights into confined LCLCs, specifically in the context of confinement geometry and surface properties, are lacking. Here, we report the emergence of time dependent textures in static disodium chromoglycate (DSCG) solutions, confined in PDMS-based microfluidic devices. We use a combination of soft lithography, surface characterization and polarized optical imaging to generate and analyze the confinement-induced LCLC textures, and demonstrate that over time, herringbone and spherulite textures emerge due to spontaneous nematic (N) to columnar M-phase transition, propagating from the LCLC-PDMS interface into the LCLC bulk. By varying the confinement geometry, anchoring conditions and the initial DSCG concentration, we can systematically tune the temporal dynamics of the N to M-phase transition and textural behaviour of the confined LCLC. Since static molecular states register the initial conditions for LC flows, the time dependent boundary and bulk conditions reported here suggest that the local surface-mediated dynamics could be central in understanding LCLC flows, and in turn, the associated transport properties of this versatile material.

cond-mat.soft↗