arXiv subjects

Manu Prakash

Publications and source records attributed to Manu Prakash.

At least 19 recordsLinked to original sources

arXiv2024

Flight-Scope: microscopy with microfluidics in microgravity

With the European Space Agency (ESA) and NASA working to return humans to the moon and onwards to Mars, it has never been more important to study the impact of altered gravity conditions on biological organisms. These include astronauts but also useful micro-organisms they may bring with them to produce food, medicine, and other useful compounds by synthetic biology. Parabolic flights are one of the most accessible microgravity research platforms but present their own challenges: relatively short periods of altered gravity (~20s) and aircraft vibration. Live-imaging is necessary in these altered-gravity conditions to readout any real-time phenotypes. Here we present Flight-Scope, a new microscopy and microfluidics platform to study dynamic cellular processes during the short, altered gravity periods on parabolic flights. We demonstrated Flight-Scopes capability by performing live and dynamic imaging of fluorescent glucose uptake by yeast, S. cerevisiae, on board an ESA parabolic flight. Flight-Scope operated well in this challenging environment, opening the way for future microgravity experiments on biological organisms.

physics.bio-ph↗

arXiv2023

Droplet tilings in precessive fields: hysteresis, elastic defects, and annealing

Two-component Marangoni contracted droplets can be arranged into arbitrary two-dimensional tiling patterns where they display rich dynamics due to vapor mediated long-range interactions. Recent work has characterized the centered hexagonal honeycomb lattice, showing it to be a highly frustrated system with many metastable states and relaxation occurring over multiple timescales [Molina et al., PNAS, 2021, 18, 34]. Here, we study this system under the influence of a rotating gravitational field. High amplitudes are able to completely disrupt droplet-droplet interactions, making it possible to identify a transition between field-dominated to interaction-dominated regimes. The system displays complex hysteresis behavior, the details of which are connected to the emergence of linear mesoscale structures. These mesoscale features display an elasticity that is governed by the balance between gravity and long-ranged vapor-mediated attractions. We find that disorder plays an important role in determining the dynamics of these features. Finally, we demonstrate the ability to anneal the system by progressively reducing the field amplitude, a process that reduces configurational energy compared to a rapid quench. The ability to manipulate vapor-mediated interactions in deliberately designed droplet tilings provides a novel platform for table-top explorations of multi-body interactions.

cond-mat.soft↗

arXiv2023

Hidden Comet-Tails of Marine Snow Impede Ocean-based Carbon Sequestration

Global carbon-cycle on our planet ties together the living and the non-living world, coupling ecosystem function to our climate. Gravity driven downward flux of carbon in our oceans in the form of marine snow, commonly referred to as biological pump directly regulates our climate. Multi-scale nature of this phenomena, biological complexity of the marine snow particles and lack of direct observations of sedimentation fundamentally limits a mechanistic understanding of this downward flux. The absence of a physics based understanding of sedimentation of these multi-phase particles in a spatially and temporally heterogeneous ocean adds significant uncertainty in our carbon flux predictions. Using a newly invented scale-free vertical tracking microscopy, we measure for the first time, the microscopic sedimentation and detailed fluid-structure dynamics of marine snow aggregates in field settings. The microscopically resolved in-situ PIV of large number of field-collected marine snow reveals a comet tail like flow morphology that is universal across a range of hydrodynamic fingerprints. Based on this dataset, we construct a reduced order model of Stokesian sedimentation and viscoelastic distortions of mucus to understand the sinking speeds and tail lengths of marine snow dressed in mucus. We find that the presence of these mucus-tails doubles the mean residence time of marine snow in the upper ocean, reducing overall carbon sequestration due to microbial remineralization. We set forth a theoretical framework within which to understand marine snow sinking flux, paving the way towards a predictive understanding of this crucial transport phenomena in the open ocean.

physics.ao-ph↗

arXiv2023

Rapid, antibiotic incubation-free determination of tuberculosis drug resistance using machine learning and Raman spectroscopy

Tuberculosis (TB) is the world's deadliest infectious disease, with over 1.5 million deaths annually and 10 million new cases reported each year. The causative organism, Mycobacterium tuberculosis (Mtb) can take nearly 40 days to culture, a required step to determine the pathogen's antibiotic susceptibility. Both rapid identification of Mtb and rapid antibiotic susceptibility testing (AST) are essential for effective patient treatment and combating antimicrobial resistance. Here, we demonstrate a rapid, culture-free, and antibiotic incubation-free drug susceptibility test for TB using Raman spectroscopy and machine learning. We collect few-to-single-cell Raman spectra from over 25,000 cells of the MtB complex strain Bacillus Calmette Guerin (BCG) resistant to one of the four mainstay anti-TB drugs, isoniazid, rifampicin, moxifloxacin and amikacin, as well as a pan susceptible wildtype strain. By training a neural network on this data, we classify the antibiotic resistance profile of each strain, both on dried samples and in patient sputum samples. On dried samples, we achieve >98% resistant versus susceptible classification accuracy across all 5 BCG strains. In patient sputum samples, we achieve ~79% average classification accuracy. We develop a feature recognition algorithm in order to verify that our machine learning model is using biologically relevant spectral features to assess the resistance profiles of our mycobacterial strains. Finally, we demonstrate how this approach can be deployed in resource-limited settings by developing a low-cost, portable Raman microscope that costs <$5000. We show how this instrument and our machine learning model enables combined microscopy and spectroscopy for accurate few-to-single-cell drug susceptibility testing of BCG.

physics.bio-ph↗

arXiv2023

Active dislocations and topological traps govern dynamics of spiraling filamentous cyanobacteria

Activity can organize matter in unique configurations inaccessible to equilibrium systems, including a sundry of spiraling shapes seen in nature that range from galaxies to living tissues to fossilized stromatolites. How these dynamic yet stable patterns form in motile active systems that span a range of length and time scales remains an open question. Here we study the collective gliding dynamics of ultra-long filamentous cyanobacteria confined in two dimensions and present the discovery of an emergent pattern we call ``active spirals". Individual filaments in the spiral bulk remain confluent due to adhesion forces and exhibit reversible gliding motility. Thus individual filaments undergo bidirectional movement and the spiral object as a whole has no fixed vorticity. Using single filament tracking, we discover that spirals permit the radial flux of material as filaments shear past one another. We demonstrate that these rearrangements can be entirely described by topological rules of interaction between filaments tips. We thus reduce the dynamics of a spiral to a set of active dislocations (corresponding to the filament tips) on a polar coordinate lattice and show that we can reproduce and predict the material flux in the system. Finally, we present a discovery of a novel topological trap present in these spirals, and is induced purely by the geometric chirality of long winding filaments with winding number greater than zero. A topological trap creates boundaries in the spiral across which material cannot flow, leading to persistent structures that are topologically locked for the lifetime of the system. The emergent mechanics of active spirals presented here sheds light on the critical role of adhesion forces, activity and geometry in the formation of long-term, stable, yet dynamic active patterns.

cond-mat.soft↗

arXiv2023

Inkwell: Design and Validation of a Low-Cost Open Electricity-Free 3D Printed Device for Automated Thin Smearing of Whole Blood

Microscopy plays a crucial role in hematology and diagnosis of infectious diseases worldwide. For malaria alone, more than 200 million slides are read by manual microscopists every year. High quality thin blood smears are essential for subsequent microscopy examinations including malaria microscopy, but are hard to make in field settings. Existing devices for assisting in making thin smears are available but are limited by cost or complexity for wider use. Here we present Inkwell, a portable mechanical device capable of making high quality thin blood smears in field settings. Inkwell is simple, low-cost, does not use electricity, and requires minimal training prior to use. By utilizing passive dissipative dynamics of a spiral spring coupled to an air dashpot with a tunable valve - we demonstrate a highly tunable mechanism for constant velocity smears at prescribed angle. Inkwell is capable of producing high quality blood smears of tunable cell density with more than 12 million individually distinguishable red blood cells on a single slide. The current design, which exploits precision manufacturing of a 17 cents plastic syringe and a spring, can be printed on a standard 3D printer with overall unit cost of less than a few dollars in large quantities. We further present usability tests to confirm performance over 10,000 unit cycle operations with no degradation in quality of the smear and demonstrate ease of use with minimal training. Inkwell enhances the broader toolbox of open innovations in diagnostics for providing high quality medical care in low and medium resource settings. Combined with rise of 3D printing, Inkwell presents an alternative to traditional centralized manufacturing and opens up distributed manufacturing of medical diagnostics in global context.

physics.med-ph↗

arXiv2023

Self-learning mechanical circuits

Computation, mechanics and materials merge in biological systems, which can continually self-optimize through internal adaptivity across length scales, from cytoplasm and biofilms to animal herds. Recent interest in such material-based computation uses the principles of energy minimization, inertia and dissipation to solve optimization problems. Although specific computations can be performed using dynamical systems, current implementations of material computation lack the ability to self-learn. In particular, the inverse problem of designing self-learning mechanical systems which can use physical computations to continuously self-optimize remains poorly understood. Here we introduce the concept of self-learning mechanical circuits, capable of taking mechanical inputs from changing environments and constantly updating their internal state in response, thus representing an entirely mechanical information processing unit. Our circuits are composed of a new mechanical construct: an adaptive directed spring (ADS), which changes its stiffness in a directional manner, enabling neural network-like computations. We provide both a theoretical foundation and experimental realization of these elastic learning units and demonstrate their ability to autonomously uncover patterns hidden in environmental inputs. By implementing computations in an embodied physical manner, the system directly interfaces with its environment, thus broadening the scope of its learning behavior. Our results pave the way towards the construction of energy-harvesting, adaptive materials which can autonomously and continuously sense and self-optimize to gain function in different environments.

cond-mat.soft↗

arXiv2022

Active Foam: The Adaptive Mechanics of 2D Air-Liquid Foam under Cyclic Inflation

Foam is a canonical example of disordered soft matter where local force balance leads to the competition of many metastable configurations. Here we present an experimental and theoretical framework for "active foam" where an individual voxel inflates and deflates periodically. We explore structural adaptations of this disordered material with respect to added activity. Periodic injection of local activity leads to a small number of irreversible and reversible T1 transitions throughout the foam. Regardless of the presence of T1 transitions, individual vertices will displace outwards and subsequently return back to their approximate original radial position; this radial displacement follows an inverse law. Surprisingly, each return trajectory does not retrace its outbound path but rather encloses a finite area, with either a CW or CCW direction - which we define as a local swirl. These swirls form coherent patterns spanning the entire scale of the material. Using a reduced order dynamical model, we demonstrate that swirl arises as a direct consequence of spatial disorder in the local micro-structure. Building a first principles model, we demonstrate that disorder and strain rate control a crossover between cooperation and competition between swirls in adjacent vertices. Over longer timescales, the region around the active voxel structurally adapts from a higher-energy metastable state to a lower energy state, indicative of a localized annealing process. Finally, we develop a statistical toy-model that evolves edge lengths based on a set of simple rules to explore how this class of materials adapts over time as a function of initial structure. Adding activity to foam couples structural disorder and adaptive dynamics to encourage the development of a new class of abiotic, cellularized active matter.

cond-mat.soft↗

arXiv2021

A Swimming Rheometer: Self-propulsion of a freely-suspended swimmer enabled by viscoelastic normal stresses

Self-propulsion at low Reynolds number is notoriously restricted, a concept that is commonly known as the "scallop theorem". Here we present a truly self-propelled swimmer (force- and torque- free) that, while unable to swim in a Newtonian fluid due to the scallop theorem, propels itself in a non-Newtonian fluid as a result of fluid elasticity. This propulsion mechanism is demonstrated using a robotic swimmer, comprised of a "head" sphere and a "tail" sphere, whose swimming speed is shown to have reasonable agreement with a microhydrodynamic asymptotic theory and numerical simulations. Schlieren imaging demonstrates that propulsion of the swimmer is driven by a strong viscoelastic jet at the tail, which develops due to the fore-aft asymmetry of the swimmer. Optimized cylindrical and conic tail geometries are shown to double the propulsive signal, relative to the optimal spherical tail. Finally, we show that we can use observations of this robot to infer rheological properties of the surrounding fluid. We measure the primary normal stress coefficient at shear rates less than 1 Hz, and show reasonable agreement with extrapolated benchtop measurements (between 0.8 to 1.2 Pa sec2 difference). We also discuss how our swimmer can be used to measure the second normal stress coefficient and other rheological properties. The study experimentally demonstrates the exciting potential for a "swimming rheometer", bringing passive physics-driven fluid sensing to numerous applications in chemical and bioengineering.

physics.flu-dyn↗

arXiv2021

Excitable mechanics embodied in a walking cilium

Rapid transduction of sensory stimulation to action is essential for an animal to survive. To this end, most animals use the sub-second excitable and multistable dynamics of a neuromuscular system. Here, studying an animal without neurons or muscles, we report analogous excitable and multistable dynamics embedded in the physics of a 'walking' cilium. We define a 'walking cilium' as a phenomena where the locomotive force is generated through contact with a substrate which is periodically reset by steps in the direction of motion. We begin by showing that cilia can walk without specialized gait control and identify the characteristic scales of spatio-temporal height fluctuations of the tissue. With the addition of surface interaction, we construct a low-order dynamical model of this single-cilium sub-unit. In addition to studying the dynamics of a single cilium in isolation, we subsequently examine collections of these walking cilia. En route to an emergent model for ciliary walking, we demonstrate the limits of substrate mediated synchronization between cilia. In the desynchronized limit, our model shows evidence of localized multi-stability mediated by the crosstalk between locomotive forcing and height. The out-of-equilibrium mechanics -- which govern this emergent excitable bistability -- directly control the locomotive forcing of a walking cilia. This direct coupling bypasses the role of the synaptic junctions between neurons and muscles. We show a minimal mechanism -- trigger waves -- by which these walking cells may work together to achieve organism-scale collaboration, such as coordination of hunting strikes across $10^5$ cells without central control.

physics.bio-ph↗

arXiv2021

Ciliary flocking and emergent instabilities enable collective agility in a non-neuromuscular animal

Effective organismal behavior responds appropriately to changes in the surrounding environment. Attaining this delicate balance of sensitivity and stability is a hallmark of the animal kingdom. By studying the locomotory behavior of a simple animal (\textit{Trichoplax adhaerens}) without muscles or neurons, here, we demonstrate how monociliated epithelial cells work collectively to give rise to an agile non-neuromuscular organism. Via direct visualization of large ciliary arrays, we report the discovery of sub-second ciliary reorientations under a rotational torque that is mediated by collective tissue mechanics and the adhesion of cilia to the underlying substrate. In a toy model, we show a mapping of this system onto an "active-elastic resonator". This framework explains how perturbations propagate information in this array as linear speed traveling waves in response to mechanical stimulus. Next, we explore the implications of parametric driving in this active-elastic resonator and show that such driving can excite mechanical 'spikes'. These spikes in collective mode amplitudes are consistent with a system driven by parametric amplification and a saturating nonlinearity. We conduct extensive numerical experiments to corroborate these findings within a polarized active-elastic sheet. These results indicate that periodic and stochastic forcing are valuable for increasing the sensitivity of collective ciliary flocking. We support these theoretical predictions via direct experimental observation of linear speed traveling waves which arise from the hybridization of spin and overdamped density waves. We map how these ciliary flocking dynamics result in agile motility via coupling between an amplified resonator and a tuning (Goldstone-like) mode of the system. This sets the stage for how activity and elasticity can self-organize into behavior which benefits the organism as a whole.

physics.bio-ph↗

arXiv2021

Mobile defects born from an energy cascade shape the locomotive behavior of a headless animal

The physics of behavior seeks simple descriptions of animal behavior. The field has advanced rapidly by using techniques in low dimensional dynamics distilled from computer vision. Yet, we still do not generally understand the rules which shape these emergent behavioral manifolds in the face of complicated neuro-construction -- even in the simplest of animals. In this work, we introduce a non-neuromuscular model system which is complex enough to teach us something new but also simple enough for us to understand. In this simple animal, the manifolds underlying the governing dynamics are shaped and stabilized by a physical mechanism: an active-elastic, inverse-energy cascade. Building upon pioneering work in the field, we explore the formulation of the governing dynamics of a polarized active elastic sheet in terms of the normal modes of an elastic structure decorated by a polarized activity at every node. By incorporating a torque mediated coupling physics, we show that power is pumped from the shortest length scale up to longer length scale modes via a combination of direct mode coupling and preferential dissipation. We use this result to motivate the study of organismal locomotion as an emergent simplicity governing organism-scale behavior. To master the low dimensional dynamics on this manifold, we present a zero-transients limit study of the dynamics of +1 or vortex-like defects in the ciliary field. We show, experimentally, numerically and analytically that these defects arise from this energy cascade to generate long-lived, stable modes of locomotive behavior. Using a geometric model, we can link defects to organism locomotion. We extend this framework to study larger organisms with non-circular shape and introduce local activity modulation for defect steering. We expect this work to inform the foundations of organismal control of distributed actuation without muscles or neurons.

physics.bio-ph↗

arXiv2020

Evaporative self-assembly of motile droplets

Self-assembly is the underlying building principle of biological systems and represents a promising approach for the future of manufacturing, but the yields are often limited by undesirable metastable states. Meanwhile, annealing methods have long been an important means to guide complex systems towards optimal states. Despite their importance, there have been few attempts to experimentally visualize the microscopic dynamics that occur during annealing. Here, we present an experimental system that enables the study of interacting many-body dynamics by exploiting the physics of multi-droplet evaporation on a prescribed lattice network. Ensembles of motile binary droplets are seeded into a hexagonal lattice template where interactions are mediated through the vapor phase and can be manipulated through the application of a global gravitational field. We show that for finite systems (61 droplets) the interacting droplets have an effective long-ranged interaction that results in the formation of frustrated, metastable states. Application of a periodic, global gravitational field can drive the system through a non-equilibrium phase transition separating phase-locked synchronization from interaction-dominated behavior. Finally, we directly visualize field-driven annealing that leads to terminal states that are less frustrated. Overall, our results represent a new platform for studying many-body physics with long-ranged interactions, enabling the design of field-based control strategies for programming the self-assembly of complex many-body systems.

cond-mat.soft↗

arXiv2020

Project 1000 x 1000: Centrifugal melt spinning for distributed manufacturing of N95 filtering facepiece respirators

The COVID-19 pandemic has caused a global shortage of personal protective equipment. While existing supply chains are struggling to meet the surge in demand, the limited supply of N95 filtering facepiece respirators (FFRs) has placed healthcare workers at risk. This paper presents a method for scalable and distributed manufacturing of FFR filter material based on a combination of centrifugal melt spinning utilizing readily available cotton candy machines as an example. The proposed method produces nonwoven polypropylene fabric material with filtering efficiency of up to 96% for particles 0.30-0.49 μm in diameter. We additionally demonstrate a scalable means to test for filtration efficiency and pressure drop to ensure a standardized degree of quality in the output material. We perform preliminary optimization of relevant parameters for scale-up and propose that this is a viable method to rapidly produce up to one million N95 FFRs per day in distributed manner with just six machines per site operating across 200 locations. We share this work as a starting point for others to rapidly construct, replicate and develop their own affordable modular processes aimed at producing high quality filtration material to address the current FFR shortage globally.

physics.app-ph↗

arXiv2020

Engineering reconfigurable flow patterns via surface-driven light-controlled active matter

Surface-driven flows are ubiquitous in nature, from subcellular cytoplasmic streaming to organ-scale ciliary arrays. Here, we model how confined geometries can be used to engineer complex hydrodynamic patterns driven by activity prescribed solely on the boundary. Specifically, we simulate light-controlled surface-driven active matter, probing the emergent properties of a suspension of active colloids that can bind and unbind pre-patterned surfaces of a closed microchamber, together creating an active carpet. The attached colloids generate large scale flows that in turn can advect detached particles towards the walls. Switching the particle velocities with light, we program the active suspension and demonstrate a rich design space of flow patterns characterised by topological defects. We derive the possible mode structures and use this theory to optimise different microfluidic functions including hydrodynamic compartmentalisation and chaotic mixing. Our results pave the way towards designing and controlling surface-driven active fluids.

physics.bio-ph↗

arXiv2018

Rapid behavioral transitions produce chaotic mixing by a planktonic microswimmer

Despite their vast morphological diversity, many invertebrates have similar larval forms characterized by ciliary bands, innervated arrays of beating cilia that facilitate swimming and feeding. Hydrodynamics suggests that these bands should tightly constrain the behavioral strategies available to the larvae; however, their apparent ubiquity suggests that these bands also confer substantial adaptive advantages. Here, we use hydrodynamic techniques to investigate "blinking," an unusual behavioral phenomenon observed in many invertebrate larvae in which ciliary bands across the body rapidly change beating direction and produce transient rearrangement of the local flow field. Using a general theoretical model combined with quantitative experiments on starfish larvae, we find that the natural rhythm of larval blinking is hydrodynamically optimal for inducing strong mixing of the local fluid environment due to transient streamline crossing, thereby maximizing the larvae's overall feeding rate. Our results are consistent with previous hypotheses that filter feeding organisms may use chaotic mixing dynamics to overcome circulation constraints in viscous environments, and it suggests physical underpinnings for complex neurally-driven behaviors in early-divergent animals.

physics.flu-dyn↗

arXiv2017

Synchronous magnetic control of water droplets in bulk ferrofluid

We present a microfluidic platform for two-dimensional manipulation of water droplets immersed in bulk oil-based ferrofluid. Although non-magnetic, the droplets are exclusively controlled by magnetic fields, without any pressure-driven flow. The diphasic fluid layer is trapped in a submillimeter Hele-Shaw chamber that includes permalloy tracks on its substrate. An in-plane rotating magnetic field magnetizes the permalloy tracks, thus producing local magnetic gradients, while an orthogonal magnetic field magnetizes the bulk ferrofluid. To minimize the magnetostatic energy of the system, droplets are attracted towards the locations of the tracks where ferrofluid is repelled. Using this technique, we demonstrate synchronous generation and propagation of water droplets, analyze PIV data of the bulk ferrofluid flow and study the kinematics of propagation. In addition, we show controlled break-up of droplets and droplet-to-droplet interactions. Finally, we discuss future applications owing to the potential biocompatibility of the droplets.

physics.flu-dyn↗

arXiv2017

Two-component Marangoni-contracted droplets: friction and shape

When a mixture of propylene glycol and water is deposited on a clean glass slide, it forms a droplet of a given apparent contact angle rather than spreading as one would expect on such a high-energy surface. The droplet is stabilized by a Marangoni flow due to the non-uniformity of the components' concentrations between the border and the center of the droplet, itself a result of evaporation. These self-contracting droplets have unusual properties such as absence of pinning and the ability to move under an external humidity gradient. The droplets' apparent contact angle is a function of their concentration and the external humidity. Here we study the motion of such droplets sliding down slopes, how they deform when moving at large speeds, and compare the results to normal non-volatile droplets. We precisely control the external humidity and explore the influence of the volume, viscosity, surface tension, and contact angle. We find that the droplets suffer a negligible pinning force so that for small velocities the capillary number ($\mathrm{Ca}$) is directly proportional to the Bond number ($\mathrm{Bo}$): $\mathrm{Ca}=\mathrm{Bo} \sinα$ with $α$ the angle of the slope. When the droplets move at larger velocities they deform when Ca exceeds a threshold, and deposit smaller droplets when $\mathrm{Ca}$ reaches twice this threshold.

cond-mat.soft↗