We use interdisciplinary approaches including theory and experiments to understand how computation is embodied in biological matter. Examples include cognition in single cell protists and morphological computing in animals with no neurons and origins of complex behavior in multi-cellular systems. Broadly, we invent new tools for studying non-model organisms with significant focus on life in the ocean - addressing fundamental questions such as how do cells sense pressure or gravity? Finally, we are dedicated towards inventing and distributing “frugal science” tools to democratize access to science (previous inventions used worldwide: Foldscope, Abuzz), diagnostics of deadly diseases like malaria and convening global citizen science communities to tackle planetary scale environmental challenges such as mosquito surveillance or plankton surveillance by citizen sailors mapping the ocean in the age of Anthropocene.
Core Leadership Team, Stanford Center for Innovation in Global Health (2017 - Present)
Board member,, Jasper Ridge Reserve, Stanford (https://jrbp.stanford.edu) (2017 - Present)
Honors & Awards
MIT Ideas Sustainability Prize, MIT (2003)
Lemelson MIT Student Finalist Award, Lemelson Foundation (2008)
Junior Fellow (Physics), Harvard Society of Fellows (2008-2011)
Frederick E. Terman Fellow, Stanford University (2011-2013)
TED Senior Fellow, Technology, Entertainment and Design (TED) (2011-2013)
Pew Scholar, Pew Foundation (2013-2017)
Brilliant 10, Popular Science Brilliant 10 (2014)
TR35, MIT Technology Review (2014)
Emerging Explorer, National Geographic (2015)
MacArthur Fellow, MacArthur Foundation (2016)
HHMI-Gates Faculty Scholar, HHMI (2016-2021)
25 People Shaping the Future, Rolling Stone Magazine (2017)
Chan Zuckerberg BioHub Investigator, Chan Zuckerberg BioHub (2017)
INDEX Design Award, INDEX (2017)
NSF “Vizzies” Experts’ Choice Award, Popular Science (2017)
Tau Beta Pi Teaching Award, Tau Beta Pi (2017)
WIRED’s Next List, WIRED (2017)
Design of the Year Award (Paperfuge), Beazley (2018)
Inaugural Fellow, Leading Interdisciplinary Collaborations, Stanford Woods Institute (2018)
Town & Country's 50, Town & Country Magazine (2018)
The Creative Class of 2019, Newsweek (2019)
Humanitarian Award for Contributions in Science, Technology and Robotics, Rotary International (2020)
Unilever Colworth Prize, Microbiology Society (2020)
Boards, Advisory Committees, Professional Organizations
Co-founder, Foldscope Instruments (2017 - Present)
Board Member, Ciencia Puerto Rico (https://www.cienciapr.org) (2017 - Present)
Board Member, PIVOT (http://pivotworks.org) (2017 - Present)
Ph.D., Massachusetts Institute of Technology, Field of Study: Applied Physics (MAS) (2008)
M.S., Massachusetts Institute of Technology, Field of Study: Applied Physics (MAS) (2004)
B.Tech, Indian Institute of Technology, Field of Study: Computer Science and Engineering (2002)
Community and International Work
Low-cost scientific instruments
India Dept of Biotechnology
Opportunities for Student Involvement
Low-cost scanning of oral cavity, Kenya and India
Opportunities for Student Involvement
Zhang, S., Mershin, A., Kaiser, K., Cook, B., Graveland-Bikker, J.F., Prakash, M., Kong, D., Maguire, Y.,. "United States Patent US9714941 Bio-sensing nanodevice", Jul 25, 2017
Prakash M., Cybulski J., Clements J.. "United States Patent US9696535 Foldscope: Ultra-low-cost fluorescence microscope constructed via folding", Leland Stanford Junior University,, Jul 4, 0017
Prakash M., Gershenfeld N.. "United States Patent US9404835 Microfluidic bubble logic", Massachusetts Institute of Technology, Aug 2, 0016
Chow B., Joo J., Prakash M.. "United States Patent US8367435 Methods and apparatus for control of hydrothermal nanowire synthesis", Massachusetts Institute of Technology, Jun 16, 0013
- Frugal Science
BIOE 271 (Win)
- Senior Capstone Design I
BIOE 141A (Aut)
- Senior Capstone Design II
BIOE 141B (Win)
Independent Studies (9)
- Bioengineering Problems and Experimental Investigation
BIOE 191 (Aut, Win, Spr, Sum)
- Directed Investigation
BIOE 392 (Aut, Win, Spr, Sum)
- Directed Reading in Biophysics
BIOPHYS 399 (Aut, Win, Spr, Sum)
- Directed Studies in Applied Physics
APPPHYS 290 (Aut)
- Directed Study
BIOE 391 (Aut, Win, Spr, Sum)
- Graduate Research
BIOPHYS 300 (Aut, Win, Spr, Sum)
- Out-of-Department Graduate Research
BIO 300X (Aut, Win, Spr, Sum)
- Ph.D. Research
MATSCI 300 (Aut, Win, Spr, Sum)
- Ph.D. Research Rotation
ME 398 (Win)
- Bioengineering Problems and Experimental Investigation
- Prior Year Courses
Doctoral Dissertation Reader (AC)
Jeremy Binagia, Sam Bray, Chew Chai, Shreya Deshmukh, Tingting Gong, Amalia Hadjitheodorou, Pengyang Li, Sasha Zemsky
Postdoctoral Faculty Sponsor
JIJUMON A S, Samhita Banavar, Rahul Chajwa, Melanie Hannebelle, Shailabh Kumar, Adam Larson, Vishal Patil
Doctoral Dissertation Advisor (AC)
Charlotte Brannon, Ray Chang, Ellie Flaum, Laurel Kroo, Ethan Li, Hongquan Li, Anton Molina, Pranav Vyas, Grace Zhong
Julie Chang, Ray Chang, Gustavo Chau Loo Kung, Shreya Deshmukh, Ian Ho, Louai Labanieh, Micah Lawrence, Jiawei Sun, Lara Weed
A microfluidic platform for highly parallel bite by bite profiling of mosquito-borne pathogen transmission.
2021; 12 (1): 6018
Mosquito bites transmit a number of pathogens via salivary droplets deposited during blood-feeding, resulting in potentially fatal diseases. Little is known about the genomic content of these nanodroplets, including the transmission dynamics of live pathogens. Here we introduce Vectorchip, a low-cost, scalable microfluidic platform enabling high-throughput molecular interrogation of individual mosquito bites. We introduce an ultra-thin PDMS membrane which acts as a biting interface to arrays of micro-wells. Freely-behaving mosquitoes deposit saliva droplets by biting into these micro-wells. By modulating membrane thickness, we observe species-dependent differences in mosquito biting capacity, utilizable for selective sample collection. We demonstrate RT-PCR and focus-forming assays on-chip to detect mosquito DNA, Zika virus RNA, as well as quantify infectious Mayaro virus particles transmitted from single mosquito bites. The Vectorchip presents a promising approach for single-bite-resolution laboratory and field characterization of vector-pathogen communities, and could serve as a powerful early warning sentinel for mosquito-borne diseases.
View details for DOI 10.1038/s41467-021-26300-0
View details for PubMedID 34650045
- Modeling epithelial tissues as active-elastic sheets reproduce contraction pulses and predict rip resistance COMMUNICATIONS PHYSICS 2021; 4 (1)
Droplet tilings for rapid exploration of spatially constrained many-body systems.
Proceedings of the National Academy of Sciences of the United States of America
2021; 118 (34)
Geometry in materials is a key concept which can determine material behavior in ordering, frustration, and fragmentation. More specifically, the behavior of interacting degrees of freedom subject to arbitrary geometric constraints has the potential to be used for engineering materials with exotic phase behavior. While advances in lithography have allowed for an experimental exploration of geometry on ordering that has no precedent in nature, many of these methods are low throughput or the underlying dynamics remain difficult to observe directly. Here, we introduce an experimental system that enables the study of interacting many-body dynamics by exploiting the physics of multidroplet evaporation subject to two-dimensional spatial constraints. We find that a high-energy initial state of this system settles into frustrated, metastable states with relaxation on two timescales. We understand this process using a minimal dynamical model that simulates the overdamped dynamics of motile droplets by identifying the force exerted on a given droplet as being proportional to the two-dimensional vapor gradients established by its neighbors. Finally, we demonstrate the flexibility of this platform by presenting experimental realizations of droplet-lattice systems representing different spin degrees of freedom and lattice geometries. Our platform enables a rapid and low-cost means to directly visualize dynamics associated with complex many-body systems interacting via long-range interactions. More generally, this platform opens up the rich design space between geometry and interactions for rapid exploration with minimal resources.
View details for DOI 10.1073/pnas.2020014118
View details for PubMedID 34417307
- Choosing Wisely for COVID-19: ten evidence-based recommendations for patients and physicians. Nature medicine 2021
- India's COVID-19 crisis: a call for international action. Lancet (London, England) 2021
- Motility-induced fracture reveals a ductile-to-brittle crossover in a simple animal's epithelia NATURE PHYSICS 2021
Modified full-face snorkel masks as reusable personal protective equipment for hospital personnel.
2021; 16 (1): e0244422
Here we adapt and evaluate a full-face snorkel mask for use as personal protective equipment (PPE) for health care workers, who lack appropriate alternatives during the COVID-19 crisis in the spring of 2020. The design (referred to as Pneumask) consists of a custom snorkel-specific adapter that couples the snorkel-port of the mask to a rated filter (either a medical-grade ventilator inline filter or an industrial filter). This design has been tested for the sealing capability of the mask, filter performance, CO2 buildup and clinical usability. These tests found the Pneumask capable of forming a seal that exceeds the standards required for half-face respirators or N95 respirators. Filter testing indicates a range of options with varying performance depending on the quality of filter selected, but with typical filter performance exceeding or comparable to the N95 standard. CO2 buildup was found to be roughly equivalent to levels found in half-face elastomeric respirators in literature. Clinical usability tests indicate sufficient visibility and, while speaking is somewhat muffled, this can be addressed via amplification (Bluetooth voice relay to cell phone speakers through an app) in noisy environments. We present guidance on the assembly, usage (donning and doffing) and decontamination protocols. The benefit of the Pneumask as PPE is that it is reusable for longer periods than typical disposable N95 respirators, as the snorkel mask can withstand rigorous decontamination protocols (that are standard to regular elastomeric respirators). With the dire worldwide shortage of PPE for medical personnel, our conclusions on the performance and efficacy of Pneumask as an N95-alternative technology are cautiously optimistic.
View details for DOI 10.1371/journal.pone.0244422
View details for PubMedID 33439902
Applying heat and humidity using stove boiled water for decontamination of N95 respirators in low resource settings.
2021; 16 (9): e0255338
Global shortages of N95 respirators have led to an urgent need of N95 decontamination and reuse methods that are scientifically validated and available world-wide. Although several large scale decontamination methods have been proposed (hydrogen peroxide vapor, UV-C); many of them are not applicable in remote and low-resource settings. Heat with humidity has been demonstrated as a promising decontamination approach, but care must be taken when implementing this method at a grassroots level. Here we present a simple, scalable method to provide controlled humidity and temperature for individual N95 respirators which is easily applicable in low-resource settings. N95 respirators were subjected to moist heat (>50% relative humidity, 65-80°C temperature) for over 30 minutes by placing them in a sealed container immersed in water that had been brought to a rolling boil and removed from heat, and then allowing the containers to sit for over 45 minutes. Filtration efficiency of 0.3-4.99 μm incense particles remained above 97% after 5 treatment cycles across all particle size sub-ranges. This method was then repeated at a higher ambient temperature and humidity in Mumbai, using standard utensils commonly found in South Asia. Similar temperature and humidity profiles were achieved with no degradation in filtration efficiencies after 6 cycles. Higher temperatures (>70°C) and longer treatment times (>40 minutes) were obtained by insulating the outer vessel. We also showed that the same method can be applied for the decontamination of surgical masks. This simple yet reliable method can be performed even without electricity access using any heat source to boil water, from open-flame stoves to solar heating, and provides a low-cost route for N95 decontamination globally applicable in resource-constrained settings.
View details for DOI 10.1371/journal.pone.0255338
View details for PubMedID 34591858
Sensory Discrimination of Blood and Floral Nectar by Aedes aegypti Mosquitoes.
Blood-feeding mosquitoes survive by feeding on nectar for metabolic energy but require a blood meal to develop eggs. Aedes aegypti females must accurately discriminate blood and nectar because each meal promotes mutually exclusive feeding programs with distinct sensory appendages, meal sizes, digestive tract targets, and metabolic fates. We investigated the syringe-like blood-feeding appendage, the stylet, and discovered that sexually dimorphic stylet neurons taste blood. Using pan-neuronal calcium imaging, we found that blood is detected by four functionally distinct stylet neuron classes, each tuned to specific blood components associated with diverse taste qualities. Stylet neurons are insensitive to nectar-specific sugars and respond to glucose only in the presence of additional blood components. The distinction between blood and nectar is therefore encoded in specialized neurons at the very first level of sensory detection in mosquitoes. This innate ability to recognize blood is the basis of vector-borne disease transmission to millions of people worldwide.
View details for DOI 10.1016/j.neuron.2020.09.019
View details for PubMedID 33049200
BiteOscope, an open platform to study mosquito biting behavior.
Female mosquitoes need a blood meal to reproduce, and in obtaining this essential nutrient they transmit deadly pathogens. Although crucial for the spread of mosquito-borne diseases, blood feeding remains poorly understood due to technological limitations. Indeed, studies often expose human subjects to assess biting behavior. Here, we present the biteOscope, a device that attracts mosquitoes to a host mimic which they bite to obtain an artificial blood meal. The host mimic is transparent, allowing high-resolution imaging of the feeding mosquito. Using machine learning we extract detailed behavioral statistics describing the locomotion, pose, biting, and feeding dynamics of Aedes aegypti, Aedes albopictus, Anopheles stephensi, and Anopheles coluzzii. In addition to characterizing behavioral patterns, we discover that the common insect repellent DEET repels Anopheles coluzzii upon contact with their legs. The biteOscope provides a new perspective on mosquito blood feeding, enabling the high-throughput quantitative characterization of this lethal behavior.
View details for DOI 10.7554/eLife.56829
View details for PubMedID 32960173
Scale-free vertical tracking microscopy.
The behavior and microscale processes associated with freely suspended organisms, along with sinking particles underlie key ecological processes in the ocean. Mechanistically studying such multiscale processes in the laboratory presents a considerable challenge for microscopy: how to measure single cells at microscale resolution, while allowing them to freely move hundreds of meters in the vertical direction? Here we present a solution in the form of a scale-free, vertical tracking microscope, based on a 'hydrodynamic treadmill' with no bounds for motion along the axis of gravity. Using this method to bridge spatial scales, we assembled a multiscale behavioral dataset of nonadherent planktonic cells and organisms. Furthermore, we demonstrate a 'virtual-reality system for single cells', wherein cell behavior directly controls its ambient environmental parameters, enabling quantitative behavioral assays. Our method and results exemplify a new paradigm of multiscale measurement, wherein one can observe and probe macroscale and ecologically relevant phenomena at microscale resolution. Beyond the marine context, we foresee that our method will allow biological measurements of cells and organisms in a suspended state by freeing them from the confines of the coverslip.
View details for DOI 10.1038/s41592-020-0924-7
View details for PubMedID 32807956
- Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays NATURE PHYSICS 2020
The multiscale physics of cilia and flagella
Nature Physics Review
2020; 2: 74–88
View details for DOI 10.1038/s42254-019-0129-0
An investigation of Dirofilaria immitis infection and its effects on mosquito wingbeat frequencies.
2020; 283: 109112
Each mosquito species has a different wingbeat frequency by which they attract mates. With just a brief recording (<1/10th of a second) these acoustic signatures can be analyzed to quickly determine if mosquitoes belong to a species that is known to transmit different pathogens. A recent study has shown that mobile phones are capable of capturing acoustic data from mosquito wingbeats. We examined wingbeat signatures and flight duration patterns of D. immitis infected and non-infected Aedes aegypti to determine if mobile phone recordings of wingbeat frequencies can be used to distinguish infected mosquitoes from non-infected ones. Female mosquitoes were recorded prior to and at various time points after feeding on infected or non-infected dog blood by placing individual mosquitoes into a collection vial and recording for 60 s using the Voice Memo app for iPhone 7 plus and 8. To uniformly analyze audio data, recordings were processed using a previously described automated algorithm in Python 3.0 to determine wingbeat frequency. A total of 1669 recordings were gathered, and mosquitoes were dissected to confirm the presence and number of D. immitis larvae. Our findings indicate that there was a significant effect on wingbeat frequency with an increasing number of L3 larvae. Specifically, as the number of L3, infective stage larvae increases, a decrease in wingbeat frequency is seen. However, there was no significant effect of increasing number of L1 or L2 larvae causing increasing wingbeat frequencies. The detection of a significant difference in wingbeat frequencies between mosquitoes harboring infective stage D. immitis larvae is unique and suggests the possibility of using wingbeat recordings as a tool for vector species and pathogen surveillance and monitoring.
View details for DOI 10.1016/j.vetpar.2020.109112
View details for PubMedID 32512421
Coupled Active Systems Encode an Emergent Hunting Behavior in the Unicellular Predator Lacrymaria olor.
Current biology : CB
Many single-celled protists use rapid morphology changes to perform fast animal-like behaviors. To understand how such behaviors are encoded, we analyzed the hunting dynamics of the predatory ciliate Lacrymaria olor, which locates and captures prey using the tip of a slender "neck" that can rapidly extend more than seven times its body length (500mum from its body) and retract in seconds. By tracking single cells in real-time over hours and analyzing millions of sub-cellular postures, we find that these fast extension-contraction cycles underlie an emergent hunting behavior that comprehensively samples a broad area within the cell's reach. Although this behavior appears complex, we show that it arises naturally as alternating sub-cellular ciliary and contractile activities rearrange the cell's underlying helical cytoskeleton to extend or retract the neck. At short timescales, a retracting neck behaves like an elastic filament under load, such that compression activates a series of buckling modes that reorient the head and scramble its extensile trajectory. At longer timescales, the fundamental length of this filament can change, altering the location in space where these transitions occur. Coupling these fast and slow dynamics together, we present a simple model for how Lacrymaria samples the range of geometries and orientations needed to ensure dense stochastic sampling of the immediate environment when hunting to locate and strike at prey. More generally, coupling active mechanical and chemical signaling systems across different timescales may provide a general strategy by which mechanically encoded emergent cell behaviors can be understood or engineered.
View details for DOI 10.1016/j.cub.2019.09.034
View details for PubMedID 31679941
Collective intercellular communication through ultra-fast hydrodynamic trigger waves.
The biophysical relationships between sensors and actuators1-5 have been fundamental to the development of complex life forms. Swimming organisms generate abundant flows that persist in aquatic environments6-13, and responding promptly to external stimuli is key to survival14-19. Here we present the discovery of 'hydrodynamic trigger waves' in cellular communities of the protist Spirostomum ambiguum that propagate-in a manner similar to a chain reaction20-22-hundreds of times faster than their swimming speed. By coiling its cytoskeleton, Spirostomum can contract its long body by 60% within milliseconds23, experiencing accelerations that can reach forces of 14g. We show that a single cellular contraction (the transmitter) generates long-ranged vortex flows at intermediate Reynolds numbers that can, in turn, trigger neighbouring cells (the receivers). To measure the sensitivity to hydrodynamic signals in these receiver cells, we present a high-throughput suction-flow device for probing mechanosensitive ion channels24 by back-calculating the microscopic forces on the cell membrane. We analyse and quantitatively model the ultra-fast hydrodynamic trigger waves in a universal framework of antenna and percolation theory25,26, and reveal a phase transition that requires a critical colony density to sustain collective communication. Our results suggest that this signalling could help to organize cohabiting communities over large distances and influence long-term behaviour through gene expression (comparable to quorum sensing16). In more immediate terms, because contractions release toxins27, synchronized discharges could facilitate the repulsion of large predators or immobilize large prey. We postulate that numerous aquatic organisms other than protists could coordinate their behaviour using variations of hydrodynamic trigger waves.
View details for DOI 10.1038/s41586-019-1387-9
View details for PubMedID 31292551
BITES, BLOOD AND BEHAVIOR: BIOPHYSICAL APPROACHES TO UNDERSTANDING MOSQUITO BLOOD-FEEDING BEHAVIOR
AMER SOC TROP MED & HYGIENE. 2019: 444
View details for Web of Science ID 000507364504156
Frugal Science in the Age of Curiosity Manu Prakash, Jim Cybulski, Rebecca Konte, Team Foldscope and the global Foldscope community
MIT PRESS. 2019: 26–29
View details for Web of Science ID 000546472600005
VECTOR CHIP: A MINIATURIZED PLATFORM FOR HIGH-THROUGHPUT INTERROGATION OF MOSQUITO-PATHOGEN DYNAMICS
AMER SOC TROP MED & HYGIENE. 2019: 421–22
View details for Web of Science ID 000507364504082
OPENMM - A LOW-COST, MODULAR, AND AUTONOMOUS MICROSCOPE FOR MALARIA DIAGNOSIS AND BEYOND
AMER SOC TROP MED & HYGIENE. 2019: 484
View details for Web of Science ID 000507364504290
ABUZZ : A MOBILE PHONE BASED CITIZEN SCIENCE PLATFORM FOR CROWDSOURCING ECOLOGICAL DATA FOR MOSQUITO SURVEILLANCE
AMER SOC TROP MED & HYGIENE. 2019: 448
View details for Web of Science ID 000507364504170
Ultrafast epithelial contractions provide insights into contraction speed limits and tissue integrity.
Proceedings of the National Academy of Sciences of the United States of America
By definition of multicellularity, all animals need to keep their cells attached and intact, despite internal and external forces. Cohesion between epithelial cells provides this key feature. To better understand fundamental limits of this cohesion, we study the epithelium mechanics of an ultrathin (25 mum) primitive marine animal Trichoplax adhaerens, composed essentially of two flat epithelial layers. With no known extracellular matrix and no nerves or muscles, T. adhaerens has been claimed to be the "simplest known living animal," yet is still capable of coordinated locomotion and behavior. Here we report the discovery of the fastest epithelial cellular contractions known in any metazoan, to be found in T. adhaerens dorsal epithelium (50% shrinkage of apical cell area within one second, at least an order of magnitude faster than other known examples). Live imaging reveals emergent contractile patterns that are mostly sporadic single-cell events, but also include propagating contraction waves across the tissue. We show that cell contraction speed can be explained by current models of nonmuscle actin-myosin bundles without load, while the tissue architecture and unique mechanical properties are softening the tissue, minimizing the load on a contracting cell. We propose a hypothesis, in which the physiological role of the contraction dynamics is to resist external stresses while avoiding tissue rupture ("active cohesion"), a concept that can be further applied to engineering of active materials.
View details for PubMedID 30309963
- Two-component marangoni-contracted droplets: friction and shape SOFT MATTER 2018; 14 (37): 7724–30
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 apex 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 angles are a function of their concentration and the external humidity. Here we study the motion of such droplets sliding down slopes 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 (Ca) is directly proportional to the Bond number (Bo): Ca = Bosinalpha with alpha the angle of the slope. Lastly we study the successive shapes the droplets take when sliding at larger and larger velocities.
View details for PubMedID 30191241
The principles of cascading power limits in small, fast biological and engineered systems
2018; 360 (6387): 397-+
Mechanical power limitations emerge from the physical trade-off between force and velocity. Many biological systems incorporate power-enhancing mechanisms enabling extraordinary accelerations at small sizes. We establish how power enhancement emerges through the dynamic coupling of motors, springs, and latches and reveal how each displays its own force-velocity behavior. We mathematically demonstrate a tunable performance space for spring-actuated movement that is applicable to biological and synthetic systems. Incorporating nonideal spring behavior and parameterizing latch dynamics allows the identification of critical transitions in mass and trade-offs in spring scaling, both of which offer explanations for long-observed scaling patterns in biological systems. This analysis defines the cascading challenges of power enhancement, explores their emergent effects in biological and engineered systems, and charts a pathway for higher-level analysis and synthesis of power-amplified systems.
View details for PubMedID 29700237
Synchronous magnetic control of water droplets in bulk ferrofluid
2018; 14 (5): 681–92
We present a microfluidic platform for magnetic 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 fluids are dispensed in a sub-millimeter Hele-Shaw chamber that includes permalloy tracks on its substrate. An in-plane rotating magnetic field magnetizes the permalloy tracks, producing local magnetic gradients, while an orthogonal magnetic field magnetizes the bulk ferrofluid. To minimize the magnetostatic energy of the system, the water droplets are attracted towards the locations on the tracks where the bulk ferrofluid is repelled. Using this technique, we demonstrate synchronous generation and propagation of water droplets, study the kinematics of propagation, and analyze the flow of the bulk ferrofluid. 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.
View details for PubMedID 29205244
Ultra Fast Contractions and Emergent Dynamics in a Living Active Solid - The Epithelium of the Primitive Animal Trichoplax adhaerens
CELL PRESS. 2018: 649A
View details for Web of Science ID 000430563300236
Local Epithelial Fracture and Healing Mechanics Dictate Morphogenesis and Asexual Reproduction in Trichoplax adhaerens
CELL PRESS. 2018: 651A–652A
View details for Web of Science ID 000430563300252
Using mobile phones as acoustic sensors for high-throughput mosquito surveillance
The direct monitoring of mosquito populations in field settings is a crucial input for shaping appropriate and timely control measures for mosquito-borne diseases. Here, we demonstrate that commercially available mobile phones are a powerful tool for acoustically mapping mosquito species distributions worldwide. We show that even low-cost mobile phones with very basic functionality are capable of sensitively acquiring acoustic data on species-specific mosquito wingbeat sounds, while simultaneously recording the time and location of the human-mosquito encounter. We survey a wide range of medically important mosquito species, to quantitatively demonstrate how acoustic recordings supported by spatio-temporal metadata enable rapid, non-invasive species identification. As proof-of-concept, we carry out field demonstrations where minimally-trained users map local mosquitoes using their personal phones. Thus, we establish a new paradigm for mosquito surveillance that takes advantage of the existing global mobile network infrastructure, to enable continuous and large-scale data acquisition in resource-constrained areas.
View details for PubMedID 29087296
Flowtrace: simple visualization of coherent structures in biological fluid flows
JOURNAL OF EXPERIMENTAL BIOLOGY
2017; 220 (19): 3411–18
We present a simple, intuitive algorithm for visualizing time-varying flow fields that can reveal complex flow structures with minimal user intervention. We apply this technique to a variety of biological systems, including the swimming currents of invertebrates and the collective motion of swarms of insects. We compare our results with more experimentally difficult and mathematically sophisticated techniques for identifying patterns in fluid flows, and suggest that our tool represents an essential 'middle ground' allowing experimentalists to easily determine whether a system exhibits interesting flow patterns and coherent structures without resorting to more intensive techniques. In addition to being informative, the visualizations generated by our tool are often striking and elegant, illustrating coherent structures directly from videos without the need for computational overlays. Our tool is available as fully documented open-source code for MATLAB, Python or ImageJ at www.flowtrace.org.
View details for PubMedID 28729343
Generation of droplet arrays with rational number spacing patterns driven by a periodic energy landscape
PHYSICAL REVIEW E
2017; 96 (3): 033108
The generation of droplets at low Reynolds numbers is driven by nonlinear dynamics that give rise to complex patterns concerning both the droplet-to-droplet spacing and the individual droplet sizes. Here we demonstrate an experimental system in which a time-varying energy landscape provides a periodic magnetic force that generates an array of droplets from an immiscible mixture of ferrofluid and silicone oil. The resulting droplet patterns are periodic, owing to the nature of the magnetic force, yet the droplet spacing and size can vary greatly by tuning a single bias pressure applied on the ferrofluid phase; for a given cycle period of the magnetic force, droplets can be generated either at integer multiples (1, 2, ...), or at rational fractions (3/2, 5/3, 5/2, ...) of this period with mono- or multidisperse droplet sizes. We develop a discrete-time dynamical systems model not only to reproduce the phenotypes of the observed patterns but also to provide a framework for understanding systems driven by such periodic energy landscapes.
View details for PubMedID 29346989
- Vortex arrays and ciliary tangles underlie the feeding-swimming trade-off in starfish larvae NATURE PHYSICS 2017; 13 (4): 380-386
- Schistosoma mansoni cercariae swim effciently by exploiting an elastohydrodynamic coupling NATURE PHYSICS 2017; 13 (3): 266-271
- Hand-powered ultralow-cost paper centrifuge NATURE BIOMEDICAL ENGINEERING 2017; 1 (1)
Mapping Load-Bearing in the Mammalian Spindle Reveals Local Kinetochore Fiber Anchorage that Provides Mechanical Isolation and Redundancy.
Current biology : CB
2017; 27 (14): 2112–22.e5
Active forces generated at kinetochores move chromosomes, and the dynamic spindle must robustly anchor kinetochore fibers (k-fibers) to bear this load. The mammalian spindle bears the load of chromosome movement far from poles, but we do not know where and how-physically and molecularly-this load distributes across the spindle. In part, this is because probing spindle mechanics in live cells is difficult. Yet answering this question is key to understanding how the spindle generates and responds to force and performs its diverse mechanical functions. Here, we map load-bearing across the mammalian spindle in space-time and dissect local anchorage mechanics and mechanism. To do so, we laser-ablate single k-fibers at different spindle locations and in different molecular backgrounds and quantify the immediate relaxation of chromosomes, k-fibers, and microtubule speckles. We find that load redistribution is locally confined in all directions: along the first 3-4 μm from kinetochores, scaling with k-fiber length, and laterally within ∼2 μm of k-fiber sides, without detectable load sharing between neighboring k-fibers. A phenomenological model suggests that dense, transient crosslinks to the spindle along k-fibers bear the load of chromosome movement but that these connections do not limit the timescale of spindle reorganization. The microtubule crosslinker NuMA is needed for the local load-bearing observed, whereas Eg5 and PRC1 are not detectably required, suggesting specialization in mechanical function. Together, the data and model suggest that NuMA-mediated crosslinks locally bear load, providing mechanical isolation and redundancy while allowing spindle fluidity. These features are well suited to support robust chromosome segregation.
View details for PubMedID 28690110
USING MOBILE PHONES AS ACOUSTIC SENSORS FOR HIGH-THROUGHPUT SURVEILLANCE OF MOSQUITO ECOLOGY
AMER SOC TROP MED & HYGIENE. 2017: 21
View details for Web of Science ID 000423215202065
- Wetting: Bumps lead the way. Nature materials 2016; 15 (4): 378-379
Surface tension dominates insect flight on fluid interfaces.
journal of experimental biology
2016; 219: 752-766
Flight on the 2D air-water interface, with body weight supported by surface tension, is a unique locomotion strategy well adapted for the environmental niche on the surface of water. Although previously described in aquatic insects like stoneflies, the biomechanics of interfacial flight has never been analysed. Here, we report interfacial flight as an adapted behaviour in waterlily beetles (Galerucella nymphaeae) which are also dexterous airborne fliers. We present the first quantitative biomechanical model of interfacial flight in insects, uncovering an intricate interplay of capillary, aerodynamic and neuromuscular forces. We show that waterlily beetles use their tarsal claws to attach themselves to the interface, via a fluid contact line pinned at the claw. We investigate the kinematics of interfacial flight trajectories using high-speed imaging and construct a mathematical model describing the flight dynamics. Our results show that non-linear surface tension forces make interfacial flight energetically expensive compared with airborne flight at the relatively high speeds characteristic of waterlily beetles, and cause chaotic dynamics to arise naturally in these regimes. We identify the crucial roles of capillary-gravity wave drag and oscillatory surface tension forces which dominate interfacial flight, showing that the air-water interface presents a radically modified force landscape for flapping wing flight compared with air.
View details for DOI 10.1242/jeb.127829
View details for PubMedID 26936640
View details for PubMedCentralID PMC4811005
- Synchronous universal droplet logic and control NATURE PHYSICS 2015; 11 (7): 588-596
Diagnosis of Schistosoma haematobium Infection with a Mobile Phone-Mounted Foldscope and a Reversed-Lens CellScope in Ghana
AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE
2015; 92 (6): 1253-1256
We evaluated two novel, portable microscopes and locally acquired, single-ply, paper towels as filter paper for the diagnosis of Schistosoma haematobium infection. The mobile phone-mounted Foldscope and reversed-lens CellScope had sensitivities of 55.9% and 67.6%, and specificities of 93.3% and 100.0%, respectively, compared with conventional light microscopy for diagnosing S. haematobium infection. With conventional light microscopy, urine filtration using single-ply paper towels as filter paper showed a sensitivity of 67.6% and specificity of 80.0% compared with centrifugation for the diagnosis of S. haematobium infection. With future improvements to diagnostic sensitivity, newer generation handheld and mobile phone microscopes may be valuable tools for global health applications.
View details for DOI 10.4269/ajtmh.14-0741
View details for Web of Science ID 000355785400028
View details for PubMedID 25918211
Vapour-mediated sensing and motility in two-component droplets.
2015; 519 (7544): 446-450
Controlling the wetting behaviour of liquids on surfaces is important for a variety of industrial applications such as water-repellent coatings and lubrication. Liquid behaviour on a surface can range from complete spreading, as in the 'tears of wine' effect, to minimal wetting as observed on a superhydrophobic lotus leaf. Controlling droplet movement is important in microfluidic liquid handling, on self-cleaning surfaces and in heat transfer. Droplet motion can be achieved by gradients of surface energy. However, existing techniques require either a large gradient or a carefully prepared surface to overcome the effects of contact line pinning, which usually limit droplet motion. Here we show that two-component droplets of well-chosen miscible liquids such as propylene glycol and water deposited on clean glass are not subject to pinning and cause the motion of neighbouring droplets over a distance. Unlike the canonical predictions for these liquids on a high-energy surface, these droplets do not spread completely but exhibit an apparent contact angle. We demonstrate experimentally and analytically that these droplets are stabilized by evaporation-induced surface tension gradients and that they move in response to the vapour emitted by neighbouring droplets. Our fundamental understanding of this robust system enabled us to construct a wide variety of autonomous fluidic machines out of everyday materials.
View details for DOI 10.1038/nature14272
View details for PubMedID 25762146
- Vapour-mediated sensing and motility in two-component droplets NATURE 2015; 519 (7544): 446-?
Punch card programmable microfluidics.
2015; 10 (3)
Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series of holes in punched paper tapes, we demonstrate independent control of 15 on-chip pumps with enhanced mixing, normally-closed valves and a novel on-demand impact-based droplet generator. We demonstrate robustness of operation by encoding a string of characters representing the word "PUNCHCARD MICROFLUIDICS" using the droplet generator. Multiplexing is demonstrated by implementing an example colorimetric water quality assays for pH, ammonia, nitrite and nitrate content in different water samples. With its portable and robust design, low cost and ease-of-use, we envision punch card programmable microfluidics will bring complex control of microfluidic chips into field-based applications in low-resource settings and in the hands of children around the world.
View details for DOI 10.1371/journal.pone.0115993
View details for PubMedID 25738834
View details for PubMedCentralID PMC4349784
- Punch card programmable microfluidics. PloS one 2015; 10 (3)
- Emergent mechanics of biological structures MOLECULAR BIOLOGY OF THE CELL 2014; 25 (22): 3461-3465
Emergent mechanics of biological structures.
Molecular biology of the cell
2014; 25 (22): 3461-3465
Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework "emergent mechanics." Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead.
View details for DOI 10.1091/mbc.E14-03-0784
View details for PubMedID 25368421
View details for PubMedCentralID PMC4230603
- Foldscope: Origami-Based Paper Microscope PLOS ONE 2014; 9 (6)
Probing the Mechanical Coupling of the Cell Membrane to the Nucleus with Vertical Nanopillar Arrays
57th Annual Meeting of the Biophysical-Society
CELL PRESS. 2013: 546A–546A
View details for Web of Science ID 000316074305286
Hydraulic stress induced bubble nucleation and growth during pupal metamorphosis
Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB)/Symposium on New Frontiers from Marine Snakes to Marine Ecosystems
OXFORD UNIV PRESS INC. 2012: E140–E140
View details for Web of Science ID 000303165001028
Flying in two dimensions
Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB)/Symposium on New Frontiers from Marine Snakes to Marine Ecosystems
OXFORD UNIV PRESS INC. 2012: E141–E141
View details for Web of Science ID 000303165001029
- The hungry fly: Hydrodynamics of feeding in the common house fly PHYSICS OF FLUIDS 2011; 23 (9)
Face-selective electrostatic control of hydrothermal zinc oxide nanowire synthesis
2011; 10 (8): 596-601
Rational control over the morphology and the functional properties of inorganic nanostructures has been a long-standing goal in the development of bottom-up device fabrication processes. We report that the geometry of hydrothermally grown zinc oxide nanowires can be tuned from platelets to needles, covering more than three orders of magnitude in aspect ratio (~0.1-100). We introduce a classical thermodynamics-based model to explain the underlying growth inhibition mechanism by means of the competitive and face-selective electrostatic adsorption of non-zinc complex ions at alkaline conditions. The performance of these nanowires rivals that of vapour-phase-grown nanostructures, and their low-temperature synthesis (<60 °C) is favourable to the integration and in situ fabrication of complex and polymer-supported devices. We illustrate this capability by fabricating an all-inorganic light-emitting diode in a polymeric microfluidic manifold. Our findings indicate that electrostatic interactions in aqueous crystal growth may be systematically manipulated to synthesize nanostructures and devices with enhanced structural control.
View details for DOI 10.1038/NMAT3069
View details for Web of Science ID 000293000000019
View details for PubMedID 21743451
Hydraulic stress induced bubble nucleation and growth during pupal metamorphosis
Annual Meeting of the American-Society-for-Cell-Biology (ASCB)
AMER SOC CELL BIOLOGY. 2011
View details for Web of Science ID 000305505501236
- Face-selective electrostatic control of nanowire synthesis Nature Materials 2011; 10: 596-601
- Interfacial Propulsion by Directional Adhesion International Journal of Non-Linear Mechanics 2011; 46 (4): 607-615
- On a tweezer for droplets Advances in Colloid and Interface Science 2010; 161: 10-14
- Drop propulsion in tapered tubes Euro Physics Letters, 2009; 86: 1-5
Surface tension transport of prey by feeding shorebirds: The capillary ratchet
2008; 320 (5878): 931-934
The variability of bird beak morphology reflects diverse foraging strategies. One such feeding mechanism in shorebirds involves surface tension-induced transport of prey in millimetric droplets: By repeatedly opening and closing its beak in a tweezering motion, the bird moves the drop from the tip of its beak to its mouth in a stepwise ratcheting fashion. We have analyzed the subtle physical mechanism responsible for drop transport and demonstrated experimentally that the beak geometry and the dynamics of tweezering may be tuned to optimize transport efficiency. We also highlight the critical dependence of the capillary ratchet on the beak's wetting properties, thus making clear the vulnerability of capillary feeders to surface pollutants.
View details for DOI 10.1126/science.1156023
View details for Web of Science ID 000255868300042
View details for PubMedID 18487193
Microfluidic bubble logic
2007; 315 (5813): 832-835
We demonstrate universal computation in an all-fluidic two-phase microfluidic system. Nonlinearity is introduced into an otherwise linear, reversible, low-Reynolds number flow via bubble-to-bubble hydrodynamic interactions. A bubble traveling in a channel represents a bit, providing us with the capability to simultaneously transport materials and perform logical control operations. We demonstrate bubble logic AND/OR/NOT gates, a toggle flip-flop, a ripple counter, timing restoration, a ring oscillator, and an electro-bubble modulator. These show the nonlinearity, gain, bistability, synchronization, cascadability, feedback, and programmability required for scalable universal computation. With increasing complexity in large-scale microfluidic processors, bubble logic provides an on-chip process control mechanism integrating chemistry and computation.
View details for DOI 10.1126/science.1136907
View details for Web of Science ID 000244069000065
View details for PubMedID 17289994
- The Integument of Water-walking Arthropods: Form and Function Advances in Insect Physiology 2007; 34: 117-192
- Water walking devices Experiments in Fluids 2007; 43: 769-778
- Microfludic Bubble Logic Science 2007; 315: 832-835
- Personal fabrication Telektronikk 2004; 3: 22-26