Biology subjects

Bhamla, M. S.

Publications and source records attributed to Bhamla, M. S..

At least 19 recordsLinked to original sources

bioRxiv2024

Ultrafast elastocapillary fans control agile maneuvering in ripple bugs and robots

Millimeter-sized ripple bugs in the genus Rhagovelia exhibit exceptional agility and rapid maneuvers in fast, unsteady streams, comparable to animal fliers. Their remarkable interfacial transit and turning skills stem from a specialized fan structure on their middle legs. While researchers have suggested active fan actuation, the role of capillary forces and unique microstructure in self-spreading remains unclear. We reveal that Rhagovelias fans possess a flat-ribbon architecture with directional stiffness, enabling ultrafast elastocapillary morphing for passive actuation in under 10 ms, independent of muscle control, while producing high-thrust momentum through unsteady vortical wakes. These self-morphing fans allow Rhagovelia to execute [~]90 {degrees} turns at a rate of [~]4200 {degrees}/s, in [~]50 ms, with speeds reaching [~]120 BL/s - on par with the fastest recorded turns in animal fliers like fruit flies. Inspired by these, we develop an ultralight, ultrafast elastocapillary robotic fan ([~]1 mg, [~]100 ms opening/closing time) and integrate it into an insect-scaled robot (Rhagobot, [~]0.2 g). The engineered fans passively balance surface tension and water drag through stiffness anisotropy, enabling the robot to achieve high agility with speeds up to [~]2 BL/s and turning rates of 206 {degrees}/sec. Experiments with both insects and robots, with and without fans, show that a self-spreading passive fan significantly improves thrust, braking, and turning - key factors for controlled, high-speed maneuvers. This elastocapillary innovation enables ripple bugs to survive and thrive in turbulent streams and offers new insights for agile aquatic robotics.

biophysics↗

bioRxiv2024

Epineuston vortex recapture enhances thrust in tiny water skaters

Vortex recapture underpins the exceptional mobility of natures finest fliers and swimmers. Utilized by agile fruit flies and efficient jellyfish, this phenomenon is well-documented in bulk fluids. Despite extensive studies on organismal locomotion at the waters surface, a vital fluidic interface where diverse life forms interact, hydrodynamics of interfacial vortex recapture remains unexplored. We investigate interfacial (on water) vortical hydrodynamics in Microvelia americana, one of the smallest and fastest water striders, skating at 50 body lengths per second (BL/s) or 15 cm/s. Their middle legs shed counter-rotating vortices, re-energized by their hind legs, demonstrating interfacial vortex recapture. High-speed imaging, particle imaging velocimetry, physical models, and CFD simulations show re-energization increases thrust by creating positive pressure at the hind tarsi, acting as a virtual wall. This vortex capture is facilitated by the tripod gait, leg morphology, and precise spatio-temporal placement of the hind tarsi during the power stroke. Our study extends vortex recapture principles from bulk fluids to the interface, offering insights into efficient interfacial locomotion, where surface tension and capillary waves challenge movement. Understanding interfacial vortex hydrodynamics can guide the development of energy-efficient microrobots to explore the planets water surface niches, critical frontlines of climate change and pollution. Significance StatementInterfacial Vortex Recapture in Microvelia americana extends the vortex recapture principles to the air-water interface, revealing an efficient locomotory mode in a challenging ecological niche. By demonstrating thrust enhancement through precise vortex interactions, our study bridges biology and fluid dynamics. This discovery informs the design of energy-efficient amphibious microrobots, capable of navigating the water interface with a new tripod gait paradigm, diverging from the conventional drag-based rowing designs. These findings are foundational for exploring and monitoring the water surface, an ecological interface vital for addressing climate change and pollution impacts.

biophysics↗

bioRxiv2024

Reversible kink instability drives ultrafast jumping in nematodes and soft robots

Entomopathogenic nematodes (EPNs) exhibit a bending-elastic instability, or kink, before becoming airborne, a feature hypothesized but not proven to enhance jumping performance. Here, we provide the evidence that this kink is crucial for improving launch performance. We demonstrate that EPNs actively modulate their aspect ratio, forming a liquid-latched closed loop over a slow timescale O(1 s), then rapidly open it O (10 {micro}s), achieving heights of 20 body lengths (BL) and generating [~] 104 W/Kg of power. Using jumping nematodes, a bio-inspired Soft Jumping Model (SoftJM), and computational simulations, we explore the mechanisms and implications of this kink. EPNs control their takeoff direction by adjusting their head position and center of mass, a mechanism verified through phase maps of jump directions in simulations and SoftJM experiments. Our findings reveal that the reversible kink instability at the point of highest curvature on the ventral side enhances energy storage using the nematodes limited muscular force. We investigated the impact of aspect ratio on kink instability and jumping performance using SoftJM, and quantified EPN cuticle stiffness with AFM, comparing it with C. elegans. This led to a stiffness-modified SoftJM design with a carbon fiber backbone, achieving jumps of [~]25 BL. Our study reveals how harnessing kink instabilities, a typical failure mode, enables bidirectional jumps in soft robots on complex substrates like sand, offering a novel approach for designing limbless robots for controlled jumping, locomotion, and even planetary exploration.

biophysics↗

bioRxiv2024

Leeches Predate on Fast-Escaping and Entangling Blackworms by Spiral Entombment

We investigate how the Helobdella spp. freshwater leeches capture and consume Lumbriculus variegatus blackworms despite the blackworms ultrafast helical swimming escape reflex and ability to form large tangled blobs. We describe our discovery of a unique spiral entombment strategy used by these leeches to overcome the blackworms active and collective defenses. Unlike their approach to less reactive and solitary prey like mollusks, where leeches simply attach and suck, Helobdella leeches employ this spiral entombment strategy specifically adapted for blackworms. Our findings highlight the complex interactions between predator and prey in freshwater ecosystems, providing insights into ecological adaptability and predator-prey dynamics.

animal behavior and cognition↗

bioRxiv2024

Wax "tails" enable planthopper nymphs to self-right midair and land on their feet

The striking appearance of wax tails -- posterior wax projections on planthopper nymphs -- has captivated entomologists and naturalists alike. Despite their intriguing presence, the functional roles of these structures remain largely unexplored. This study leverages high-speed imaging to uncover the biomechanical implications of these wax formations in the aerial dynamics of planthopper nymphs (Ricania sp.). We quantitatively demonstrate that removing wax tails significantly increases body rotations during jumps. Specifically, nymphs without wax projections undergo continuous rotations, averaging 4.3 {+/-} 1.9 per jump, in contrast to wax-intact nymphs, who narrowly complete a full rotation, averaging only 0.7 {+/-} 0.2 per jump. This suggests that wax structures effectively counteract rotation through aerodynamic drag forces. These stark differences in body rotation correlate with landing success: nymphs with wax intact achieve a near perfect landing rate of 98.5%, while those without wax manage only a 35.5% success rate. Jump trajectory analysis reveals transitions from parabolic to Tartaglia shapes at higher take-off velocities for wax-intact nymphs, illustrating how wax structures assist nymphs in achieving stable, controlled descents. Our findings confirm the aerodynamic self-righting functionality of wax tails in stabilizing planthopper landings, advancing our understanding of the complex interplay between wax morphology and aerial maneuverability, with broader implications for the evolution of flight in wingless insects and bioinspired robotics.

bioengineering↗

bioRxiv2024

Tiny amphibious insects use tripod gait for seamless transition across land, water, and duckweed

Insects exhibit remarkable adaptability in their locomotive strategies across diverse environments, a crucial trait for foraging, survival, and predator avoidance. Microvelia, tiny 2-3 mm insects that adeptly walk on water surfaces, exemplify this adaptability by using the alternating tripod gait in both aquatic and terrestrial terrains. These insects commonly inhabit low-flow ponds and streams cluttered with natural debris like leaves, twigs, and duckweed. Using high-speed imaging and pose-estimation software, we analyze Microvelia spp.s movement across water, sandpaper (simulating land), and varying duckweed densities (10%, 25%, and 50% coverage). Our results reveal Microvelia maintain consistent joint angles and strides of their upper and hind legs across all duckweed coverages, mirroring those seen on sandpaper. Microvelia adjust the stride length of their middle legs based on the amount of duckweed present, decreasing with increased duckweed coverage and at 50% duckweed coverage, their middle legs strides closely mimic their strides on sandpaper. Notably, Microvelia achieve speeds up to 56 body lengths per second on water, nearly double those observed on sandpaper and duckweed (both rough, frictional surfaces), highlighting their higher speeds on low friction surfaces such as the waters surface. This study highlights Microvelias ecological adaptability, setting the stage for advancements in amphibious robotics that emulate their unique tripod gait for navigating complex terrains.

animal behavior and cognition↗

bioRxiv2024

Limb loss and specialized leg dynamics in tiny water-walking insects

The air-water of the planets water bodies, such as ponds, lakes and streams, presents an uncertain ecological niche with predatory threats from above and below. As Microvelia move across the water surface in small ponds, they face potential injury from attacks by birds, fish, and underwater invertebrates. Thus, our study investigates the effects of losing individual or pairs of tarsi on the Microvelias ability to walk on water. Removal of both hind tarsi causes Microvelia spp. to rock their bodies (yaw) while running across the water surface at {+/-}19{degrees}, compared to {+/-}7{degrees} in non-ablated specimens. This increase in yaw, resulting from the removal of hind tarsi, indicates that Microvelia use their hind legs as rudders to regulate yaw, originating from the contralateral middle legs strokes on the waters surface through an alternating tripod gait. Ablation of the ipsilateral middle and hind tarsi disrupts directionality, making Microvelia turn in the direction of their intact limbs. This loss of directionality does not occur with the removal of contralateral middle and hind tarsi. However, Microvelia lose their ability to use the alternating tripod gait to walk for water walking on the day of contralateral ablation. Remarkably, by the next day Microvelia adapt and regain the ability to walk on water using the alternating tripod gait. Our findings elucidate the specialized leg dynamics within the alternating tripod gait of Microvelia spp., and their adaptability to tarsal loss. This research could guide the development and design strategies of small, adaptive, and resilient micro-robots that can adapt to controller malfunction or actuator damage for walking on water and terrestrial surfaces.

animal behavior and cognition↗

bioRxiv2024

Trackoscope: A Low-Cost, Open, Autonomous Tracking Microscope for Long-Term Observations of Microscale Organisms

Cells and microorganisms are motile, yet the stationary nature of conventional microscopes impedes comprehensive, long-term behavioral and biomechanical analysis. The limitations are twofold: a narrow focus permits high-resolution imaging but sacrifices the broader context of organism behavior, while a wider focus compromises microscopic detail. This trade-off is especially problematic when investigating rapidly motile ciliates, which often have to be confined to small volumes between coverslips affecting their natural behavior. To address this challenge, we introduce Trackoscope, a 2-axis autonomous tracking microscope designed to follow swimming organisms ranging from 10{micro}m to 2mm across a 325cm2 area (equivalent to an A5 sheet) for extended durations--ranging from hours to days--at high resolution. Utilizing Trackoscope, we captured a diverse array of behaviors, from the air-water swimming locomotion of Amoeba to bacterial hunting dynamics in Actinosphaerium, walking gait in Tardigrada, and binary fission in motile Blepharisma. Trackoscope is a cost-effective solution well-suited for diverse settings, from high school labs to resource-constrained research environments. Its capability to capture diverse behaviors in larger, more realistic ecosystems extends our understanding of the physics of living systems. The low-cost, open architecture democratizes scientific discovery, offering a dynamic window into the lives of previously inaccessible small aquatic organisms.

microbiology↗

bioRxiv2023

OpenCell: A Low-cost, Open-Source, 3-in-1 device for DNA Extraction

High-cost DNA extraction procedures pose significant challenges for budget-constrained laboratories. To address this, we introduce OpenCell, an economical, open-source, 3-in-1 laboratory device that combines the functionalities of a bead homogenizer, a microcentrifuge, and a vortex mixer. OpenCell utilizes modular attachments that magnetically connect to a central rotating brushless motor. This motor couples to an epicyclic gearing mechanism, enabling efficient bead homogenization, vortex mixing, and centrifugation within one compact unit. OpenCells design incorporates multiple redundant safety features, ensuring both the devices and operators safety. Additional features such as RPM measurement, programmable timers, battery operation, and optional speed control make OpenCell a reliable and reproducible laboratory instrument. In our study, OpenCell successfully isolated DNA from Spinacia oleracea (spinach), with an average yield of 2.3 {micro}g and an A260/A280 ratio of 1.77, demonstrating its effectiveness for downstream applications such as Polymerase Chain Reaction (PCR) amplification. With its compact size (20 cm x 28 cm x 6.7 cm) and lightweight design (0.8 kg), comparable to the size and weight of a laptop, OpenCell is portable, making it an attractive component of a lab-in-a-backpack for resource-constrained environments in low-and-middle-income countries and synthetic biology in remote field stations. Leveraging the accessibility of 3D printing and off-the-shelf components, OpenCell can be manufactured and assembled at a low unit cost of less than $50, providing an affordable alternative to expensive laboratory equipment costing over $4000. OpenCell aims to overcome the barriers to entry in synthetic biology research and contribute to the growing collection of frugal and open hardware.

bioengineering↗

bioRxiv2023

Collecting-Gathering Biophysics of the Blackworm L. variegatus

Many organisms exhibit collecting and gathering behaviors as a foraging and survival method. Certain benthic macroinvertebrates are classified as collector-gatherers due to their collection of particulate matter as a food source, such as the aquatic oligochaete Lumbriculus variegatus (California blackworms). Blackworms demonstrate the ability to ingest organic and inorganic materials, including microplastics, but previous work has only qualitatively described their possible collecting behaviors for such materials. The mechanism through which blackworms consolidate discrete particles into a larger clumps remains unexplored quantitatively. By analyzing a group of blackworms in a large arena with an aqueous algae solution, we discover that their relative collecting efficiency is proportional to population size. Examining individual blackworms under a microscope reveals that both algae and microplastics physically adhere to the worms body due to external mucus secretions, which cause the materials to clump around the worm. We observe that this clumping reduces the worms exploration of its environment, potentially due to thigmotaxis. To validate the observed biophysical mechanisms, we create an active polymer model of a worm moving in a field of particulate debris with a short-range attractive force on its body to simulate its adhesive nature. We find that the attractive force increases gathering efficiency. This study offers insights into the mechanisms of collecting-gathering behavior, informing the design of robotic systems, as well as advancing our understanding the ecological impacts of microplastics on benthic invertebrates.

ecology↗

bioRxiv2022

A unified model for the dynamics of ATP-independent ultrafast contraction

In nature, several ciliated protists possess the remarkable ability to execute ultrafast motions using protein assemblies called myonemes, which contract in response to Ca2+ ions. Existing theories, such as actomyosin contractility and macroscopic biomechanical latches, do not adequately describe these systems, necessitating new models to understand their mechanisms. In this study, we image and quantitatively analyze the contractile kinematics observed in two ciliated protists (Vorticella sp and Spirostomum sp), and, based on the mechanochemistry of these organisms, we propose a minimal mathematical model that reproduces our observations as well as those published previously. Analyzing the model reveals three distinct dynamic regimes, differentiated by the rate of chemical driving and the importance of inertia. We characterize their unique scaling behaviors and kinematic signatures. Besides providing insights into Ca2+-powered myoneme contraction in protists, our work may also inform the rational design of ultrafast bioengineered systems such as active synthetic cells.

biophysics↗

bioRxiv2022

Plate-Q: A Frugal Microplate-Reader for Bacterial Signal Quantification

Microplate readers are laboratory instruments used to measure biological properties and reactions within a microplate. A microplate consists of small wells in which separated reactions take place. These reactions convert the progression of biochemical processes into optical signals. A microplate reader detects these signals and quantifies a parameter of interest. Most lab-grade microplate readers can cost up to $20,000, making them unaffordable for underfunded labs and developing countries. In light of this, we developed Plate-Q, a $150 frugal microplate reader capable of quantifying green fluorescence protein and optical density of bacterial samples from 96-hole microplates. Rather than using optical sensors found in laboratory microplate readers, Plate-Q takes advantage of a Raspberry-Pi camera to capture images of a microplate and manually extract brightness values using computer vision algorithms. Plate-Q utilizes 440nm excitation lights with a 510nm emission filter to measure GFP expression and 600nm lights for optical density readings. However, camera-based technologies have three main problems: lens distortion, signal interference, and brightness calculations. Plate-Q addresses these problems through camera movement over the well-plate, image optimization, 3D printed well-plate covers and mathematical regression algorithms. In testing with fusarium dual-plasmid biosensors, Plate-Q showed comparable accuracy to commercial microplate readers with an average error of .034 and a root mean squared error of .012 for fluorescence and an average error of .045 and root mean squared error of .023 error for optical density. Users can scan for other fluorescent proteins by changing the light source and filter for different wavelengths. With all aspects of Plate-Q being open source, labs worldwide can quantify samples in an affordable and time-efficient manner.

bioengineering↗

bioRxiv2021

The ultrafast snap of a finger is mediated by skin friction

The snap of a finger has been used as a form of communication and music for millennia across human cultures. However, a systematic analysis of the dynamics of this rapid motion has not yet been performed. Using high-speed imaging and force sensors, we analyze the dynamics of the finger snap. Our analysis reveals the central role of skin friction in mediating the snap dynamics by acting as a latch to control the resulting high velocities. We evaluate the role of this frictional latch experimentally, by covering the thumb and middle finger with different materials to produce different friction coefficients and varying compressibility. In doing so, we reveal that the compressible, frictional latch of the finger pads likely operate in a regime optimally tuned for both friction and compression. We also develop a soft, compressible friction-based latch-mediated spring actuated (LaMSA) model to further elucidate the key role of friction and how it interacts with a compressible latch. Our mathematical model reveals that friction plays a dual role in the finger snap, both aiding in force loading and energy storage while hindering energy release. Our work reveals how friction between surfaces can be harnessed as a tunable latch system and provide design insight towards the frictional complexity in many robotics and ultra-fast energy-release structures.

biophysics↗

bioRxiv2021

Emergent collective locomotion in an active polymer model of entangled worm blobs

Numerous worm and arthropod species form physically-connected aggregations in which interactions among individuals give rise to emergent macroscale dynamics and functionalities that enhance collective survival. In particular, some aquatic worms such as the California blackworm (Lumbriculus variegatus) entangle their bodies into dense blobs to shield themselves against external stressors and preserve moisture in dry conditions. Motivated by recent experiments revealing emergent locomotion in blackworm blobs, we investigate the collective worm dynamics by modeling each worm as a self-propelled Brownian polymer. Though our model is two-dimensional, compared to real three-dimensional worm blobs, we demonstrate how a simulated blob can collectively traverse temperature gradients via the coupling between the active motion and the environment. By performing a systematic parameter sweep over the strength of attractive forces between worms, and the magnitude of their directed self-propulsion, we obtain a rich phase diagram which reveals that effective collective locomotion emerges as a result of finely balancing a tradeoff between these two parameters. Our model brings the physics of active filaments into a new meso- and macroscale context and invites further theoretical investigation into the collective behavior of long, slender, semi-flexible organisms.

biophysics↗

bioRxiv2020

A Tunable, Simplified Model for Biological Latch Mediated Spring Actuated Systems

We develop a model of latch-mediated spring actuated (LaMSA) systems relevant to comparative biomechanics and bioinspired design. The model contains five components: two motors (muscles), a spring, a latch, and a load mass. One motor loads the spring to store elastic energy and the second motor subsequently removes the latch, which releases the spring and causes movement of the load mass. We develop open-source software to accompany the model, which provides an extensible framework for simulating LaMSA systems. Output from the simulation includes information from the loading and release phases of motion, which can be used to calculate kinematic performance metrics that are important for biomechanical function. In parallel, we simulate a comparable, directly actuated system that uses the same motor and mass combinations as the LaMSA simulations. By rapidly iterating through biologically relevant input parameters to the model, simulated kinematic performance differences between LaMSA and directly actuated systems can be used to explore the evolutionary dynamics of biological LaMSA systems and uncover design principles for bioinspired LaMSA systems. As proof of principle of this concept, we compare a LaMSA simulation to a directly actuated simulation that includes a either Hill-type force-velocity trade-off or muscle activation dynamics, or both. For the biologically-relevant range of parameters explored, we find that the muscle force-velocity trade-off and muscle activation have similar effects on directly actuated performance. Including both of these dynamic muscle properties increases the accelerated mass range where a LaMSA system outperforms a directly actuated one.

biophysics↗

bioRxiv2020

Collective protection and transport in entangled biological and robotic active matter

Living systems at all scales aggregate in large numbers for a variety of functions including mating, predation, and survival. The majority of such systems consist of unconnected individuals that collectively flock, school or swarm. However some aggregations involve physically entangled individuals, which can confer emergent mechanofunctional material properties to the collective. Here we study in laboratory experiments and rationalize in theoretical and robotic models the dynamics of physically entangled and motile self-assemblies of centimeter long California blackworms (L. Variegatus). Thousands of individual worms form braids with their long, slender and flexible bodies to make a three-dimensional, soft and shape-shifting blob. The blob behaves as a living material capable of mitigating damage and assault from environmental stresses through dynamic shape transformations, including minimizing surface area for survival against desiccation and enabling transport (negative thermotaxis) from hazardous environments (like heat). We specifically focus on the locomotion of the blob to understand how an amorphous entangled ball of worms is able to break symmetry to move across a substrate. We hypothesize that the collective blob displays rudimentary differentiation of function across itself, which when combined with entanglement dynamics facilitates directed persistent blob locomotion. To test this, we develop robophysical blobs, which display emergent locomotion in the collective without sophisticated control or programming of any individual robot. The emergent dynamics of the living functional blob and robophysical model can inform the rational design of exciting new classes of adaptive mechanofunctional living materials and emergent swarm robotics. Significance StatementLiving organisms form collectives across all scales, from bacteria to whales, enabling biological functions not accessible by individuals alone. In a few small cases, the individuals are physically connected to each other, forming to a new class of entangled active matter systems with emergent mechanofunctionalities of the collective. Here, we describe the dynamics of macroscopic aquatic worms that braid their long, soft bodies to form large entangled worm blobs. We discover that the worm blob behaves as a living material to undergo dynamic shape transformations to reduce evaporation or break-symmetry and locomote to safety against thermal stresses. We show that the persistent blob locomotion emerges as a consequence of physical entanglement and functional differentiation of individuals based on spatial location within a blob. We validate these principles in robophysical swarming blobs, that pave the way for new classes of mechanofunctional active matter systems and collective emergent robotics.

biophysics↗

bioRxiv2019

Addressing age related hearing loss through engineering accessible and affordable hearing technology

Hearing Aids have dominated the audiological market for decades. While the costs of the electronic components have reduced substantially, the cost of a hearing aid has risen steadily to the point that it has become unaffordable for the vast majority of the population with Age Related Hearing Loss (ARHL). Here, we present an ultra-low-cost, affordable and accessible hearing aid device ( LoCHAid), specifically targeted for ARHL in elderly patients. The LoCHAid costs only 98 cents (< $1) to mass manufacture and can be personalized for each user through a 3D-printable case. It is designed to be an over-the-counter (OTC) self-serviceable solution for elderly individuals with ARHL. Electroacoustic measurements show that the device meets most of the targets set out by the WHO Preferred Product Profile and Consumer Technology Association for Hearing Aids. The frequency response of the hearing aid shows selectable gain in the range of 4-8 kHz, and mild to moderate gain between 200-1000 Hz, and shows very limited total distortion (1%). Simulated gain measurements show that the LoCHAid is well fitted to a range of ARHL profiles for males and females between the ages of 60-79 years. Overall, the measurements show that the device has the potential to benefit individuals with ARHL. Thus, our proposed design addresses a long-standing and grand challenge of affordable and accessible hearing technology for every elderly person on this planet.

bioengineering↗

bioRxiv2019

A 3D-printed hand-powered centrifuge for molecular biology

The centrifuge is an essential tool for many aspects of research and medical diagnostics. However, conventional centrifuges are often inaccessible outside of conventional laboratory settings, such as remote field sites, require a constant external power source, and can be prohibitively costly in resource-limited settings and STEM-focused programs. Here we present the 3D-Fuge, a 3D-printed hand-powered centrifuge, as a novel alternative to standard benchtop centrifuges. Based on the design principles of a paper-based centrifuge, this 3D-printed instrument increases the volume capacity to 2 mL and can reach hand-powered centrifugation speeds up to 6,000 rpm. The 3D-Fuge devices presented here are capable of centrifugation of a wide variety of different solutions such as spinning down samples for biomarker applications and performing nucleotide extractions as part of a portable molecular lab setup. We introduce the design and proof-of-principle trials that demonstrate the utility of low-cost 3D printed centrifuges for use in remote and educational settings.

bioengineering↗