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Results for “Biological fluid dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Topological structure and dynamics of three-dimensional active nematics

Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination loops that undergo complex dynamics and recombination events. Our work suggests a framework for analyzing the nonequilibrium dynamics of bulk anisotropic systems as diverse as driven complex fluids, active metamaterials, biological tissues, and collections of robots or organisms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Online Machine Learning for Accelerating Molecular Dynamics Modeling of Cells

We developed a biomechanics-informed online learning framework to learn the dynamics with ground truth generated with multiscale modeling simulation. It was built on Summit-like supercomputers, which were also used to benchmark and validate our framework on one physiologically significant modeling of deformable biological cells. We generalized the century-old equation of Jeffery orbits to a new equation of motion with additional parameters to account for the flow conditions and the cell deformability. Using simulation data at particle-based resolutions for flowing cells and the learned parameters from our framework, we validated the new equation by the motions, mostly rotations, of a human platelet in shear blood flow at various shear stresses and platelet deformability. Our online framework, which surrogates redundant computations in the conventional multiscale modeling by solutions of our learned equation, accelerates the conventional modeling by three orders of magnitude without visible loss of accuracy.

multiscale modeling↗
DOE OSTI2020

Water and vapor transport in algal‐fungal lichen: Modeling constrained by laboratory experiments, an application for Flavoparmelia caperata

ABSTRACT Algal‐fungal symbionts share water, nutrients, and gases via an architecture unique to lichens. Because lichen activity is controlled by moisture dynamics, understanding water transport is prerequisite to understand their fundamental biology. We propose a model of water distributions within foliose lichens governed by laws of fluid motion. Our model differentiates between water stored in symbionts, on extracellular surfaces, and in distinct morphological layers. We parameterize our model with hydraulic properties inverted from laboratory measurements of Flavoparmelia caperata and validate for wetting and drying. We ask: (1) Where is the bottleneck to water transport? (2) How do hydration and dehydration dynamics differ? and (3) What causes these differences? Resistance to vapor flow is concentrated at thallus surfaces and acts as the bottleneck for equilibrium, while internal resistances are small. The model captures hysteresis in hydration and desiccation, which are shown to be controlled by nonlinearities in hydraulic capacitance. Muting existing nonlinearities slowed drying and accelerated wetting, while exaggerating nonlinearities accelerated drying and slowed wetting. The hydraulic nonlinearity of F. caperata is considerable, which may reflect its preference for humid and stable environments. The model establishes the physical foundation for future investigations of transport of water, gas, and sugar between symbionts.

Potkay, Aaron↗
DOE OSTI2023

Milligrams to kilograms: making microbes work at scale

Energy is one of the most complex fields of study and an issue that influences nearly every aspect of modern life. Over the past century, combustion of fossil fuels, particularly in the transportation sector, has been the dominant form of energy release. Refining of petroleum and natural gas into liquid transportation fuels is also the centerpiece of the modern chemical industry used to produce materials, solvents, and other consumer goods. In the face of global climate change, the world is searching for alternative, sustainable means of producing energy carriers and chemical building blocks. The use of biofuels in engines predates modern refinery optimization and today represents a small but significant fraction of liquid transportation fuels burnt each year. Similarly, white biotechnology has been used to produce many natural products through fermentation. The evolution of recombinant DNA technology into modern synthetic biology has expanded the scope of biofuels and bioproducts that can be made by biocatalysts. This opinion examines the current trends in this research space, highlighting the substantial growth in computational tools and the growing influence of renewable electricity in the design of metabolic engineering strategies. In short, advanced biofuel and bioproduct synthesis remains a vibrant and critically important field of study whose focus is shifting away from the conversion of lignocellulosic biomass towards a broader consideration of how to reduce carbon dioxide to fuels and chemical products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effect of interfacial vibrational coupling on surface wettability and water transport

Here, we report that the atomic-scale vibrational coupling at the solid-fluid interface can substantially alter the interfacial properties such as wettability and fluid slip. The wettability of water droplets on substrates subjected to various vibrational frequencies is studied using molecular dynamics simulation. The contact angle increases (i.e., becomes more hydrophobic) when the oscillation frequency of the substrate matches the intermolecular bending frequency of liquid water. We investigate the underlying mechanism by examining the dynamics of water molecules at the interface and find that the temporal contact between the solid and fluid is shorter when the frequencies match, resulting in weak solid-fluid adsorption. We further report that the vibrational match at the interface reduces wall-fluid friction and enhances water transport through the nanopore. Our findings demonstrate the importance of the atomic-scale vibrational coupling at the solid-fluid interface on the physicochemical behavior of nanodevices and biological nanochannels.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Active liquid crystals powered by force-sensing DNA-motor clusters

Significance Single-molecule techniques have elucidated how isolated molecular motors generate piconewton forces with unprecedented detail. However, in diverse biological and synthetic settings, force-generating proteins collectively power nonequilibrium dynamics, including continuous large-scale rearrangements and persistent fluid flows. Characterizing motor-generated forces in these dense and dynamical environments remains a challenge. We assembled a reversible DNA-based force-sensing probe that, by an optical readout, reveals the molecular arrangements and the force loads experienced by kinesin motors. These probes provide insight into motor-generated forces that collectively power the unique dynamics of microtubule-based active nematics, a noteworthy example of an internally driven active matter system. DNA-based force probes can be extended to study forces and stresses in various synthetic systems as well as diverse cellular environments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Shape-preserving amorphous-to-crystalline transformation of CaCO3 revealed by in situ TEM

Organisms use inorganic ions and macromolecules to regulate crystallization from amorphous- precursors, endowing natural biominerals with complex morphologies and enhanced properties. The mechanisms by which modifiers enable these shape preserving transformations are poorly understood. We used in situ liquid-phase transmission electron microscopy to follow the evolution from amorphous calcium carbonate to calcite in the presence of additives. A combination of contrast analysis and infrared spectroscopy shows that Mg ions, which are widely present in seawater and biological fluids, alter the transformation pathway in a concentration-dependent manner. The ions bring excess (structural) water into the amorphous bulk so that a direct transformation is triggered by dehydration in the absence of morphological changes. Molecular dynamics simulations suggest Mg-incorporated water induces structural fluctuations, allowing transformation without the need to nucleate a separate crystal. Thus, the obtained calcite retains the original morphology of the amorphous state, biomimetically achieving the morphological control of crystals seen in biominerals

crystallization, biomineralization, calcium carbon↗
DOE OSTI2023

Activity-induced propulsion and separation of passive chiral particles in liquids

Recent literature shows that chiral particles driven by vorticity gradients of a base Newtonian liquid can separate only in nonlinear or nonstationary flows. Here, we show that a base Newtonian liquid endowed with rotational degrees of freedom, can give rise to chiral particle propulsion and separation even in the Stokes flow approximation. We consider active mechanisms generating spatially inhomogeneous vorticity in the base liquid in a channel such as a magnetic torque, a pressure gradient and a sliding wall. These mechanisms generate regions of spatially inhomogeneous vorticity maintained by the internal angular momentum, propelling the chiral particles according to their handedness. Similar conclusions can be reached when one of the channel walls is replaced by a free surface acted on by surface shear. This behavior is in contrast to the case of standard Newtonian liquids where chiral particle propulsion generated by vorticity gradients is not possible in Stokes flow. Furthermore, this effect can find applications in industry, biology and medicine.

42 ENGINEERING↗
DOE OSTI2020

Quantitative Protein Corona Composition and Dynamics on Carbon Nanotubes in Biological Environments

When nanoparticles enter biological environments, proteins adsorb to form the "protein corona" which alters nanoparticle biodistribution and toxicity. Herein, we measure protein corona formation on DNA-functionalized single-walled carbon nanotubes (ssDNA-SWCNTs), a nanoparticle used widely for sensing and delivery, in blood plasma and cerebrospinal fluid. We characterize corona composition by mass spectrometry, revealing high-abundance corona proteins involved in lipid binding, complement activation, and coagulation. We investigate roles of electrostatic and entropic interactions driving selective corona formation. Lastly, we study real-time protein binding on ssDNA-SWCNTs, obtaining agreement between enriched proteins binding strongly and depleted proteins binding marginally, while highlighting cooperative adsorption mechanisms. Knowledge of protein corona composition, formation mechanisms, and dynamics informs nanoparticle translation from in vitro design to in vivo application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Quantifying electron transport in aggregated colloidal suspensions in the strong flow regime

Electron transport in complex fluids, biology, and soft matter is a valuable characteristic in processes ranging from redox reactions to electrochemical energy storage. These processes often employ conductor–insulator composites in which electron transport properties are fundamentally linked to the microstructure and dynamics of the conductive phase. While microstructure and dynamics are well recognized as key determinants of the electrical properties, a unified description of their effect has yet to be determined, especially under flowing conditions. In this work, the conductivity and shear viscosity are measured for conductive colloidal suspensions to build a unified description by exploiting both recent quantification of the effect of flow-induced dynamics on electron transport and well-established relationships between electrical properties, microstructure, and flow. These model suspensions consist of conductive carbon black (CB) particles dispersed in fluids of varying viscosities and dielectric constants. In a stable, well-characterized shear rate regime where all suspensions undergo self-similar agglomerate breakup, competing relationships between conductivity and shear rate were observed. To account for the role of variable agglomerate size, equivalent microstructural states were identified using a dimensionless fluid Mason number, Mn f , which allowed for isolation of the role of dynamics on the flow-induced electron transport rate. At equivalent microstructural states, shear-enhanced particle–particle collisions are found to dominate the electron transport rate. This work rationalizes seemingly contradictory experimental observations in literature concerning the shear-dependent electrical properties of CB suspensions and can be extended to other flowing composite systems.

Science & Technology - Other Topics↗
DOE OSTI2025

Autonomous sensor suite for evaluating fish-turbine interactions and environmental impacts in marine renewable energy and hydropower

Marine renewable energy (MRE) harnesses ocean-based resources such as waves, tides, currents, and thermal or salinity gradients for sustainable power generation. It has the potential to complement existing renewable resources, support remote communities, and contribute to decarbonization efforts. However, understanding the hydrodynamic forces created by MRE devices and their impacts on marine life is critical for responsible deployment. Here, to address these concerns, advanced sensor devices, including the Marine Sensor Fish (MSF), Sensor Fish Mini (SF Mini), and Flexible Sensor Fish (FSF), were developed to measure interactions between aquatic organisms and MRE systems. This paper details the design, manufacturing, calibration, and field deployment of these sensor suites, highlighting their ability to capture key physical stressors such as shear forces, pressure changes, and collision impacts. The MSF successfully evaluated turbine interactions at a tidal turbine in the Salish Sea, capturing data on turbulence, collision impact, and pressure gradients. The SF Mini validated hydrodynamic conditions in scaled hydraulic models, supporting computational fluid dynamics simulations. The FSF, with its flexible silicone body, measured species-specific impacts in turbulent environments. This research demonstrates the potential of Sensor Fish technology to advance sustainable marine energy systems by reducing biological impacts and informing environmentally sustainable designs.

Ecological impacts↗
DOE OSTI2024

Pattern formation in odd viscoelastic fluids

Nonreciprocal interactions fueled by local energy consumption can be found in biological and synthetic active matter at scales where viscoelastic forces are important. Such systems can be described by “odd” viscoelasticity, which assumes fewer material symmetries than traditional theories. Here we study odd viscoelasticity analytically and using lattice Boltzmann simulations. We identify a pattern-forming instability which produces an oscillating array of fluid vortices, and we elucidate which features govern the growth rate, wavelength, and saturation of the vortices. Our observation of pattern formation through odd mechanical response can inform models of biological patterning and guide engineering of odd dynamics in soft active matter systems. Published by the American Physical Society 2024

Floyd, Carlos (ORCID:0000000262707250)↗
DOE OSTI2026

Primary biomolecular adsorption energetics of core–shell nanocomplexes: Implications for biological interactions

Molecular organization at the nano-bio interface governing the colloidal stability, reactivity, immune recognition, and drug delivery performance of nanoparticles remains difficult to predict. Quantifying the primary hydration energetics of biomolecule-coated nanomaterials can determine those interactions and provide a basis for engineered nanocarriers with tailored behavior in biological systems. Here, we measured the thermodynamics of water adsorption on patchy dry magnetite (Fe 3 O 4 ) nanoparticles coated with three model biomolecules, bovine serum albumin, potato starch, and lauric acid and compared these properties to the hydration energetics of the corresponding free dry biomolecules. The results demonstrate how the surface functionalization alters the hydrophilicity, the accessible hydrophilic surface, and the interaction potential of the nanocomplex surface with biological media. The protein coating increases the interaction potential of the surface of the nanocomplex. The weaker interaction potential of the polysaccharide coating and the relatively large hydrophilic surface area allow dynamic and reversible binding, while the fatty acid rearranges into a partial bilayer with very strong hydrophilicity. The findings establish the hydration enthalpy as a quantitative basis to determine and interpret nanoparticle interactions with proteins, membranes, and biological fluids, and provide a thermodynamic foundation for designing nanocarriers with predictable biological reactivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Outsourced hearing in an orb-weaving spider that uses its web as an auditory sensor

Hearing is a fundamental sense of many animals, including all mammals, birds, some reptiles, amphibians, fish, and arthropods. The auditory organs of these animals are extremely diverse in anatomy after hundreds of millions of years of evolution, yet all are made up of cellular tissue and are morphologically part of the bodies of animals. Here, we show that hearing in the orb-weaving spider Larinioides sclopetarius is not constrained by the organism’s body but is extended through outsourcing hearing to its extended phenotype, the proteinaceous, self-manufactured orb web. We find that the wispy, wheel-shaped orb web acts as a hyperacute acoustic antenna to capture the sound-induced air particle movements that approach the maximum physical efficiency better than the acoustic responsivity of all previously known eardrums. By sensing the motion of web threads, the spider remotely detects and localizes the source of an incoming airborne acoustic wave, such as those emitted by approaching prey or predators. By outsourcing its acoustic sensors to its web, the spider is released from body size constraints and permits the araneid spider to increase its sound-sensitive surface area enormously, up to 10,000 times greater than the spider itself. The spider also enables the flexibility to functionally adjust and regularly regenerate its external "eardrum" according to its needs. The outsourcing and supersizing of auditory function in spiders provides unique features for studying extended and regenerative sensing and designing novel acoustic flow detectors for precise fluid dynamic measurement and manipulation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Structural Heterogeneity and Hydrodynamics of an Intrinsically Disordered Protein Condensate

Biology demonstrates precise control over the free-energy landscape through the selective partitioning of biomacromolecules into membraneless organelles, enabling essential functions such as biochemical transformations, signaling cascades, and mechanical reinforcement. Although the function of these condensates depends on their underlying structure and hydrodynamics, molecular-scale information on these systems remains sparse. Here, in this study, neutron scattering is used to probe the organization and dynamics of the intrinsically disordered N-terminal domain of Galectin-3, an extracellular lectin responsible for facilitating liquid–liquid phase separation on the cellular surface, in both dilute and condensed phases. Dilute solutions contain isolated protein chains in equilibrium with mesoscopic clusters, whereas the condensed phase adopts a bicontinuous, microemulsion-like morphology. The dilute phase behavior is quantitatively described by coarse-grained polymer models from soft-matter physics, demonstrating their predictive power for complex biological proteins. At elevated concentrations, the proteins self-assemble akin to block copolymers, microphase separating through the aggregation of hydrophobic domains along the protein contour. The resulting condensate remains fluid-like despite a 25-fold increase in concentration; its internal hydrodynamics slow by only a factor of 3 relative to dilute protein chains. These results provide a molecular-level framework for how disordered proteins achieve both the structural complexity and dynamic fluidity of biomolecular condensates.

Carrick, Brian R. [Massachusetts Inst. of Technolo↗
DOE OSTI2025

Incorporating the molecular-scale into a hydrodynamic description of confined aqueous systems

Hydrodynamics provides a continuum-level description of fluid motion, but its applicability at the nanoscale becomes uncertain due to the emerging importance of molecular-level effects such as spatial heterogeneity. Hydrodynamic boundary conditions that incorporate molecular details allow us to partition the system into a near-wall region and a bulk fluid region. We identify a hydrodynamic wall located inside the fluid that determines where slip begins. By extending the hydrodynamic wall with the slip length, the position of the extrapolated wall is established. This offers a unified description of both slip and stagnant flow behaviors, with wall hydrophobicity characterized by the relative location of the extrapolated wall with respect to the physical wall. Employing this concept in analyses of equilibrium molecular dynamics (MD) and non-equilibrium MD simulations of Couette and Poiseuille flows, our results demonstrate consistency between equilibrium and non-equilibrium approaches across different flow types and confinement levels. This demonstrates the robust nature of linear response theory. We then explore the effects of fluid-wall and bulk fluid interactions on the hydrodynamic properties. These findings enhance the effectiveness of molecular-based simulations for investigating complex confined systems in nanofluidics, biology, and colloidal science, offering a complementary molecular-scale perspective to traditional continuum approaches.

flow simulations↗
DOE OSTI2025

Hydropower Biological Evaluation Toolset (HBET) Version 3.0: User Guide

The Hydropower Biological Evaluation Tools (HBET) software package, developed by Pacific Northwest National Laboratory (PNNL), is designed to assemble, organize, and process data collected by Sensor Fish and live fish. HBET enable users to characterize the hydraulic conditions of hydropower structures and estimate fish injury and mortality rates from various stressors. Future updates of the software may support other technologies, such as bead tracking in physical models and computational fluid dynamics. The HBET program can be customized to analyze different hydraulic applications, including turbines, spillways, weirs, pumped storage, and other user-defined functions, and therefore, help researchers, turbine designers, hydropower operators, and regulators better evaluate hydropower structures regarding their environmental sustainability and cost-effectiveness. Added content to the user guide about the new feature for predicting absolute injury rates.

13 HYDRO ENERGY↗