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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
NASA NTRS1997

Peptide Folding and Translocation Across the Water-Membrane Interface

The ability of small peptides to organize at aqueous interfaces was examined by performing a series of large-scale, molecular dynamics computer simulations of several peptides composed of two amino acids, nonpolar leucine (L) and polar glutamine (Q). The peptides differed in size and sequence of the amino acids. Studies on dipeptides LL, LQ, QL and QQ were extended to two heptamers, LQQLLQL and LQLQLQL, designed to maximize interfacial stability of an alpha-helix and a beta-strand, respectively, by exposing polar side chains to water and nonpolar side chains to a nonpolar phase. Finally, a transition of an undecamer, composed entirely of leucine residues, from a disordered structure in water to an alpha-helix in a nonpolar phase representing the interior of the membrane was investigated. Complete folding of a peptide in solution was accomplished for the first time in computer simulations. The simulations revealed several basic principles governing the sequence-dependent organization of peptides at interfaces. Short peptides tend to accumulate at interfaces and acquire ordered structures, providing that they have a proper sequence of polar and nonpolar amino acids. The dominant factor determining the interfacial structure of peptides is the hydrophobic effect, which is manifested at aqueous interfaces as a tendency for polar and nonpolar groups of the solute to segregate into the aqueous and nonpolar phases, respectively. If peptides consist of nonpolar residue's only, they become inserted into the nonpolar phase. As demonstrated by the example of the leucine undecamer, such peptides fold into an alpha-helix as they partition into the nonpolar medium. The folding proceeds through an intermediate, called 3-10-helix, which remains in equilibrium with the alpha-helix. Once in the nonpolar environment, the peptides can readily change their orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with changing external conditions may have provided a simple mechanism of transmitting signals from the environment to the interior of a cell.

Pohorille, Andrew↗
DOE OSTI2022

Imaginary admittance and charge transfer resistance correlate to the physiological status of Shewanella oneidensis cultures in real time

Monitoring microbial activity is essential for industrial and environmental applications to proceed efficiently. To minimize time and labor-intensive monitoring, a new paradigm is required for in-situ, real time analysis. Since bioconversion of organics is accomplished by microorganisms through the oxidation of feedstocks linked to the reduction of electron acceptors, microorganisms can be viewed as electrochemical catalysts. In this respect, cell membranes have an electrical potential, which is analogous to a conventional capacitor and linked dynamically to cellular activity. Here, in this study, we demonstrate the use of electrochemical impedance spectrometry (EIS) and cyclic voltammetry (CV) for monitoring microbial metabolic activity in real time, in-situ. The effect of organic electron donors as a function of concentration to the physiological status of strains of Shewanella oneidensis was determined. In this study, the pyomelanin overproducer (S. oneidensis ΔhmgA) and the pyomelanin deficient mutant (S. oneidensis ΔmelA) were chosen due to different surface electrochemical characteristics along with differences in oxygen utilization efficiency. CV, relative admittance, phase shift and permittivity changed with growth status and correlated with electron flow from organic carbon sources and terminal electron acceptor availability. This work offers a novel and inexpensive approach to real time monitoring with the advantage of abundant data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Elucidation of the physical factors that control activated transport of penetrants in chemically complex glass-forming liquids

Understanding the activated transport of penetrant or tracer atoms and molecules in condensed phases is a challenging problem in chemistry, materials science, physics, and biophysics. Many angstrom- and nanometer-scale features enter due to the highly variable shape, size, interaction, and conformational flexibility of the penetrant and matrix species, leading to a dramatic diversity of penetrant dynamics. Based on a minimalist model of a spherical penetrant in equilibrated dense matrices of hard spheres, a recent microscopic theory that relates hopping transport to local structure has predicted a novel correlation between penetrant diffusivity and the matrix thermodynamic dimensionless compressibility, S 0 ( T ) (which also quantifies the amplitude of long wavelength density fluctuations), as a consequence of a fundamental statistical mechanical relationship between structure and thermodynamics. Moreover, the penetrant activation barrier is predicted to have a factorized/multiplicative form, scaling as the product of an inverse power law of S 0 ( T ) and a linear/logarithmic function of the penetrant-to-matrix size ratio. This implies an enormous reduction in chemical complexity that is verified based solely on experimental data for diverse classes of chemically complex penetrants dissolved in molecular and polymeric liquids over a wide range of temperatures down to the kinetic glass transition. The predicted corollary that the penetrant diffusion constant decreases exponentially with inverse temperature raised to an exponent determined solely by how S 0 ( T ) decreases with cooling is also verified experimentally. Our findings are relevant to fundamental questions in glassy dynamics, self-averaging of angstrom-scale chemical features, and applications such as membrane separations, barrier coatings, drug delivery, and self-healing.

Science & Technology - Other Topics↗
DOE OSTI2020

The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions

The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review,we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1981

Formulation of a dynamic analysis method for a generic family of hoop-mast antenna systems

Analytical studies of mast-cable-hoop-membrane type antennas were conducted using a transfer matrix numerical analysis approach. This method, by virtue of its specialization and the inherently easy compartmentalization of the formulation and numerical procedures, can be significantly more efficient in computer time required and in the time needed to review and interpret the results.

Gabriele, A.↗
DOE OSTI2025

Solution‐Like Water Transport Across Molecular to Macroscopic Length Scales in Crosslinked Poly(Ethylene Glycol Diacrylate) Networks With Tailored Sidechains

Poly(ethylene glycol) (PEG)‐based materials, like PEG‐diacrylate (PEGDA), are prized for their hydrophilic, inert properties, and leveraged in hydrogels and as membrane mimics. While network chemistry is often tuned for selective transport and antifouling, fundamental understanding of water dynamics at the network surface and the impact on bulk transport is limited. We utilize Overhauser dynamic nuclear polarization (ODNP) to measure nanoscale water diffusivity near a tethered spin label at the water‐polymer surface and compare it to bulk water diffusivity from pulsed field gradient (PFG) NMR. Via active ester chemistry, spin labels and varied sidechain chemistries are introduced, modulating network hydrophilicity. Tuning network hydration through crosslinker content and functional groups further impacts water diffusivity. Results show rapid nanoscale water transport at the polymer surface, reflecting network volumetric water content, with further modulation by sidechain functionality. These findings demonstrate PEGDA's utility as a membrane mimic and the critical impact of network chemistry on water transport.

hydrogels↗
DOE OSTI2022

Rheology and dynamics of a solvent segregation driven gel (SeedGel)

Bicontinuous structures promise applications in a broad range of research fields, such as energy storage, membrane science, and biomaterials. Kinetically arrested spinodal decomposition is found responsible for stabilizing such structures in different types of materials. A recently developed solvent segregation driven gel (SeedGel) is demonstrated to realize bicontinuous channels thermoreversibly with tunable domain sizes by trapping nanoparticles in a particle domain. As the mechanical properties of SeedGel are very important for its future applications, a model system is characterized by temperature-dependent rheology. The storage modulus shows excellent thermo-reproducibility and interesting temperature dependence with the maximum storage modulus observed at an intermediate temperature range (around 28 °C). SANS measurements are conducted at different temperatures to identify the macroscopic solvent phase separation during the gelation transition, and solvent exchange between solvent and particle domains that is responsible for this behavior. Further, the long-time dynamics of the gel is further studied by X-ray Photon Correlation Spectroscopy (XPCS). The results indicate that particles in the particle domain are in a glassy state and their long-time dynamics are strongly correlated with the temperature dependence of the storage modulus.

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

Impact of Asymmetric Microstructure on Ion Transport in Ti 3 C 2 T x Membranes

Consolidation or densification of low-dimensional MXene materials into membranes can result in the formation of asymmetric membrane structures. Nanostructural (short-range) and microstructural (long-range) heterogeneity can influence mass transport and separation mechanisms. Short-range structural dynamics include the presence of water confined between the 2D layers, while long-range structural properties include the formation of defects, micropores, and mesopores. Herein, it is demonstrated that structural heterogeneity in Ti 3 C 2 T x membranes fabricated via vacuum-assisted filtration significantly affects ion transport. Higher ion permeabilities are achieved when the dense “bottom” side of the membrane, rather than the porous “top” side, faces the feed solution. Characterization of the membrane reveals distinct differences in flake alignment, surface roughness, and porosity across the membrane. In conclusion, the directional dependence on permeability suggests that one region of the membrane experiences stronger internal concentration polarization, potentially suppressing permeability through the porous side of the membrane.

MXene↗
DOE OSTI2026

Tracking the protein conformational motions driving HIV-1 membrane fusion

HIV-1 Env (trimeric gp120/gp41) is the surface protein responsible for membrane fusion. The Env binds to the receptor proteins, which induces gp120 shedding leading to conformational changes of gp41 from the pre-fusion to post-fusion state, allowing its fusion peptide to embed in the host cell membrane and bringing the viral and host cell membranes together. The gp41 refolding is a target of several peptide inhibitors. Yet, the molecular mechanism of this dynamic process is still not well understood. In this study, we successfully simulate the conformational change of gp41 from pre-fusion to post-fusion state in atomistic resolution using all-atom structure-based models. We reveal that maintaining the directionality of protomer interactions in both pre-fusion and post-fusion states is crucial for gp41 refolding. Additionally, we find that HR1 inherently extends as a three-helical bundle toward the host-cell membrane without any bias. Importantly, we identify native contacts in the pre-fusion state that are critical for the proper refolding of gp41 towards the post-fusion state. Lastly, by incorporating the membrane-fusion inhibitors, T20 and SFT, we identify the most vulnerable stage in the fusion pathway that exhibits the greatest sensitivity to these drugs, which could aid in a better understanding of drug resistance mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A reduced-order model of concentration polarization in reverse osmosis systems with feed spacers

Feed spacers in reverse osmosis systems generate complex fluid flows that limit computational fluid dynamics (CFD) simulations to small length and time scales. That limits our ability to simulate mineral scaling and other membrane fouling phenomena, which occur over longer length and time scales. Thus motivated, we develop a reduced model that replaces the CFD simulation of the velocity field with an analytical model that mimics spacers. This focuses the remaining numerical effort on simulating the advection–diffusion equation governing solute transport. We motivate and validate the model with CFD simulations and bench-scale experiments of spacer filaments in three different arrangements, including cases of unsteady vortex shedding. We show that the model produces a roughly 10,000-fold speedup compared to CFD, and accurately reproduces CFD predictions of not only the average and maximum concentrations, but also the local concentration distribution along the membrane. Here, we also demonstrate the model for simulating a feed channel with a length-to-height ratio of 200. The model provides a simple testbed for exploratory studies of multispecies transport, precipitation, and membrane fouling phenomena for which simulating spacers is often prohibitive.

Computational fluid dynamics↗
DOE OSTI2021

cAMP binding to closed pacemaker ion channels is non-cooperative

Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP and provide direct validation of the ligand-induced flip-state model. Furthermore, this approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

What are grana in chloroplasts of vascular plants good for?

All plants and green algae contain stacked grana thylakoid membranes in their chloroplasts, underscoring an evolutionary pressure to maintain this unique structural feature. In addition, numerous studies have demonstrated that particular lateral and vertical dimensions of grana facilitate the function, regulation and repair of the photosynthetic machinery responsible for energy conversion. In this review, we present an updated overview of our understanding concerning the structure of grana thylakoids, the forces that contribute to their formation and their architectural dynamics. After establishing the structural foundation, we continue by reviewing the implications of grana formation on light harvesting, electron transport and protein maintenance in the thylakoid membranes of vascular plants. Regarding light harvesting, we discuss the implications of grana formation on energy spillover, macromolecular crowding, lateral versus vertical excitation energy transfer, and state transition. With respect to electron transport, we summarize recent findings regarding the functional connectivity of spatially separated photosystems facilitated by grana formation through small mobile electron carriers. We also explore how the dynamic responses of grana architecture regulate electron transport. Finally, we address how grana formation contributes to the organization of protein repair and biogenesis within thylakoid membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex

Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo–electron microscopy (cryo-EM) structure of yeast V o proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of V o that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V o that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, in this work, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Modeling the dynamics of phospholipids in the fluid phase of liposomes

Here, we present the derivation of a new model to describe neutron spin echo spectroscopy and quasi-elastic neutron scattering data on liposomes. We compare the new model with existing approaches and benchmark it with experimental data. The analysis indicates the importance of including all major contributions in the modeling of the intermediate scattering function. Simultaneous analysis of the experimental data on lipids with full contrast and tail contrast matched samples reveals highly confined lipid tail motion. A comparison of their dynamics demonstrates the statistical independence of tail-motion and height–height correlation of the membrane. A more detailed analysis indicates that the lipid tail relaxation is confined to a potential with cylindrical symmetry, in addition to the undulation and diffusive motion of the liposome. Despite substantial differences in the chemistry of the fatty acid tails, the observation indicates a universal behavior. The analysis of partially deuterated systems confirms the strong contribution of the lipid tail to the intermediate scattering function. Within the time range from 5 to 100 ns, the intermediate scattering function can be described by the height–height correlation function. The existence of the fast-localized tail motion and the contribution of slow translational diffusion of liposomes determine the intermediate scattering function for t < 5 ns and t > 100 ns, respectively. Taking into account the limited time window lowers the bending moduli by a factor of 1.3 (DOPC) to 2 (DMPC) compared to the full range.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

DYCAST: A finite element program for the crash analysis of structures

DYCAST is a nonlinear structural dynamic finite element computer code developed for crash simulation. The element library contains stringers, beams, membrane skin triangles, plate bending triangles and spring elements. Changing stiffnesses in the structure are accounted for by plasticity and very large deflections. Material nonlinearities are accommodated by one of three options: elastic-perfectly plastic, elastic-linear hardening plastic, or elastic-nonlinear hardening plastic of the Ramberg-Osgood type. Geometric nonlinearities are handled in an updated Lagrangian formulation by reforming the structure into its deformed shape after small time increments while accumulating deformations, strains, and forces. The nonlinearities due to combined loadings are maintained, and stiffness variation due to structural failures are computed. Numerical time integrators available are fixed-step central difference, modified Adams, Newmark-beta, and Wilson-theta. The last three have a variable time step capability, which is controlled internally by a solution convergence error measure. Other features include: multiple time-load history tables to subject the structure to time dependent loading; gravity loading; initial pitch, roll, yaw, and translation of the structural model with respect to the global system; a bandwidth optimizer as a pre-processor; and deformed plots and graphics as post-processors.

Pifko, A. B.↗
NASA NTRS2003

Basic and clinical immunology

Progress in immunology continues to grow exponentially every year. New applications of this knowledge are being developed for a broad range of clinical conditions. Conversely, the study of primary and secondary immunodeficiencies is helping to elucidate the intricate mechanisms of the immune system. We have selected a few of the most significant contributions to the fields of basic and clinical immunology published between October 2001 and October 2002. Our choice of topics in basic immunology included the description of T-bet as a determinant factor for T(H)1 differentiation, the role of the activation-induced cytosine deaminase gene in B-cell development, the characterization of CD4(+)CD25(+) regulatory T cells, and the use of dynamic imaging to study MHC class II transport and T-cell and dendritic cell membrane interactions. Articles related to clinical immunology that were selected for review include the description of immunodeficiency caused by caspase 8 deficiency; a case series report on X-linked agammaglobulinemia; the mechanism of action, efficacy, and complications of intravenous immunoglobulin; mechanisms of autoimmunity diseases; and advances in HIV pathogenesis and vaccine development. We also reviewed two articles that explore the possible alterations of the immune system caused by spaceflights, a new field with increasing importance as human space expeditions become a reality in the 21st century.

Review↗