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At least 91 records · Page 5

Expansion of Microbial Monitoring Capabilities on the International Space Station (ISS)

Microbial monitoring is one of the tools that the National Aeronautics and Space Administration (NASA) uses on the International Space Station (ISS) to help maintain crew health and safety. In combination with regular housekeeping and disinfection when needed, microbial monitoring provides important information to the crew about the quality of the environment. Rotation of astronauts, equipment, and cargo on the ISS can affect the microbial load in the air, surfaces, and water. The current ISS microbial monitoring methods are focused on culture-based enumeration during flight and require a significant amount of crew time as well as long incubation periods of up to 5 days there by proliferating potential pathogens. In addition, the samples require return to Earth for complete identification of the microorganisms cultivated. Although the current approach assess the quality of the ISS environment, molecular technology offers faster turn-around of information particularly beneficial in an off-nominal situation. In 2011, subject matter experts from industry and academia recommended implementation of molecular-based technologies such as quantitative real-time polymerase chain reaction (qPCR) for evaluation to replace current, culture-based technologies. The RAZOR EX (BioFire Defense, Inc, Salt Lake City, UT) a ruggedized, compact, COTS (commercial off the shelf) qPCR instrument was tested, evaluated and selected in the 2 X 2015 JSC rapid flight hardware demonstration initiative as part of the Water Monitoring Suite. RAZOR EX was launched to ISS on SpaceX-9 in July 2016 to evaluate the precision and accuracy of the hardware by testing various concentrations of DNA in microgravity compared to ground controls. Flight testing was completed between September 2016 and March 2017. Data presented will detail the hardware performance of flight testing results compared to ground controls. Future goals include additional operational ground-based testing and assay development to determine if this technology can meet spaceflight microbial monitoring requirements.

Khodadad, Christina L.↗

Carbazole-Based Hole Transport Polymer for Methylammonium-Free Tin-Lead Perovskite Solar Cells with Enhanced Efficiency and Stability

As the most commonly used hole transport material (HTM) in tin-lead (Sn-Pb) perovskite solar cells (PSCs), poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS) limits the power conversion efficiency (PCE) and stability of the PSCs due to its acidic characteristics. Herein, an easily synthesized polymer HTM poly[(phenyl)imino[9-(2-ethylhexyl)carbazole]-2,7-diyl] (CzAn) with a shallow highest occupied molecular orbital (HOMO) level of -4.95 eV is used in a p-i-n structure, methylammonium-free, Sn-Pb PSC to replace PEDOT:PSS. Upon optimization using doping and surface engineering, high quality Sn-Pb PSCs could be successfully fabricated, boosting the PCE to 22.6% (stabilized PCE of 21.3%) compared with 21.2% for PEDOT:PSS. The perovskite films prepared on the modified CzAn HTM possess improved crystallinity, reduced trap-state density, and larger carrier mobility resulting in PSCs with greatly improved stability.

carrier mobility↗

Intermetallic phase formation in Al-Si-Zr alloys during hot isostatic pressing revealed by experiments and molecular dynamics

Understanding phase transformations at alloy interfaces is critical for the design of advanced structural materials. Here, in this study, we investigate the formation mechanisms of the Al 2 SiZr intermetallic phase in the Al-Si-Zr system under hot isostatic pressing (HIP) using molecular dynamics (MD) simulations and thermodynamic analysis. A unique aspect of our approach in MD involves the replacement of a disordered Al 2 SiZr stoichiometry with an ordered phase at the Al-Zr interface once HIP results in the desired Al 2 SiZr stoichiometry, allowing us to compute the total energetic cost of transformation by accounting for both formation energies and diffusion barriers. Diffusion coefficients and activation energies, extracted across a range of temperatures, reveal that HIP substantially enhances atomic mobility, creating favorable stoichiometry for phase evolution. Our results show that Al 2 SiZr phase formation is kinetically unfavorable at lower temperatures but becomes feasible when the thermodynamic driving energy surpass a critical energy threshold.

Roy, Ankit [Pacific Northwest National Laboratory ↗

Solution to a gene divergence problem under arbitrary stable nucleotide transition probabilities

A nucleic acid chain, L nucleotides in length, with the specific base sequence B(1)B(2) ... B(L) is defined by the L-dimensional vector B = (B(1), B(2), ..., B(L)). For twelve given constant non-negative transition probabilities that, in a specified position, the base B is replaced by the base B' in a single step, an exact analytical expression is derived for the probability that the position goes from base B to B' in X steps. Assuming that each base mutates independently of the others, an exact expression is derived for the probability that the initial gene sequence B goes to a sequence B' = (B'(1), B'(2), ..., B'(L)) after X = (X(1), X(2), ..., X(L)) base replacements. The resulting equations allow a more precise accounting for the effects of Darwinian natural selection in molecular evolution than does the idealized (biologically less accurate) assumption that each of the four nucleotides is equally likely to mutate to and be fixed as one of the other three. Illustrative applications of the theory to some problems of biological evolution are given.

Holmquist, R.↗

Tissue Engineering and Cellular Regeneration at NASA Report to Regenetech SAB

A project overview describing three dimensional tissue models is shown. The topics include: 1) cellular regeneration; 2) haemopoietic replacement; 3) novel vaccine development; 4) pharmacology and toxicology interventions; 5) development of synthetic viruses; and 6) molecular genetics and proteomics of recapitulated models.

Goodwin, Thomas J.↗

Developing nanometer scale, atomically precise metallo-catalysts with Molecular Lego

We propose to create atomically precise, highly robust, nanometer scale macromolecules that organize biomimetic metal binding groups in designed three-dimensional pockets to accelerate specific polymerization reactions. These atomically precise catalysts will create atomically precise polymers with improved mechanical and environmental properties from renewable building blocks. We seek to create and study nanometer scale catalysts that mimic metallo-enzymes in their activity and selectivity because these larger catalysts will be able to make more extensive non-covalent contacts with the transition state of the growing polymer. These catalysts will have extended lifetimes because they will better protect the metals and higher activity because additional reactive groups can be brought in close contact with the active site to enhance reactivity. They will be far more tolerant to extremes of temperature and will not denature in non-aqueous solvents because they are held together by multiple, strong, covalent bonds. Our approach to catalysts could be used to develop catalysts to replace noble metal-based catalysts when targeting other reactions, because the geometry of the active site enforced by the Molecular Lego scaffolding will access new reactivity, mimicking how nature uses earth abundant metals for much of its catalysis. We will initially target Lewis acid-based catalysts that assemble aliphatic polyesters with improved stereoselectivity, tacticity and complex alternation of monomers. Aliphatic polyesters have received growing attention as attractive, environmentally benign, and sustainable alternatives to polymers developed from petroleum feedstocks. Aliphatic polyesters are environmentally friendly because they undergo facile hydrolytic degradation to benign products, and they have excellent properties and high biocompatibility. We will assemble these catalysts using unique “Spiroligomers” (aka Molecular Lego) chemistry developed in the Schafmeister group combined with the organometallic chemistry expertise of the Dobereiner group. Polymers are an attractive synthetic target of nanoscale atomically precise catalysts because their resulting structure, stereochemistry and tacticity has profound impact on their properties (crystalline vs amorphous) and provides a readout of the catalytic mechanism. Polymer synthesis also serves as an example of “atomically precise manufacturing” where atomically precise nanoscale catalysts construct polymers with atomic precision at increasing length scales.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Fracture of Carbon Nanotube - Amorphous Carbon Composites: Molecular Modeling

Carbon nanotubes (CNTs) are promising candidates for use as reinforcements in next generation structural composite materials because of their extremely high specific stiffness and strength. They cannot, however, be viewed as simple replacements for carbon fibers because there are key differences between these materials in areas such as handling, processing, and matrix design. It is impossible to know for certain that CNT composites will represent a significant advance over carbon fiber composites before these various factors have been optimized, which is an extremely costly and time intensive process. This work attempts to place an upper bound on CNT composite mechanical properties by performing molecular dynamics simulations on idealized model systems with a reactive forcefield that permits modeling of both elastic deformations and fracture. Amorphous carbon (AC) was chosen for the matrix material in this work because of its structural simplicity and physical compatibility with the CNT fillers. It is also much stiffer and stronger than typical engineering polymer matrices. Three different arrangements of CNTs in the simulation cell have been investigated: a single-wall nanotube (SWNT) array, a multi-wall nanotube (MWNT) array, and a SWNT bundle system. The SWNT and MWNT array systems are clearly idealizations, but the SWNT bundle system is a step closer to real systems in which individual tubes aggregate into large assemblies. The effect of chemical crosslinking on composite properties is modeled by adding bonds between the CNTs and AC. The balance between weakening the CNTs and improving fiber-matrix load transfer is explored by systematically varying the extent of crosslinking. It is, of course, impossible to capture the full range of deformation and fracture processes that occur in real materials with even the largest atomistic molecular dynamics simulations. With this limitation in mind, the simulation results reported here provide a plausible upper limit on achievable CNT composite properties and yield some insight on the influence of processing conditions on the mechanical properties of CNT composites.

Jensen, Benjamin D.↗

Modeling of Peptides with Classical and Novel Machine Learning Force Fields: A Comparison

The replacement of classical force fields (FFs) with novel neural-network-based frameworks is an emergent topic in molecular dynamics (MD) simulations. In contrast to classical FFs, which have proven their capability to provide insights into complex soft matter systems at an atomistic resolution, the machine learning (ML) potentials have yet to demonstrate their applicability for soft materials. However, the underlying philosophy, which is learning the energy of an atom in its surrounding chemical environment, makes this approach a promising tool. In particular for the exploration of novel chemical compounds, which have not been considered in the original parametrization of classical FFs. In this article, we study the performance of the ANI-2x ML model and compare the results with those of two classical FFs, namely, CHARMM27 and the GROMOS96 43a1 FF. We explore the performance of these FFs for bulk water and two model peptides, trialanine and a 9-mer of the α-aminoisobutyric acid, in vacuum and water. The results for water describe a highly ordered water structure, with a structure similar to those using ab initio molecular dynamics simulations. The energy landscape of the peptides described by Ramachandran maps show secondary structure basins similar to those of the classical FFs but differ in the position and relative stability of the basins. Details of the sampled structures show a divergent performance of the different models, which can be related either to the short-ranged nature of the ML potentials or to shortcomings of the underlying data set used for training. These findings highlight the current state of the applicability of ANI-2x ML potential for MD simulations of soft matter systems. Simultaneously, they provide insights for future improvements of current ML potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluation of advanced component concepts for an integrated environmental control/life support, resistojet control system

Flow restricting devices were studied for their suitability as liquid water propellant flow limiters for the biowaste resistojet. Flow limiting during the start-up transient is required to prevent thrustor instabilities and icing which could result in heater failure in the electrical resistance heated thrustor (resistojet). The study was directed toward simple devices which would function passively (i.e., without power except from the propellant flow itself), and would offer high reliability and simplicity. In addition to the flow limiting devices, a thermal pumping system was studied to determine whether CO2, desorbed from molecular sieves could be pumped thermally in a space station application. The thermal pump is considered a possible replacement for mechanical pumps. It involves a cyclic, constant volume cryopumping system which employs space radiators to achieve the cryotemperatures. The frozen CO2 would be vaporized periodically, using a waste heat loop, to attain sufficient pressure to transfer a large portion of the trapped CO2 to storage tanks.

Halbach, C. R.↗

Kingdom Animalia: the zoological malaise from a microbial perspective

Pain and cognitive dissonance abounds amongst biologists: the plant-animal, botany-zoology wound has nearly healed and the new gash--revealed by department and budget reorganizations--is "molecular" vs. "organismic" biology. Here I contend that resolution of these tensions within zoology requires that an autopoietic-gaian view replace a mechanical-neodarwinian perspective; in the interest of brevity and since many points have been discussed elsewhere, rather than develop detailed arguments I must make staccato statements and refer to a burgeoning literature. The first central concept is that animals, all organisms developing from blastular embryos, evolved from single protist cells that were unable to reproduce their undulipodia. The second points to the usefulness of recognizing the analogy between cyclically established symbioses and meiotic sexuality.

NASA Program Exobiology↗

Quantitative Analysis of the Semiconductor–Electrolyte Interface Using Cyclic Voltammetry Measurements

Small changes in the chemical potential at a semiconductor interface can result in dramatic changes to the space-charge layer that underpins applications in the electronic and photovoltaic industries as well as in photoelectrochemical cells for fuel production. There has hence been great interest in techniques that directly probe the space-charge layer, yet many fail at the semiconductor–electrolyte interface due to the potential drop in the electric double-layer region of the electrolyte. This article demonstrates that photovoltages, obtained from straightforward cyclic voltammetry measurements, provide an experimental and quantitative approach for characterizing the semiconductor–electrolyte interface. Key parameters accessible through this approach include the flat-band potential ( E fb ), the fraction of the total potential that drops across the space-charge layer (γ sc ) and the electric double layer, as well as the surface recombination lifetime (τ s ). Here, we report photovoltage measurements for p -type Si(111) photoelectrodes in contact with electrolytes containing redox-active species with a range of known reduction potentials that exceed the 1.1 eV bandgap. In tetrabutylammonium [NBu 4 ] + electrolyte, the flat-band potential determined for hydrogen-terminated ( p -Si–H), methyl-terminated ( p -Si–CH 3 ), and chemically oxidized ( p -Si–cSiO x ) surfaces were −0.02, −0.31, and 0.30 V vs Fc +/0 , respectively, agreeing well with expected shifts arising from surface dipole modifications. The quantitative analysis also reveals that 67% of the applied bias drops across the space-charge layer for p -Si–H, 73% for p -Si–CH 3 , and only 44% for p -Si–cSiO x . The remaining potential drop is attributed to the interfacial surface layer, which consists of a molecular dipole or oxide overlayer, and the Helmholtz layer within the electrolyte. When the larger [NBu 4 ] + electrolyte was replaced with Li + , the flat-band position showed minimal changes, but the fraction of the potential drop across the space-charge layer increased significantly, consistent with the small cation altering the structure of the electric double layer.

electrolytes↗

Fully synthetic platform to rapidly generate tetravalent bispecific nanobody–based immunoglobulins

Nanobodies bind a target antigen with a kinetic profile similar to a conventional antibody, but exist as a single heavy chain domain that can be readily multimerized to engage antigen via multiple interactions. Presently, most nanobodies are produced by immunizing camelids; however, platforms for animal-free production are growing in popularity. Here, we describe the development of a fully synthetic nanobody library based on an engineered human V H 3-23 variable gene and a multispecific antibody-like format designed for biparatopic target engagement. To validate our library, we selected nanobodies against the SARS-CoV-2 receptor–binding domain and employed an on-yeast epitope binning strategy to rapidly map the specificities of the selected nanobodies. We then generated antibody-like molecules by replacing the V H and V L domains of a conventional antibody with two different nanobodies, designed as a molecular clamp to engage the receptor-binding domain biparatopically. The resulting bispecific tetra-nanobody immunoglobulins neutralized diverse SARS-CoV-2 variants with potencies similar to antibodies isolated from convalescent donors. Subsequent biochemical analyses confirmed the accuracy of the on-yeast epitope binning and structures of both individual nanobodies, and a tetra-nanobody immunoglobulin revealed that the intended mode of interaction had been achieved. This overall workflow is applicable to nearly any protein target and provides a blueprint for a modular workflow for the development of multispecific molecules.

60 APPLIED LIFE SCIENCES↗

Report on DOE-Supported Participation in the 18th International Congress on Photosynthesis Research (IPC 2022)

Photosynthesis is the primary natural process for conversion of solar energy to chemical energy. Solar energy is the only clean, renewable source of energy that has sufficient capacity to replace fossil fuels and meet rising global energy needs. Meeting this challenge means understanding photosynthetic energy conversion at a molecular level, a task requiring perspectives from all disciplines of science. The 18th International Congress on Photosynthesis (IPC) is facilitating just that by providing a forum for scientists from all corners of the world to come together to share ideas and build new collaborations that will improve the lives of future generations. A vibrant knowledge of each of the diverse aspects of basic and applied photosynthesis research obviously depends upon a healthy scientific exchange among the members of the research community. While senior scientists are more likely able to make the long trip to this important meeting, the travel costs for students and postdocs would otherwise prohibit participation for talented junior US scientists. At the same time, this is precisely the kind of meeting that strengthens interest and careers in the important scientific directions represented by this conference. For all scientists this is an opportunity to learn firsthand about the very latest advances in the field and to meet and brainstorm with collaborators as well as make new collaborations. For junior scientists, this funding is giving an opportunity to do these things plus it is often the first tangible experience regarding the global, international significance of their own projects. Overall, the diversity of topics and technical approaches is providing an extremely stimulating multidisciplinary environment for junior and senior scientists performing research in a variety of areas that are within the scope to the US DOE mission. In collaboration with the executive members of the North American Photosynthesis Conference Association (NAPCA and the International Society of Photosynthesis research (ISPR), a competitive selection of junior participants is being made based upon the quality of the abstracts and materials submitted by self-identified candidates that have applied following a broadcast call for applications from junior US scientists. Financial support is consisting of waivers for the registration cost of the meeting and partial living expenses at local dormitory facilities at the conference site.

08 HYDROGEN↗

Graph-Based Approaches for Predicting Solvation Energy in Multiple Solvents: Open Datasets and Machine Learning Models

The solvation properties of molecules, often estimated using quantum chemical simulations, are important in the synthesis of energy storage materials, drugs, and industrial chemicals. Here, we develop machine learning models of solvation energies to replace expensive quantum chemistry calculations with inexpensive-to-compute message-passing neural network models that require only the molecular graph as inputs. Our models are trained on a new database of solvation energies for 130,258 molecules taken from the QM9 dataset computed in five solvents (acetone, ethanol, acetonitrile, dimethyl sulfoxide, and water) via an implicit solvent model. Our best model achieves a mean absolute error of 0.5 kcal/mol for molecules with nine or fewer non-hydrogen atoms and 1 kcal/mol for molecules with between 10 and 14 non-hydrogen atoms. We make the entire dataset of 651,290 computed entries openly available and provide simple web and programmatic interfaces to enable others to run our solvation energy model on new molecules. This model calculates the solvation energies for molecules using only the SMILES string and also provides an estimate of whether each molecule is within the domain of applicability of our model. We envision that the dataset and models will provide the functionality needed for the rapid screening of large chemical spaces to discover improved molecules for many applications.

25 ENERGY STORAGE↗

Laser-SPS systems analysis and environmental impact assessment

The systems feasibility and environmental impact of replacing the microwave transmitters on the Satellite Power System with laser transmitters are examined. The lasers suggested are two molecular-gas electric-discharge lasers (EDL's), namely the CO and CO2 lasers. Calculations are made on system efficiency, atmospheric transmission efficiency, and laser beam spreading. It is found that the present satellite concept using lasers is far too inefficient and massive to be economically viable. However, the safety issues associated with laser power transmission appear tractable, and no effects could be identified which present a real danger of serious injury to the environment, although certain phenomena deserve closer scrutiny.

Beverly, R. E., III↗

A search for C60 in carbonaceous chondrites

Analysis of interior samples of the Murchison meteorite by two routes yielded an upper limit of 2 ppb for its C60 content, as compared to parts per million levels for individual polycyclic aromatic hydrocarbons (PAHs ). Provided the samples contain an interstellar component, which is probable since Murchison hydrocarbons contain excess deuterium, this result argues against the ubiquitous presence of C60 in the interstellar medium. A possible explanation for the absence of C60 was found in experiments showing how PAHs replace fullerenes as stable end products when hydrogen is present during carbon condensation. As a secondary result we found high molecular weight PAHs in the Murchison and Allende meteorites. Coronene and its methyl derivatives are especially interesting since features in the coronene spectrum have been shown to match some of the unidentified interstellar infrared emission bands.

De Vries, M. S.↗

Ni( II )-binding affinity of Cc NikZ-II and its homologs: the role of the HH -prong and variable loop revealed by structural and mutational studies

Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Binding, Release and Functionalization of Intact Pnictogen Tetrahedra Coordinated to Dicopper Complexes

The bridging MeCN ligand in the dicopper(I) complexes [(DPFN)Cu 2 (μ,η 1 : η 1 -MeCN)][X] 2 (X=weakly coordinating anion, NTf 2 (1 a), FAl[OC 6 F 10 (C 6 F 5 )] 3 (1 b), Al[OC(CF 3 ) 3 ] 4 (1 c)) was replaced by white phosphorus (P 4 ) or yellow arsenic (As 4 ) to yield [(DPFN)Cu 2 (μ,η 2 : η 2 -E 4 )][X] 2 (E=P (2 a-c), As (3 a-c)). The molecular structures in the solid state reveal novel coordination modes for E 4 tetrahedra bonded to coinage metal ions. Experimental data and quantum chemical computations provide information concerning perturbations to the bonding in coordinated E 4 tetrahedra. Reactions with N-heterocyclic carbenes (NHCs) led to replacement of the E 4 tetrahedra with release of P 4 or As 4 and formation of [(DPFN)Cu 2 (μ,η 1 : η 1 - Me NHC)][X] 2 (4 a,b) or to an opening of one E-E bond leading to an unusual E 4 butterfly structural motif in [(DPFN)Cu 2 (μ,η 1 : η 1 -E 4 Dipp NHC)][X] 2 (E=P (5 a,b), E=As (6)). With a cyclic alkyl amino carbene ( Et CAAC), cleavage of two As-As bonds was observed to give two isomers of [(DPFN)Cu 2 (μ,η 2 : η 2 -As 4 Et CAAC)][X] 2 (7 a,b) with an unusual As 4 -triangle+1 unit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗