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Martin, Richard L.

Publications and source records attributed to Martin, Richard L..

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cognitive analysis of metabolomics data for systems biology

Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. Additionally, the four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1–4 h or more to complete, depending on the processing time of the various software used.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Energy-Degeneracy-Driven Covalency in Actinide Bonding

Evaluating the nature of chemical bonding for actinide elements represents one of the most important and long-standing problems in actinide science. In this work, we directly address this challenge and contribute a Cl K-edge X-ray absorption spectroscopy and relativistic density functional theory study that quantitatively evaluates An–Cl covalency in AnCl 6 2– (An IV = Th, U, Np, Pu). Lastly, the results showed significant mixing between Cl 3p- and An IV 5f- and 6d-orbitals (t 1u */t 2u * and t 2g */e g *), with the 6d-orbitals showing more pronounced covalent bonding than the 5f-orbitals. Moving from Th to U, Np, and Pu markedly changed the amount of M–Cl orbital mixing, such that An IV 6d- and Cl 3p-mixing decreased and metal 5f- and Cl 3p-orbital mixing increased across this series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Oxidation State of 229 Th Recoils Implanted into MgF 2 Crystals

A solid-state nuclear clock based on the low-lying isomeric state in 229 Th has attracted growing interest. One potential problem for the solid-state nuclear clock approach is the suitability of the doped environment for photon emission of the nuclear isomeric state. Specifically, Th n+ n < 4 ions could open non-radiative decay routes for deexcitation, hindering the photon emission. Here we have used time-resolved photoluminescence (TRPL) and density functional theory (DFT) calculations to characterize MgF 2 crystals that have been implanted with 229 Th recoils via a-decay from a 233 U source with the goal of determining the charge state of the implanted thorium atoms. The DFT calculations predicted Th4+ to be the lowest energy oxidation state with Th3+ the next lowest in the MgF2 crystal environment. The DFT calculations also show Th4+:MgF 2 system has a band gap large enough so that the internal electron conversion decay channel is suppressed. Experimentally, we found no evidence for thorium in oxidations state other than +4 using TRPL spectroscopy that has a detection limit for Thn+ n < 4 ions several orders of magnitude smaller than the number of implanted 229Th recoils. This work shows that the solid-state approach is a viable option for a nuclear clock.

229Th Isomeric State↗
DOE OSTI2017

Quantitative Evidence for Lanthanide-Oxygen Orbital Mixing in CeO 2 , PrO 2 , and TbO 2

We report that understanding the nature of covalent (band-like) vs ionic (atomic-like) electrons in metal oxides continues to be at the forefront of research in the physical sciences. In particular, the development of a coherent and quantitative model of bonding and electronic structure for the lanthanide dioxides, LnO 2 (Ln = Ce, Pr, and Tb), has remained a considerable challenge for both experiment and theory. Herein, relative changes in mixing between the O 2p orbitals and the Ln 4f and 5d orbitals in LnO 2 are evaluated quantitatively using O K-edge X-ray absorption spectroscopy (XAS) obtained with a scanning transmission X-ray microscope and density functional theory (DFT) calculations. For each LnO 2 , the results reveal significant amounts of Ln 5d and O 2p mixing in the orbitals of t 2g (σ-bonding) and e g (π-bonding) symmetry. The remarkable agreement between experiment and theory also shows that significant mixing with the O 2p orbitals occurs in a band derived from the 4f orbitals of a 2u symmetry (σ-bonding) for each compound. However, a large increase in orbital mixing is observed for PrO 2 that is ascribed to a unique interaction derived from the 4f orbitals of t 1u symmetry (σ- and π-bonding). Lastly, O K-edge XAS and DFT results are compared with complementary L 3 -edge and M 5,4 -edge XAS measurements and configuration interaction calculations, which shows that each spectroscopic approach provides evidence for ground state O 2p and Ln 4f orbital mixing despite inducing very different core-hole potentials in the final state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Impact of the strength and spatial distribution of adsorption sites on methane deliverable capacity in nanoporous materials

The methane deliverable capacity of adsorbent materials is a critical performance metric that will determine the viability of using adsorbed natural gas (ANG) technology in vehicular applications. ARPA-E recently set a target deliverable capacity of 315 cc(STP)/cc that a viable adsorbent material should achieve to yield a driving range competitive with incumbent fuels. However, recent computational screening of hundreds of thousands of materials suggests that the target is unattainable. In this work, we aim to determine whether the observed limits in deliverable capacity (similar to 200 cc(STP)/cc) are fundamental limits arising from thermodynamic or material design constraints. Our efforts focus on simulating methane adsorption isotherms in a large number of systems, resulting in a broad exploration of different combinations of spatial distributions and energetics of adsorption sites. All systems were classified into five adsorption scenarios with varying degrees of realism in the manner that adsorption sites are created and endowed with energetics. The scenarios range from methane adsorption on discrete idealized lattice sites to adsorption in metal-organic frameworks with coordinatively unsaturated sites (CUS) provided by metalated catechol groups. Our findings strongly suggest that the ARPA-E target is unattainable, although not due to thermodynamic constraints but due to material design constraints. On the other hand, we also find that the currently observed deliverable capacity limits may be moderately surpassed. For instance, incorporation of CUS in IRMOF-10 is predicted to yield a 217 cc(STP)/cc deliverable capacity. The modified material has a similar to 0.85 void fraction and a heat of adsorption of similar to 15 kJ/mol. This suggests that similar, moderate improvements over existing materials could be achieved as long as CUS incorporation still maintains a relatively large void fraction. Nonetheless, we conclude that more significant improvements in deliverable capacity will require changes in the currently proposed operation conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Computer-Aided Search for Materials to Store Natural Gas for Vehicles

Most cars use gasoline as a fuel. But cars can run on other fuels, such as natural gas (NG), the same gas that is used for cooking and for heating our homes. NG is cheaper and possibly better for the environment than gasoline. However, gasoline is much more dense than NG since gasoline is a liquid and NG is a gas. So, to run a car on NG, we need to increase its density so that we can fit enough NG in the fuel tank to drive a similar distance as with a tank of gasoline. Researchers around the world are working on synthesizing materials that act as sponges that adsorb NG. By putting these sponge-like materials inside of the fuel tank, we can increase the density of NG to efficiently store it onboard the vehicle. In our study, we show that how computers can be used to search for the most promising sponge-like materials to store NG.

03 NATURAL GAS↗
DOE OSTI2015

Evaluation of nitrogen-rich macrocyclic ligands for the chelation of therapeutic bismuth radioisotopes

The use of α-emitting isotopes for radionuclide therapy is a promising treatment strategy for small micro-metastatic disease. The radioisotope ²¹³Bi is a nuclide that has found substantial use for targeted α-therapy (TAT). The relatively unexplored aqueous chemistry of Bi³⁺, however, hinders the development of bifunctional chelating agents that can successfully deliver these Bi radioisotopes to the tumor cells. Here, a novel series of nitrogen-rich macrocyclic ligands is explored for their potential use as Bi-selective chelating agents. The ligands, 1,4,7,10-tetrakis(pyridin-2-ylmethyl)-1,4,7,10-tetraazacyclododecane (L py ), 1,4,7,10-tetrakis(3-pyridazylmethyl)-1,4,7,10-tetraazacyclododecane (L pyd ), 1,4,7,10-tetrakis(4-pyrimidylmethyl)-1,4,7,10-tetraazacyclododecane (L pyr ), and 1,4,7,10-tetrakis(2-pyrazinylmethyl)-1,4,7,10-tetraazacyclododecane (L pz ), were prepared by a previously reported method and investigated here for their abilities to bind Bi radioisotopes. The commercially available and commonly used ligands 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) and N-[ (R) -2-amino-3-( p -isothiocyanato-phenyl)propyl]- trans -(S,S)- cyclohexane-1,2-diamine- N,N,N',N",N" -pentaacetic acid (CHX-A''-DTPA) were also explored for comparative purposes. Radio-thin-layer chromatography (TLC) was used to measure the binding kinetics and stabilities of the complexes formed. The long-lived isotope, ²⁰⁷Bi (t 1/2 = 32 years), was used for these studies. Density functional theory (DFT) calculations were also employed to probe the ligand interactions with Bi³⁺ and the generator parent ion Ac³⁺.In contrast to DOTA and CHX-A''-DTPA, these nitrogen-rich macrocycles selectively chelate Bi³⁺ in the presence of the parent isotope Ac³⁺. Among the four tested, L py was found to exhibit optimal Bi³⁺-binding kinetics and complex stability. L py complexes Bi³⁺ more rapidly than DOTA, yet the resulting complexes are of similar stability. DFT calculations corroborate the experimentally observed selectivity of these ligands for Bi³⁺ over Ac³⁺. Taken together, these data implicate L py as a valuable chelating agent for the delivery of ²¹³Bi. Its selectivity for Bi³⁺ and rapid and stable labeling properties warrant further investigation and biological studies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Oxidation and Hydration of U 3 O 8 Materials Following Controlled Exposure to Temperature and Humidity

Chemical signatures correlated with uranium oxide processing are of interest to forensic science for inferring sample provenance. Identification of temporal changes in chemical structures of process uranium materials as a function of controlled temperatures and relative humidities may provide additional information regarding sample history. In our study, a high-purity α-U 3 O 8 sample and three other uranium oxide samples synthesized from reaction routes used in nuclear conversion processes were stored under controlled conditions over 2–3.5 years, and powder X-ray diffraction analysis and X-ray absorption spectroscopy were employed to characterize chemical speciation. We measured signatures from the α-U 3 O 8 sample indicated that the material oxidized and hydrated after storage under high humidity conditions over time. Impurities, such as uranyl fluoride or schoepites, were initially detectable in the other uranium oxide samples. After storage under controlled conditions, the analyses of the samples revealed oxidation over time, although the signature of the uranyl fluoride impurity diminished. The presence of schoepite phases in older uranium oxide material is likely indicative of storage under high humidity and should be taken into account for assessing sample history. Finally, the absence of a signature from a chemical impurity, such as uranyl fluoride hydrate, in an older material may not preclude its presence at the initial time of production.

36 MATERIALS SCIENCE↗
DOE OSTI2015

In silico prediction of MOFs with high deliverable capacity or internal surface area

Metal–organic frameworks (MOFs) offer unprecedented atom-scale design and structural tunability, largely due to the vast number of possible organic linkers which can be utilized in their assembly. Exploration of this space of linkers allows identification of ranges of achievable material properties as well as discovery of optimal materials for a given application. Experimental exploration of the linker space has to date been quite limited due to the cost and complexity of synthesis, while high-throughput computational studies have mainly explored MOF materials based on known or readily available linkers. Here an evolutionary algorithm for de novo design of organic linkers for metal–organic frameworks is used to predict MOFs with either high methane deliverable capacity or methane accessible surface area. Known chemical reactions are applied in silico to a population of linkers to discover these MOFs. Through this design strategy, MOF candidates are found in the ten symmetric networks acs, cds, dia, hxg, lvt, nbo, pcu, rhr, sod, and tbo. Furthermore, the correlation between deliverable capacities and surface area is network dependent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

The materials genome in action: identifying the performance limits for methane storage

Analogous to the way the Human Genome Project advanced an array of biological sciences by mapping the human genome, the Materials Genome Initiative aims to enhance our understanding of the fundamentals of materials science by providing the information we need to accelerate the development of new materials. This approach is particularly applicable to recently developed classes of nanoporous materials, such as metal–organic frameworks (MOFs), which are synthesized from a limited set of molecular building blocks that can be combined to generate a very large number of different structures. In this Perspective, we describe how a materials genome approach can be used to search for high-performance adsorbent materials to store natural gas in a vehicular fuel tank. Drawing upon recent reports of large databases of existing and predicted nanoporous materials generated in silico , we have collected and compared on a consistent basis the methane uptake in over 650 000 materials based on the results of molecular simulation. The data that we have collected provide candidate structures for synthesis, reveal relationships between structural characteristics and performance, and suggest that it may be difficult to reach the current Advanced Research Project Agency-Energy (ARPA-E) target for natural gas storage.

03 NATURAL GAS↗
DOE OSTI2014

Covalency in Metal-Oxygen Multiple Bonds Evaluated Using Oxygen K-edge Spectroscopy and Electronic Structure Theory

Advancing theories of how metal oxygen bonding influences metal oxo properties can expose new avenues for innovation in materials science, catalysis, and biochemistry. Historically, spectroscopic analyses of the transition metal peroxyanions, MO4x-, have formed the basis for new M O bonding theories. Herein, relative changes in M O orbital mixing in MO42- (M = Cr, Mo, W) and MO41- (M = Mn, Tc, Re) are evaluated for the first time by non-resonant inelastic X-ray scattering, X-ray absorption spectroscopy using fluorescence and transmission (via a scanning transmission X-ray microscope), and linear-response density functional theory. The results suggest that moving from Group 6 to Group 7 or down the triads increases M O e () mixing. Meanwhile, t2 mixing ( + ) remains relatively constant within the same Group. These unexpected changes in frontier orbital energy and composition are evaluated in terms of periodic trends in d orbital energy and radial extension.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Optimizing nanoporous materials for gas storage

In this work, we address the question of which thermodynamic factors determine the deliverable capacity of methane in nanoporous materials. The deliverable capacity is one of the key factors that determines the performance of a material for methane storage in automotive fuel tanks. To obtain insights in how the molecular characteristics of a material are related to this deliverable capacity, we developed several statistical thermodynamic models. The predictions of these models are compared with the classical thermodynamics approach of Bhatia and Myers [Bhatia and Myers Langmuir, 2005, 22, 1688] and with the results of molecular simulations in which we screen the IZA zeolite structures and a hypothetical zeolite database of over 100,000 structures. Both the simulations and our models do not support the rule of thumb that, for methane storage, one should aim for an optimal heat of adsorption of 18.8 kJ/mol -1 . Instead, our models show that one can identify an optimal heat of adsorption, but that this optimal heat of adsorption depends on the structure of the material. The different models we have developed are aimed to provide guidelines on how this optimal heat of adsorption is related to the molecular structure of the material.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Modeling Methane Adsorption in Interpenetrating Porous Polymer Networks

Porous polymer networks (PPNs) are a class of porous materials of particular interest in a variety of energy-related applications because of their stability, high surface areas, and gas uptake capacities. Computationally derived structures for five recently synthesized PPN frameworks, PPN-2, -3, -4, -5, and -6, were generated for various topologies, optimized using semiempirical electronic structure methods, and evaluated using classical grand canonical Monte Carlo simulations. We show that a key factor in modeling the methane uptake performance of these materials is whether, and how, these material frameworks interpenetrate and demonstrate a computational approach for predicting the presence, degree, and nature of interpenetration in PPNs that enables the reproduction of experimental adsorption data.

Martin, RL↗