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At least 523 records · Page 29

Direct tests of cytochrome c and c 1 functions in the electron transport chain of malaria parasites

The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c-2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c-2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c1 for inducible knockdown. Translational repression of cyt c and cyt c1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c-2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.

60 APPLIED LIFE SCIENCES↗

Elucidating the atomistic origin of anharmonicity in tetragonal CH3NH3PbI3 with Raman scattering

Halide perovskite (HP) semiconductors exhibit unique strong coupling between the electronic and structural dynamics. In this work, we use Raman polarization-orientation (PO) measurements and ab initio molecular dynamics (AIMD) to investigate the origin and temperature evolution of the strong structural anharmonicity throughout the tetragonal phase of CH 3 NH 3 PbI 3 . Raman PO measurements reveal a soft modelike spectral feature. This mode shows an unusual continuous increase in damping with temperature which is indicative of an anharmonic potential surface. The analysis of AIMD trajectories identifies two major sources of anharmonicity: the orientational unlocking of the [CH 3 NH 3 ] + ions and large-amplitude octahedral tilting that continuously increases with temperature. Our work suggests that the standard phonon picture cannot describe the structural dynamics of tetragonal CH 3 NH 3 PbI 3 .

36 MATERIALS SCIENCE↗

Evaporation Induced Entrainment of Contaminants from Evaporating and Burning Liquids.

This interim report details model development, theory, and a literature review focusing on the evaporation induced entrainment (sub-boiling) of contaminated liquids. Entrainment from a variety of sources is the topic of DOE Handbook 3010, and this report deals more broadly with fire related airborne sources of contaminants in hazardous operations. Relatively few studies have examined sub-boiling behavior in the past, however, it can be a phenomenon that presents a fire related risk under hazardous operations. Molecular dynamics simulations are used to infer the gaseous evolution of coordinated complexes, and a model for a water/plutonium/nitrate system is deduced from the simulation results by evaluating the statistical trends of the results. Questions remain as to the chemical reactivity and longevity of entrained species. A generalized computer model capability and simple analytical model assumptions are developed for predicting the results of these and other (boiling and solid entrainment) scenarios. Verification related predictions using these models are illustrated.

36 MATERIALS SCIENCE↗

Present state and chemical evolution of the atmospheres of Titan, Triton, and Pluto

An evaluation is made of the current understanding of the atmospheres of Titan, Triton, and Pluto, as well as of theoretical models for their origin and evolution. All three atmospheres contain methane, while Titan, and probably Triton, have nitrogen. The primary driver in the evolution of the Titan atmosphere has been the irreversible photolysis of methane. If a surface reservoir of liquid methane exists to resupply the atmosphere, it is subject to enrichment in ethane due to the long-term photolysis of methane. The key issue in the origin and early evolution of Titan's atmosphere is the source of molecular nitrogen; two schemes for the conversion of ammonia to nitrogen have been considered.

Lunine, J. I.↗

Relating space radiation environments to risk estimates

A number of considerations must go into the process of determining the risk of deleterious effects of space radiation to travelers. Among them are (1) determination of the components of the radiation environment (particle species, fluxes and energy spectra) which will encounter, (2) determination of the effects of shielding provided by the spacecraft and the bodies of the travelers which modify the incident particle spectra and mix of particles, and (3) determination of relevant biological effects of the radiation in the organs of interest. The latter can then lead to an estimation of risk from a given space scenario. Clearly, the process spans many scientific disciplines from solar and cosmic ray physics to radiation transport theeory to the multistage problem of the induction by radiation of initial lesions in living material and their evolution via physical, chemical, and biological processes at the molecular, cellular, and tissue levels to produce the end point of importance.

Curtis, Stanley B.↗

Volcanic CO2 Abundance of Kilauea Plume Retrieved by Meand of AVIRIS Data

Absorbing the electromagnetic radiation in several regions of the solar spectrum, CO2 plays an important role in the Earth radiation budget since it produces the greenhouse effect. Many natural processes in the Earth s system add and remove carbon dioxide. Overall, measurements of atmospheric carbon dioxide at different sites around the world show an increased carbon dioxide concentration in the atmosphere. At Mauna Loa Observatory (Hawaii) the measured carbon dioxide increased from 315 to 365 ppm, in the period 1958 2000 [Keeling et al., 2001]. While at the large scale, the relationship between CO2 increase and global warming is established [IPCC, 1996], at the local scale, many studies are still needed to understand regional and local sources of carbon dioxide, such as volcanoes. The volcanic areas are particularly rich in carbon dioxide; this is due to magma degassing in the summit craters region of active volcanoes, and to the presence of fractures and active faults [Giammanco et al., 1998]. Several studies estimate a global flux of volcanic CO2 (34+/-24)10(exp 6) tons/day from effusive volcanic emissions, such as the tropospheric volcanic plume (Table 1) [McClelland et al., 1989]. Plumes are a turbulent mixture of gases, solid particles and liquid droplets, emitted continuously at high temperature from summit craters, fumarolic fields or during eruptive episodes. Inside the plume, water vapour represents 70 90% of the volcanic gases. The main gaseous components are CO2, SO2, HCl, H2, H2S, HF, CO, N2 and CH4. Other plume components are volcanic ash, aqueous and acid droplets and solid sulphur-derived particles [Sparks et al., 1997]. Volcanic gases and aerosols are evidences of volcanic activity [Spinetti et al., 2003] and they have important climatic and environmental effects [Fiocco et al., 1994]. For example, Etna volcano is one of the world s major volcanic gas sources [Allard et al., 1991]. New studies on volcanic gaseous emissions have pointed out that a variation of the gas ratio CO2/SO2 is related to eruptive episodes [Caltabiano et al., 1994]. However, measurements and monitoring of volcanic carbon dioxide are difficult and often hazardous, due to the high background presence of atmospheric CO2 and the inaccessibility of volcanic sites. Hyperspectral remote sensing is a suitable technique to overcome the difficulties of ground measurement. It permits a rapid, comprehensive view of volcanic plumes and their evolution over time, detection of all gases with absorption molecular lines within the sensor s multispectral range and, in general, measurement of all the volatile components evolving from craters. The molecular and particle plume components scatter and absorb incident solar radiation. The integral of the radiation difference composes the signal measured by the remote spectrometer. The inversion technique consists of retrieving the plume component concentrations, hence decomposing the signal into the different contributions. The accuracy of remote sensing techniques depends primarily on the sensor capability and sensitivity.

Spinetti, C.↗

Can Massive Stars Be Formed by Accretion?

Although massive stars play a critical role in the production of turbulent energy in the ISM, in the formation and destruction of molecular clouds, and ultimately in the dynamical and chemodynamical evolution of galaxies, our understanding of the sequence of events which leads to their formation is still rather limited.

Star formation accretion disks radiation hydrodyna↗

Unveiling the Mechanism of Mn Dissolution Through a Dynamic Cathode‐Electrolyte Interphase on LiMn2O4

Abstract Understanding the formation and evolution of the cathode‐electrolyte interphase (CEI), which forms at the interface between the cathode and electrolyte, is crucial for revealing degradation mechanisms in cathode materials, especially for developing strategies to stabilize the interphase in the strongly oxidizing conditions that evolve at high operating voltages in next‐generation Li‐ion batteries. However, The present understanding of the CEI is challenged by its complex and dynamic nature. In this work, near‐edge X‐ray absorption fine structure spectroscopy, electrochemical characterization, and reactive molecular dynamics simulations are combined to reveal a mechanism for CEI formation and evolution above model LiMn 2 O 4 (LMO) thin‐film electrodes in contact with conventional carbonate‐based electrolytes. It is found that Mn dissolution from LMO can be understood in terms of repetitive Mn 3 O 4 formation and dissolution behavior during cycling, which is closely connected to electrolyte decomposition and a key aspect of the CEI formation and growth. The behavior of the CEI in this model system offers detailed insight into the dynamic chemistry of the interphase, underscoring the important role of electrolyte composition and cathode surface structure in interphase degradation.

Ou, Wenhan↗

Cyclopentadiene evolution during pyrolysis-gas chromatography of PMR polyimides

The effect of formulated molecular weight (FMW), extent of cure, and cumulative aging on the amount of cyclopentadiene (CPD) evolved from Polymerization of Monomeric Reactants (PMR) polyimides were investigated by pyrolysis-gas chromotography (PY-GC). The PMR polyimides are additional crosslinked resins formed from an aromatic diamine, a diester of an aromatic tetracarboxylic acid and a monoester of 5-norbornene-2, 3-dicarboxylic acid. The PY-GC results were related to the degree of crosslinking and to the thermo-oxidative stability (weight loss) of PMR polyimides. Thus, PY-GC has shown to be a valid technique for the characterization of PMR polyimide resins and composites via correlation of the CPD evolved versus the thermal history of the PMR sample.

Alston, William B.↗

The collapse of clouds and the formation and evolution of stars and disks

We consider the interrelationships among the structure of molecular clouds; the collapse of rotating cloud cores; the formation of stars and disks; the origin of molecular outflows, protostellar winds, and highly collimated jets; the birth of planetary and binary systems; and the dynamics of star/disk/satellite interactions. Our discussion interweaves theory with the results of observations that span from millimeter wavelengths to X-rays.

Shu, Frank↗

Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will be maintained only if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74%–94% of the variance in aneuploid strains’ growth rates is explained by the cumulative cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of small nucleolar RNAs (snoRNAs) and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.

genic load↗

ALMA Observations of the Molecular Gas in the Debris Disk of the 30 Myr Old Star HD 21997

The 30 Myr old A3-type star HD 21997 is one of the two known debris dust disks having a measurable amount of cold molecular gas. With the goal of understanding the physical state, origin, and evolution of the gas in young debris disks, we obtained CO line observations with the Atacama Large Millimeter/submillimeter Array (ALMA). Here, we report on the detection of (12)CO and (13)CO in the J = 2-1 and J = 3-2 transitions and C(18)O in the J = 2-1 line. The gas exhibits a Keplerian velocity curve, one of the few direct measurements of Keplerian rotation in young debris disks. The measured CO brightness distribution could be reproduced by a simple star+disk system, whose parameters are r(sub in) < 26 AU, r(sub out) = 138 +/- 20 AU, Stellar M = 1.8 +0.5/−0.2 Solar M, and i = 32. Deg. 6 +/- 3 deg..1. The total CO mass, as calculated from the optically thin C(18)O line, is about (4-8) ×10(exp −2 ) Solar M, while the CO line ratios suggest a radiation temperature on the order of 6-9 K. Comparing our results with those obtained for the dust component of the HD 21997 disk from ALMA continuum observations by Moor et al., we conclude that comparable amounts of CO gas and dust are present in the disk. Interestingly, the gas and dust in the HD 21997 system are not colocated, indicating a dust-free inner gas disk within 55 AU of the star. We explore two possible scenarios for the origin of the gas. A secondary origin, which involves gas production from colliding or active planetesimals, would require unreasonably high gas production rates and would not explain why the gas and dust are not colocated. We propose that HD 21997 is a hybrid system where secondary debris dust and primordial gas coexist. HD 21997, whose age exceeds both the model predictions for disk clearing and the ages of the oldest T Tauri-like or transitional gas disks in the literature, may be a key object linking the primordial and the debris phases of disk evolution.

molecular gas↗

Transient Pulse-Response Time-of-Flight Mass Spectrometry for Complex, Deactivating Heterogeneous Catalytic Systems: Application to Ethane Dehydroaromatization

The study of complex, multistep bond-forming and -breaking reactions in heterogeneous catalytic systems often encounters challenges associated with the involvement of large numbers of intermediates among branching pathways. Kinetic information obtained from traditional steady-state measurements can be complemented with that from time-resolved methods to uncover details of the underlying chemistry. Herein, we describe an approach for tracking the complete time-resolved chemical composition (ca. 4–200 u) of a reactor effluent in response to a reactant pulse. We use a six-port rotary valve with a metered sampling loop to pulse reactants at ambient pressure into a flow reactor packed with a catalyst bed within the isothermal region of a heated furnace. The temporal evolution of effluent species is tracked using time-resolved molecular-beam time-of-flight mass spectrometry. We highlight the possibilities that this method has to offer by studying the complex bifunctional mechanism of ethane dehydroaromatization over an HZSM-5-supported platinum catalyst. We demonstrate that energy-tunable ionization sources, which facilitate isomer resolution, enable the measurement of the full mass spectral time-dependent system response. This includes the evolution of major products and mechanistically relevant reactive intermediates such as 1,3-butadiene and cyclopentadiene; these species have not previously been observed from this reaction. In additional studies, we also assess the role of platinum in the catalyst by examining temporal responses to ethane and ethylene feeds. Results show that two temporally distinct formation pathways exist for methane and benzene, and that their importance depends on both catalyst composition and reactant identity. Additionally, characteristics of catalyst deactivation are uniquely observable in the time-resolved mass spectral response, including the selective deactivation of a benzene formation pathway. The combination of time-of-flight mass spectrometry with tunable ionization enables the simultaneous observation of all effluents in a complex mixture of intermediates with isomer/isobar differentiation capabilities that can be applied to any complex reaction system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microgravity research in plant biological systems: Realizing the potential of molecular biology

The sole all-pervasive feature of the environment that has helped shape, through evolution, all life on Earth is gravity. The near weightlessness of the Space Station Freedom space environment allows gravitational effects to be essentially uncoupled, thus providing an unprecedented opportunity to manipulate, systematically dissect, study, and exploit the role of gravity in the growth and development of all life forms. New and exciting opportunities are now available to utilize molecular biological and biochemical approaches to study the effects of microgravity on living organisms. By careful experimentation, we can determine how gravity perception occurs, how the resulting signals are produced and transduced, and how or if tissue-specific differences in gene expression occur. Microgravity research can provide unique new approaches to further our basic understanding of development and metabolic processes of cells and organisms, and to further the application of this new knowledge for the betterment of humankind.

Lewis, Norman G.↗

Prediction of vacancy defect diffusion paths in high entropy alloys via machine learning on molecular dynamics data

Identifying the diffusion path of point defects is a critical step in understanding their evolution and the mechanisms of related phenomena. Defect diffusion occurs at small length and time scales, with impacts on material properties that may continue to evolve over ns to μs, ms, and the continuum scale (s, min, etc., and cm, m, etc.). The time scale accessible to molecular dynamics (MD) simulations is limited by small step sizes, typically in the fs range. Thus, surrogate models of MD simulations through machine learning (ML)-based algorithms are of great interest, especially for complex systems such as high entropy alloys (HEAs). In this work, dynamics governing vacancy migration in HEA were approximated with graph convolutional network (GCN) models as ansatzes for kinetic Monte Carlo (KMC) rate catalogs. Network design considered that diffusion in crystalline solids generally depends on interactions between defects and their immediate neighbor atoms. Graphs represented the vacancy surroundings, MD-generated trajectories provided training and comparison datasets, and unsupervised GCN models approximated interatomic dynamics governing vacancy migration in HEAs as ansatzes for KMC. A proof-of-concept model trained on MD data for the Fe, Ni, Cr, Co, and Cu HEA environment was used with two different neighbor interactions to assess the feasibility of training a GCN to predict vacancy defect transition rates in the HEA environment. The resulting setup rapidly generated MD-formatted synthetic trajectories based on dynamics learned from the MD training set, with a time acceleration of roughly two orders of magnitude and a similar diffusion coefficient to MD observations. Additionally, Nudged Elastic Band (NEB) calculations were performed on randomly generated FeNiCrCoCu HEA structures to determine vacancy migration barriers across nearest-neighbor sites. Transition probabilities for each jump, categorized by atomic type, were extracted from these calculations. NEB-based and GCN-based approaches led to similar outcomes.

Reimer, C↗

Ultraviolet observations of interstellar extinction near the Cepheus OB3 molecular cloud

New IUE observations and available data for O and B stars new Cep OB3 are presented, and extinction curves for the stars are derived. The differences in those curves are examined in detail, showing that while the level of the far-UV extinction differs greatly throughout the region, the shape of the 2175 A bump does not. The different curves form a family which can be parametrized by the strength of the bump per E(B-V). This suggests that some single physical process dominates the modification of the grains in the region. Evidence is presented which indicates that this process is related to the evolution of the grains once they emerge from the Cep OB3 molecular cloud. The practicality of using the strength of the bump per E(B-V) for dereddening stars in a region where the form of the UV extinction differs from place to place is demonstrated.

Massa, D.↗

Analyzing the effect of pressure on the properties of point defects in $\gamma\mathrm{U–Mo}$ through atomistic simulations

Uranium–molybdenum (U–Mo) alloys in monolithic fuel foil are the primary candidate for the conversion of high-performance research reactors in the USA. Monolithic fuel is utilized in a plate-type design with a zirconium diffusion barrier and aluminum cladding. These fuel types are unique in that they contain no plenum for the release of fission gases, which, in conjunction with the aluminum cladding, can lead to large stress states within the fuel. The nature of how fundamental processes of radiation damage, including the evolution of point defects, under such stresses occur is unknown. In this work, we present molecular dynamics simulations of the formation energy of point defects under applied stress. We report this work will allow for the implementation of stress-dependent microstructural evolution models of nuclear fuels, including those for both fission gas bubble growth and creep, which are critical to ensure the stable and predictable behavior of research reactor fuels.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗