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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Output Data: gcam_usa_v5p3_im3

Output databases and tables supporting the publication: Khan, Z., Zhao, M., Ahsan, H., Wolfram, P., Vernon, C., Rice, J., Iyer, G., Binsted, M., Snyder, A., Graham, N., Kyle, P., 2023. Coevolution of future water, energy and land systems across the United States in response to national and global socioeconomic, climate, and energy policy drivers. (In progress) Earths Future, DOI: XXX with further details available at the meta-repository: https://immm-sfa.github.io/khan-etal_2023_im3gcamusa Folder: gcam_usa_im3_outputs (GCAM USA v 5.3 used for IM3 experiment Output Databases): database_rcp45cooler_ssp3.tar.gz database_rcp45cooler_ssp5.tar.gz database_rcp45hotter_ssp5.tar.gz database_rcp45hotter_ssp5.tar.gz database_rcp85cooler_ssp3.tar.gz database_rcp85cooler_ssp5.tar.gz database_rcp85hotter_ssp5.tar.gz database_rcp85hotter_ssp5.tar.gz Folder: gcam_usa_im3_gcamextractor_outputs (gcamextractor post-processing of the GCAM databases for specific downstream models ): dataGCAM_cerf.tar.gz (For CERF Model) dataGCAM_demeter.tar.gz (For Demeter model) dataGCAM_go.tar.gz (For GO model) gcamDataTable.tar.gz (All IM3 scenarios)

Climate Change↗
NASA NTRS1991

No-net-rotation model of current plate velocities incorporating plate motion model NUVEL-1

NNR-NUVEL1 is presented which is a model of plate velocities relative to the unique reference frame defined by requiring no-net-rotation of the lithosphere while constraining relative plate velocities to equal those in global plate motion model NUVEL-1 (DeMets et al., 1990). In NNR-NUVEL1, the Pacific plate rotates in a right-handed sense relative to the no-net-rotation reference frame at 0.67 deg/m.y. about 63 deg S, 107 deg E. At Hawaii the Pacific plate moves relative to the no-net-rotation reference frame at 70 mm/yr, which is 25 mm/yr slower than the Pacific plate moves relative to the hotspots. Differences between NNR-NUVEL1 and HS2-NUVEL1 are described. The no-net-rotation reference frame differs significantly from the hotspot reference frame. If the difference between reference frames is caused by motion of the hotspots relative to a mean-mantle reference frame, then hotspots beneath the Pacific plate move with coherent motion towards the east-southeast. Alternatively, the difference between reference frames can show that the uniform drag, no-net-torque reference frame, which is kinematically equivalent to the no-net-rotation reference frame, is based on a dynamically incorrect premise.

Argus, Donald F.↗
NASA NTRS1992

Plate tectonics from VLBI and SLR global data

This study is based on data derived from fifteen years of observations of the SLR (side-looking radar) network and six years of the VLBI (very long baseline interferometry) network. In order to use all available information VLBI and SLR global data sets were combined in a least squares fashion to calculate station horizontal velocities. All significant data pertaining to a single site contribute to the station horizontal motion. The only constraint on the solution is that no vertical motion is allowed. This restriction does not greatly affect the precision of the overall solution given the fact that the expected vertical motion for most stations, even those experiencing post glacial uplift, is well under 1 cm/yr. Since the average baseline is under 4,000 km, only a small fraction of the station vertical velocity is translated into baseline rates so that the error introduced in the solution by restricting up-down station movement is minimal. As a reference, station velocities were then compared to the ones predicted by the NUVEL-1 geological model of DeMets et al. (1990). The focus of the study is on analyzing these discrepancies for global plate tectonics as well as regional tectonic settings. The method used also allows us not only to derive horizontal motion for individual stations but also to calculate Euler vectors for those plates that have enough stations located on the stable interior like North America, Pacific, Eurasia, and Australia.

Harrison, Christopher G. A.↗
NASA NTRS2003

Perfection of Apoferritin Crystals: An Advanced X-Ray Imaging and Diffraction Study

Ferritin is a well-known iron-storage protein, and is a spherical shell that consists of 24 identical subunits packed in a 432 symmetry. The typically large protein size and its distinction from lysozyme as to chemical and physical characteristics make ferritin an attractive model protein for crystal growth and perfection investigation-as an alternative to the most widely studied lysozyme. In this contribution, the latest results obtained from coherence-based x-ray diffraction imaging and diffraction experiments will be presented on octahedral apoferritin (a demetalized form of ferritin) crystals grown from various growth conditions. Crystal specimens, which have the measured rocking-curve widths varying from a few arcseconds to several tens arcseconds (or more), are comparatively examined by intrinsically highly sensitive mapping of lattice perfection and defects. The richness of the observed defects and growth features offers insight into perfection and growth of protein crystals. Beautiful interference fringe patterns formed in diffraction images and fine oscillation structure of rocking curves observed will be discussed for understanding of physical origins and the underlying impact.

Hu, Z. W.↗
NASA NTRS2004

Near Space Tracking of the EM Phenomena Associated with the Main Earthquakes

Searching for electromagnetic (EM) phenomena originating in the Earth's crust prior to major earthquakes (M>5) are the object of this exploratory study. We present the idea of a possible relationship between: (1) electro-chemical and thermodynamic processes in the Earth's crust and (2) ionic enhancement of the atmosphere/ionosphere with tectonic stress and earthquake activity. The major source of these signals are proposed to originate from electromagnetic phenomenon which are responsible for these observed pre-seismic processes, such as, enhanced IR emission, also born as thermal anomalies, generation of long wave radiation, light emission caused by ground-to-air electric discharges, Total Electron Content (TEC) ionospheric anomalies and ionospheric plasma variations. The source of these data will include: (i) ionospheric plasma perturbations data from the recently launched DEMETER mission and currently available TEC/GPS network data; (ii) geomagnetic data from ORSTED and CHAMP; (iii) Thermal infra-red (TIR) transients mapped by the polar orbiting (NOAA/AVHRR, MODIS) and (iv) geosynchronous weather satellites measurements of GOES, METEOSAT. This approach requires continues observations and data collecting, in addition to both ground and space based monitoring over selected regions in order to investigate the various techniques for recording possible anomalies. During the space campaign emphasis will be on IR emission, obtained from TIR (thermal infrared) satellites, that records land/sea surface temperature anomalies and changes in the plasma and total electron content (TEC) of the ionosphere that occur over areas of potential earthquake activity.

Ouzounov, Dimitar↗
NASA NTRS1999

Glacial Isostatic Adjustment Observed with VLBI and SLR

In global geodetic solutions vertical rates of site motion are usually estimated relative to the geocenter (center of figure) of the solid earth. The velocity of the geocenter is estimated assuming that the plates are rigid, that the velocities of the plates equal those in NUVEL-1A (DeMets et al. 1990, 1994) and that the uplift, subsidence, and intraplate deformation due to glacial isostatic adjustment is negligible.

postglacial rebould mantel viscosity crustal movem↗
NASA NTRS2011

Theory and Simulations of Solar System Plasmas

"Theory and simulations of solar system plasmas" aims to highlight results from microscopic to global scales, achieved by theoretical investigations and numerical simulations of the plasma dynamics in the solar system. The theoretical approach must allow evidencing the universality of the phenomena being considered, whatever the region is where their role is studied; at the Sun, in the solar corona, in the interplanetary space or in planetary magnetospheres. All possible theoretical issues concerning plasma dynamics are welcome, especially those using numerical models and simulations, since these tools are mandatory whenever analytical treatments fail, in particular when complex nonlinear phenomena are at work. Comparative studies for ongoing missions like Cassini, Cluster, Demeter, Stereo, Wind, SDO, Hinode, as well as those preparing future missions and proposals, like, e.g., MMS and Solar Orbiter, are especially encouraged.

Goldstein, Melvyn L.↗
NASA NTRS2010

Validating of Atmospheric Signals Associated with some of the Major Earthquakes in Asia (2003-2009)

The recent catastrophic earthquake in Haiti (January 2010) has provided and renewed interest in the important question of the existence of precursory signals related to strong earthquakes. Latest studies (VESTO workshop in Japan 2009) have shown that there were precursory atmospheric signals observed on the ground and in space associated with several recent earthquakes. The major question, still widely debated in the scientific community is whether such signals systematically precede major earthquakes. To address this problem we have started to validate the anomalous atmospheric signals during the occurrence of large earthquakes. Our approach is based on integration analysis of several physical and environmental parameters (thermal infrared radiation, electron concentration in the ionosphere, Radon/ion activities, air temperature and seismicity) that were found to be associated with earthquakes. We performed hind-cast detection over three different regions with high seismicity Taiwan, Japan and Kamchatka for the period of 2003-2009. We are using existing thermal satellite data (Aqua and POES); in situ atmospheric data (NOAA/NCEP); and ionospheric variability data (GPS/TEC and DEMETER). The first part of this validation included 42 major earthquakes (M greater than 5.9): 10 events in Taiwan, 15 events in Japan, 15 events in Kamchatka and four most recent events for M8.0 Wenchuan earthquake (May 2008) in China and M7.9 Samoa earthquakes (Sep 2009). Our initial results suggest a systematic appearance of atmospheric anomalies near the epicentral area, 1 to 5 days prior to the largest earthquakes, that could be explained by a coupling process between the observed physical parameters, and the earthquake preparation processes.

Ouzounov, D. P.↗
NASA NTRS2012

Validation of Atmosphere/Ionosphere Signals Associated with Major Earthquakes by Multi-Instrument Space-Borne and Ground Observations

The latest catastrophic earthquake in Japan (March 2011) has renewed interest in the important question of the existence of pre-earthquake anomalous signals related to strong earthquakes. Recent studies have shown that there were precursory atmospheric/ionospheric signals observed in space associated with major earthquakes. The critical question, still widely debated in the scientific community, is whether such ionospheric/atmospheric signals systematically precede large earthquakes. To address this problem we have started to investigate anomalous ionospheric / atmospheric signals occurring prior to large earthquakes. We are studying the Earth's atmospheric electromagnetic environment by developing a multisensor model for monitoring the signals related to active tectonic faulting and earthquake processes. The integrated satellite and terrestrial framework (ISTF) is our method for validation and is based on a joint analysis of several physical and environmental parameters (thermal infrared radiation, electron concentration in the ionosphere, lineament analysis, radon/ion activities, air temperature and seismicity) that were found to be associated with earthquakes. A physical link between these parameters and earthquake processes has been provided by the recent version of Lithosphere-Atmosphere-Ionosphere Coupling (LAIC) model. Our experimental measurements have supported the new theoretical estimates of LAIC hypothesis for an increase in the surface latent heat flux, integrated variability of outgoing long wave radiation (OLR) and anomalous variations of the total electron content (TEC) registered over the epicenters. Some of the major earthquakes are accompanied by an intensification of gas migration to the surface, thermodynamic and hydrodynamic processes of transformation of latent heat into thermal energy and with vertical transport of charged aerosols in the lower atmosphere. These processes lead to the generation of external electric currents in specific regions of the atmosphere and the modifications, by dc electric fields, in the ionosphere-atmosphere electric circuit. We retrospectively analyzed temporal and spatial variations of four different physical parameters (gas/radon counting rate, lineaments change, long-wave radiation transitions and ionospheric electron density/plasma variations) characterizing the state of the lithosphere/atmosphere coupling several days before the onset of the earthquakes. Validation processes consist in two phases: A. Case studies for seven recent major earthquakes: Japan (M9.0, 2011), China (M7.9, 2008), Italy (M6.3, 2009), Samoa (M7, 2009), Haiti (M7.0, 2010) and, Chile (M8.8, 2010) and B. A continuous retrospective analysis was preformed over two different regions with high seismicity- Taiwan and Japan for 2003-2009. Satellite, ground surface, and troposphere data were obtained from Terra/ASTER, Aqua/AIRS, POES and ionospheric variations from DEMETER and COSMIC-I data. Radon and GPS/TEC were obtaining from monitoring sites in Taiwan, Japan and Italy and from global ionosphere maps (GIM) respectively. Our analysis of ground and satellite data during the occurrence of 7 global earthquakes has shown the presence of anomalies in the atmosphere. Our results for Tohoku M9.0 earthquake show that on March 7th, 2011 (4 days before the main shock and 1 day before the M7.2 foreshock of March 8, 2011) a rapid increase of emitted infrared radiation was observed by the satellite data and an anomaly was developed near the epicenter. The GPS/TEC data indicate an increase and variation in electron density reaching a maximum value on March 8. From March 3 to 11 a large increase in electron concentration was recorded at all four Japanese ground-based ionosondes, which returned to normal after the main earthquake. Similar approach for analyzing atmospheric and ionospheric parameters has been applied for China (M7.9, 2008), Italy (M6.3, 2009), Samoa (M7, 2009), Haiti (M7.0, 2010) and Chile (M8.8, 2010) eahquakes. Results have revealed the presence of related variations of these parameters implying their connection with the earthquake process. The second phase (B) of this validation included 102 major earthquakes (M>5.9) in Taiwan and Japan. We have found anomalous behavior before all of these events with no false negatives. False alarm ratio for false positives is less then 10% and has been calculated for the same month of the earthquake occurrence for the entire period of analysis (2003-2009). The commonalities for detecting atmospheric/ionospheric anomalies are: i.) Regularly appearance over regions of maximum stress (i.e., along plate boundaries); ii.) Anomaly existence over land and sea; and iii) association with M>5.9 earthquakes not deeper than 100km. Due to their long duration over the same region these anomalies are not consistent with a meteorological origin. Our initial results from the ISTF validation of multi-instrument space-borne and ground observations show a systematic appearance of atmospheric anomalies near the epicentral area, one to seven (average) days prior to the largest earthquakes, and suggest that it could be explained by a coupling process between the observed physical parameters and the pre-earthquake preparation processes.

Ouzounov, Dimitar↗
NASA NTRS2012

Inter-Disciplinary Validation of Pre Earthquake Signals. Case Study for Major Earthquakes in Asia (2004-2010) and for 2011 Tohoku Earthquake

We carried out multi-sensors observations in our investigation of phenomena preceding major earthquakes. Our approach is based on a systematic analysis of several physical and environmental parameters, which we found, associated with the earthquake processes: thermal infrared radiation, temperature and concentration of electrons in the ionosphere, radon/ion activities, and air temperature/humidity in the atmosphere. We used satellite and ground observations and interpreted them with the Lithosphere-Atmosphere- Ionosphere Coupling (LAIC) model, one of possible paradigms we study and support. We made two independent continues hind-cast investigations in Taiwan and Japan for total of 102 earthquakes (M>6) occurring from 2004-2011. We analyzed: (1) ionospheric electromagnetic radiation, plasma and energetic electron measurements from DEMETER (2) emitted long-wavelength radiation (OLR) from NOAA/AVHRR and NASA/EOS; (3) radon/ion variations (in situ data); and 4) GPS Total Electron Content (TEC) measurements collected from space and ground based observations. This joint analysis of ground and satellite data has shown that one to six (or more) days prior to the largest earthquakes there were anomalies in all of the analyzed physical observations. For the latest March 11 , 2011 Tohoku earthquake, our analysis shows again the same relationship between several independent observations characterizing the lithosphere /atmosphere coupling. On March 7th we found a rapid increase of emitted infrared radiation observed from satellite data and subsequently an anomaly developed near the epicenter. The GPS/TEC data indicated an increase and variation in electron density reaching a maximum value on March 8. Beginning from this day we confirmed an abnormal TEC variation over the epicenter in the lower ionosphere. These findings revealed the existence of atmospheric and ionospheric phenomena occurring prior to the 2011 Tohoku earthquake, which indicated new evidence of a distinct coupling between the lithosphere and atmosphere/ionosphere.

Ouzounov, D.↗
DOE OSTI2021

Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH3)4]q, q = -2, -1, +2, +3

Iron-sulfur clusters play important roles in biology as parts of electron transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron-sulfur cluster of rubredoxin and its cationic counterparts. Specifically, we report results for the ground and low-lying electronically excited states of the complex [Fe(SCH3)4]2-/1-/2+/3+, using Multi-Reference (CASSCF, MRCISD), and Coupled Cluster [CCSD(T)] methodology in order to provide accurate adiabatic reduction energies, dissociation energies and insights into the bonding analysis. The nature of the Fe-S chemical bond and the magnitude of the ionization potentials in the anionic and cationic [Fe(SCH3)4] complexes offer a physical rationale for the relative stabilization, structure and speciation of these complexes. Anionic and cationic complexes present different types of chemical bonds: prevalently ionic in [Fe(SCH3)4]2-/1- complexes and covalent in [Fe(SCH3)4]2+/3+ complexes. The ionic bonds result in an energy gain for the transition [Fe(SCH3)4]2-®[Fe(SCH3)4]- (i.e., FeII®FeIII) of 1.5 eV, while the covalent bonds result in an energy loss for the transition [Fe(SCH3)4]2+®[Fe(SCH3)4]3+ of 16.6 eV, almost half of the IP of Fe2+. The ionic vs covalent bond character influences the Fe-S bond strength and length, i.e., ionic Fe-S bonds are longer than covalent ones by about 0.2 Å (for FeII) and 0.04 Å (for FeII). Finally, the average Fe-S heterolytic bond strength is 6.7 eV (FeII) and 14.6 (FeIII) eV at the RCCSD(T) level of theory.

Tzeli, Demeter↗
DOE OSTI2022

The Effect of Geometry, Spin, and Orbital Optimization in Achieving Accurate, Correlated Results for Iron–Sulfur Cubanes

Iron–sulfur clusters comprise an important functional motif in the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from correlated, large active space calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. Here, to provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of the [Fe(II/III) 4 S 4 (SMe) 4 ] -2 clusters using two complementary, correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (<1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the singlet and the spin state 2S + 1 = 19, corresponding to a maximal number of Fe-d electrons being unpaired and of parallel spin, is strongly geometry dependent, changing by a factor of 3 upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap compared to typical mean-field orbital approaches. Our results show the need for performing large active space calculations to unveil the challenging electronic structure of these complex catalytic centers and should serve as accurate starting points for fully correlated treatments upon inclusion of dynamical correlation outside the active space.

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

Importance of Electron Correlation on the Geometry and Electronic Structure of [2Fe–2S] Systems: A Benchmark Study of the [Fe 2 S 2 (SCH 3 ) 4 ] 2–,3–,4– , [Fe 2 S 2 (SCys) 4 ] 2– , [Fe 2 S 2 (S- p -tol) 4 ] 2– , and [Fe 2 S 2 (S- o -xyl) 4 ] 2– Complexes

Iron–sulfur clusters are crucial for biological electron transport and catalysis. Obtaining accurate geometries, energetics, manifolds of their excited electronic states, and reduction energies is important to understand their role in these processes. Here, using a [2Fe–2S] model complex with Fe II and Fe III oxidation states, which leads to different charges, i.e., [Fe 2 S 2 (SMe) 4 ] 2–,3–,4– , we benchmarked a variety of computational methodologies ranging from density functional theory (DFT) to post-Hartree–Fock methods, including complete active space self-consistent field (CASSCF), multireference configuration interaction, the second-order N-electron valence state perturbation theory (NEVPT2), and the linearized integrand approximation of adiabatic connection (AC0) approaches. Additionally, we studied three experimentally well-characterized complexes, [Fe 2 S 2 (SCys) 4 ] 2– , [Fe 2 S 2 (S-o-tol) 4 ] 2– , and [Fe 2 S 2 (S-o-xyl) 4 ] 2– , via DFT methods. We conclude that the dynamic electron correlation is important for accurately predicting the geometry of these complexes. Broken symmetry (BS) DFT correctly predicts experimental geometries of low-spin multiplicity, while CASSCF does not. However, BS-DFT significantly overestimates the difference between the low- and high-spin electronic states for a given oxidation state. At the same time, CASSCF underestimates it but provides relative energies closer to the reference NEVPT2 results. Finally, AC0 provides energetics of NEVPT2 quality with the additional advantage of being able to use large CASSCF sizes. NEVPT2 gives the best estimates of the Fe III /Fe III → Fe II /Fe III (4.27 eV) and Fe II /F III → Fe II /F II (7.72 eV) reduction energies. The results provide insight into the electronic structure of these complexes and assist in the understanding of their physical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The Many-Body Expansion for Metals: II. Nonadditive Terms in Clusters Composed of Metals with n s 1 , n s 2 , and n s 2 p 1 Configurations

The many-body expansion (MBE) was applied to homometallic and heterometallic trimers of metals with ns 1 , ns 2 , and ns 2 p 1 configurations to investigate its convergence, the magnitude and nature (stabilizing/destabilizing) of the individual terms and seek an understanding of their variation across the different families of clusters. In particular, we examined the series of alkali metals (Li 3 , Na 3 , K 3 , Li 2 Na, LiNa 2 ), alkali metal borides (Li 2 B and LiB 2 ), and alkaline earth metals (Be 3 , Be 2 Mg, BeMg 3 , and Mg 3 ) trimers, as well as sodium clusters Na n , n = 2–5. Here, we found that there is no uniform contribution (stabilizing or destabilizing) across the series in the different families of trimers. For instance, the 2-B term stabilizes the ground states of the Na 3 (doublet), Na 4 (singlet), and Na 5 (doublet) clusters, and the 3-B term destabilizes them; however, the opposite holds for the quartet state of the Li 3 , Li 2 Na, LiNa 2 , and Na 3 clusters (destabilizing 2-B, stabilizing 3-B). Substituting Li with B in the quartet state of Li 3 results in a significant reduction of the 3-B term amounting to 16% (Li 2 B) and 5% (LiB 3 ) of the binding energy. On the contrary, the ground states of the alkaline earth metal clusters (Be 3 , Be 2 Mg, BeMg 3 , and Mg 3 ) are stabilized by the 3-B term, while the 2-B term destabilizes them. Overall, we find that the 3-B terms significantly stabilize the high-spin multiplicity states of the ns 1 configurations and the low-spin states of the ns 2 configurations. Finally, as the size of the metal increases, the contribution of the 3-B term to the binding energy decreases due to the longer metal–metal bond distances.

Alkali metals↗
DOE OSTI2023

Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder

Adhesion G protein-coupled receptors (aGPCRs) are cell-surface proteins with large extracellular regions that bind to multiple ligands to regulate key biological functions including neurodevelopment and organogenesis. Modulating a single function of a specific aGPCR isoform while affecting no other function and no other receptor is not trivial. Here, we engineered an antibody, termed LK30, that binds to the extracellular region of the aGPCR ADGRL3, and specifically acts as an agonist for ADGRL3 but not for its isoform, ADGRL1. The LK30/ADGRL3 complex structure revealed that the LK30 binding site on ADGRL3 overlaps with the binding site for an ADGRL3 ligand – teneurin. In cellular-adhesion assays, LK30 specifically broke the trans-cellular interaction of ADGRL3 with teneurin, but not with another ADGRL3 ligand – FLRT3. Our work provides proof of concept for the modulation of isoform- and ligand-specific aGPCR functions using unique tools, and thus establishes a foundation for the development of fine-tuned aGPCR-targeted therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ultrafast structural changes direct the first molecular events of vision

Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs). A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-transconformation, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The many-body expansion for metals. I. The alkaline earth metals Be, Mg, and Ca

We examine the many-body expansion (MBE) for alkaline earth metal clusters, Be n , Mg n , Ca n ( n = 4, 5, 6), at the Møller–Plesset second order perturbation theory, coupled-cluster singles and doubles with perturbative triples, multi-reference perturbation theory, and multi-reference configuration interaction levels of theory. The magnitude of each term in the MBE is evaluated for several geometrical configurations. We find that the behavior of the MBE for these clusters depends strongly on the geometrical arrangement and, to a lesser extent, on the level of theory used. Another factor that affects the MBE is the in situ (ground or excited) electronic state of the individual atoms in the cluster. For most geometries, the three-body term is the largest, followed by a steady decrease in absolute energy for subsequent terms. Though these systems exhibit non-negligible multi-reference effects, there was little qualitative difference in the MBE when employing single vs multi-reference methods. Useful insights into the connectivity and stability of these clusters have been drawn from the respective potential energy surfaces and quasi-atomic orbitals for the various dimers, trimers, and tetramers. Through these analyses, we investigate the similarities and differences in the binding energies of different-sized clusters for these metals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗