Simple estimation of absolute free energies for biomolecules

One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is irrelevant, however, if the absolute free energy of each state can be computed. We present a method for calculating the absolute free energy that employs a simple construction of an exactly computable reference system which possesses high overlap with the state of interest. The approach requires only a physical ensemble of conformations generated via simulation, and an auxiliary calculation of approximately equal central-processing-unit (CPU) cost. Moreover, the calculations can converge to the correct free energy value even when the physical ensemble is incomplete or improperly distributed. As a "proof of principle," we use the approach to correctly predict free energies for test systems where the absolute values can be calculated exactly, and also to predict the conformational equilibrium for leucine dipeptide in implicit solvent.Comment: To appear in J. Chem. Phys., 10 pages, 6 figure

An X-ray Spectroscopic Study of the Hot Interstellar Medium Toward the Galactic Bulge

We present a detailed spectroscopic study of the hot gas toward the Galactic bulge along the 4U 1820-303 sight line by a combination analysis of emission and absorption spectra. In addition to the absorption lines of OVII Kalpha, OVII Kbeta, OVIII Kalpha and NeIX Kalpha by Chandra LTGS as shown by previous works, Suzaku detected clearly the emission lines of OVII, OVIII, NeIX and NeX from the vicinity. We used simplified plasma models with constant temperature and density. Evaluation of the background and foreground emission was performed carefully, including stellar X-ray contribution based on the recent X-ray observational results and stellar distribution simulator. If we assume that one plasma component exists in front of 4U1820-303 and the other one at the back, the obtained temperatures are T= 1.7 +/- 0.2 MK for the front-side plasma and T=3.9(+0.4-0.3) MK for the backside. This scheme is consistent with a hot and thick ISM disk as suggested by the extragalactic source observations and an X-ray bulge around the Galactic center.Comment: 14 pages, 15 figures, accepted to be published in PASJ (Replace figure files to fix latex problem

The Effect of Fe-Al Substitution on the Crystal Structure of MgSiO3 Bridgmanite

The crystal chemistry of ten well-characterized bridgmanite single-crystals with Fe and Al contents ranging from 0 to 0.40 atoms per two-cation formula units were investigated by single-crystal X-ray diffraction. Structural refinements indicate that Fe3+ and Al mainly occupy the Mg and Si sites, respectively, when present in similar proportions. Molar volumes of bridgmanite endmember components were refined using data from this and previous studies and found to decrease in the order Fe3+Fe3+O3 > MgFe3+O2.5 > Fe3+AlO3 > MgAlO2.5 > AlAlO3 > Fe2+SiO3 > MgSiO3. Fe3+AlO3 charge-coupled substitution leads to an anisotropic increase of B-O bond distances, resulting in more distorted octahedral B sites and in a more significant increase of the c-axis with respect to the a- and b-axes. Valence bond calculations indicate that the A site is more compressible than the B site for all bridgmanite samples studied, implying that octahedral tilting and distortion will dominate the bridgmanite compression mechanism. Guided by these crystal chemical observations, bulk moduli of bridgmanite endmember components were estimated using results of previous studies. The volume changes of equilibria controlling the speciation of bridgmanite components were then calculated at conditions relevant to the top of Earth's lower mantle. The proportion of oxygen vacancy components is predicted to decrease with pressure. While the stability of the bridgmanite Fe3+AlO3 component will drive charge disproportionation to produce iron metal at the top of the lower mantle, this appears to be much less favorable by 50 GPa. An increase in the proportion of the Fe3+Fe3+O3 bridgmanite component, however, may favor the formation of iron metal at higher pressures

Effect of Fe3+ on Phase Relations in the Lower Mantle : Implications for Redox Melting in Stagnant Slabs

Recent studies have revealed that Earth's deep mantle may have a wider range of oxygen fugacities than previously thought. Such a large heterogeneity might be caused by material subducted into the deep mantle. However, high-pressure phase relations are poorly known in systems including Fe3+ at the top of the lower mantle, where the subducted slab may be stagnant. We therefore conducted high-pressure and high-temperature experiments using a multi-anvil apparatus to study the phase relations in a Fe3+-bearing system at 26 GPa and 1573–2073 K, at conditions prevailing at the top of the lower mantle. At temperatures below 1923 K, MgSiO3-rich bridgmanite, an Fe3+-rich oxide phase, and SiO2 coexist in the recovered sample. Quenched partial melt was observed above 1973 K, which is significantly lower than the solidus temperature of an equivalent Fe3+-free bulk composition. The partial melt obtained from the Fe3+-rich bulk composition has a higher iron content than coexisting bridgmanite, similar to the Fe2+-dominant system. The results suggest that strong mantle oxygen fugacity anomalies might alter the subsolidus and melting phase relations under lower mantle conditions. We conclude that (1) a small amount of melt may be generated from an Al-depleted region of a stagnant slab, such as subducted former banded-iron-formation, and (2) Fe3+ is not transported into the deep part of the lower mantle because of its incompatibility during melting

Experimental Constraints on the Ferric Fe Content and Oxygen Fugacity in Subducted Serpentinites

Serpentinites play an important role in the delivery of water into subduction zones. In addition, serpentinites also contain ferric Fe and can transport significant redox potential. We present high-pressure and high-temperature experiments and Mössbauer spectroscopy measurements on natural lizardite and antigorite samples equilibrated at various oxygen fugacities in order to quantify the relationship between the oxygen fugacity f(O2) and the Fe3+/Fetot ratio in these two phases. In antigorite, Fe3+ partitions into the octahedral site and is charge balanced by tetrahedral Al. In lizardite, tetrahedral Fe3+ is observed only at low temperature as well as under high f(O2), whereas Fe3+ prefers the octahedral site at temperatures exceeding 500 °C and at 3 to 5 GPa. Although metastable, lizardite remains in redox equilibrium in our experiments at conditions above the lizardite to antigorite phase transformation at 300 °C and demonstrates a similar stability to antigorite. The Al concentration of lizardite is found to be temperature dependent, and it was possible to reequilibrate the Fe3+/Fetot ratio of lizardite from 0.1 to 0.9 by using redox buffers such as Fe metal, graphite, graphite–calcite, Re–ReO2 and Ru–RuO2. Our experiments on antigorite demonstrate that antigorite does not adjust its Al concentration on experimental time scales. Since Fe3+ is charge balanced by Al, it was also not possible to manipulate the Fe3+/Fetot ratio of antigorite. The coexisting phases, however, show chemical equilibration with this antigorite composition. We have retrieved the standard Gibbs energy for Fe3+- and Al-endmembers of antigorite and lizardite and calculated the metamorphic evolution of subducting serpentinites. The lizardite to antigorite transformation does not cause a decrease in the bulk Fe3+/Fetot ratio under f(O2) buffered conditions, in contrast to observations from some natural settings, but does result in the formation of additional magnetite due to antigorite having a lower Fe3+/Fetot ratio than lizardite at equilibrium. If the f(O2) of antigorite serpentinite is buffered during subduction, such as due to the presence of graphite and carbonate, the bulk Fe3+/Fetot ratio decreases progressively. On the other hand, in a closed system where the bulk serpentinite Fe3+/Fetot ratio remains constant, the f(O2) increases during subduction. In this scenario, the f(O2) of an antigorite serpentinite with a typical Fe3+/Fetot ratio of 0.4 increases from the fayalite–magnetite–quartz to the hematite–magnetite f(O2) buffer during dehydration. These f(O2) results confirm earlier inferences that fluids produced by antigorite dehydration may not contain sufficient oxidised sulphur species to oxidise the mantle wedge. Sufficiently high levels of f(O2) to mobilise oxidised sulphur species may be reached upon antigorite dehydration, however, if closed system behaviour maintains a high bulk redox potential across the lizardite to antigorite phase transformation. Alternatively, oxidation of the mantle wedge might be achieved by oxidising agents from sources in subducted oceanic crust and sediments

LEM All-Sky Survey: Soft X-ray Sky at Microcalorimeter Resolution

The Line Emission Mapper (LEM) is an X-ray Probe with with spectral resolution ~2 eV FWHM from 0.2 to 2.5 keV and effective area >2,500 cm$^2$ at 1 keV, covering a 33 arcmin diameter Field of View with 15 arcsec angular resolution, capable of performing efficient scanning observations of very large sky areas and enabling the first high spectral resolution survey of the full sky. The LEM-All-Sky Survey (LASS) is expected to follow the success of previous all sky surveys such as ROSAT and eROSITA, adding a third dimension provided by the high resolution microcalorimeter spectrometer, with each 15 arcsec pixel of the survey including a full 1-2 eV resolution energy spectrum that can be integrated over any area of the sky to provide statistical accuracy. Like its predecessors, LASS will provide both a long-lasting legacy and open the door to the unknown, enabling new discoveries and delivering the baseline for unique GO studies. No other current or planned mission has the combination of microcalorimeter energy resolution and large grasp to cover the whole sky while maintaining good angular resolution and imaging capabilities. LASS will be able to probe the physical conditions of the hot phases of the Milky Way at multiple scales, from emission in the Solar system due to Solar Wind Charge eXchange, to the interstellar and circumgalactic media, including the North Polar Spur and the Fermi/eROSITA bubbles. It will measure velocities of gas in the inner part of the Galaxy and extract the emissivity of the Local Hot Bubble. By maintaining the original angular resolution, LASS will also be able to study classes of point sources through stacking. For classes with ~$10^4$ objects, it will provide the equivalent of 1 Ms of high spectral resolution data. We describe the technical specifications of LASS and highlight the main scientific objectives that will be addressed. (Abridged)Comment: White Paper in support of a mission concept to be submitted for the 2023 NASA Astrophysics Probes opportunity. This White Paper will be updated when required. 30 pages, 25 figure