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1. Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations

   https://doi.org/10.1128/msystems.00588-22  

   Dufault-Thompson, Keith ; Nie, Chang ; Jian, Huahua ; Wang, Fengping ; Zhang, Ying ( August 2022 , mSystems)

   Mackelprang, Rachel (Ed.)

   ABSTRACT Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (Δ r G ′), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism’s ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism. 

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2. All electron GW with linearized augmented plane waves for metals and semiconductors

   https://doi.org/10.1016/j.cpc.2023.108986  

   Haule, Kristjan ; Mandal, Subhasish ( February 2024 , Computer Physics Communications)

   GW approximation is one of the most popular parameter-free many-body methods that go beyond the limitations of the standard density functional theory (DFT) to determine the excitation spectra for moderately correlated materials and in particular the semiconductors. It is also the first step in developing the diagrammatic Monte Carlo method into an electronic structure tool, which would offer a numerically exact solution to the solid-state problem. While most electronic structure packages offer support for GW calculations for band-insulating materials, the level of support for metallic systems is somewhat limited. This limitation can be partly attributed to the relatively minor differences often observed between GW and DFT results in treating metallic systems, which is not expected to persist to higher orders in perturbation theory. Describing metals within the GW framework presents a challenge, as it requires accurate resolution of Fermi surface singularities, which, in turn, calls for a dense momentum mesh. Here we implement the GW algorithm within the all-electron Linear Augmented Plane Wave framework, where we pay special attention to the metallic systems, the convergence with respect to momentum mesh, and proper treatment of the deep laying core states, as needed for the future variational diagrammatic Monte Carlo implementation. Our improved algorithm for resolving Fermi surface singularities allows us a stable and accurate analytic continuation of imaginary axis data, which is carried out for GW excitation spectra throughout the Brillouin zone in both the metallic and insulating materials and is compared to numerically more stable contour deformation integration technique. We compute band structures for elemental metallic systems Li, Na, and Mg as well as for various narrow and wide bandgap insulators such as Si, BN, SiC, MgO, LiF, ZnS, and CdS and compare our results with previous GW calculations and available experiments data. Our results are in good agreement with the available literature. Thus our software allows users to compute full bandstructures for metals and insulators using all-electron potential without downfolding to Wannier orbital basis. 

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3. Characterizing local metallic bonding variation induced by external perturbation

   https://doi.org/10.1039/C9CP05954G  

   Wang, Hongwei ; Fuller, Jon ; Chen, Peng ; Morozov, Sergey I. ; An, Qi ( January 2020 , Physical Chemistry Chemical Physics)

   The subtle variation of metallic bonding, induced by external influence, plays an essential role in determining physical, mechanical, and chemical properties of metals. However, it is extremely difficult to describe this variation because of the delocalization nature of metallic bonding. Here, we utilize the reduced density gradient and topological analysis of electron density to capture the local metallic bonding variations (LMBV) caused by lattice distortion and carrier injection in many face-centered cubic (fcc) metals. We find that the LMBV determines the traits of fcc metals such as strength, malleability, and ductility. Moreover, the fcc metals can become more flexible/stronger with the electron/hole injection, providing an important guidance to tune metals for desired mechanical properties. 

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4. Experimental and Computational Studies on Superhard Material Rhenium Diboride under Ultrahigh Pressures

   https://doi.org/10.3390/ma13071657  

   Burrage, Kaleb C. ; Lin, Chia-Min ; Chen, Wei-Chih ; Chen, Cheng-Chien ; Vohra, Yogesh K. ( April 2020 , Materials)

   An emerging class of superhard materials for extreme environment applications are compounds formed by heavy transition metals with light elements. In this work, ultrahigh pressure experiments on transition metal rhenium diboride (ReB2) were carried out in a diamond anvil cell under isothermal and non-hydrostatic compression. Two independent high-pressure experiments were carried out on ReB2 for the first time up to a pressure of 241 GPa (volume compression V/V0 = 0.731 ± 0.004), with platinum as an internal pressure standard in X-ray diffraction studies. The hexagonal phase of ReB2 was stable under highest pressure, and the anisotropy between the a-axis and c-axis compression increases with pressure to 241 GPa. The measured equation of state (EOS) above the yield stress of ReB2 is well represented by the bulk modulus K0 = 364 GPa and its first pressure derivative K0´ = 3.53. Corresponding density-functional-theory (DFT) simulations of the EOS and elastic constants agreed well with the experimental data. DFT results indicated that ReB2 becomes more ductile with enhanced tendency towards metallic bonding under compression. The DFT results also showed strong crystal anisotropy up to the maximum pressure under study. The pressure-enhanced electron density distribution along the Re and B bond direction renders the material highly incompressible along the c-axis. Our study helps to establish the fundamental basis for anisotropic compression of ReB2 under ultrahigh pressures. 

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5. Robust anomalous metallic states and vestiges of self-duality in two-dimensional granular In-InOx composites

   https://doi.org/10.1038/s41535-021-00329-2  

   Zhang, Xinyang ; Hen, Bar ; Palevski, Alexander ; Kapitulnik, Aharon ( March 2021 , npj Quantum Materials)

   Many experiments investigating magnetic-field tuned superconductor-insulator transition (H-SIT) often exhibit low-temperature resistance saturation, which is interpreted as an anomalous metallic phase emerging from a ‘failed superconductor’, thus challenging conventional theory. Here we study a random granular array of indium islands grown on a gateable layer of indium-oxide. By tuning the intergrain couplings, we reveal a wide range of magnetic fields where resistance saturation is observed, under conditions of careful electromagnetic filtering and within a wide range of linear response. Exposure to external broadband noise or microwave radiation is shown to strengthen the tendency of superconductivity, where at low field a global superconducting phase is restored. Increasing magnetic field unveils an ‘avoided H-SIT’ that exhibits granularity-induced logarithmic divergence of the resistance/conductance above/below that transition, pointing to possible vestiges of the original emergent duality observed in a true H-SIT. We conclude that anomalous metallic phase is intimately associated with inherent inhomogeneities, exhibiting robust behavior at attainable temperatures for strongly granular two-dimensional systems.

    

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