Inversion using a new low-dimensional representation of complex binary geological media based on a deep neural network

Efficient and high-fidelity prior sampling and inversion for complex geological media is still a largely unsolved challenge. Here, we use a deep neural network of the variational autoencoder type to construct a parametric low-dimensional base model parameterization of complex binary geological media. For inversion purposes, it has the attractive feature that random draws from an uncorrelated standard normal distribution yield model realizations with spatial characteristics that are in agreement with the training set. In comparison with the most commonly used parametric representations in probabilistic inversion, we find that our dimensionality reduction (DR) approach outperforms principle component analysis (PCA), optimization-PCA (OPCA) and discrete cosine transform (DCT) DR techniques for unconditional geostatistical simulation of a channelized prior model. For the considered examples, important compression ratios (200 - 500) are achieved. Given that the construction of our parameterization requires a training set of several tens of thousands of prior model realizations, our DR approach is more suited for probabilistic (or deterministic) inversion than for unconditional (or point-conditioned) geostatistical simulation. Probabilistic inversions of 2D steady-state and 3D transient hydraulic tomography data are used to demonstrate the DR-based inversion. For the 2D case study, the performance is superior compared to current state-of-the-art multiple-point statistics inversion by sequential geostatistical resampling (SGR). Inversion results for the 3D application are also encouraging

Editor\u27s Notes, Chiba Medical Journal 90-1

Multiple sequence alignment of deduced amino acid sequences of 25 wheat annexin genes with rice annexin OsAnn2 (Os05g31760) obtained by ClustalW. (PDF 212 kb

Binary Compound Bilayer and Multilayer with Vertical Polarizations: Two-Dimensional Ferroelectrics, Multiferroics, and Nanogenerators

Vertical ferroelectricity in two-dimensional (2D) materials is desirable for high-density data storage without quantum tunneling or high power consumption/dissipation, which still remains elusive due to the surface-depolarizing field. Herein, we report the first-principles evidence of 2D vertical ferroelectricity induced by interlayer translation, which exists extensively in the graphitic bilayer of BN, AlN, ZnO, MoS₂, GaSe, <i>etc.</i>; the bilayer of some 2D ferromagnets like MXene, VS₂, and MoN₂ can be even multiferroics with switchable magnetizations upon ferroelectric switching, rendering efficient reading and writing for high-density data storage. In particular, the electromechanical coupling between interlayer translation and potential can be used to drive the flow of electrons as nanogenerators for harvesting energy from human activities, ocean waves, mechanical vibration, <i>etc.</i> A ferroelectric superlattice with spatial varying potential can be formed in a bilayer Moire pattern upon a small twist or strain, making it possible to generate periodic n/p doped-domains and shape the periodicity of the potential energy landscape. Finally, some of their multilayer counterparts with wurtzite structures like a ZnO multilayer are revealed to exhibit another type of vertical ferroelectricity with greatly enhanced polarizations

Lewis Acid-catalyzed [3 + 2]Cyclo-addition of Alkynes with <i>N</i>-Tosyl-aziridines via Carbon–Carbon Bond Cleavage: Synthesis of Highly Substituted 3-Pyrrolines

A novel, efficient, and highly regioselective Lewis acid-catalyzed [3 + 2] cycloaddition of alkynes with azomethine ylides, which are easily obtained from <i>N</i>-tosylaziridines via C–C bond heterolysis at room temperature was developed. Moderate enantioselectivity (70% ee) can be achieved by the application of the commercially available chiral Pybox 7 as the ligand

Chemical Syntheses of Oligodeoxyribonucleotides Containing Spore Photoproduct

5-(α-Thyminyl)-5,6-dihydrothymine, also called spore photoproduct or SP, is commonly found in the genomic DNA of UV-irradiated bacterial endospores. Despite the fact that SP was discovered nearly 50 years ago, its biochemical impact is still largely unclear due to the difficulty of preparing SP-containing oligonucleotide in high purity. Here, we report the first synthesis of the phosphoramidite derivative of dinucleotide SP TpT, which enables successful incorporation of SP TpT into oligodeoxyribonucleotides with high efficiency via standard solid-phase synthesis. This result provides the scientific community a reliable means to prepare SP-containing oligonucleotides, laying the foundation for future SP biochemical studies. Thermal denaturation studies of the SP-containing oligonucleotide found that SP destabilizes the duplex by 10–20 kJ/mol, suggesting that its presence in the spore-genomic DNA may alter the DNA local conformation

Direct Simulation Evidence of Generation of Oxygen Vacancies at the Golden Cage Au₁₆ and TiO₂ (110) Interface for CO Oxidation

We show Born–Oppenheimer molecular dynamics (BOMD) simulation evidence of the generation of oxygen vacancies at the golden cage Au₁₆ and TiO₂ (110) interface for CO oxidation. Unlike the conventional Langmuir–Hinshelwood (L-H) mechanism, the CO molecule adsorbed at the perimeter Au sites of Au₁₆ tends to attack a nearby lattice oxygen atom on the TiO₂ (110) surface rather than the neighboring co-adsorbed molecular O₂. Our large-scale BOMD simulation provides, to our knowledge, the first real-time demonstration of feasibility of the Mars–van Krevelen (M-vK) mechanism as evidenced by the generation of oxygen vacancies on the TiO₂ surface in the course of the CO oxidation. Furthermore, a comparative study of the CO oxidation at the golden cage Au₁₈ and TiO₂ interface suggests that the L-H mechanism is more favorable than the M-vK mechanism due to higher structural robustness of the Au₁₈ cage. It appears that the selection of either M-vK or L-H mechanism for the CO oxidation is dependent on the structural fluxionality of the Au cage clusters on the TiO₂ support

Interference Effects in Femtosecond Sum Frequency Spectra of Model Cellulose Films

Application of sum frequency spectroscopy (SFS) to thin film structures results in complex spectra, which require theoretical deconvolution. In the present work, a new copropagating model for SF emission from model cellulose surfaces has been developed, thereby enabling the study of cellulose surface characteristics and various aspects of wood utilization. Immobilized model cellulose films have been prepared on gold-coated silicon wafers for characterization by SFS. Before quantitatively analyzing SF spectra derived from cellulose, the thickness-dependent interference effect between multiple SF sources in the cellulose/gold system was investigated theoretically. Comparisons between experimental and simulated SF spectra enable an accurate understanding of thickness/phase and thickness/intensity interference effects, which are essential to the application of SFS to cellulose and other thin films on gold. It was shown that the resonant SF signal generated at the cellulose/gold interface is small, is constant with film thickness, and that the cellulose orientation is opposite that at the cellulose/air interface. As such, resonant SF signals generated at the air/cellulose interface dominate the SF spectra, although a minor contribution from the cellulose/gold interface does exist

Highly <i>Cis</i>-1,4-Selective Living Polymerization of 3‑Methylenehepta-1,6-diene and Its Subsequent Thiol–Ene Reaction: An Efficient Approach to Functionalized Diene-Based Elastomer

Living polymerization of 3-methylenehepta-1,6-diene (MHD) catalyzed by bis­(phosphino)­carbazoleide-ligated yttrium alkyl complex afforded a new product bearing pendant terminal vinyl groups with high stereotacticity (<i>cis</i>-1,4-selectivity up to 98.5%), proved by the NMR (¹H, ¹³C, and 1D ROESY) spectroscopic analyses, which demonstrates overwhelmingly favorable chemoselectivity toward conjugated diene over α-olefin moieties. High <i>cis</i>-1,4 random copolymers of MHD and isoprene could also be obtained with pendant vinyl groups ranging from 10% to 90%. These vinyl groups in every chain unit can be cleanly and quantitatively converted into various functionalities via light-mediated thiol–ene reaction, resulting in homo- and copolymers of various functional butadiene derivatives, which display versatile thermal properties

Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics

Pf2001 esterase (Pf2001) from Pyrococcus furiosus has hyperthermophilic properties and exerts a biocatalytic function in a dimeric state. Crystal structures revealed that the structural rearrangement of the cap domain is responsible for the Pf2001 dimer formation. However, the details of the cap domain remodeling and the effects of temperature on the dimerization process remain elusive at the molecular level, taking into account that experimental methods are difficult to capture the dynamic process of dimerization to some extent. Herein, four dimer models based on the monomeric crystal structure (PDB ID: 5G59) were constructed to investigate the conformational transition details and temperature effects in the dimerization by conventional molecular dynamics and accelerated molecular dynamics simulations. Our simulation results indicate that the monomer undergoes a conformational change into a “preparatory state” at high temperatures, which is more favorable for its transformation into a stable dimer. The subsequent free energy landscape analysis further identifies four intermediate states (from separated state to dimeric state) and discloses that a more accessible α-helix driven by stronger hydrophobic interactions induces a rearrangement of the cap domain, displaying a “tic-tac-toe” activation feature that is important for stabilizing the dimer interface and facilitating the formation of hydrophobic pockets. In addition, the electrostatic potential surface analysis illustrates that the weaker electrostatic repulsion (Lys and Arg) in the dimer interface at high temperatures is also a key factor for dimer stabilization. Altogether, our results can provide molecular-level insight into the dimer formation process of hyperthermophilic esterase and would be useful to understand the enzymatic specificity of α/β-hydrolase

Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics

Pf2001 esterase (Pf2001) from Pyrococcus furiosus has hyperthermophilic properties and exerts a biocatalytic function in a dimeric state. Crystal structures revealed that the structural rearrangement of the cap domain is responsible for the Pf2001 dimer formation. However, the details of the cap domain remodeling and the effects of temperature on the dimerization process remain elusive at the molecular level, taking into account that experimental methods are difficult to capture the dynamic process of dimerization to some extent. Herein, four dimer models based on the monomeric crystal structure (PDB ID: 5G59) were constructed to investigate the conformational transition details and temperature effects in the dimerization by conventional molecular dynamics and accelerated molecular dynamics simulations. Our simulation results indicate that the monomer undergoes a conformational change into a “preparatory state” at high temperatures, which is more favorable for its transformation into a stable dimer. The subsequent free energy landscape analysis further identifies four intermediate states (from separated state to dimeric state) and discloses that a more accessible α-helix driven by stronger hydrophobic interactions induces a rearrangement of the cap domain, displaying a “tic-tac-toe” activation feature that is important for stabilizing the dimer interface and facilitating the formation of hydrophobic pockets. In addition, the electrostatic potential surface analysis illustrates that the weaker electrostatic repulsion (Lys and Arg) in the dimer interface at high temperatures is also a key factor for dimer stabilization. Altogether, our results can provide molecular-level insight into the dimer formation process of hyperthermophilic esterase and would be useful to understand the enzymatic specificity of α/β-hydrolase