Pressure-induced superconductivity of Ac-B-H hydrides.

The search for room-temperature superconductors among high-pressure hydrides is a hot research topic. In this study, the structures, stabilities and superconducting properties of ternary Ac-B-H hydrides were studied using a genetic algorithm (GA) combined with density functional theory (DFT) calculations. It was shown that the R3̄m-AcBH8 and I4/mmm-AcB2H8 structures were thermodynamically and dynamically stable above 70 and 125 GPa, respectively. In the R3̄m-AcBH8 structure, the BH6 unit and the dispersed H atoms were bonded to form a corrugated structure. The I4/mmm-AcB2H8 structure contained a cage and the Ac atom located at the cage center. The calculations of the electron-phonon coupling showed that the R3̄m-AcBH8 and I4/mmm-AcB2H8 structures had Tc values of 140 K (70 GPa) and 99 K (125 GPa), respectively. The analyses of the phonon dispersion curves revealed that electron-phonon coupling was closely related to the vibrations of the B-H bonds.

Study of fusion peptide release for the spike protein of SARS-CoV-2.

The spike protein of SARS-CoV-2 can recognize the ACE2 membrane protein on the host cell and plays a key role in the membrane fusion process between the virus envelope and the host cell membrane. However, to date, the mechanism for the spike protein recognizing host cells and initiating membrane fusion remains unknown. In this study, based on the general assumption that all three S1/S2 junctions of the spike protein are cleaved, structures with different forms of S1 subunit stripping and S2' site cleavage were constructed. Then, the minimum requirement for the release of the fusion peptide was studied by all-atom structure-based MD simulations. The results from simulations showed that stripping an S1 subunit from the A-, B- or C-chain of the spike protein and cleaving the specific S2' site on the B-chain (C-chain or A-chain) may result in the release of the fusion peptide, suggesting that the requirement for the release of FP may be more relaxed than previously expected.

AmberMDrun: A Scripting Tool for Running Amber MD in an Easy Way.

MD simulations have been widely applied and become a powerful tool in the field of biomacromolecule simulations and computer-aided drug design, etc., which can estimate binding free energy between receptor and ligand. However, the inputs and force field preparation for performing Amber MD is somewhat complicated, and challenging for beginners. To address this issue, we have developed a script for automatically preparing Amber MD input files, balancing the system, performing Amber MD for production, and predicting receptor-ligand binding free energy. This script is open-source, extensible and can support customization. The core code is written in C++ and has a Python interface, providing both efficient performance and convenience.

Ground and excited states of even-numbered Hubbard ring at half-filling: comparison of the extended Gutzwiller approach with exact diagonalization.

It remains a great challenge in condensed matter physics to develop a method to treat strongly correlated many-body systems with balanced accuracy and efficiency. We introduce an extended Gutzwiller (EG) method incorporating a manifold technique, which builds an effective manifold of the many-body Hilbert space, to describe the ground-state (GS) and excited-state (ES) properties of strongly correlated electrons. We systematically apply an EG projector onto the GS and ES of a non-interacting system. Diagonalization of the true Hamiltonian within the manifold formed by the resulting EG wavefunctions gives the approximate GS and ES of the correlated system. To validate this technique, we implement it on even-numbered fermionic Hubbard rings at half-filling with periodic boundary conditions, and compare the results with the exact diagonalization (ED) method. The EG method is capable of generating high-quality GS and low-lying ES wavefunctions, as evidenced by the high overlaps of wavefunctions between the EG and ED methods. Favorable comparisons are also achieved for other quantities including the total energy, the double occupancy, the total spin and the staggered magnetization. With the capability of accessing the ESs, the EG method can capture the essential features of the one-electron removal spectral function that contains contributions from states deep in the excited spectrum. Finally, we provide an outlook on the application of this method on large extended systems.

A rotationally invariant approach based on Gutzwiller wave function for correlated electron systems.

We introduce a rotationally invariant approach combined with the Gutzwiller conjugate gradient minimization method to study correlated electron systems. In the approach, the Gutzwiller projector is parametrized based on the number of electrons occupying the onsite orbitals instead of the onsite configurations. The approach efficiently groups the onsite orbitals according to their symmetry and greatly reduces the computational complexity, which yields a speedup of20∼50×in the minimal basis energy calculation of dimers. The computationally efficient approach promotes more accurate calculations beyond the minimal basis that is inapplicable in the original approach. A large-basis energy calculation of F2demonstrates favorable agreements with standard quantum-chemical calculations Bytautaset al(2007J. Chem. Phys.127164317).

Structures and localized vibrational states of defects in graphite by tight-binding calculations.

The structural and vibrational properties of pristine graphite and point defects in graphite are studied by tight-binding (TB) calculations using a three-center TB potential model. We showed that the three-center TB potential without "ad hoc" van der Waals interaction corrections can accurately describe the inter-layer distance of graphite and the lowest-energy structures and stabilities of typical point defects in graphite. The results from our TB calculations are in good agreement with those from density-functional theory calculations with van der Waals interaction corrections. We also investigated the vibrational properties to gain better understanding on the localization of vibrational states induced by the point defects. Our calculation results show that although localized or quasi-localized vibrational modes can be found in all defected graphite, the localization induced by Frenkel pair, dual-vacancy, and dual-interstitial defects is much stronger. Atomic displacements associated with the localized vibrational modes induced by these three point defects are also analyzed.

Energy decomposition analysis of cationic carbene analogues with group 13 and 16 elements as a central atom: a comparative study.

Decomposition of the molecular interaction energies into physically intuitive components provides insight to the chemical bonding between fragments. Extended transition state-natural orbital for chemical valence (ETS-NOCV) and natural energy decomposition analysis (NEDA) are methodologically different schemes to partition the interaction energies into physically similar components. To answer the question if the two energy decomposition analysis (EDA) schemes render the same interpretations of reactions, both schemes are employed to study the reactions of two cationic carbene analogues: (1) bis(tri-tert-butylphosphane) group-13-element monocations [(PtBu3)2M+ (M = B, Al, Ga, In, and Tl)] and (2) N-heterocyclic carbene (NHC) dications with a group 16 element as the central atom [(Dipp2DAB)M2+, M = O, S, Se, and Te; Dipp2DAB = 1,4-(2,6-diisopropyl)phenyl-1,4-diaza-1,3-butadiene]. Comparison of the EDA components obtained using the ETS-NOCV and NEDA schemes suggests that, for each individual reaction, the two EDA schemes may not necessarily lead to a consensus about the interpretation or "understanding" of the reaction. However, if the whole families of the studied cationic carbene analogue reactions with simple hydrocarbons are considered, the ETS-NOCV and NEDA schemes agree that the most dominant effects on the interaction energies are the orbital interactions, with the second most dominant being electrostatics, and Pauli exclusions being the least effective.

The Gutzwiller conjugate gradient minimization method for correlated electron systems.

We review our recent work on the Gutzwiller conjugate gradient minimization method, anab initioapproach developed for correlated electron systems. The complete formalism has been outlined that allows for a systematic understanding of the method, followed by a discussion of benchmark studies of dimers, one- and two-dimensional single-band Hubbard models. In the end, we present some preliminary results of multi-band Hubbard models and large-basis calculations of F2to illustrate our efforts to further reduce the computational complexity.

Lithium Diffusion in Silicon Encapsulated with Graphene.

The model of a graphene (Gr) sheet putting on a silicon (Si) substrate is used to simulate the structures of Si microparticles wrapped up in a graphene cage, which may be the anode of lithium-ion batteries (LIBS) to improve the high-volume expansion of Si anode materials. The common low-energy defective graphene (d-Gr) structures of DV5-8-5, DV555-777 and SV are studied and compared with perfect graphene (p-Gr). First-principles calculations are performed to confirm the stable structures before and after Li penetrating through the Gr sheet or graphene/Si-substrate (Gr/Si) slab. The climbing image nudged elastic band (CI-NEB) method is performed to evaluate the diffusion barrier and seek the saddle point. The calculation results reveal that the d-Gr greatly reduces the energy barriers for Li diffusion in Gr or Gr/Si. The energy stability, structural configuration, bond length between the atoms and layer distances of these structures are also discussed in detail.

Localized electronic and vibrational states in amorphous diamond.

Amorphous diamond structures are generated by quenching high-density high-temperature liquid carbon using tight-binding molecular-dynamics simulations. We show that the generated amorphous diamond structures are predominated by strong tetrahedral bonds with the sp3 bonding fraction as high as 97%, thus exhibit an ultra-high incompressibility and a wide band gap close to those of crystalline diamond. A small amount of sp2 bonding defects in the amorphous sample contributes to localized electronic states in the band gap while large local strain gives rise to localization of vibrational modes at both high and low frequency regimes.

Spin-Filtering Ferroelectric Tunnel Junctions as Multiferroic Synapses for Neuromorphic Computing.

As nanoelectronic synapses, memristive ferroelectric tunnel junctions (FTJs) have triggered great interest due to the potential applications in neuromorphic computing for emulating biological brains. Here, we demonstrate multiferroic FTJ synapses based on the ferroelectric modulation of spin-filtering BaTiO3/CoFe2O4 composite barriers. Continuous conductance change with an ON/OFF current ratio of ∼54 400% and long-term memory with the spike-timing-dependent plasticity (STDP) of synaptic weight for Hebbian learning are achieved by controlling the polarization switching of BaTiO3. Supervised learning simulations adopting the STDP results as database for weight training are performed on a crossbar neural network and exhibit a high accuracy rate above 97% for recognition. The polarization switching also alters the band alignment of CoFe2O4 barrier relative to the electrodes, giving rise to the change of tunneling magnetoresistance ratio by about 10 times and even the reversal of its sign depending upon the resistance states. These results, especially the electrically switchable spin polarization, provide a new approach toward multiferroic neuromorphic devices with energy-efficient electrical manipulations through potential barrier design. In addition, the availability of spinel ferrite barriers epitaxially grown with ferroelectric oxides also expends the playground of FTJ devices for a broad scope of applications.

Characterization of three phases of liquid carbon by tight-binding molecular dynamics simulations.

We have performed systematic molecular dynamics simulations to study the structures of liquid carbon at 5000 K with the weight density ranging from 1.4 to 3.5 g cm-3, using a three-center tight-binding potential of carbon. The simulation results show that the bonding characteristics of the liquid changes predominately from twofold to threefold, and then to fourfold coordination as the density increases. Signals of two structural changes at the densities of about 1.9 and 3.0 g cm-3 respectively are revealed by the slope changes in the density dependence of structural, electronic and dynamical properties. Our simulation results suggest that there are three distinct liquid carbon phases in this density range. However, further thermodynamics calculations, e.g., free energy calculations, would be required to clarify the possible liquid-liquid transitions.

Functional analysis of UGT201D3 associated with abamectin resistance in Tetranychus cinnabarinus (Boisduval).

Uridine diphosphate (UDP)-glycosyltransferases (UGTs) are widely distributed within living organisms and share roles in biotransformation of various lipophilic endo- and xenobiotics with activated UDP sugars. In this study, it was found that the activity of UGTs in abamectin-resistant (AbR) strain was significantly higher (2.35-fold) than that in susceptible strain (SS) of Tetranychus cinnabarinus. Further analysis showed that 5-nitrouracil, the inhibitor of UGTs, could enhance the lethal effect of abamectin on mites. From the previous microarray results, we found an UGT gene (UGT201D3) overexpressed in AbR strain. Quantitative PCR analysis showed that UGT201D3 was highly expressed and more inducible with abamectin exposure in the AbR strain. After silencing the transcription of UGT201D3, the activity of UGTs was decreased and the susceptibility to abamectin was increased in AbR strain whereas it was not in SS. Furthermore, UGT201D3 gene was then successfully expressed in Escherichia coli. The recombinant UGT201D3 exhibited α-naphthol activity (2.81 ± 0.43 nmol/mg protein/min), and the enzyme activity could be inhibited by abamectin (inhibitory concentration at 50%: 57.50 ± 3.54 µmol/L). High-performance liquid chromatography analysis demonstrated that the recombinant UGT201D3 could effectively deplete abamectin (15.77% ± 3.72%) incubating with 150 µg protein for 6 h. These results provided direct evidence that UGT201D3 was involved in abamectin resistance in T. cinnabarinus.

Ring-Stacking Water Clusters: Morphology and Stabilities.

The structures and interaction energies of water clusters with ring stacking motifs are studied by using ab initio calculations. The structures of the water clusters are constructed by stacking either single rings or multi-rings of tetramer, pentamer, and hexamer. We found that, in the single-ring-stacking motif, the most stable isomers exhibit an alternative clockwise-anticlockwise stacking pattern. We also show that four-layer single-ring-stacking isomers are not energetically favorable in comparison with those of two-layer multi-ring-stacking isomers. The relative stability of the isomers is also analyzed in terms of H-bond strength and elastic distortions of the water molecules.

Novel superconducting structures of BH2 under high pressure.

The crystal structures of boron hydrides in a pressure range of 50-400 GPa were studied using the genetic algorithm (GA) method combined with first-principles density functional theory calculations. BH4 and BH5 are predicted to be thermodynamically unstable. Two new BH2 structures with Cmcm and C2/c space group symmetries, respectively, were predicted, in which the B atoms tend to form two-dimensional sheets. The calculated band structures showed that in the pressure range of 50-150 GPa, the Cmcm-BH2 phase has very small gaps, while the C2/c-BH2 phase at 200-400 GPa is metallic. The superconductivity of the C2/c-BH2 structure was also investigated, and electron-phonon coupling calculations revealed that the estimated Tc values of C2/c-BH2 are about 28.18-37.31 K at 250 GPa.

Benchmark of correlation matrix renormalization method in molecule calculations.

We report benchmark calculations of the correlation matrix renormalization (CMR) approach for 23 molecules in the well-established G2 molecule set. This subset represents molecules with spin-singlet ground state in a variety of chemical bonding and coordination environments. The QUAsi-atomic minimal basis-set orbitals (QUAMBOs) are used as local orbitals in both CMR and full configuration interaction (FCI) calculations for comparison. The results obtained from the calculations are also compared with available experimental data. It is shown that the CMR method produces binding and dissociation energy curves in good agreement with the QUAMBO-FCI calculations as well as experimental results. The CMR benchmark calculations yield a standard deviation of 0.09 Å for the equilibrium bond length and 0.018 Hartree/atom for the formation energy, with a gain of great computational efficiency which scales like Hartree-Fock method.

Theoretical Prediction of Si2-Si33 Absorption Spectra.

The optical absorption spectra of Si2-Si33 clusters were systematically studied by a time-dependent density functional theory approach. The calculations revealed that the absorption spectrum becomes significantly broad with increasing cluster size, stretching from ultraviolet to the infrared region. The absorption spectra are closely related to the structural motifs. With increasing cluster size, the absorption intensity of cage structures gradually increases, but the absorption curves of the prolate and the Y-shaped structures are very sensitive to cluster size. If the transition energy reaches ∼12 eV, it is noted that all the clusters have remarkable absorption in deep ultraviolet region of 100-200 nm, and the maximum absorption intensity is ∼100 times that in the visible region. Further, the optical responses to doping in the Si clusters were studied.

High-pressure structures of yttrium hydrides.

In this work, the crystal structures of YH3 and YH4 at high pressure (100-250 GPa) have been explored using a genetic algorithm combined with first-principles calculations. New structures of YH3 with space group symmetries of P21/m and I4/mmm were predicted. The electronic structures and the phonon dispersion properties of various YH3 and YH4 structures at different temperatures and pressures were investigated. Among YH3 phases, the P21/m structure of YH3 was found to have a relatively high superconducting transformation temperature T c of 19 K at 120 GPa, which is reduced to 9 K at 200 GPa. Other YH3 structures have much lower T cs. Compared with YH3, the T c of the YH4 compound is much higher, i.e. 94 K at 120 GPa and 55 K at 200 GPa.

Tight-binding calculation studies of vacancy and adatom defects in graphene.

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. Here, we show that a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to four vacancies and four embedded atoms in graphene. Our calculations reveal low-energy defect structures and provide a more comprehensive understanding of the structures and stability of defects in graphene.

Si78 double cage structure and special optical properties.

We performed first-principles calculations to study the structural stability of Si78 clusters with or without hydrogen passivation. The calculations reveal that an endohedral double cage isomer is more stable than the diamond-like structure, whereas the opposite is found for the hydrogen passivated isomers. In particular, the hydrogenated double cage and diamond-like structure may display blue shifts to the visible and UV regions, respectively. The IR vibration spectra, ionization potential (IP) and electronic density-of-states of the clusters were calculated and discussed.