Identification of Dual-Target Inhibitors for Epidermal Growth Factor Receptor and AKT: Virtual Screening Based on Structure and Molecular Dynamics Study.

Epidermal growth factor EGFR is an important target for non-small cell lung (NSCL) cancer, and inhibitors of the AKT protein have been used in many cancer treatments, including those for NSCL cancer. Therefore, searching small molecular inhibitors which can target both EGFR and AKT may help cancer treatment. In this study, we applied a ligand-based pharmacophore model, molecular docking, and MD simulation methods to search for potential inhibitors of EGFR and then studied dual-target inhibitors of EGFR and AKT by screening the immune-oncology Chinese medicine (TCMIO) database and the human endogenous database (HMDB). It was found that TCMIO89212, TCMIO90156, and TCMIO98874 had large binding free energies with EGFR and AKT, and HMDB0012243 also has the ability to bind to EGFR and AKT. These results may provide valuable information for further experimental study.

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.

Stable structures and superconducting properties of Ca-La-H compounds under pressure.

The calcium hydrides and lanthanum hydrides under high pressures have been reported to have good superconducting properties with high-TC. In this work, the structures and superconductivities of Ca-La-H ternary hydrides have been studied by genetic algorithm and density functional theory calculations. Our results show that at the pressure range of 100-300 GPa, the most stable structure of CaLaH12has aCmmmsymmetry, in which there is a H24hydrogen cage. It can be expected to have high possibility to be synthesized due to its large stability. Furthermore, the predictedTCof theCmmm-CaLaH12structure is about 140 K at 150 GPa, and when the pressure decreases to 30 GPa, the CaLaH12structure with aC2/msymmetry has a predictedTCof about 49 K. The CaLaH12is suggested to be a stable good superconductor with large stability and performs well at relatively low pressures.

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.

Study on superconducting Li-Se-H hydrides.

The structures, stabilities and superconducting properties of LiSeHn (n = 4-10) hydrides at 150-300 GPa were studied by the genetic algorithm (GA) and DFT calculation method. Three stable stoichiometries of LiSeH4, LiSeH6 and LiSeH10 were uncovered under high pressure. Four other metastable stoichiometries of LiSeH5, LiSeH7, LiSeH8, and LiSeH9 were also studied. By analyzing the electronic band structure and electronic density of states, C2 LiSeH4, Pmm2 LiSeH6 and C2 LiSeH10 were all found to be metal phases above 150 GPa. Electron-phonon coupling calculations showed that C2 LiSeH4 and Pmm2 LiSeH6 were promising superconductors. The predicted Tc values of C2 LiSeH4 and Pmm2 LiSeH6 were 77 K at 200 GPa and 111 K at 250 GPa, respectively.

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.

Ultra-coarse-graining modeling of liquid water.

It is a great challenge to develop ultra-coarse-grained models in simulations of biological macromolecules. In this study, the original coarse-graining strategy proposed in our previous work [M. Li and J. Z. H. Zhang, Phys. Chem. Chem. Phys. 23, 8926 (2021)] is first extended to the ultra-coarse-graining (UCG) modeling of liquid water, with the NC increasing from 4-10 to 20-500. The UCG force field is parameterized by the top-down strategy and subsequently refined on important properties of liquid water by the trial-and-error scheme. The optimal cutoffs for non-bonded interactions in the NC = 20/100/500 UCG simulations are, respectively, determined on energy convergence. The results show that the average density at 300 K can be accurately reproduced from the well-refined UCG models while it is largely different in describing compressibility, self-diffusion coefficient, etc. The density-temperature relationships predicted by these UCG models are in good agreement with the experiment result. Besides, two polarizable states of the UCG molecules are observed after simulated systems are equilibrated. The ion-water RDFs from the ion-involved NC = 100 UCG simulation are nearly in accord with the scaled AA ones. Furthermore, the concentration of ions can influence the ratio of two polarizable states in the NC = 100 simulation. Finally, it is illustrated that the proposed UCG models can accelerate liquid water simulation by 114-135 times, compared with the TIP3P force field. The proposed UCG force field is simple, generic, and transferable, potentially providing valuable information for UCG simulations of large biomolecules.

Tracking Electron Dynamics of Single Molecules in Scanning Tunneling Microscopy Junctions with Laser Pulses.

On the basis of real-time simulations, we devise a method to extend the capability of scanning tunneling microscopy (STM) to track the electronic dynamics of molecules on a material's surface with the ultrafast temporal resolution of laser pulses. The intrinsic mechanism of visualization of electronic dynamics by measuring tunneling charge is attributed to the interference between the electronic oscillations stimulated by pump and probe pulses. The charge-transfer rate from molecule to the surrounding environment can be estimated with the decay time of electronic dynamics, which can also be detected by measuring the tunneling charge across the STM junction. Moreover, it is found that the tunneling charge can be varied precisely by changing the carrier-envelope phase (CEP) of the pulses, and this phase-dependence of tunnelling diminishes as the duration of incident laser pulses increases. The proposed scheme provides an alternative means for visualization of electron dynamics of single molecules by measuring tunnelling charges.

Transcriptome analysis revealed that multiple genes were related to the cyflumetofen resistance of Tetranychus cinnabarinus (Boisduval).

Metabolic resistance is one of the main causes of acaricide resistance. Many previous studies focused on the function of specific genes in insecticides/acaricides resistance. However, during the development of resistance, the overall dynamic of expression levels of detoxification enzyme genes in mites is still unclear. Tetranychus cinnabarinus, a major agricultural pest, which is notorious for developing resistance to acaricides rapidly. In this study, a field susceptible strain (YS) was continuously selected for 16, 25 and 32 generations, and developed to low resistance (7.83-fold, L), medium resistance (17.23-fold, M) and high resistance (86.05-fold, H), respectively. Transcriptome sequencing was performed in YS, L, M and H strains. Overall, compared with YS strain, the number of differential expression genes increased slightly with the development of cyflumetofen-resistance. As for detoxification genes, the median of fold change of up-regulated P450、CCE and GST genes was higher than those of all up-regulated genes in three resistance level, but only the number and the median of fold change of up-regulated P450 genes was increased slightly with the development of resistance. In addition, synergism experiments also proved that P450 and GST genes were the major contributors to the metabolic resistance of cyflumetofen of T. cinnabarinus. These results showed that the resistance of T. cinnabarinus to cyflumetofen was related to many resistant genes, among which P450 genes could play crucial roles in cyflumefen resistance.

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.

A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles.

As coarse-grained (CG) studies of large biomolecules increase, developments of reliable CG solvent models become particularly important. In this work, we reduce five water molecules into a three-point CG model with permanent dipole and quadrupole moments. In the CG force field, the modified Morse potential is utilized and an ideal three-water cluster is designed to derive CG-level permanent multipoles. The new CG model is parametrized on the AMOEBA polarizable force field. Various important properties of liquid water are examined to validate the new CG model. Results show that the new CG model can correctly reproduce certain important experimental properties such as density, isothermal compressibility and relative static dielectric permittivity, even better than the existing AA models. Additionally, the CPU tests reveal that the CG model can accelerate molecular dynamics simulations by a factor of 19 compared to the popular AA force field. Compared with the fix-point-charge model widely used in other CG models, the permanent-multipole-based CG model describes more rigid electrostatic attractions. This study also illustrates that the permanent multipole moments contribute a lot to the electrostatic calculations in CG simulation.

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.

Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy.

Coarse-grained (CG) model has been a powerful tool in bridging the gap between theoretical studies and experimental phenomena in biological computing field. The reconstruction from a CG model to an atomic-detail structure is especially important in CG studies of biological systems. In this work, a rigid-fragment- and local-frame-based (RF-LF) backmapping method was proposed to achieve reverse mapping from CG models to atomic-level structures. The initial atomic-level structures were further refined to yield the final backmapping ones. With the popular Martini force field, the performance of the RF-LF method was extensively examined in the CG → AA (CG to AA) backmapping of protein/DNA/RNA systems. Besides, the RF-LF method was also extended to the backmapping of the TMFF model. Numerical results illustrate that the RF-LF backmapping method is generic and parameter-free and can provide a promising way to tackle atomic-level studies in CG models.