量子力学和分子力学组合方法及其应用

QM/MM组合方法在研究凝聚态中的化学反应及生物大分子的结构和活性之间的关系等方面已取得重要进展.这一方法的要点在于将大体系配分成几部分,根据需要对不同部分进行不同级别的处理,因此既利用了量子力学的精确性,又利用了分子力学的高效性.对QM/MM组合理论及其一些最新进展作一简单介绍,并以最近进行的几个工作为例说明QM/MM组合方法的应用.

Electron acceleration in interaction of magnetic islands in large temporal-spatial turbulent magnetic reconnection

A new combined Fermi, betatron, and turbulent electron acceleration mechanism is proposed in interaction of magnetic islands during turbulent magnetic reconnection evolution in explosive astrophysical phenomena at large temporal-spatial scale(LTSTMR), the ratio of observed current sheets thickness to electron characteristic length, electron Larmor radius for low-β and electron inertial length for high-β, is on the order of 10^(10)–10^(11); the ratio of observed evolution time to electron gyroperiod is on the order of 10~7–10~9).The original combined acceleration model is known to be one of greatest importance in the interaction of magnetic islands; it assumes that the continuous kinetic-dynamic temporal-spatial scale evolution occurs as two separate independent processes.In this paper, we reconsider the combined acceleration mechanism by introducing a kinetic-dynamic-hydro full-coupled model instead of the original micro-kinetic or macro-dynamic model.We investigate different acceleration mechanisms in the vicinity of neutral points in magnetic islands evolution, from the stage of shrink and breakup into smaller islands(kinetic scale), to the stage of coalescence and growth into larger islands(dynamic scale), to the stages of constant and quasi-constant(contracting-expanding) islands(hydro scale).As a result, we give for the first time the acceleration efficiencies of different types of acceleration mechanisms in magnetic islands' interactions in solar atmosphere LTSTMR activities(pico-, 10^(–2)–10~5 m; nano-, 10~5–10~6 m; micro-, 10~6–10~7 m; macro-, 10~7–10~8 m; large-,10~8–10~9 m).

Computational Studies of Photocatalysis with Metal-Organic Frameworks

Metal–organic frameworks (MOFs) as photocatalysts and photocatalyst supports combine several advantages of homogeneous and heterogeneous catalyses, including stability, post-reaction separation, catalyst reusability,and tunability, and they have been intensively studied for photocatalytic applications. There are several reviews that focus mainly or even entirely on experimental work. The present review is intended to complement those reviews by focusing on computational work that can provide a further understanding of the photocatalytic properties of MOF photocatalysts. We first present a summary of computational methods, including density functional theory, combined quantum mechanical and molecular mechanical methods, and force fields for MOFs. Then, computational investigations on MOF-based photocatalysis are briefly discussed. The discussions focus on the electronic structure, photoexcitation, charge mobility, and photoredox catalysis of MOFs, especially the widely studied Ui O-66-based MOFs.

The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

Pedigree information is of fundamental importance in breeding programs and related genetics efforts.However,many individuals have unknown pedigrees.While methods to identify and confirm direct parent–offspring relationships are routine,those for other types of close relationships have yet to be effectively and widely implemented with plants,due to complications such as asexual propagation and extensive inbreeding.The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes(referred to in this study as“summed potential lengths of shared haplotypes”,SPLoSH).A custom Python script,HapShared,was developed to generate SPLoSH data in apple and sweet cherry.HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops.These distributions were then used to estimate previously unknown relationships.Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data.For cherry,a full-sib relationship was deduced for‘Emperor Francis,and‘Schmidt’,a half-sib relationship for‘Van’and‘Windsor’,and the paternal grandparents of‘Stella’were confirmed.For apple,29 cultivars were found to share an unknown parent,the pedigree of the unknown parent of‘Cox’s Pomona’was reconstructed,and‘Fameuse’was deduced to be a likely grandparent of‘McIntosh’.Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets,integrated genetic maps,and previously identified pedigree relationships.Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

Reactions with Criegee intermediates are the dominant gas-phase sink for formyl fluoride in the atmosphere

Atmospheric oxidation processes are of central importance in atmospheric climate models.It is often considered that volatile organic molecules are mainly removed by hydroxyl radical;however,the kinetics of some reactions of hydroxyl radical with volatile organic molecules are slow.Here we report rate constants for rapid reactions of formyl fluoride with Criegee intermediates.These rate constants are calculated by dual-level multistructural canonical variational transition state theory with small-curvature tunneling(DL-MS-CVT/SCT).The treatment contains beyond-CCSD(T)electronic structure calculations for transition state theory,and it employs validated density functional input for multistructural canonical variational transition state theory with small-curvature tunneling and for variable-reaction-coordinate variational transition state theory.We find that the M11-L density functional has higher accuracy than CCSD(T)/CBS for the HC(O)F+CH2OO and HC(O)F+anti-CH_(3)CHOO reactions.We find significant negative temperature dependence in the ratios of the rate constants for HC(O)F+CH2OO/anti-CH_(3)CHOO to the rate constant for HC(O)F+OH.We also find that different Criegee intermediates have different rate-determining-steps in their reactions with formyl fluoride,and we find that the dominant gas-phase removal mechanism for HC(O)F in the atmosphere is the reaction with CH2OO and/or anti-CH_(3)CHOO Criegee intermediates.

2011年3月11日日本地震海啸数值模拟

为了有效利用数值模拟的方法来更好的预测海啸,利用美国国家地质调查局(US Geological Survey,USGS)给出的震源机制及断层参数,对日本仙台地震海啸进行数值模拟,运用模拟结果对沿岸海啸灾害分布进行分析,以期给出更为合理的海啸预警方案.数值模型由震后表面变形模拟和基于二维浅水波方程的海啸传播程序两部分组成,模拟结果表现了海啸传播过程的特征,与岸边观测点对于海啸到达时间及波高的记录基本吻合.使用该模型在地震发生后对于海啸到达的地区及其波高进行预测,可以给出更准确的海啸预警,降低海啸对人类造成的损失.

港口海浪安全数值模拟方法

在特定条件下海浪会在海湾内发生共振效应,与海湾本身的地形和固有频率有关,当入射波与此频率相近或具有倍数关系时,共振效应导致的波高放大会带来严重危害.传统的理论研究方法只能对规则形状的港口进行考察,本文将地震海啸和平面入射波的数值模拟结合频谱分析方法应用于考察港口海浪安全.利用浅水波方程和有限差分方法,建立了海浪传播的数值模型,用来模拟港口中的波浪行为.针对模拟结果的时间序列做频谱分析研究其共振效应,得出港口中特定点的敏感频率.数值模拟的结果结合当地的波浪观测历史数据可以在未来对港口及其周边区域潜在的灾害分布做出评估.

Electro-Pulse-Boring(EPB): Novel Super-Deep Drilling Technology for Low Cost Electricity

The inexhaustible heat deposit in great depths （5-10 km） is a scientific fact. Such deposit occurs around the globe. Thereby, everybody is enabled to generate autonomously clean and renewable energy, ample electricity and heat. The economical exploration and exploitation of this superdeep geothermal heat deposit requires a novel drilling technique, because the currently only deep drilling method （Rotary） is limited to about 5 km, due to the rising costs, depending exponentially on depth. Electro-pulse-boring （EPB） is a valuable option to Rotary drilling. EPB, originally investigated in Russia, is ready to be developed for industrialization. The feasibility of EPB is proven by many boreholes drilled up to 200 m in granite （crystalline）. Estimates show outstanding low costs for drilling by EPB： 100 E/m for a borehole with a large diameter （φ） such as 20 （50 cm）, independent on depth and applicable likewise for sediments and crystalline rocks, such as granite. The current rate of penetration （ROP） of 3 m per hour is planned to be augmented up to 35 m per hour, and again, irrespective whether in sedimentary or crystalline formations. Consequently, a 10 km deep borehole with φ 50 cm will ultimately be drilled within 12 days. EPB will create new markets, such as： （i） EPB shallow drilling for geotechnics, energy piles, measures in order to mitigate natural hazards, etc., （ii） EPB deep drilling （3-5 km） for hydro-geothermics, exploration campaigns etc. and （iii） EPB super-deep drilling （5-10 km） for petro-geothermies, enabling the economic generation of electricity. The autonomous and unlimited supply with cost efficient electricity, besides ample heat, ensures reliably clean and renew- able energy, thus, high supply security. Such development will provide a substantial relief to cope with the global challenge to limit the climate change below 2 ℃. The diminution of fossil fuels, due to the energy transition in order to mitigate the climate change, implies likewise the decrease of air pollution.

Numerical simulation of March 11,2011 Honshu,Japan tsunami

In order to predict tsunami hazards through numerical simulation,by using the focal mechanisms as well as fault parameters of Japan's 2011 Tohoku Earthquake provided by National Geological Survey(referred to as USGS),we proposed a numerical model to simulate the Honshu,Japan tsunami.Numerical computing is conducted to investigate the security along the coast.We also analyzed the simulation results and distribution of tsunami disaster,trying to achieve a more reasonable tsunami warning program.Our numerical model is composed of simulation of surface deformation after the earthquake and the tsunami propagation process which is based on two dimensional shallow water equations.The simulation results show the characteristics of the tsunami propagation,and arrival times on recorder points are consistent with tsunami observation.This model can be applied to evaluate the security of the coastal area and obtain more accurate tsunami warning.

SEPRAN: A Versatile Finite-Element Package for a Wide Variety of Problems in Geosciences

Numerical modelling of geological processes, such as mantle convection, flow in porous media, and geothermal heat transfer, has become quite common with the increase in computing and the availability of usable software. Today modelling these dynamical processes entails the solving of the governing equations involving the mass, momentum, energy and chemical transport. These equations represent partial differential equations and must be solved on powerful enough computers because they require sufficient spatial and temporal resolution to be useful. We describe here the salient and outstanding features of the SEPRAN software package, developed in the Netherlands, as a case study for a robust and user-friendly soft- ware, which the geological community can utilize in handling many thermal-mechanical-chemical problems found in geology, which will include geothermal situations, where many types of partial differential equations must be solved at the same time with thermodynamical input parameters.

Parallel Numerical Analysis on the Rheology of the Martian Ice-Rock Mixture

The distribution and amount of ground ice on Mars is an important issue to be addressed for the future exploration of the planet.The occurrence of interstitial ice in Martian frozen ground is indicated by landforms,such as fluidized ejecta craters,softened terrain,and fretted channels.How-ever,experimental data on the rheology of ice-rock mixture under Martian physical conditions are sparse,and the amount of ground ice that is required to produce the viscous deformation observed in Martian ice-related landforms is still unknown.In our study,we put forward a three-dimensional non-Newtonian viscous finite element model to investigate the behavior of ice-rock mixtures numeri-cally.The randomly distributed tetrahedral elements are generated in regular domain to represent the natural distribution of ice-rock materials.Numerical simulation results show that when the volume of rock is less than 40%,the rheology of the mixture is dominated by ice,and there is occurrence of a brittle-ductile transition when ice fraction reaches a certain value.Our preliminary results contribute to the knowledge of the determination of the rheology and ice content in Martian ice-rock mixture.The presented model can also be utilized to evaluate the amount of ground ice on Mars.

ZFN,TALEN and CRISPR-Cas9 mediated homology directed gene insertion in Arabidopsis:A disconnect between somatic and germinal cells

Breakthroughs in the generation of programmable sequence-specific nucleases (SSNs), such as zinc finger nucleases (ZFNs),TAL effector nucleases (TALENs) and the RNA-directed nuclease CRISPR-associated protein 9 (Cas9), have greatly increased the ease of plant genome engineering (Voytas, 2013; Malzahn et al.,2017). Programmable SSNs introduce a DNA double-strand break

Melt Evolution above a Spontaneously Retreating Subducting Slab in a Three-Dimensional Model

Dehydration of the subducting slab favors the melting of the surrounding mantle. Water content and melt evolution atop a spontaneously retreating subducting slab are reported in a three- dimensional （3-D） model. We find that fluids, including water and melts in the rocks, vary substantially along the trench, which cannot be found in two-dimensional （2-D） models. Their maxima along the subducting slab are mainly located at about 50 to 70 and 120 to 140 kin. Volumetric melt production rate changes spatially and episodically atop the slab, which may reflect the intensity and variations of volcanoes.

EASE-DGGS:a hybrid discrete global grid system for Earth sciences

Although we live in an era of unprecedented quantities and access to data,deriving actionable information from raw data is a hard problem.Earth observation systems(EOS)have experienced rapid growth and uptake in recent decades,and the rate at which we obtain remotely sensed images is increasing.While significant effort and attention has been devoted to designing systems that deliver analytics ready imagery faster,less attention has been devoted to developing analytical frameworks that enable EOS to be seamlessly integrated with other data for quantitative analysis.Discrete global grid systems(DGGS)have been proposed as one potential solution that addresses the challenge of geospatial data integration and interoperability.Here,we propose the systematic extension of EASE-Grid in order to provide DGGS-like characteristics for EOS data sets.We describe the extensions as well as present implementation as an application programming interface(API),which forms part of the University of Minnesota’s GEMS(Genetic x Environment x Management x Socioeconomic)Informatics Center’s API portfolio.

Influences of Lower-Mantle Properties on the Formation of Asthenosphere in Oceanic Upper Mantle

Asthenosphere is a venerable concept based on geological intuition of Reginald Daly nearly 100 years ago. There have been various explanations for the existence of the asthenosphere. The concept of a plume-fed asthenosphere has been around for a few years due to the ideas put forth by Yamamoto et al.. Using a two-dimensional Cartesian code based on finite-volume method, we have investigated the influences of lower-mantle physical properties on the formation of a low-viscosity zone in the oceanic upper mantle in regions close to a large mantle upwelUng. The rheological law is Newtonian and depends on both temperature and depth. An extended-Boussinesq model is assumed for the energetics and the olivine to spinel, the spinel to perovskite and perovskite to post-perovskite （ppv） phase transitions are considered. We have compared the differences in the behavior of hot upweilings passing through the transition zone in the mid-mantle for a variety of models, starting with constant physical properties in the lower-mantle and culminating with complex models which have the post-perovskite phase transition and depth-dependent coefficient of thermal expansion and thermal conductivity. We found that the formation of the asthenosphere in the upper mantle in the vicinity of large upwellings is facilitated in models where both depth-dependent thermal expansivity and conductivity are included. Models with constant thermal expansivity and thermal conductivity do not produce a hot low-viscosity zone, resembling the asthenosphere. We have also studied the influences of a cylindrical model and found similar results as the Cartesian model with the important difference that upper-mantle temperatures were much cooler than the Cartesian model by about 600 to 700 K. Our findings argue for the potentially important role played by lower-mantle material properties on the development of a plume-fed asthenosphere in the oceanic upper mantle.

Bioinspired mechanically interlocking holey graphene@SiO_(2)anode

Mechanically interlocking structures that can enhance adhesion at the interface and regulate the stress distribution have been widely observed in biological systems.Inspired by the biological structures in the wings of beetles,we synthesized a holey graphene@SiO_(2)anode with strong mechanical interlocking,characterized it electrochemically,and explained its performance by finite element analysis and density functional calculations.The mechanically interlocking structure enhances lithium-ion(Li^(+))storage by transmitting the strain from SiO_(2)to the holey graphene and by a mechano-electrochemical coupling effect.The interlocking fit hinders the abscission of SiO_(2)and the distinctive structure reduces the stress and strain of SiO_(2)during(de)lithiation.The positive mechano-electrochemical coupling effect preserves the amount of electrochemically active phase(LixSi)during cycles and facilitates Li+diffusion.Therefore,the capacity shows only a slight attenuation after 8000 cycles(cycling stability),and the specific capacity is~1200 mA h g^(−1)at 5 A/g(rate-performance).This study furnishes a novel way to design high-performance Li^(+)/Na+/K^(+)/Al3^(+)anodes with large volume expansion.

Regional Stress Fields under Tibet from 3D Global Flow Simulation

Tibetan area is the most active continental collision zone on earth. Several major earthquakes occurred around the boundaries of Tibetan plateau and caused massive damages and casualties. The dynamics of this area is not well understood due to the complex structure of Tibet and its surrounding area. In this study, a 3D global flow simulation with only viscous rheology is applied to studying the stress distribution in this area, and the interaction between Tibet and its surrounding areas is investigated. Finally, the possibility of combining regional modeling with global models is also discussed.

Submicron Volume Roughness & Asperity Contact Friction Model for Principle Slip Surface in Flash Heating Process

Based on focused ion beam and shear friction apparatus data, the multi-resolutions （0.2 nm-5μm） volume roughness ＆ asperity contact （VR ＆ AC） three-dimensional structure on principle slip surface interface-surface （PSS-IS） is measured on high performance computational platform; and physical plastic-creep friction model is established by using hybrid hyper-singular integral equation ＆ lattice Boltzmann ＆ lattice Green function （BE-LB-LG）. The correlation of rheological property and VR ＆ AC evolution under transient （10 μs） macro-normal stress （18-300 MPa） and slip rate （0.25-7.5 m/s） are obtained; and the PSS-IS friction in co-seismic flash heating is quantitative analyzed for the first time.

High-throughput predictions of metal-organic framework electronic properties:theoretical challenges,graph neural networks,and data exploration

With the goal of accelerating the design and discovery of metal–organic frameworks(MOFs)for electronic,optoelectronic,and energy storage applications,we present a dataset of predicted electronic structure properties for thousands of MOFs carried out using multiple density functional approximations.Compared to more accurate hybrid functionals,we find that the widely used PBE generalized gradient approximation(GGA)functional severely underpredicts MOF band gaps in a largely systematic manner for semi-conductors and insulators without magnetic character.However,an even larger and less predictable disparity in the band gap prediction is present for MOFs with open-shell 3d transition metal cations.With regards to partial atomic charges,we find that different density functional approximations predict similar charges overall,although hybrid functionals tend to shift electron density away from the metal centers and onto the ligand environments compared to the GGA point of reference.Much more significant differences in partial atomic charges are observed when comparing different charge partitioning schemes.We conclude by using the dataset of computed MOF properties to train machine-learning models that can rapidly predict MOF band gaps for all four density functional approximations considered in this work,paving the way for future high-throughput screening studies.To encourage exploration and reuse of the theoretical calculations presented in this work,the curated data is made publicly available via an interactive and user-friendly web application on the Materials Project.

Kinetics of the Toluene Reaction with OH Radical

We calculated the kinetics of chemical activation reactions of toluene with hydroxyl radical in the temperature range from 213 K to 2500 K and the pressure range from 10 Torr to the high-pressure limit by using multistructural variational transition state theory with the small-curvature tunneling approximation(MS-CVT/SCT)and using the system-specifc quantum Rice-RamspergerKassel method.Te reactions of OH with toluene are important elementary steps in both combustion and atmospheric chemistry,and thus it is valuable to understand the rate constants both in the high-pressure,high-temperature regime and in the low-pressure,low-temperature regime.Under the experimental pressure conditions,the theoretically calculated total reaction rate constants agree well with the limited experimental data,including the negative temperature dependence at low temperature.We fnd that the efect of multistructural anharmonicity on the partition functions usually increases with temperature,and it can change the calculated reaction rates by factors as small as 0.2 and as large as 4.2.We also fnd a large efect of anharmonicity on the zero-point energies of the transition states for the abstraction reactions.We report that abstraction of H from methyl should not be neglected in atmospheric chemistry,even though the low-temperature results are dominated by addition.We calculated the product distribution,which is usually not accessible to experiments,as a function of temperature and pressure.