Institute of Theoretical Physics

The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.

Molecular docking has become an increasingly important tool for drug discovery. In this review, we present a brief introduction of the available molecular docking methods, and their development and applications in drug discovery. The relevant basic theories, including sampling algorithms and scoring functions, are summarized. The differences in and performance of available docking software are also discussed. Flexible receptor molecular docking approaches, especially those including backbone flexibility in receptors, are a challenge for available docking methods. A recently developed Local Move Monte Carlo (LMMC) based approach is introduced as a potential solution to flexible receptor docking problems. Three application examples of molecular docking approaches for drug discovery are provided. Keywords: Conformational sampling, scoring, flexible protein-ligand docking, backbone flexibility, local move Monte Carlo sampling, molecular docking, drug discovery, virtual screening, high throughput screening, QSAR

Analytical expressions are derived for the evaluation of energy gradients in the zeroth order regular approximation (ZORA) to the Dirac equation. The electrostatic shift approximation is used to avoid gauge dependence problems. Comparison is made to the quasirelativistic Pauli method, the limitations of which are highlighted. The structures and first metal-carbonyl bond dissociation energies for the transition metal complexes W(CO)6, Os(CO)5, and Pt(CO)4 are calculated, and basis set effects are investigated.

A model for holographic dark energy is proposed, following the idea that the short distance cut-off is related to the infrared cut-off. We assume that the infrared cut-off relevant to the dark energy is the size of the event horizon. With the input ΩΛ=0.73, we predict the equation of state of the dark energy at the present time be characterized by w=−0.90. The cosmic coincidence problem can be resolved by inflation in our scenario, provided we assume the minimal number of e-foldings.

A protocol for quantum secure direct communication using blocks of Einstein-Podolsky-Rosen (EPR) pairs is proposed. A set of ordered N EPR pairs is used as a data block for sending secret message directly. The ordered N EPR set is divided into two particle sequences, a checking sequence and a message-coding sequence. After transmitting the checking sequence, the two parties of communication check eavesdropping by measuring a fraction of particles randomly chosen, with random choice of two sets of measuring bases. After insuring the security of the quantum channel, the sender Alice encodes the secret message directly on the message-coding sequence and sends them to Bob. By combining the checking and message-coding sequences together, Bob is able to read out the encoded messages directly. The scheme is secure because an eavesdropper cannot get both sequences simultaneously. We also discuss issues in a noisy channel.

In this paper we will calculate the effect of spin–orbit coupling on properties of closed shell molecules, using the zero-order regular approximation to the Dirac equation. Results are obtained using density functionals including density gradient corrections. Close agreement with experiment is obtained for the calculated molecular properties of a number of heavy element diatomic molecules.

A theoretical quantum key distribution scheme using Einstein-Podolsky-Rosen (EPR) pairs is presented. This scheme is efficient in that it uses all EPR pairs in distributing the key except those chosen for checking eavesdroppers. The high capacity is achieved because each EPR pair carries 2 bits of key code.

Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.

Hadrons are composite particles made of quark and gluons. Interestingly, some excited hadronic states resemble the deuteron viewed as a barely bound neutron-proton system. Such hadronic molecules are spatially extended systems lying very close to decay thresholds. This work reviews the current experimental evidence for hadronic molecules and related theoretical descriptions, including effective field theories and lattice quantum chromodynamics.

Using the low limit of cosmic ages from globular cluster and the white dwarfs: t0>12Gyr, together with recent new high redshift supernova observations from the HST/GOODS program and previous supernova data, we give a considerable estimation of the equation of state for dark energy, with uniform priors as weak as 0.2<Ωm<0.4 or 0.1<Ωmh2<0.16. We find cosmic age limit plays a significant role in lowering the upper bound on the variation amplitude of dark energy equation of state. We propose in this Letter a new scenario of dark energy dubbed quintom, which gives rise to the equation of state larger than −1 in the past and less than −1 today, satisfying current observations. In addition we have also considered the implications of recent X-ray gas mass fraction data on dark energy, which favors a negative running of the equation of state.

This chapter contains sections titled: Introduction The Kohn-Sham Molecular Orbital Model MO-Theoretical Analysis of Chemical Bonding: Beyond a Qualitative MO Theory The Electron Pair Bond and Pauli Repulsion The Three-Electron Bond and One-Electron Bonding The Role of Steric Repulsion in Bonding Models Strongly Polar Electron Pair Bonding Conclusions and Outlook

The Jiangmen Underground Neutrino Observatory (JUNO), a 20 kton multi-purpose\nunderground liquid scintillator detector, was proposed with the determination\nof the neutrino mass hierarchy as a primary physics goal. It is also capable of\nobserving neutrinos from terrestrial and extra-terrestrial sources, including\nsupernova burst neutrinos, diffuse supernova neutrino background, geoneutrinos,\natmospheric neutrinos, solar neutrinos, as well as exotic searches such as\nnucleon decays, dark matter, sterile neutrinos, etc. We present the physics\nmotivations and the anticipated performance of the JUNO detector for various\nproposed measurements. By detecting reactor antineutrinos from two power plants\nat 53-km distance, JUNO will determine the neutrino mass hierarchy at a 3-4\nsigma significance with six years of running. The measurement of antineutrino\nspectrum will also lead to the precise determination of three out of the six\noscillation parameters to an accuracy of better than 1\\%. Neutrino burst from a\ntypical core-collapse supernova at 10 kpc would lead to ~5000\ninverse-beta-decay events and ~2000 all-flavor neutrino-proton elastic\nscattering events in JUNO. Detection of DSNB would provide valuable information\non the cosmic star-formation rate and the average core-collapsed neutrino\nenergy spectrum. Geo-neutrinos can be detected in JUNO with a rate of ~400\nevents per year, significantly improving the statistics of existing geoneutrino\nsamples. The JUNO detector is sensitive to several exotic searches, e.g. proton\ndecay via the $p\\to K^++\\bar\\nu$ decay channel. The JUNO detector will provide\na unique facility to address many outstanding crucial questions in particle and\nastrophysics. It holds the great potential for further advancing our quest to\nunderstanding the fundamental properties of neutrinos, one of the building\nblocks of our Universe.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

&lt;p&gt;The discovery of gravitational waves (GWs) by the LIGO collaboration in 2016 has provided a direct test on the prediction made by Albert Einstein a century ago based on his general theory of relativity. It has caused a significant influence worldwide on the basic research in science.&lt;/p&gt;

We study the thermodynamic properties and phase structures of topological black holes in Einstein theory with a Gauss-Bonnet term and a negative cosmological constant. The event horizon of these topological black holes can be a hypersurface with positive, zero, or negative constant curvature. When the horizon is a zero curvature hypersurface, the thermodynamic properties of black holes are completely the same as those of black holes without the Gauss-Bonnet term, although the two black hole solutions are quite different. When the horizon is a negative constant curvature hypersurface, the thermodynamic properties of the Gauss-Bonnet black holes are qualitatively similar to those of black holes without the Gauss-Bonnet term. When the event horizon is a hypersurface with positive constant curvature, we find that the thermodynamic properties and phase structures of black holes drastically depend on the spacetime dimension d and the coefficient of the Gauss-Bonnet term: when $d&gt;~6$, the properties of black holes are also qualitatively similar to the case without the Gauss-Bonnet term, but when $d=5,$ a new phase of locally stable small blacks holes occurs under a critical value of the Gauss-Bonnet coefficient, and beyond the critical value, the black holes are always thermodynamically stable. However, the locally stable small black hole is not globally preferred; instead a thermal anti--de Sitter space is globally preferred. We find that there is a minimal horizon radius, below which the Hawking-Page phase transition will not occur since for these black holes the thermal anti--de Sitter space is always globally preferred.

Dark energy, the mysterious cause of the accelerating expansion of the universe, is one of the most important fields of research in astrophysics and cosmology today. Introducing the theoretical ideas, observational methods and results, this textbook is ideally suited to graduate courses on dark energy, and will also supplement advanced cosmology courses. Providing a thorough introduction to this exciting field, the textbook covers the cosmological constant, quintessence, k-essence, perfect fluid models, extra-dimensional models, and modified gravity. Observational research is reviewed, from the cosmic microwave background to baryon acoustic oscillations, weak lensing and cluster abundances. Every chapter ends with problems, with full solutions provided, and any calculations are worked through step-by-step.

Himalayan-Tibetan Underplate The Himalayas formed from the collision of India with Eurasia beginning about 50 million years ago, but the fate and position of the subducted Indian crust was not well defined until the Hi-CLIMB seismic experiment was initiated. The centerpiece of the project is an 800-kilometer-long, closely spaced, linear array of broadband seismographs, extending from the Ganges lowland, across the Himalayas, and onto the central Tibetan plateau. Nábělek et al. (p. 1371 ) present images of the crust and upper mantle of the Southern Tibetan plateau underthrust northward by the Indian plate, in which they trace the base of the Indian plate to 31°N. The character of the crust-mantle interface in this region suggests that the Indian crust is at least partly decoupled from the mantle beneath.

We review the problem of dark energy, including a survey of theoretical models and some aspects of numerical studies.

In order to describe quantum heat engines, here we systematically study isothermal and isochoric processes for quantum thermodynamic cycles. Based on these results the quantum versions of both the Carnot heat engine and the Otto heat engine are defined without ambiguities. We also study the properties of quantum Carnot and Otto heat engines in comparison with their classical counterparts. Relations and mappings between these two quantum heat engines are also investigated by considering their respective quantum thermodynamic processes. In addition, we discuss the role of Maxwell's demon in quantum thermodynamic cycles. We find that there is no violation of the second law, even in the existence of such a demon, when the demon is included correctly as part of the working substance of the heat engine.

Abstract A new method is described for setting up the effective potential for electrons in non-transition metals, including liquid metals and alloys. It is based on a model potential fitted to the spectroscopically measured energy levels of the free ions. The potential between the atomic cores is obtained from the dielectric screening calculation of Cohen and Phillips (1961) with some refinements. The method is tested on the band structures of the (solid) alkali metals. The Fermi surfaces of K, Rb and Cs are found to be considerably less distorted than calculated by Ham (1962), and thus in better agreement with experiment.