11 research outputs found
Describing Strong Correlation with Block-Correlated Coupled Cluster Theory
A block-correlated coupled cluster (BCCC) method based on the generalized
valence bond (GVB) wave function (GVB-BCCC in short) is proposed and
implemented at the ab initio level, which represents an attractive
multireference electronic structure method for strongly correlated systems. The
GVB-BCCC method is demonstrated to provide accurate descriptions for multiple
bond breaking in small molecules, although the GVB reference function is
qualitatively wrong for the studied processes. For a challenging prototype of
strongly correlated systems, tridecane with all 12 single C-C bonds at various
distances, our calculations have shown that the GVB-BCCC2b method can provide
highly comparable results as the density matrix renormalization group method
for potential energy surfaces along simultaneous dissociation of all C-C bonds
Automatic Reaction Pathway Search via Combined Molecular Dynamics and Coordinate Driving Method
We proposed and implemented
a combined molecular dynamics and coordinate
driving (MD/CD) method for automatically searching multistep reaction
pathways of chemical reactions. In this approach, the molecular dynamic
(MD) method at the molecular mechanics (MM) or semiempirical quantum
mechanical (QM) level is employed to explore the conformational space
of the minimum structures, and the modified coordinate driving (CD)
method is used to build reaction pathways for representative conformers.
The MD/CD method is first applied to two model reactions (the Claisen
rearrangement and the intermolecular aldol reaction). By comparing
the obtained results with those of the existing methods, we found
that the MD/CD method has a comparable performance in searching low-energy
reaction pathways. Then, the MD/CD method is further applied to investigate
two reactions: the electrocyclic reaction of benzocyclobutene-7-carboxaldehyde
and the intramolecular Diels–Alder reaction of ketothioester
with 11 effectively rotatable single bonds. For the first reaction,
our results can correctly account for its torquoselectivity. For the
second one, our method predicts eight reaction channels, leading to
eight different stereo- and regioselective products. The MD/CD method
is expected to become an efficient and cost-effective theoretical
tool for automatically searching low-energy reaction pathways for
relatively complex chemical reactions
Block-Correlated Coupled Cluster Theory with up to Four-Pair Correlation for Accurate Static Correlation of Strongly Correlated Systems
A block-correlated coupled cluster
method with up to
four-pair
correlation based on the generalized valence bond wave function (GVB-BCCC4)
is first implemented, which offers an alternative method for electronic
structure calculations of strongly correlated systems. We developed
some techniques to derive a set of compact and cost-effective equations
for GVB-BCCC4, which include the definition of n-block
(n = 1–4) Hamiltonian matrices, the combination
of excitation operators, and the definition of independent amplitudes.
We then applied the GVB-BCCC4 method to investigate several potential
energy surfaces of strongly correlated systems with singlet ground
states. Our calculations demonstrate that the GVB-BCCC4 method can
provide nearly exact static correlation energies as the density matrix
renormalization group method (on the basis of the same GVB orbitals).
This work highlights the significance of four-pair correlation in
quantitative descriptions of static correlation energy for strongly
correlated systems
Adsorption Mechanism of 4-Amino-5-mercapto-1,2,4-triazole as Flotation Reagent on Chalcopyrite
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder
Transitional cell carcinoma (TCC) is the most common type of bladder cancer. Here we sequenced the exomes of nine individuals with TCC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with TCC with different tumor stages and grades. In our study, we discovered a variety of genes previously unknown to be mutated in TCC. Notably, we identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP-EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with TCC. Of these genes, we showed UTX to be altered substantially more frequently in tumors of low stages and grades, highlighting its potential role in the classification and diagnosis of bladder cancer. Our results provide an overview of the genetic basis of TCC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer
Sequencing of 50 human exomes reveals adaptation to high altitude
Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exornes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPASl shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPASl in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude. Copyright 2010 by the American Association for the Advancement of Science; all rights reserved.Link_to_subscribed_fulltex