A dilemma about whether thionitroxide radical (RSNHO) or S-nitrosothiol (RSNO) is observed in protein S-nitrosylation has arisen recently. To illustrate the effect of chemical environment on these structures, this pap...
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A dilemma about whether thionitroxide radical (RSNHO) or S-nitrosothiol (RSNO) is observed in protein S-nitrosylation has arisen recently. To illustrate the effect of chemical environment on these structures, this paper presents quantum mechanical molecular dynamics of thionitroxide, and cis-and trans-S-nitrosothiols in the gas phase, methanol, and water. By using Car-Parrinello molecular dynamics (CPMD), we have observed that there is free rotation about the S-N bond at 300 K in thionitroxide, but no such rotation is observed for S-nitrosothiol. The C-S-N-O torsion angle distribution in thionitroxide is s-ignificantly dependent upon the surrounding environment, leading to either gauche-, cis-, or trans-conformation. In the case of S-nitrosothiol the C-S-N-O plane is twisted slightly by 5°-15° in the cis-isomer, while the periplanar structure is well-retained in the trans-isomer. The calculated results are in agreement with the X-ray crystallographic data of small molecular RSNO species. Interestingly, for both compounds, the CPMD simulations show that solvation can cause a decrease in the S-N bond length. Moreover, the oxygen atom of thionitroxide is found to be a good hydrogen-bond acceptor, forming an oxyanion-hole-like hydrogen bonding network.
In this section, we introduce some outstanding research achievements made by CAS scientists in 2010, as listed in the Chinese version of Science Development Report published in March 2011.
In this section, we introduce some outstanding research achievements made by CAS scientists in 2010, as listed in the Chinese version of Science Development Report published in March 2011.
The multi-symplectic formulations of the Good Boussinesq equation were considered. For the multi-symplectic formulation, a new fifteen-point difference scheme which is equivalent to the multi-symplectic Preissman inte...
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The multi-symplectic formulations of the Good Boussinesq equation were considered. For the multi-symplectic formulation, a new fifteen-point difference scheme which is equivalent to the multi-symplectic Preissman integrator was derived. The numerical experiments show that the multi-symplectic schemes have excellent long-time numerical behavior.
The extended magnetohydrodynamic models are derived based on the moment closure of the Vlasov-Maxwell （VM） equations. We adopt the Grad type moment expansion which was firstly proposed for the Boltzmann equation. A ...
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The extended magnetohydrodynamic models are derived based on the moment closure of the Vlasov-Maxwell （VM） equations. We adopt the Grad type moment expansion which was firstly proposed for the Boltzmann equation. A new regularization method for the Grad＇s moment system was recently proposed to achieve the globally hyperbolicity so that the local well-posedness of the moment system is attained. For the VM equations, the moment expansion of the convection term is exactly the same as that in the Boltzmann equation, thus the new developed regularization applies. The moment expansion of the electromagnetic force term in the VM equations turns out to be a linear source term, which can preserve the conservative properties of the distribution function in the VM equations perfectly.
This paper studied subspace properties of the Celis–Dennis–Tapia(CDT)subproblem that arises in some trust-region algorithms for equality constrained opti*** analysis is an extension of that presented by Wang and Yu...
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This paper studied subspace properties of the Celis–Dennis–Tapia(CDT)subproblem that arises in some trust-region algorithms for equality constrained opti*** analysis is an extension of that presented by Wang and Yuan(***.104:241–269,2006)for the standard trust-region *** suitable conditions,it is shown that the trial step obtained from the CDT subproblem is in the subspace spanned by all the gradient vectors of the objective function and of the constraints computed until the current *** on this observation,a subspace version of the Powell–Yuan trust-region algorithm is proposed for equality constrained optimization problems where the number of constraints is much lower than the number of variables. The convergence analysis is given and numerical results arealso reported.
作者：
白中治State Key Laboratory of Scientific/Engineering Computing
Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and System Sciences Chinese Academy of Sciences Beijing 100080 P.R. China
For the large sparse block two-by-two real nonsingular matrices, we establish a general framework of structured preconditioners through matrix transformation and matrix approximations. For the specific versions such a...
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For the large sparse block two-by-two real nonsingular matrices, we establish a general framework of structured preconditioners through matrix transformation and matrix approximations. For the specific versions such as modified block Jacobi-type, modified block Gauss-Seidel-type, and modified block unsymmetric (symmetric) Gauss-Seidel-type preconditioners, we precisely describe their concrete expressions and deliberately analyze eigenvalue distributions and positive definiteness of the preconditioned matrices. Also, we show that when these structured preconditioners are employed to precondition the Krylov subspace methods such as GMRES and restarted GMRES, fast and effective iteration solvers can be obtained for the large sparse systems of linear equations with block two-by-two coefficient matrices. In particular, these structured preconditioners can lead to high-quality preconditioning matrices for some typical matrices from the real-world applications.
The teracluster LSSC-II installed at the statekeylaboratory of scientific and engineeringcomputing, Chinese Academy of Sciences is one of the most powerful PC clusters in China. It has a peek performance of 2Tflops...
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The teracluster LSSC-II installed at the statekeylaboratory of scientific and engineeringcomputing, Chinese Academy of Sciences is one of the most powerful PC clusters in China. It has a peek performance of 2Tflops. With a Linpack performance of 1.04Tflops, it is ranked at the 43rd place in the 20th TOP500 List (November 2002), 51st place in the 21st TOP500 List (June 2003), and the 82nd place in the 22nd TOP500 List (November 2003) with a new Linpack performance of 1.3Tflops. In this paper, we present some design principles of this cluster, as well as its applications in some large-scale numerical simulations.
We have previously reported an L2-gradient flow (L2GF) method for cryo-electron tomography and single-particle reconstruction, which has a reasonably good performance. The aim of this paper is to further upgrade both ...
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With the rapid development of artificial intelligence (AI), the game between the human and machine/AI becomes more and more common. The related theoretical analysis becomes significant and necessary, which however is ...
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