New algorithm for tensor contractions on multi‐core CPUs,GPUs, and accelerators enables CCSD and EOM‐CCSD calculations with over 1000 basis functions on a single compute node

A new hardware‐agnostic contraction algorithm for tensors of arbitrary symmetry and sparsity is presented. The algorithm is implemented as a stand‐alone open‐source code libxm . This code is also integrated with general tensor library libtensor and with the Q‐Chem quantum‐chemistry package. An overview of the algorithm, its implementation, and benchmarks are presented. Similarly to other tensor software, the algorithm exploits efficient matrix multiplication libraries and assumes that tensors are stored in a block‐tensor form. The distinguishing features of the algorithm are: (i) efficient repackaging of the individual blocks into large matrices and back, which affords efficient graphics processing unit (GPU)‐enabled calculations without modifications of higher‐level codes; (ii) fully asynchronous data transfer between disk storage and fast memory. The algorithm enables canonical all‐electron coupled‐cluster and equation‐of‐motion coupled‐cluster calculations with single and double substitutions (CCSD and EOM‐CCSD) with over 1000 basis functions on a single quad‐GPU machine. We show that the algorithm exhibits predicted theoretical scaling for canonical CCSD calculations, O (N ⁶), irrespective of the data size on disk. © 2017 Wiley Periodicals, Inc.     

Adaptive‐numerical‐bias metadynamics

A metadynamics scheme is presented in which the free energy surface is filled with progressively adding adaptive biasing potentials, obtained from the accumulated probability distribution of the collective variables. Instead of adding Gaussians with assigned height and width in conventional metadynamics method, here we add a more realistic adaptive biasing potential to the Hamiltonian of the system. The shape of the adaptive biasing potential is adjusted on the fly by sampling over the visited states. As the top of the barrier is approached, the biasing potentials become wider. This decreases the problem of trapping the system in the niches, introduced by the addition of Gaussians of fixed height in metadynamics. Our results for the free energy profiles of three test systems show that this method is more accurate and converges more quickly than the conventional metadynamics, and is quite comparable (in accuracy and convergence rate) with the well‐tempered metadynamics method. © 2017 Wiley Periodicals, Inc.     

Lipophilic counterion effect on aggregation and adsorption behavior of quaternary ammonium surfactants

The obvious different aggregation and adsorption behavior of six newly quaternary ammonium surfactants with different lipophilic counterions has been discoverd by measurements of equilibrium and dynamic surface tension, fluorescence and conductivity. Interestingly, the critical micelle concentration (CMC) and its surface tension γ_CMC decrease with the increasing counterion chain length. However, three methods have confirmed that an exception of CMC increases slightly from C₁₆NC₁ to C₁₆NC₂. According to experimental results, a balanced mechanism between hydrophobicity and electrostatic of counterion is proposed. Besides, the dynamic surface tension results show the diffusion coefficient increases with the increasing counterion length both at a short time (D_t?→?0) and long time (D_t?→?∞), which indicates a faster adsorption process. Unlike the inorganic counterion, the diffusion coefficient decreases with the increase of hydrophobic chain length. This is attributed to the strong electrostatic interactions between counterions and cationic headgroups.     

Computational method for optimal control of switched systems with input and state constraints

In this paper, we consider an optimal control problem of switched systems with input and state constraints. Since the complexity of such constraint and switching laws, it is difficult to solve the problem using standard optimization techniques. In addition, although conjugate gradient algorithms are very useful for solving nonlinear optimization problem, in practical implementations, the existing Wolfe condition may never be satisfied due to the existence of numerical errors. And the mode insertion technique only leads to suboptimal solutions, due to only certain mode insertions being considered. Thus, based on an improved conjugate gradient algorithm and a discrete filled function method, an improved bi-level algorithm is proposed to solve this optimization problem. Convergence results indicate that the proposed algorithm is globally convergent. Three numerical examples are solved to illustrate the proposed algorithm converges faster and yields a better cost function value than existing bi-level algorithms.     

Some Topological Properties of Charming Spaces

In this paper, we mainly discuss the class of charming spaces. First, we show that there exists a charming space such that the Tychonoff product is not a charming space. Then we discuss some properties of charming spaces and give some characterizations of some class of charming spaces. Finally, we show that the Suslin number of an arbitrary charming rectifiable space is countable.     

Computational analysis for the determination of deleterious nsSNPs in human MTHFD1 gene

Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol. Out of 327 nsSNPs form human MTHFD1 gene, total 45 SNPs were predicted as functionally most significant SNPs, among which 17 were highly conserved and functional, 17 were highly conserved and structural residues. Among 45 most significant SNPs, 15 were predicted to be involved in post translational modifications. The p.Gly165Arg may interfere in homodimer interface formation. The p.Asn439Lys and p.Asp445Asn may interfere in binding interactions of MTHFD1 protein with cesium cation and potassium. The two SNPs (p.Asp562Gly and p.Gly637Cys) might interfere in interactions of MTHFD1 with ligand.     

High-Fidelity,Narcissistic Self-Sorting in the Synthesis of Organometallic Assemblies from Poly-NHC Ligands

Highly selective, narcissistic self-sorting has been observed in the one-pot synthesis of three organometallic molecular cylinders of type [M₃{L-(NHC)₃}₂](PF₆)₃ (M=Ag⁺, Au⁺; L=1,3,5-benzene, triphenylamine, or 1,3,5-triphenylbenzene) from L-(NHC)₃ and silver(I) or gold(I) ions. The molecular cylinders contain only one type of tris-NHC ligand with no crossover products detectable. Transmetalation of the tris-NHC ligands from Ag⁺ to Au⁺ in a one-pot reaction with retention of the supramolecular structures is also demonstrated. High-fidelity self-sorting was also observed in the one-pot reaction of benzene-bridged tris-NHC and tetrakis-NHC ligands with Ag₂O. This study for the first time extends narcissistic self-sorting in metal–ligand interactions from Werner-type complexes to organometallic derivatives.     

[2+1] Cycloaddition Affording Methylene‐ and Vinylidenecyclopropane Derivatives: A Journey around the Reactivity of Metal‐Phosphinito–Phosphinous Acid Complexes

Metal–phosphinito–phosphinous acid complexes are interesting catalysts exhibiting unique reactivities. In this account, we intend to provide a clear overview of palladium– and platinum–phosphinito–phosphinous acid complexes, their preparation from secondary phosphine oxides, and their applications in catalysis. They have been mainly used to develop [2+1] cycloadditions to afford methylenecyclopropane derivatives using norbornenes and various alkynes as partners. As a function of the catalyst, the reaction conditions, or the nature of the reagents, different synthetic transformations have been observed: [2+1] cycloadditions, giving rise to either alkylidenecyclopropanes or vinylidenecyclopropanes; tandem [2+1]/[3+2] cycloadditions, and so forth. The mechanisms of these reactions have been studied to rationalize the different reactivities observed.