The impact of polystyrene resins in solid-phase organic synthesis

Summary A major objective of the DIVERSOMER^® technology is to provide pure and characterized compounds for biological testing in order to prevent false negatives in our libraries. On several occasions, analysis of the final products by¹H-NMR and MS, has revealed by-products from the polystyrene solid support. Subsequently, three alternative methods were studied to remove polystyrene by-products; (i) prewashing of the resin prior to execution of the synthesis; (ii) pretreatment of the resin with the cleavage conditions consistent with the solid-phase synthesis reaction scheme; and (iii) parallel purification.     

氨-碘酸盐介质中白喉类毒素的平行催化氢波

在 0 .4mol/LNH3 NH4Cl (pH 8.3 1 )介质中 ,白喉类毒素 (DT)于 - 1 .89V(vs.SCE)处产生的极谱催化氢波可被碘酸钾进一步催化 ,峰电流明显增大 ,但峰电位不变 ,产生一种氢的新动力波 ,建议称其为平行催化氢波。在 0 .4mol/LNH3 NH4Cl(pH 8.3 1 ) - 5 .0× 1 0 - 3 mol/LKIO3介质中 ,DT平行催化氢波的二阶导数峰电流与其浓度在 0 .2 μg/mL～ 1 .0 μg/mL内呈线性关系 ,可用于生物制品中DT含量的测定。     

PRIRODA-04: a quantum-chemical program suite. New possibilities in the study of molecular systems with the application of parallel computing

Main characteristics are described of the PRIRODA quantum-chemical program suite designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing. A number of examples of calculations are presented.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 804–810, March, 2005.     

A parallel implementation of the COLUMBUS multireference configuration interaction program

Summary In this work a parallel implementation of the COLUMBUS MRSDCI program system is presented. A coarse grain parallelization approach using message passing via the portable toolkit TCGMSG is used. The program is very well portable and runs on shared memory machines like the Cray Y-MP, Alliant FX/2800 or Convex C2 and on distributed memory machines like the iPSC/860. Further implementations on a network of workstations and on the Intel Touchstone Delta are in progress. Overall, results are quite satisfactory considering the complexity and the prodigious requirements, especially the I/O bandwidth, of MRCI programs in general. For our largest test case we obtain a speedup of a factor of 7.2 on an eight processor Cray Y-MP for that section of the program (hamiltonian matrix times trial vector product) which has been parallelized. The speedup for one complete diagonalization iteration amounts to 5.9. An absolute speed close to 1 GFLOPS is found. Results for the iPSC/860 show that ordinary disk I/O is certainly not sufficient in order to guarantee a satisfactory performance. As a solution for that problem, the implementation of a fully asynchronous distributed-memory model for certain data files is in preparation. On leave from: Bereich Informatik, Universität Leipzig, Augustusplatz 10/11, O-7010 Leipzig, Germany     

Benchmark studies of the BCRLM reactive scattering code: Implications for accurate quantum calculations

Summary The Bending Corrected Rotating Linear Model (BCRLM), developed by Hayes and Walker, is a simple approximation to the true multidimensional scattering problem for reactions of the type: A + BC AB + C. While the BCRLM method is simpler than methods designed to obtain accurate three-dimensional quantum scattering results, this turns out to be a major advantage in terms of our benchmarking studies. The computer code used to obtain BCRLM scattering results is written for the most part in standard FORTRAN and has been ported to several scalar, vector, and parallel architecture computers including the IBM 3090-600J, the Cray XMP and YMP, the Ardent Titan, IBM RISC System/6000, Convex C-1 and the MIPS 2000. Benchmark results will be reported for each of these machines with an emphasis on comparing the scalar, vector, and parallel performance for the standard code with minimum modifications. Detailed analysis of the mapping of the BCRLM approach onto both shared and distributed memory parallel architecture machines indicates the importance of introducing several key changes in the basic strategy and algorithms used to calculate scattering results. This analysis of the BCRLM approach provides some insights into optimal strategies for mapping three-dimensional quantum scattering methods, such as the Parker-Pack method, onto shared or distributed memory parallel computers.     

Numerical solution of minimax problems of optimal control,part 1

This paper contains general transformation techniques useful to convert minimax problems of optimal control into the Mayer-Bolza problem of the calculus of variations [Problem (P)]. We consider two types of minimax problems: minimax problems of Type (Q), in which the minimax function depends on the state and does not depend on the control; and minimax problems of Type (R), in which the minimax function depends on both the state and the control. Both Problem (Q) and Problem (R) can be reduced to Problem (P).For Problem (Q), we exploit the analogy with a bounded-state problem in combination with a transformation of the Jacobson type. This requires the proper augmentation of the state vectorx(t), the control vectoru(t), and the parameter vector , as well as the proper augmentation of the constraining relations. As a result of the transformation, the unknown minimax value of the performance index becomes a component of the parameter vector being optimized.For Problem (R), we exploit the analogy with a bounded-control problem in combination with a transformation of the Valentine type. This requires the proper augmentation of the control vectoru(t) and the parameter vector , as well as the proper augmentation of the constraining relations. As a result of the transformation, the unknown minimax value of the performance index becomes a component of the parameter vector being optimized.In a subsequent paper (Part 2), the transformation techniques presented here are employed in conjunction with the sequential gradient-restoration algorithm for solving optimal control problems on a digital computer; both the single-subarc approach and the multiple-subarc approach are discussed.This research was supported by the National Science Foundation, Grant No. ENG-79-18667, and by Wright-Patterson Air Force Base, Contract No. F33615-80-C3000. This paper is a condensation of the investigations reported in Refs. 1–7. The authors are indebted to E. M. Coker and E. M. Sims for analytical and computational assistance.     

One pot solid phase synthesis of 2-substituted 2,3-dihydropyridin-4(1H)-ones on Rinkamide-resin

A novel solid phase synthesis of 2-substituted 2,3-dihydropyridin-4(1H)-ones using Rinkamide-polystyrene-resin is described. The key step involves a hetero-Diels-Alder reaction of Danishefsky's diene with solid phase bound imines, which was carefully optimized. Using this method even ketones are transformed into 2,2-disubstituted dihydropyridones.     

Elimination of the diagonalization bottleneck in parallel Direct-SCF methods

Summary It is shown that the matrix diagonalization bottleneck associated with thesequential O(N _BFN ³ ) diagonalization of the fock matrix within each iteration of the Direct-SCF procedure may be eliminated, and replaced instead with a combination ofparallel O(N _BFN ^<4 ) andsequential O(N _Sub ³ ) steps. For large basis sets, the relation N_Sub N_BFN between the dimension of the expansion subspace and the number of basis functions leads to a method of wave-function optimization in which the sequential bottleneck is eliminated. As a side benefit, the second-order iterative procedure on which this method is based displays superior convergence properties, and provides greater insight into the behavior of the energy with respect to orbital variations, than the traditional first-order, fixed-point, iterative approaches. The implementation of this method may be incorporated into essentially any existing Direct-SCF program with only minimal, and localized, changes.     

Discontinuous Galerkin methods on graphics processing units for nonlinear hyperbolic conservation laws

We present a novel implementation of the modal DG method for hyperbolic conservation laws in two dimensions on graphics processing units (GPUs) using NVIDIA's Compute Unified Device Architecture. Both flexible and highly accurate, DG methods accommodate parallel architectures well as their discontinuous nature produces element‐local approximations. High‐performance scientific computing suits GPUs well, as these powerful, massively parallel, cost‐effective devices have recently included support for double‐precision floating‐point numbers. Computed examples for Euler equations over unstructured triangle meshes demonstrate the effectiveness of our implementation on an NVIDIA GTX 580 device. Profiling of our method reveals performance comparable with an existing nodal DG‐GPU implementation for linear problems. Copyright © 2014 John Wiley & Sons, Ltd.     

The Construction of DNA Logic Gates Restricted to Certain Live Cells Based on the Structure Programmability and Aptamer-Cell Affinity of G-Quadruplexes

DNA computation is considered a fascinating alternative to silicon-based computers; it has evoked substantial attention and made rapid advances. Besides realizing versatile functions, implementing spatiotemporal control of logic operations, especially at the cellular level, is also of great significance to the development of DNA computation. However, developing simple and efficient methods to restrict DNA logic gates performing in live cells is still a challenge. In this work, a series of DNA logic gates was designed by taking full advantage of the diversity and programmability of the G-quadruplex (G4) structure. More importantly, by further using the high affinity and specific endocytosis of cells to aptamer G4, an INHIBIT logic gate has been realized whose operational site is precisely restricted to specific live cells. The design strategy might have great potential in the field of molecular computation and smart bio-applications.