S. Chin

Gaussian density functional calculations on the allyl and polyene radicals: C3H5 to C11H13

The electronic structure of the allyl radical C3H5 and the polyene radicals C5H7, C7H9, C9H11, and C11H13 have been calculated using the linear combination of Gaussian‐type orbitals‐local spin density method. In contrast to the results obtained using the Hartree–Fock model, which show large errors, the geometries are in excellent agreement with multiconfiguration self‐consistent‐field calculations and with experiment. LSD yields a C2v symmetry for the allyl radical, while the polyenes C5H7 to C11H13 have C–C bonds alternating between single and double bonds. The harmonic vibrational frequencies were calculated for the allyl radical and C5H7 (the 1,4‐pentadienyl radical). The unscaled vibrational frequencies calculated for the allyl radical are in excellent agreement with experiment.

Biological and artificial intelligence systems

I. Biological Systems: Proteins.- Approaches to the Multiple-Minima Problem in Conformational Energy Calculations on Polypeptides and Proteins.- Protein Dynamics and Function.- Brownian Motions in Molecular Networks.- Fluorescence of Tryptophan and Protein Dynamics.- Structural Studies of Unfolded and Partly Folded Proteins Using NMR Spectroscopy.- Protonic Percolation in Biomaterials.- II. Biological Systems: DNA.- DNA Conformational Studies by IR and Raman Spectroscopies.- Minihairpin Loops in DNA: Experimental and Theoretical Studies.- Imaging Biopolymers Under Water by Scanning Tunneling Microscopy.- Structural Information in Deterministic Fluctuations of Base Sequences in DNAs. Theoretical Prediction of DNA Superstructures.- Conformational Behavior and Water Shells of Different DNA Duplexes. Computer Simulation and Biological Significance.- III. Bridge from Biological to Artificial Intelligence Systems.- Electronic Devices from Molecules: Overview, Prospects and Theoretical Chemistry.- A Theoretical Approach to Highly Conducting and Non-linear Optically Active Polymers.- Towards Unified Natural Science.- Evolutionary Adaptation to a Real and an Artificial World.- IV. Artificial Intelligence Systems: Parallel Computers.- Programming Generality and Parallel Computers.- The Warp Computer: A Cost-Effective Solution to Supercomputing.- Supercomputing and Super Computers: for Science and Engineering in General and for Chemistry and Biosciences in Particular.- Experiences with Computers of Highly Parallel Architectures.- Machines, Languages and Compilers for Parallel Symbolic Computing.- V. Artificial Intelligence Systems: Pattern Recognition.- Computer Vision.- Pattern Recognition by Statistically-Coupled Processors with Hierarchy.- A Single-chip Image Sensor and Processor: A Strategic Project.- Integrated Vision Project on the Computer Network.- VI. Artificial Intelligence Systems: Voice Recognition.- Associative Coding and The Perception of Speech.- Experiments With the Acoustic Processor of A Hidden Markov Model-Based, Large Vocabulary Speech Recognition System.- A Statistical Approach to French/English Translation.- VII. Artificial Intelligence Systems: Robotics.- Theoretical and Experimental Perspectives on Arm Trajectory Formation: A Distributed Model of Motor Redundancy.

A systematic study on the basis set superposition error in the calculation of interaction energies of systems of biological interest

A systematic study on the basis set superposition error in the calculation of interaction energies of strongly bonded molecular associations is presented. Twenty‐four different basis sets (ranging from minimal to triple‐zeta plus polarization) have been used to compute the interaction energies of four conformations of two alanine molecules interacting through their respective carboxylic groups giving rise to a double hydrogen‐bonded association. The basis set superposition error has been calculated in all the cases by using the functional counterpoise method of Boys and Bernardi. It is shown that the basis set superposition error is still important at the double‐zeta and valence triple‐zeta levels of accuracy. In most cases the correction by the counterpoise method seems to be adequate providing interaction energies which, when compared with the uncorrected ones, are in better agreement with those coming from the largest basis set used in this work ( full triple‐zeta plus polarization). The use of basis s...

Large-scale computations on a scalar, vector and parallel ‘supercomputer’

Abstract We discuss two experimental parallel computer systems 1CAP-1 and 1CAP-2 which can be applied to the entire spectrum of scientific and engineering applications. These systems achieve ‘supercomputer’ levels of performance by spreading large scale computations across multiple cooperating processors—several with vector capabilities. We outline system hardware and software, and discuss our programming strategy for migrating codes from a conventional sequential system to a parallel one. The performance of a variety of applications programs is analyzed to demonstrate the merits of this approach. Finally, we discuss 1CAP-3, an extension to this computing system, which has been recently assembled.

Parallelism in computational chemistry: Applications in quantum and statistical mechanics

Abstract Often very fundamental biochemical and biophysical problems defy simulations because of limitation in todays computers. We present and discuss a distributed system composed of two IBM-4341 and one IBM-4381, as front-end processors, and ten FPS-164 attached array processors. This parallel system-called LCAP-has presently a peak performance of about 120 MFlops; extensions to higher performance are discussed. Presently, the system applications use a modified version of VM/SP as the operating system: description of the modifications is given. Three applications programs have migrated from sequential to parallel; a molecular quantum mechanical, a Metropolis-Monte Carlo and a Molecular Dynamics program. Descriptions of the parallel codes are briefly outlined. As examples and tests of these applications we report on a study for proton tunneling in DNA base-pairs, very relevant to spontaneous mutations in genetics. As a second example, we present a Monte Carlo study of liquid water at room temperature where not only two- and three-body interactions are considered but-for the first time-also four-body interactions are included. Finally we briefly summarize a molecular dynamics study where two- and three-body interactions have been considered. These examples, and very positive performance comparison with todays supercomputers allow us to conclude that parallel computers and programming of the type we have considered, represent a pragmatic answer to many computer intensive problems.

Large Scale Computations on the Loosely Coupled Array of Processors

An experimental parallel computer system which is expected to achieve supercomputing performance across the entire spectrum of scientific and engineering applications is described. This system allows the execution of single large scale scientific and engineering applications on multiple processors. The system hardwares and softwares will be briefly described, as well as the programming strategies used to migrate codes from sequential to parallel. The validity of this approach to solving large scale problems is verified by analyzing the performance results of a variety of application programs. The type of scientific/engineering applications which may be investigated using this type of system is demonstrated by discussing one of our applications in biochemistry; namely the statistical and quantum mechanical study of DNA. Finally, ongoing and future extensions to this system are presented.

Non-empirical Pair Potentials for the Interaction Between Amino Acids

A pair potential describing the potential hypersurface between interacting aliphatic amino acids (without sulphur) is presented. This pair potential has been derived entirely from ab initio calculations at the Hartree-Fock level. Almost two thousand SCF calculations have been performed and used as input for a nonlinear least-squares fitting in order to obtain the parameters for the atom-atom analytical pair potential.

XWIB: an X-Windows interface builder for scientific and engineering application programs

Input to scientific programs (particularly, numerical simulation programs) traditionally requires an in-depth knowledge of complex and interdependent syntactic, semantic, and conceptual information. The effort to acquire this knowledge can deter a novice user from learning a program or cause an expert user to make errors. The XWIB (X-Windows Interface Builder) tool is designed to reduce this cognitive burden by supporting the specification and execution of a graphical user interface oriented toward creating input files for scientific programs.