Silicon Graphics

The new formalism is especially useful for parallel and distributed computers, since the communication intensity is exceptionally low and excellent load balancing is easy to achieve. In fact, we have used cluster of workstations (Silicon Graphics) and parallel computers - Terra 2000 and IBM SP/2 - to study dynamics of proteins. 

The simulations were carried out on a Silicon Graphics Iris Indigo workstation using the CERIUS molecular modeling and the associated HRTEM module. The multislice simulation technique was applied using the following parameters electron energy 400 kV (lambda = 0.016 A) (aberration coefficient) = 2.7 mm focus value delta/ = 66 nm beam spread = 0.30 mrad. 

O.P. acknowledges support of the Ministry of Science and Technology (CONACyT) of Mexico (Grant No. 25301-E) and the National University of Mexico (project INI 11597). O.P. is also grateful to Silicon Graphics Inc.-Cray Research of Mexico for partial financial support and generous allocation of computer time. 

This period was dominated computationally by Silicon Graphics, which provided the combination of computational and graphics performance that was accessible to all laboratories. The increased computer power, linked to graphics, led to development of semiautomated fitting of electron density... 

The adsorption of the modifier-substrate complex onto Pt (111) surface was investigated using the Soiids-Docking module of the Insightll package. This module determines the conformations of the adsorbed molecules by a combined approach of high temperature molecular dynanuc simulations with molecular mechanics minimization. All the calculated structures were visualized on a Silicon Graphics workstation. 

Hardware supported includes IBM-PC, SUN, Silicon Graphics, HP, IBM RS/6000, and DEC Unix workstations VAX workstations, Encore Unix systems. 

MLC++ was initially developed at Stanford University (Kohavi, R., Sommerfield, D. and Dougherty, J.) and was public domain. The new version 2.0 is freely distributed by Silicon Graphics, Inc. 

This work was supported in part by NIH RR-1081, DAAG29-83-G-0080, Evans and Sutherland, Silicon Graphics and IntelliCorp. We also wish to thank Dennis Miller, IJ>, Kuntz, Don Kneller, Greg Couch, Ken Arnold, and Willa Crowell for help and discussion. 

Fig. 4. Representation of B-, Z-, and A-DNA. Graphics display was performed with QUANTA (MSI) on Silicon Graphics 4D25G Personal Iris workstation, hard copies obtained with Tektronix RGBII. LEDSS, Universite J. Fourier, Grenoble, France...

Calculations of connectivity indexes and subsequent dielectric constant predictions were accomplished by using Molecular Simulations Inc. Synthia polymer module running under the Insight II interface on a Silicon Graphics Crimson workstation. All calculations were performed on the polymer s repeat unit, which was first energy-minimized through a molecular-mechanics-based algorithm. 

Structure Refinement. The refinement of the structure was based on an energy function approach (Brunger etal., 1987) arbitrary combinations of empirical and effective energy terms describing crystallographic data as implemented in XPLOR. Molecular model building was done on an IRIS Workstation (Silicon Graphics) with the software TOM, a version of FRODO (Jones, 1978). 

Continuous support by Prof. W. Thiel is greatfully acknowledged, as is a Liebig fellowship from the Fonds der chemischen Industrie. I thank Prof. W. v. Philipsbom for his interest and for a preprint of reference (5). Calculations were performed on a Silicon Graphics PowerChallenge (Organisch-chemisches Institut, Universitat Zurich) and on IBM RS6000 workstations (C4 cluster, ETH Zurich), as well as on a NEC-SX4 (CSCS, Manno, Switzerland). 

Figure 24.1 A surface reconstruction of a male antennal lobe of the moth Spodoptera littoralis. The brain was immunostained with synapsin antibody and optically sectioned using a confocal microscope. Stacks of images were integrated with the software Imaris 2,7 (Bitplane AG, Switzerland) on a Silicon Graphics workstation to obtain surface projections of the lobe. The macroglomerular complex (MGC) is located close to the entrance of the antennal nerve. M, medial D, dorsal (modified from Carlsson et at, 2002). B Synaptic organization of the major types of antennal lobe neurons. Sensory neurons (ORNs) make uniglomerular synapses both directly with projection neurons (PNs) and indirectly via local interneurons (LNs). In addition, local interneurons innervate several glomeruli and generally make inhibitory synapses. Cell bodies of PNs and LNs are located within the antennal lobe.

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