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We describe a method for predicting the conformations of loops in proteins and its application to four of the complementarity determining regions [CDRs] in the crystallographically determined structure of MCPC603. The method is based on the generation of a large number of randomly generated conformations for the backbone of the loop being studied, followed by either minimization or molecular dynamics followed by minimization starting from these random structures. The details of the algorithm for the generation of the loops are presented in the first paper in this series (Shenkin et al. [submitted]). The results of minimization and molecular dynamics applied to these loops is presented here. For the two shortest CDRs studied (H1 and L2, which are five and seven amino acids long), minimizations and dynamics simulations which ignore interactions of the loop amino acids beyond the carbon beta replicate the conformation of the crystal structure closely. This suggests that these loops fold independently of sequence variation. For the third CDR (L3, which is nine amino acids), those portions of the CDR near its base which are hydrogen bonded to framework are well replicated by our procedures, but the top of the loop shows significant conformational variability. This variability persists when side chain interactions for the MCPC603 sequence are included. For a fourth CDR (H3, which is 11 amino acids long), new low-energy backbone conformations are found; however, only those which are close to the crystal are compatible with the sequence when side chain interactions are taken into account. Results from minimization and dynamics on single CDRs with all other CDRs removed are presented. These allow us to explore the extent to which individual CDR conformations are determined by interactions with framework only.

The discovery of structural phase transitions in a series of alkanenitriles, acetonitrile (CH3CN), propionitrile (CH3CH2CN), nonadecanitrile [CD3(CH2)19CN], but not butyronitrile (CH3CH2CH2CN), at the air/water is described. Using sum frequency spectroscopy, the phase transition is manifested by an abrupt change in the orientation and an abrupt change in the vibrational frequency of the CN head group of the interface nitrile molecules. The competition between the distance dependent nitrile−nitrile dipolar interactions and the hydrogen bonding and solvation of the CN moieties is used to describe the phase transitions. A new application of second harmonic and sum frequency generation to study the interfaces of centrosymmetric microscopic particles is presented. Examples of this new use to the adsorption of molecules to a polystyrene microsphere/aqueous interface and the polarization of bulk water molecules by a charged microsphere of polystyrene sulfate are discussed.

Abstract-A complete review of the data vortex optical packet switched (OPS) interconnection network architecture is presented. The distributed multistage network topology is based on a banyan structure and incorporates a deflection routing scheme ideally suited for implementation with optical components. An implemented 12-port system prototype employs broadband semiconductor optical amplifier switching nodes and is capable of successfully routing multichannel wavelength-division multiplexing packets while maintaining practically error-free signal integrity (BER 10 12 ) with median latencies of 110 ns. Packet contentions are resolved without the use of optical buffers via a distributed deflection routing control scheme. The entire payload path in the optical domain exhibits a capacity of nearly 1 Tb/s. Further experimental measurements investigate the OPS interconnection network's flexibility and robustness in terms of optical power dynamic range and network timing. Subsequent experimental investigations support the physical layer scalability of the implemented architecture and serve to substantiate the merits of the data vortex OPS network architectural paradigm. Finally, modified design considerations that aim to increase the network throughput and device-level performance are presented.Index Terms-Interconnection networks (multiprocessor), optical interconnections, packet switching, photonic switching systems, wavelength-division multiplexing.

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