OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

The semiempirical methods of the OMx family (orthogonalization models OM1, OM2, and OM3) are known to describe biochemical systems more accurately than standard semiempirical approaches such as AM1. We investigate the benefits of augmenting these methods with an empirical dispersion term (OMx-D) taken from recent density functional work, without modifying the standard OMx parameters. Significant improvements are achieved for non-covalent interactions, with mean unsigned errors of 1.41 kcal/mol (OM2-D) and 1.31 kcal/mol (OM3-D) for the binding energy of the complexes in the JSCH-2005 data base. This supports the use of these augmented methods in quantum mechanical/molecular mechanical (QM/MM) studies of biomolecules, for example during system preparation and equilibration. As an illustrative application, we present QM and QM/MM calculations on the binding between antibody 34E4 and a hapten, where OM3-D performs better than the methods without dispersion terms (AM1, OM3)

Static stability and control effectiveness of models 12-0 and 34-0 of the vehicle 3 configuration, volume 3

Static stability and control effectiveness characteristics of two 0.004 scale models of the vehicle 3 configuration are reported. The components investigated consisted of a single aft body, vertical/rudder, OMS pods with two interchangeable wings, four interchangeable forward bodies, four trimmers, and a spoiler. The test was conducted in 14 x 14 inch trisonic wind tunnel over a Mach number range from 0.6 to 4.96. Angles of attack from 0 to 60 degrees and angles of sideslip from -10 to 10 degrees at 0, 10, 20,30, and 40 degrees angle of attack were tested. Elevon, body flap, and speed brake deflection composed the parametric considerations. No grit was placed on the models during the test. The tabulated source data and incremental data figures are presented

Static stability and control effectiveness of models 12-0 and 34-0 of the vehicle 3 configuration, volume 2

Static stability and control effectiveness characteristics of two 0.004 scale models of the vehicle 3 configuration are presented. The components investigated consisted of a single aft body, vertical/rudder, OMS pods with two interchangeable wings, four interchangeable forward bodies, four trimmers, and a spoiler. The test was conducted in a 14 x 14 inch trisonic wind tunnel over a Mach number range from 0.6 to 4.96. Angles of attack from 0 to 60 degrees and angles of sideslip from -10 to 10 degrees at 0, 10, 20, 30, and 40 degrees angle of attack were tested. Elevon, body flap, and speed brake deflection composed the parametric considerations. No grit was placed on the models during the test. The lateral-directional characteristics are presented along with some additional longitudinal data

Bonded Invar Clip Removal Using Foil Heaters

A new process uses local heating and temperature monitoring to soften the adhesive under Invar clips enough that they can be removed without damaging the composite underneath or other nearby bonds. Two 1x1 in. (approx.2.5x2.5 cm), 10-W/sq in. (approx.1.6-W/sq cm), 80-ohm resistive foil Kapton foil heaters, with pressure-sensitive acrylic adhesive backing, are wired in parallel to a 50-V, 1-A limited power supply. At 1 A, 40 W are applied to the heater pair. The temperature is monitored in the clip radius and inside the tube, using a dual thermocouple readout. Several layers of aluminum foil are used to speed the heat up, allowing clips to be removed in less than five minutes. The very local heating via the foil heaters allows good access for clip removal and protects all underlying and adjacent materials

Using a Cold Radiometer to Measure Heat Loads and Survey Heat Leaks

We have developed an inexpensive cold radiometer for use in thermal/vacuum chambers to measure heat loads, characterize emissivity and specularity of surfaces and to survey areas to evaluate stray heat loads. We report here the results of two such tests for the James Webb Space Telescope to measure heat loads and effective emissivities of 2 major pieces of optical ground support equipment that will be used in upcoming thermal vacuum testing of the Telescope

CHARMM force field parameterization protocol for self-assembling peptide amphiphiles : the Fmoc moiety

Aromatic peptide amphiphiles are known to self-assemble into nanostructures but the molecular level structure and the mechanism of formation of these nanostructures is not yet understood in detail. Molecular dynamic simulations using the CHARMM force field have been applied to a wide variety of peptide-based systems to obtain molecular level details of processes that are inaccessible with experimental techniques. However, this force field does not include parameters for the aromatic moieties which dictate the self-assembly of these systems. The standard CHARMM force field parameterization protocol uses hydrophilic interactions for the non-bonding parameters evaluation. However, to effectively reproduce the self-assembling behaviour of these molecules, the balance between the hydrophilic and hydrophobic nature of the molecule is essential. In this work, a modified parameterization protocol for the CHARMM force field for these aromatic moieties is presented. This protocol is applied for the specific case of the Fmoc moiety. The resulting set of parameters satisfies the conformational and interactions analysis and is able to reproduce experimental results such as the Fmoc-S-OMe water/octanol partition free energy and the self-assembly of Fmoc-S-OH and Fmoc-Y-OH into spherical micelles and fibres, respectively, while also providing detailed information on the mechanism of these processes. The effectiveness of the parameters for the Fmoc moiety validates the protocol as a robust approach to paramterise this class of compounds

Derivation of Suitability Metrics for Remote Access Mode Experiments

When considering the possible use of an online mode of experimentation it is important to evaluate the suitability of the remote access mode to a particular learning exercise. Within a large and diverse set of possible experiment-oriented learning exercises, it follows that not all laboratory experiments are well-suited for conversion to the remote access mode. In this paper we consider a range of factors that should be considered before the decision is taken to implement a remote laboratory. These factors fit broadly into four categories: learning factors, equipment factors, cohort factors and accreditation factors. Some of the factors may demonstrate a tendency to belong to more than one category, and some may present with a more significant weighting than others, but the categorical organization of the factors adds an ability to apply an objective assessment to remote access mode suitability

Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries

There is a significant interest in the use of unmodified self-assembling peptides as building blocks for functional, supramolecular biomaterials. Recently, dynamic peptide libraries (DPLs) have been proposed to select self-assembling materials from dynamically exchanging mixture of dipeptide inputs in the presence of a nonspecific protease enzyme, where peptide sequences are selected and amplified based on their self-assembling tendencies. It was shown that the results of DPL of mixed sequences (e.g. starting from a mixture of dileucine, L2 and diphenylalanine, F2) did not give the same outcome as the separate L2 and F2 libraries (which give rise to formation of F6 and L6), implying that interaction between these sequences could disrupt the self-assembly. In this study, coarse grained molecular dynamic (CG-MD) simulations are used to understand the DPL results for F2, L2 and mixed libraries. CG-MD simulations demonstrate that interactions between precursors can cause the low formation yield of hexapeptides in mixtures of dipeptides and show that this ability to disrupt is influenced by the concentration of the different species in the DPL. The disrupting self-assembly effect between the species in DPL is an important effect to take into account in dynamic combinatorial chemistry as it affects the possible discovery of new materials. The work shows that combined computational and experimental screening can be used complementary and in combination provide a powerful means to discover new supramolecular peptide nanostructures