Fast empirical pKa prediction by Ewald summation

pK(a) calculations for macromolecules are normally performed by solving the Poisson-Boltzmann equation, accounting for the different dielectric constants of solvent and solute, as well as the ionic strength. Despite the large number of successful applications, there are some situations where the current algorithms are not suitable: (1) large scale, high-throughput analysis which requires calculations to be completed within a fraction of a second, e.g. when permanently monitoring pK(a) shifts during a molecular dynamics simulation; (2) prediction of pK(a)s in periodic boundaries, e.g. when reconstructing entire protein crystal unit cells from PDB files, including the correct protonation patterns at experimental pH. Such in silico crystals are needed by 'self-parameterizing' molecular dynamics force fields like YASARA YAMBER, that optimize their parameters while energy-minimizing high-resolution protein crystals. To address both problems, we define an empirical equation that expresses the pK(a) as a function of electrostatic potential, hydrogen bonds and accessible surface area. The electrostatic potential is evaluated by Ewald summation, which captures periodic crystal environments and the uncertainty in atom positions using Gaussian charge densities. The empirical proportionality constants are derived from 217 experimentally determined pK(a)s, and despite its simplicity, this pK(a) calculation method reaches a high overall jack-knifed accuracy, and is fast enough to be used during a molecular dynamics simulation. A reliable null-model to judge pK(a) prediction accuracies is also presented.     

épée A support environment for process engineering software

This paper describes épée, a distributed environment for the integration of software applications. It was developed with the aim of aiding the process of design by providing the necessary support for a design information management system. The software environment is first described in general terms and then our specific application of épée to process engineering design is presented. épée uses an object-oriented approach to data management. Data are represented as objects whose definitions, via templates, reflect the process engineering design environment. The use of focussed methods promotes a consistent look and feel to the tools in the environment. Method reuse reduces software development costs and increases users' confidence in the reliability of the methods. The benefits of the history recording mechanism in épée and its object publishing facilities are described. A history record is a critical component of a high level design management system. This, together with the sharing of data through object publishing, provides the necessary support for collaborative design. The application of épée to process engineering design illustrates the benefits of object-oriented techniques to the process systems and design community. The inherent extensibility of object definitions facilitates the application of the support system to any area of design. The dynamic nature of object definitions in épée encourages exploration and experimentation with new data types and methods.     

The Complexity of Problems for Quantified Constraints

In this paper we are interested in quantified propositional formulas in conjunctive normal form with “clauses” of arbitrary shapes. i.e., consisting of applying arbitrary relations to variables. We study the complexity of the evaluation problem, the model checking problem, the equivalence problem, and the counting problem for such formulas, both with and without a bound on the number of quantifier alternations. For each of these computational goals we get full complexity classifications: We determine the complexity of each of these problems depending on the set of relations allowed in the input formulas. Thus, on the one hand we exhibit syntactic restrictions of the original problems that are still computationally hard, and on the other hand we identify non-trivial subcases that admit efficient algorithms.     

AlON: A brief history of its emergence and evolution

In the early 1970s in Japan, the United States and France it was found that additions of nitrogen into aluminum oxide resulted in new spinel-like phases. At about the same time there was much increased interest in oxynitrides, stimulated by Professor K. Jack in the UK and Y. Oyama in Japan. Following these activities a major research program in this area was initiated at the Army Materials and Mechanics Research Center in Watertown, Massachusetts in 1974. These efforts resulted in the first complete Al₂O₃–AlN phase equilibrium diagram and a process to reactively sinter to nearly full density, translucent aluminum oxynitride spinel ceramic, which was named AlON. Subsequently, the Raytheon Company further developed AlON into a highly transparent material (ALON?) with many applications including transparent armor and EM domes and windows, among others—the technology was recently transferred to the Surmet Corporation. This paper will review the early history, phase equilibrium, crystal chemistry, and properties of this material, along with more recent work in our laboratory on transient liquid phase sintering and new data on lattice parameter measurements. In addition, recent results of collaborative work on AlON's dynamic mechanical properties using plate impact, Kolsky bar and edge-on impact (EoI) experimental techniques, including preliminary modeling at the microstructural scale of AlON in the EoI test, will be presented.     

Local damage to Ultra High Performance Concrete structures caused by an impact of aircraft engine missiles

The impact of an aircraft engine missile causes high stresses, deformations and a severe local damage to conventional reinforced concrete. As a consequence the design of R/C protective structural elements results in components with rather large dimensions.Fiber reinforced Ultra High Performance Concrete (UHPC) is a concrete based material which combines ultra high strength, high packing density and an improved ductility with a significantly increased energy dissipation capacity due to the addition of fiber reinforcement. With those attributes the material is potentially suitable for improved protective structural elements with a reduced need for material resources.The presented paper reports on an experimental series of scaled aircraft engine impact tests with reinforced UHPC panels. The investigations are focused on the material behavior and the damage intensity in comparison to conventional concrete. The fundamental work of [Sugano et al., 1993a] and [Sugano et al., 1993b] is taken as reference for the evaluation of the results. The impactor model of a Phantom F4 GE-J79 engine developed and validated by Sugano et al. is used as defined in the original work. In order to achieve best comparability, the experimental configuration and method are adapted for the UHPC experiments. With ‘penetration’, ‘scabbing’ and ‘perforation’ all relevant damage modes defined in [Sugano et al., 1993a] and [Sugano et al., 1993b] are investigated so that a full set of results are provided for a representative UHPC structural configuration.     

A methodology aimed at better integration of functional verification and RTL design

The advent of new 65 nm/90 nm VLSI technology and SoC design methodologies has brought an explosive growth in the complexity of modern electronic circuits. As a result, functional verification has become the major bottleneck in any digital design flow. Thus, new methods for easier, faster and more reusable verification are required. This paper proposes a verification methodology (VeriSC2) that guides the implementation of working testbenches during hierarchical decomposition and refinement of the design, even before the RTL implementation starts. This approach uses the SystemC Verification Library (SCV), in a tool capable of automatically generating testbench templates. A case study from a MPEG-4 decoder design is used to show the effectiveness of this approach.