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.     

Geometry and Attribute Compression for Voxel Scenes

Voxel‐based approaches are today's standard to encode volume data. Recently, directed acyclic graphs (DAGs) were successfully used for compressing sparse voxel scenes as well, but they are restricted to a single bit of (geometry) information per voxel. We present a method to compress arbitrary data, such as colors, normals, or reflectance information. By decoupling geometry and voxel data via a novel mapping scheme, we are able to apply the DAG principle to encode the topology, while using a palette‐based compression for the voxel attributes, leading to a drastic memory reduction. Our method outperforms existing state‐of‐the‐art techniques and is well‐suited for GPU architectures. We achieve real‐time performance on commodity hardware for colored scenes with up to 17 hierarchical levels (a 128K³voxel resolution), which are stored fully in core.     

Development of an integrated process for electrochemical reaction and chromatographic SMB-separation

A new continuous process combining electrochemical reaction and chromatographic simulated-moving-bed (SMB) separation is presented. To demonstrate the potential of process integration, this reactor concept is applied to the direct electrochemical production of arabinose by means of simulation. Experimentally verified models of reactor and column units are combined with a model of the electrochemical SMB-reactor. These process units are characterized individually and their model parameters are discussed. The electrochemical reaction inside the microreactor can be described by a series reaction, which has an impact on the design of the integrated process: as the reaction should take place in areas of the SMB-process with maximum educt concentration, the reactors are switched on and off during operation. The integrated process shows interaction between the reaction and the separation to diminish side reactions. Case studies prove the theoretical feasibility of the integrated process. Compared to a conventional process with a reactor followed by a SMB-separation, higher yields can be obtained.     

Reaction of lipids containing hydroxy groups with trimethylsulfonium hydroxide: Formation ofO-methyl derivatives

Base-catalyzed transesterification of acyl lipids with trimethylsulfonium hydroxide (TMSH) is an easy and convenient method for the preparation of fatty acid methyl esters (FAME) for gas chromatography (GC) analyses. We have found, however, that lipids containing hydroxy groups are partially converted to the correspondingO-methyl ether derivatives which may interfere with FAME in GC separations. For example, long-chain alcohols are found to be converted to alkyl methyl ethers,rac-1-O-alkylglycerols to the corresponding 2-O-and 3-O-monomethyl ethers, as well as 2,3-di-O-methyl ethers, hydroxy fatty acids to methoxy FAME, and cholesterol to cholesteryl 3β-methyl ether. From our results, it is obvious that TMSH derivatization method is not recommended without limitation for lipids containing hydroxy groups; it may be, however, of some diagnostic value for the analysis of such lipids by GC/mass spectrometry.     

Rißausbreitung bei Leichtbauwerkstoffen

Fatigue Crack Propagation of High Strength Alloys Investigations of the crack propagation behaviour under variable amplitude loading conditions show a strong influence of sequence effects. The fatigue crack propagation as a consequence of changes in the loading conditions is not linear. New continuum mechanical analyses enable an interpretation of the influence of sequence effects on fatigue crack propagation by considering the plastic deformations and displacements around the crack tip and their correlation to the crack closure behaviour. In order to enable a direct investigation of the crack propagation and crack closure behaviour in the scanning electron microscope a special loading equipment was designed. The investigations led to the following results:

• there existed only a weak correlation between the crack propagation rates and mechanisms at the side surfaces and on the fracture surfaces of the specimens,
• the crack propagation behaviour was significantly influenced by the microstructural constitution of the alloy,
• the continuum mechanical analyses could be corroborated in the tests.

For the tests the high strength aluminum alloys 2024-T3 and X-7075 were applied.     

The Contribution of the Project Management Office: A Balanced Scorecard Perspective

Many organizations turn to project management offices (PMOs) in order to increase project efficiency, cut costs, and improve success rates in project delivery. However, many PMOs face the challenge of a lack of recognition of their contribution, leading to the need to repeatedly justify their existence. This article provides new insights into the success and failure of PMOs and also provides the rationale and structure for a holistic approach to establishing and sustaining a PMO.     

Scalable Remote Rendering with Depth and Motion‐flow Augmented Streaming

In this paper, we focus on efficient compression and streaming of frames rendered from a dynamic 3D model. Remote rendering and on‐the‐fly streaming become increasingly attractive for interactive applications. Data is kept confidential and only images are sent to the client. Even if the client's hardware resources are modest, the user can interact with state‐of‐the‐art rendering applications executed on the server. Our solution focuses on augmented video information, e.g., by depth, which is key to increase robustness with respect to data loss, image reconstruction, and is an important feature for stereo vision and other client‐side applications. Two major challenges arise in such a setup. First, the server workload has to be controlled to support many clients, second the data transfer needs to be efficient. Consequently, our contributions are twofold. First, we reduce the server‐based computations by making use of sparse sampling and temporal consistency to avoid expensive pixel evaluations. Second, our data‐transfer solution takes limited bandwidths into account, is robust to information loss, and compression and decompression are efficient enough to support real‐time interaction. Our key insight is to tailor our method explicitly for rendered 3D content and shift some computations on client GPUs, to better balance the server/client workload. Our framework is progressive, scalable, and allows us to stream augmented high‐resolution (e.g., HD‐ready) frames with small bandwidth on standard hardware.     

ManyLoDs: Parallel Many‐View Level‐of‐Detail Selection for Real‐Time Global Illumination

Level‐of‐Detail structures are a key component for scalable rendering. Built from raw 3D data, these structures are often defined as Bounding Volume Hierarchies, providing coarse‐to‐fine adaptive approximations that are well‐adapted for many‐view rasterization. Here, the total number of pixels in each view is usually low, while the cost of choosing the appropriate LoD for each view is high. This task represents a challenge for existing GPU algorithms. We propose ManyLoDs, a new GPU algorithm to efficiently compute many LoDs from a Bounding Volume Hierarchy in parallel by balancing the workload within and among LoDs. Our approach is not specific to a particular rendering technique, can be used on lazy representations such as polygon soups, and can handle dynamic scenes. We apply our method to various many‐view rasterization applications, including Instant Radiosity, Point‐Based Global Illumination, and reflection/refraction mapping. For each of these, we achieve real‐time performance in complex scenes at high resolutions.     

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.