chARpack: The Chemistry Augmented Reality Package.

Off-loading visualization and interaction into virtual reality (VR) using head-mounted displays (HMDs) has gained considerable popularity in simulation sciences, particularly in chemical modeling. Because of its unique way of soft immersion, augmented reality (AR) HMD technology has even more potential to be integrated into the everyday workflow of computational chemists. In this work, we present our environment to explore the prospects of AR in chemistry and general molecular sciences: The chemistry in Augmented Reality package (chARpack). Besides providing an extensible framework, our software focuses on a seamless transition between a 3D stereoscopic view with true 3D interactions and the traditional desktop PC setup to provide users with the best setup for all tasks in their workflow. Using feedback from domain experts, we discuss our design requirements for this kind of hybrid working environment (AR + PC), regarding input, features, degree of immersion, and collaboration.

Automatic detection of venous air embolism using transesophageal echocardiography in patients undergoing neurological surgery in the semi-sitting position: a pilot study.

Neurological surgery in the semi-sitting position is linked with a pronounced incidence of venous air embolism (VAE) which can be fatal and therefore requires continuous monitoring. Transesophageal echocardiography (TEE) provides a high sensitivity for the intraoperative detection of VAE; however, continuous monitoring with TEE requires constant vigilance by the anaesthesiologist, which cannot be ensured during the entire surgical procedure. We implemented a fully automatic VAE detection system for TEE based on a statistical model of the TEE images. In the sequence of images, the cyclic heart activity is regarded as a quasi-periodic process, and air bubbles are detected as statistical outliers. The VAE detection system was evaluated by means of receiver operating characteristic (ROC) curves using a data set consisting of 155.14 h of intraoperatively recorded TEE video and a manual classification of periods with visible VAE. Our automatic detection system accomplished an area under the curve (AUC) of 0.945 if all frames with visible VAE were considered as detection target, and an AUC of 0.990 if frames with the least severe optical grade of VAE were excluded from the analysis. Offline-review of the recorded TEE videos showed that short embolic events (≤ 2 min) may be overseen when monitoring TEE video manually. Automatic detection of VAE is feasible and could provide significant support to anaesthesiologists in clinical practice. Our proposed algorithm might possibly even offer a higher sensitivity compared to manual detection. The specificity, however, requires improvement to be acceptable for practical application. Trial Registration: German Clinical Trials Register (DRKS00011607).

2019 IEEE Scientific Visualization Contest Winner: Visual Analysis of Structure Formation in Cosmic Evolution.

Simulations of cosmic evolution are a means to explain the formation of the universe as we see it today. The resulting data of such simulations comprise numerous physical quantities, which turns their analysis into a complex task. Here, we analyze such high-dimensional and time-varying particle data using various visualization techniques from the fields of particle visualization, flow visualization, volume visualization, and information visualization. Our approach employs specialized filters to extract and highlight the development of so-called active galactic nuclei and filament structures formed by the particles. Additionally, we calculate X-ray emission of the evolving structures in a preprocessing step to complement visual analysis. Our approach is integrated into a single visual analytics framework to allow for analysis of star formation at interactive frame rates. Finally, we lay out the methodological aspects of our work that led to success at the 2019 IEEE SciVis Contest.

Enabling Detailed, Biophysics-Based Skeletal Muscle Models on HPC Systems.

Realistic simulations of detailed, biophysics-based, multi-scale models often require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are typically designed to allow for high flexibility and generality in model development. Flexibility and model development, however, are often a limiting factor for large-scale simulations. Therefore, new models are typically tested and run on small-scale compute facilities. By using a detailed biophysics-based, chemo-electromechanical skeletal muscle model and the international open-source software library OpenCMISS as an example, we present an approach to upgrade an existing muscle simulation framework from a moderately parallel version toward a massively parallel one that scales both in terms of problem size and in terms of the number of parallel processes. For this purpose, we investigate different modeling, algorithmic and implementational aspects. We present improvements addressing both numerical and parallel scalability. In addition, our approach includes a novel visualization environment which is based on the MegaMol framework and is capable of handling large amounts of simulated data. We present the results of a number of scaling studies at the Tier-1 supercomputer HazelHen at the High Performance Computing Center Stuttgart (HLRS). We improve the overall runtime by a factor of up to 2.6 and achieve good scalability on up to 768 cores.

A dsDNA model optimized for electrokinetic applications.

We present a coarse-grained (CG) model of a charged double-stranded DNA immersed in an electrolyte solution that can be used for a variety of electrokinetic applications. The model is based on an earlier rigid and immobile model of Weik et al. and includes now semi-flexibility and mobility, so that DNA dynamics can be sufficiently captured to simulate a full nanopore translocation process. To this end we couple the DNA hydrodynamically via a raspberry approach to a lattice-Boltzmann fluid and parametrize the counterions with a distant dependent friction. The electrokinetic properties of the CG DNA model inside an infinite cylinder is fitted against experimental data from Smeets et al. and all-atom simulation data from Kesselheim et al. The stiffness of our CG DNA is modeled via a harmonic angle potential fitted against experimental data of Brunet et al. Finally, the quality of our tuned parameters is tested by measuring the electrophoretic mobility of our DNA model for various numbers of base pairs and salt concentrations. Our results compare excellently with the experimental data sets of Stellwagen et al. and Hoagland et al.

Structural and Kinetic Studies on the Formation of Platinum(II) and Palladium(II) Complexes with L-Cysteine-Derived Ligands.

Complex-formation reactions of the L-cysteine-derived ligands (alpha)N-acetyl-S-methylene-(2'-pyridine)-L-cysteine (py-CH(2)-accys) and (alpha)N-acetyl-S-ethylene-2-(2'-pyridine)-L-cysteine (py-C(2)H(4)-accys) with [Pt(en)(H(2)O)(2)](2+) and [Pd(en)(H(2)O)(2)](2+) were investigated structurally by NMR spectroscopy and kinetically by UV-vis and stopped-flow spectrophotometry. The complexes [Pt(en)(py-CH(2)-accys-S,N)](NO(3))(2) (1) and [Pt(en)(py-C(2)H(4)-accys-S,N)](NO(3))(2) (2) were isolated and purified by reversed-phase HPLC. NMR spectroscopy revealed an S-thioether, N-pyridyl chelation mode with five- and six-membered chelate rings for 1 and 2 and their Pd(II) analogues 3 and 4. The amino acid functional group is not involved in coordination. Comparison of the second-order rate constants for the complex-formation reactions resulted in k(Pd(II))/k(Pt(II)) ratios of 3.7 x 10(4) for py-CH(2)-accys and 2.4 x 10(4) for py-C(2)H(4)-accys. In the presence of excess ligand, the trans effect of the Pd-coordinated sulfur donor induced labilization of the coordinated en ligand with successive displacement to give [Pd(py-CH(2)-accys)(2)] and [Pd(py-C(2)H(4)-accys)(2)]. The displacement reactions were shown to be in accordance with a preequilibrium behavior consisting of reversible formation of the ring-opened intermediate followed by successive irreversible ring closure. The results are discussed in reference to available literature data for related systems.

Complex Formation and Ligand Substitution Reactions of (2-Picolylamine)palladium(II) with Various Biologically Relevant Ligands. Characterization of (2-Picolylamine)(1,1-cyclobutanedicarboxylato)palladium(II).

The influence of a 2-picolylamine (pic) ligand on the reactivity of Pd(II) complexes was investigated by detailed equilibrium and kinetic studies. Reactions of [Pd(pic)(H(2)O)(2)](2+) with chloride, 1,1-cyclobutanedicarboxylic acid (CBDCAH(2)), inosine (ino), and inosine 5'-monophosphate (5'-IMP) were studied. A significantly higher reactivity for the first reaction step involving the displacement of one coordinated solvent molecule on [Pd(pic)(H(2)O)(2)](2+) was observed for the nucleoside inosine (k(10)( degrees )(C) = 25 400 +/- 200 M(-)(1) s(-)(1)) than for the nucleotide 5'-IMP (k(10)( degrees )(C) = 7100 +/- 300 M(-)(1) s(-)(1)) and for CBDCAH(-) (k(25)( degrees )(C) = 5380 +/- 70 M(-)(1) s(-)(1); DeltaH() = 54 +/- 2 kJ mol(-)(1); DeltaS() = 10 +/- 4 J K(-)(1) mol(-)(1); DeltaV() = -0.2 +/- 0.7 cm(3) mol(-)(1)). The results are compared and discussed in reference to data reported for closely related systems in the literature. The molecular structure of [Pd(pic)(CBDCA)] in solution and in the solid state was resolved. [Pd(pic)(CBDCA)].2H(2)O crystallizes in the space group P2(1)/c (monoclinic, a = 5.659(5) Å, b = 18.320(5) Å, c = 14.027(5) Å, beta = 97.748(5) degrees, V = 1440.94(14) Å(3), Z = 4).