Understanding the Scalability of Molecular Simulation Using Empirical Performance Modeling

The final authenticated publication is available online at https://doi.org/10.1007/978-3-030-17872-7_8.Molecular dynamics (MD) simulation allows for the study of static and dynamic properties of molecular ensembles at various molecular scales, from monatomics to macromolecules such as proteins and nucleic acids. It has applications in biology, materials science, biochemistry, and biophysics. Recent developments in simulation techniques spurred the emergence of the computational molecular engineering (CME) field, which focuses specifically on the needs of industrial users in engineering. Within CME, the simulation code ms2 allows users to calculate thermodynamic properties of bulk fluids. It is a parallel code that aims to scale the temporal range of the simulation while keeping the execution time minimal. In this paper, we use empirical performance modeling to study the impact of simulation parameters on the execution time. Our approach is a systematic workflow that can be used as a blue-print in other fields that aim to scale their simulation codes. We show that the generated models can help users better understand how to scale the simulation with minimal increase in execution time.BMBF, 01IH16008D, Verbundprojekt: TaLPas - Task-basierte Lastverteilung und Auto-Tuning in der PartikelsimulationDFG, 323299120, ExtraPeak - Automatische Leistungsmodellierung von HPC-Anwendungen mit multiplen Modellparameter

Tools for analyzing parallel I/O

Parallel application I/O performance often does not meet user expectations. Additionally, slight access pattern modifications may lead to significant changes in performance due to complex interactions between hardware and software. These issues call for sophisticated tools to capture, analyze, understand, and tune application I/O. In this paper, we highlight advances in monitoring tools to help address these issues. We also describe best practices, identify issues in measure- ment and analysis, and provide practical approaches to translate parallel I/O analysis into actionable outcomes for users, facility operators, and researchers

Domain structure of bulk ferromagnetic crystals in applied fields near saturation

We investigate the ground state of a uniaxial ferromagnetic plate with perpendicular easy axis and subject to an applied magnetic field normal to the plate. Our interest is the asymptotic behavior of the energy in macroscopically large samples near the saturation field. We establish the scaling of the critical value of the applied field strength below saturation at which the ground state changes from the uniform to a branched domain magnetization pattern and the leading order scaling behavior of the minimal energy. Furthermore, we derive a reduced sharp-interface energy giving the precise asymptotic behavior of the minimal energy in macroscopically large plates under a physically reasonable assumption of small deviations of the magnetization from the easy axis away from domain walls. On the basis of the reduced energy, and by a formal asymptotic analysis near the transition, we derive the precise asymptotic values of the critical field strength at which non-trivial minimizers (either local or global) emerge. The non-trivial minimal energy scaling is achieved by magnetization patterns consisting of long slender needle-like domains of magnetization opposing the applied fieldComment: 38 pages, 7 figures, submitted to J. Nonlin. Sci

Lower urinary tract electrical sensory assessment: A systematic review and meta-analysis

OBJECTIVE To summarize the current literature on lower urinary tract electrical sensory assessment (LUTESA), with regard to current perception thresholds (CPTs) and sensory evoked potentials (SEPs). The applied methods will be discussed in terms of technical aspects, confounding factors, and potential for lower urinary tract (LUT) diagnostics. METHODS The review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Medline (PubMed), Embase and Scopus were searched upon October 13, 2020. Meta-analyses were performed and methodological qualities of the included studies were defined by assessing risk-of-bias (RoB) as well as confounding. RESULTS After screening 9925 articles, 80 studies (5 randomized controlled trials (RCTs) and 75 non-RCTs) were included, comprising a total of 3732 patients and 692 healthy subjects. 61 studies investigated exclusively CPTs and 19 studies reported on SEPs, with or without corresponding CPTs. The recording of LUTCPTs and -SEPs was shown to represent a safe and reliable assessment of LUT afferent nerve function in healthy subjects and patients. LUTESA demonstrated significant differences in LUT sensitivity between healthy subjects and neurological patients as well as after interventions such as pelvic surgery or drug treatments. Pooled analyses revealed that several stimulation parameters (e.g. stimulation frequency, location) as well as patient characteristics might affect the main outcome measures of LUTESA (CPTs, SEP latencies, peak-to-peak amplitudes, responder rate). RoB and confounding was high in most studies. CONCLUSIONS Preliminary data show that CPT and SEP recordings are valuable tools to more objectively assess LUT afferent nerve function. LUTESA complement already established diagnostics such as urodynamics, allowing for a more comprehensive patient workup. The high RoB and confounding rate was rather related to inconsistency and inaccuracy in reporting than the technique itself. LUTESA standardization and well-designed RCTs are crucial to implement LUTESA as a clinical assessment tool

The democratic interface: technology, political organization, and diverging patterns of electoral representation

Democracies are experiencing historic disruptions affecting how people engage with core institutions such as the press, civil society organizations, parties, and elections. These processes of citizen interaction with institutions operate as a democratic interface shaping self-government and the quality of public life. The electoral dimension of the interface is important, as its operation can affect all others. This analysis explores a growing left-right imbalance in the electoral connection between citizens, parties, elections, and government. This imbalance is due, in part, to divergent left-right preferences for political engagement, organization, and communication. Support on the right for clearer social rules and simpler moral, racial and nationalist agendas are compatible with hierarchical, leader-centered party organizations that compete more effectively in elections. Parties on the left currently face greater challenges engaging citizens due to the popular meta-ideology of diversity and inclusiveness and demands for direct or deliberative democracy. What we term connective parties are developing technologies to perform core organizational functions, and some have achieved electoral success. However, when connective parties on the left try to develop shared authority processes, online and offline, they face significant challenges competing with more conventionally organized parties on the right

Comparison of a new transcutaneous bilirubinometer (Bilimed®) with serum bilirubin measurements in preterm and full-term infants

<p>Abstract</p> <p>Background</p> <p>The gold standard to assess hyperbilirubinemia in neonates remains the serum bilirubin measurement. Unfortunately, this is invasive, painful, and costly. Bilimed^®, a new transcutaneous bilirubinometer, suggests more accuracy compared to the existing non-invasive bilirubinometers because of its new technology. It furthermore takes into account different skin colours. No contact with the skin is needed during measurement, no additional material costs occur. Our aim was to assess the agreement between the Bilimed^®and serum bilirubin in preterm and term infants of different skin colours.</p> <p>Methods</p> <p>The transcutaneous bilirubin measurements were performed on the infant's sternum and serum bilirubin was determined simultaneously. The agreement between both methods was assessed by Pearson's correlation and by Bland-Altman analysis.</p> <p>Results</p> <p>A total of 117 measurement cycles were performed in 99 term infants (group1), further 47 measurements in 38 preterm infants born between 34 - 36 6/7 gestational weeks (group 2), and finally 21 measurements in 13 preterm infants born between 28 - 33 6/7 gestational weeks (group 3). The mean deviation and variability (+/- 2SD) of the transcutaneous from serum bilirubin were: -14 (+/- 144) μmol/l; -0.82 (+/- 8.4) mg/dl in group 1, +16 (+/- 91) μmol/l;+0.93(+/- 5.3) mg/dl in group 2 and -8 (+/- 76) μmol/l; -0.47 (+/- 4.4) mg/dl in group 3. These limits of agreement are too wide to be acceptable in a clinical setting. Moreover, there was to be a trend towards less good agreement with increasing bilirubin values.</p> <p>Conclusion</p> <p>Despite its new technology the Bilimed^®has no advantages, and more specifically no better agreement not only in term and near-term Caucasian infants, but also in non-Caucasian and more premature infants.</p

Ranked retrieval of Computational Biology models

<p>Abstract</p> <p>Background</p> <p>The study of biological systems demands computational support. If targeting a biological problem, the reuse of existing computational models can save time and effort. Deciding for potentially suitable models, however, becomes more challenging with the increasing number of computational models available, and even more when considering the models' growing complexity. Firstly, among a set of potential model candidates it is difficult to decide for the model that best suits ones needs. Secondly, it is hard to grasp the nature of an unknown model listed in a search result set, and to judge how well it fits for the particular problem one has in mind.</p> <p>Results</p> <p>Here we present an improved search approach for computational models of biological processes. It is based on existing retrieval and ranking methods from Information Retrieval. The approach incorporates annotations suggested by MIRIAM, and additional meta-information. It is now part of the search engine of BioModels Database, a standard repository for computational models.</p> <p>Conclusions</p> <p>The introduced concept and implementation are, to our knowledge, the first application of Information Retrieval techniques on model search in Computational Systems Biology. Using the example of BioModels Database, it was shown that the approach is feasible and extends the current possibilities to search for relevant models. The advantages of our system over existing solutions are that we incorporate a rich set of meta-information, and that we provide the user with a relevance ranking of the models found for a query. Better search capabilities in model databases are expected to have a positive effect on the reuse of existing models.</p