Hierarchy of stochastic pure states for open quantum system dynamics

We derive a hierarchy of stochastic evolution equations for pure states (quantum trajectories) to efficiently solve open quantum system dynamics with non-Markovian structured environments. From this hierarchy of pure states (HOPS) the exact reduced density operator is obtained as an ensemble average. We demonstrate the power of HOPS by applying it to the Spin-Boson model, the calculation of absorption spectra of molecular aggregates and energy transfer in a photosynthetic pigment-protein complex

Optimised planning and scheduling of grid resources

This article will present the concept and implementation of a resource management system (RMS). The central component of the RMS is the resource broker GORBA that plans resource allocation by a combination of heuristic processes and evolutionary algorithms. For resource planning, schedules are generated, which distribute the grid jobs to the grid resources in a defined time window. A test environment with extensive visualisation options was developed for GORBA, which will be presented in detail. Using this test environment, benchmark runs were carried out, which are needed to evaluate and further develop GORBA. Automated resource planning and the graphic visualisation options facilitate the usability of a grid environment

Optimised planning and scheduling of grid resources

This article will present the concept and implementation of a resource management system (RMS). The central component of the RMS is the resource broker GORBA that plans resource allocation by a combination of heuristic processes and evolutionary algorithms. For resource planning, schedules are generated, which distribute the grid jobs to the grid resources in a defined time window. A test environment with extensive visualisation options was developed for GORBA, which will be presented in detail. Using this test environment, benchmark runs were carried out, which are needed to evaluate and further develop GORBA. Automated resource planning and the graphic visualisation options facilitate the usability of a grid environment

Pure functions in C: A small keyword for automatic parallelization

© 2020, The Author(s). The need for parallel task execution has been steadily growing in recent years since manufacturers mainly improve processor performance by increasing the number of installed cores instead of scaling the processor’s frequency. To make use of this potential, an essential technique to increase the parallelism of a program is to parallelize loops. Several automatic loop nest parallelizers have been developed in the past such as PluTo. The main restriction of these tools is that the loops must be statically analyzable which, among other things, disallows function calls within the loops. In this article, we present a seemingly simple extension to the C programming language which marks functions without side-effects. These functions can then basically be ignored when the automatic parallelizer checks the parallelizability of loops. We integrated the approach into the GCC compiler toolchain and evaluated it by running several real-world applications. Our experiments show that the C extension helps to identify additional parallelization opportunities and, thus, to significantly increase the performance of applications

Stable Weyl points, trivial surface states and particle-hole compensation in WP2

A possible connection between extremely large magneto-resistance and the presence of Weyl points has garnered much attention in the study of topological semimetals. Exploration of these concepts in transition metal phosphide WP2 has been complicated by conflicting experimental reports. Here we combine angle-resolved photoemission spectroscopy (ARPES) and density functional theory (DFT) calculations to disentangle surface and bulk contributions to the ARPES intensity, the superposition of which has plagued the determination of the electronic structure in WP2. Our results show that while the hole- and electron-like Fermi surface sheets originating from surface states have different areas, the bulk-band structure of WP2 is electron-hole-compensated in agreement with DFT. Furthermore, the detailed band structure is compatible with the presence of at least 4 temperature-independent Weyl points, confirming the topological nature of WP2 and its stability against lattice distortions.Comment: 6 pages, 4 figure

Predicting protein targets for drug-like compounds using transcriptomics

An expanded chemical space is essential for improved identification of small molecules for emerging therapeutic targets. However, the identification of targets for novel compounds is biased towards the synthesis of known scaffolds that bind familiar protein families, limiting the exploration of chemical space. To change this paradigm, we validated a new pipeline that identifies small molecule-protein interactions and works even for compounds lacking similarity to known drugs. Based on differential mRNA profiles in multiple cell types exposed to drugs and in which gene knockdowns (KD) were conducted, we showed that drugs induce gene regulatory networks that correlate with those produced after silencing protein-coding genes. Next, we applied supervised machine learning to exploit drug-KD signature correlations and enriched our predictions using an orthogonal structure-based screen. As a proof-of-principle for this regimen, top-10/top-100 target prediction accuracies of 26% and 41%, respectively, were achieved on a validation of set 152 FDA-approved drugs and 3104 potential targets. We then predicted targets for 1680 compounds and validated chemical interactors with four targets that have proven difficult to chemically modulate, including non-covalent inhibitors of HRAS and KRAS. Importantly, drug-target interactions manifest as gene expression correlations between drug treatment and both target gene KD and KD of genes that act up- or down-stream of the target, even for relatively weak binders. These correlations provide new insights on the cellular response of disrupting protein interactions and highlight the complex genetic phenotypes of drug treatment. With further refinement, our pipeline may accelerate the identification and development of novel chemical classes by screening compound-target interactions.Fil: Pabon, Nicolas. University of Pittsburgh; Estados UnidosFil: Xia, Yan. University of Carnegie Mellon; Estados UnidosFil: Estabrooks, Samuel K.. University of Pittsburgh; Estados UnidosFil: Ye, Zhaofeng. Tsinghua University; ChinaFil: Herbrand, Amanda K.. Goethe Universitat Frankfurt; AlemaniaFil: Süß, Evelyn. Goethe Universitat Frankfurt; AlemaniaFil: Biondi, Ricardo Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación en Biomedicina de Buenos Aires - Instituto Partner de la Sociedad Max Planck; Argentina. Goethe Universitat Frankfurt; AlemaniaFil: Assimon, Victoria A.. University of California; Estados UnidosFil: Gestwicki, Jason E.. University of California; Estados UnidosFil: Brodsky, Jeffrey L.. University of Pittsburgh; Estados UnidosFil: Camacho, Carlos. University of Pittsburgh; Estados UnidosFil: Bar Joseph, Ziv. University of Carnegie Mellon; Estados Unido

Facilitating stress prevention in micro and small-sized enterprises:Protocol for a mixed method study to evaluate the effectiveness and implementation process of targeted web-based interventions

BACKGROUND: Workplace-related stress is a major risk factor for mental and physical health problems and related sickness absence and productivity loss. Despite evidence regarding the effectiveness of different workplace-based interventions, the implementation of stress prevention interventions is rare, especially in micro and small-sized enterprises (MSE) with fewer than 50 employees. The joint research project “PragmatiKK”(+) aims to identify and address the specific barriers to the implementation of stress prevention interventions in MSE. This study protocol describes a mixed method study design to evaluate the effectiveness of adapted stress prevention interventions and the implementation process via an integrated web-based platform (“System P”) specifically targeted at MSE. METHODS: First, we develop a web-based intervention, which accounts for the specific working conditions in MSE and addresses stress prevention at a structural and behavioral level. Second, we use common methods of implementation research to perform an effect and process evaluation. We analyze the effectiveness of the web-based stress prevention interventions by comparing depressive symptoms at baseline and follow-up (after 6 months and 12 months). Indicators for a successful implementation process include acceptability, adoption, feasibility, reach, dose, and fidelity, which we will measure with quantitative web-based questionnaires and qualitative interviews. We will also analyze the accumulated usage data from the web-based platform. DISCUSSION: Collecting data on the implementation process and the effectiveness of a web-based intervention will help to identify and overcome common barriers to stress prevention in MSE. This can improve the mental health of employees in MSE, which constitute more than 90% of all enterprises in Germany. (+) Full Project Name: „PragmatiKK - Pragmatische Lösungen für die Implementation von Maßnahmen zur Stressprävention in Kleinst- und Kleinbetrieben “(= Pragmatic solutions for the implementation of stress prevention interventions in micro and small-sized enterprises). TRIAL REGISTRATION: German Register of Clinical Studies (DRKS): DRKS00026154, date of registration: 2021-09-16. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12889-022-12921-7