A5082069859- Parallel Computing and Optimization Techniques
- Protein Structure and Dynamics
- Theoretical and Computational Physics
- COVID-19 epidemiological studies
- Distributed and Parallel Computing Systems
- Advanced Data Storage Technologies
- SARS-CoV-2 and COVID-19 Research
- Enzyme Structure and Function
- COVID-19 Pandemic Impacts
- Genetics, Bioinformatics, and Biomedical Research
- COVID-19 Clinical Research Studies
- Algorithms and Data Compression
- Complex Network Analysis Techniques
- RNA and protein synthesis mechanisms
- Stochastic processes and statistical mechanics
- Photosynthetic Processes and Mechanisms
- Distributed systems and fault tolerance
- Spectroscopy and Quantum Chemical Studies
- Scientific Computing and Data Management
- Data-Driven Disease Surveillance
- Magnetic confinement fusion research
- Forecasting Techniques and Applications
- Markov Chains and Monte Carlo Methods
- Opinion Dynamics and Social Influence
- Force Microscopy Techniques and Applications
Forschungszentrum Jülich
2009-2024
Spectrum Health
2023
Karlsruhe Institute of Technology
2020
Michigan Technological University
2009
John von Neumann Institute for Computing
2007-2008
Syracuse University
2004-2005
Michigan State University
2001-2004
Short-term forecasts of infectious disease burden can contribute to situational awareness and aid capacity planning. Based on best practice in other fields recent insights epidemiology, one maximise the predictive performance such if multiple models are combined into an ensemble. Here, we report ensembles predicting COVID-19 cases deaths across Europe between 08 March 2021 07 2022.
The novel coronavirus (SARS-CoV-2), identified in China at the end of December 2019 and causing disease COVID-19, has meanwhile led to outbreaks all over globe with about 2.2 million confirmed cases more than 150,000 deaths as April 17, 2020. In this work, mathematical models are used reproduce data early evolution COVID-19 outbreak Germany, taking into account effect actual hypothetical non-pharmaceutical interventions. Systems differential equations SEIR type extended for undetected...
Abstract Disease modelling has had considerable policy impact during the ongoing COVID-19 pandemic, and it is increasingly acknowledged that combining multiple models can improve reliability of outputs. Here we report insights from ten weeks collaborative short-term forecasting in Germany Poland (12 October–19 December 2020). The study period covers onset second wave both countries, with tightening non-pharmaceutical interventions (NPIs) subsequently a decay (Poland) or plateau renewed...
High-performance computing (HPC) is recognized as one of the pillars for further progress in science, industry, medicine, and education. Current HPC systems are being developed to overcome emerging architectural challenges order reach Exascale level performance, projected year 2020. The much larger embedded mobile market allows rapid development intellectual property (IP) blocks provides more flexibility designing an application-specific system-on-chip (SoC), turn providing possibility...
During the COVID-19 pandemic there has been a strong interest in forecasts of short-term development epidemiological indicators to inform decision makers. In this study we evaluate probabilistic real-time predictions confirmed cases and deaths from Germany Poland for period January through April 2021.
Replica exchange simulations have become the method of choice in computational protein science, but they still often do not allow an efficient sampling low-energy configurations. Here, we reconstruct replica flow temperature ladder from first passage times and use it for optimization, thereby maximizing sampling. The is applied folding thermodynamics a number proteins starting pentapeptide Met-enkephalin, through 36-residue HP-36, up to 67-residue...
Protein structures often feature beta-sheets in which adjacent beta-strands have large sequence separation. How the folding process orchestrates formation and correct arrangement of these strands is not comprehensively understood. Particularly challenging are proteins at N C termini neighbors a beta-sheet. The N-terminal beta-strand synthesized early on, but it can bind to terminus before chain fully synthesized. During this time, there danger that interacts with nearby molecules, leading...
Abstract The novel coronavirus (SARS-CoV-2), identified in China at the end of December 2019 and causing disease COVID-19, has meanwhile led to outbreaks all over globe, with about 571,700 confirmed cases 26,500 deaths as March 28th, 2020. We present here preliminary results a mathematical study directed informing on possible application or lifting control measures Germany. developed models allow spread COVID-19 among population Germany asses impact non-pharmaceutical interventions.
Abstract We report insights from ten weeks of collaborative COVID-19 forecasting for Germany and Poland (12 October – 19 December 2020). The study period covers the onset second wave in both countries, with tightening non-pharmaceutical interventions (NPIs) subsequently a decay (Poland) or plateau renewed increase (Germany) reported cases. Thirteen independent teams provided probabilistic real-time forecasts cases deaths. These were lead times one to four weeks, evaluation focused on one-...
The authors study the folding and aggregation of six chains β-amyloid fragment 16–22 using Monte Carlo simulations. While isolated prefers a helical form at room temperature, in system interacting fragments one observes both parallel antiparallel β sheets below crossover temperature Tx≈420K. have lower energy are therefore more stable. Above nucleation aggregate quickly dissolves into widely separated, weakly chains.
Abstract Utilizing the computational power of a few thousand processors on BlueGene/P, we have explored folding mechanism 67‐residue protein GS‐α 3 W. Results from our large‐scale simulation indicate diffusion‐collision for folding. However, lower‐than‐expected frequency native‐like configurations at physiological temperatures indicates shortcomings energy function. Our results suggest that studies large proteins call redevelopment and reparametrization force fields in turn require extensive...
For computational studies of protein folding, proteins with both helical and β-sheet secondary structure elements are very challenging, as they expose subtle biases the physical models. Here, we present reproducible folding a 92 residue α/β (residues 3-94 Top7, PDB ID: 1QYS) in computer simulations starting from random initial conformations using transferable model which has been previously shown to describe thermodynamic properties about 20 other smaller different folds. Top7 is de novo...
Benchmarks are essential in the design of modern HPC installations, as they define key aspects system components. Beyond synthetic workloads, it is crucial to include real applications that represent user requirements into benchmark suites, guarantee high usability and widespread adoption a new system. Given significant investments leadership-class supercomputers exascale era, this even more important necessitates alignment with vision Open Science reproducibility. In work, we present...
Using a variant of parallel tempering, we study the changes in sampling within simulation, when all-atom model is coupled to Go-like potential. We find that native structure not lowest-energy configuration force field. Adding Go term deforms energy landscape such way becomes global minimum but does lead faster thermalization.
Abstract The novel coronavirus (SARS-CoV-2), identified in China at the end of December 2019 and causing disease COVID-19, has meanwhile led to outbreaks all over globe with about 2.2 million confirmed cases more than 150,000 deaths as April 17, 2020 [37]. In view most recent information on testing activity [32], we present here an update our initial work [4]. this work, mathematical models have been developed study spread COVID-19 among population Germany asses impact non-pharmaceutical...
Two attractive and often used ideas, namely, universality the concept of a zero-temperature fixed point, are violated in infinite-range random-field Ising model. In ground state we show that exponents can depend continuously on disorder so nonuniversal. However, also at finite temperature thermal order-parameter exponent $1/2$ is restored relevant variable. Broader implications these results discussed.
Abstract Background During the COVID-19 pandemic there has been a strong interest in forecasts of short-term development epidemiological indicators to inform decision makers. In this study we evaluate probabilistic real-time predictions confirmed cases and deaths from Germany Poland for period January through April 2021. Methods We Poland. These were issued by 15 different forecasting models, run independent research teams. Moreover, performance combined ensemble forecasts. Evaluation is...
We study the surfaces of lowest energy through model polycrystalline materials in two and three dimensions. When grain boundaries are sufficiently weak, these critical manifolds (CM's) lie entirely on boundaries, while when strong, cleavage occurs. A scaling theory for intergranular to transgranular transition CM's is developed. The key parameters average size g, ratio boundary interior energy, epsilon, sample L. result that a length scale exists, L(c)(g,epsilon), so short scales l<L(c)...