Matthias S. Mueller

Bio: Matthias S. Mueller is an academic researcher from Dresden University of Technology. The author has contributed to research in topics: Xeon & InfiniBand. The author has an hindex of 6, co-authored 12 publications receiving 1274 citations. Previous affiliations of Matthias S. Mueller include University of Tennessee.

The International Exascale Software Project roadmap

Abstract: Over the last 20 years, the open-source community has provided more and more software on which the world’s high-performance computing systems depend for performance and productivity. The community has invested millions of dollars and years of effort to build key components. However, although the investments in these separate software elements have been tremendously valuable, a great deal of productivity has also been lost because of the lack of planning, coordination, and key integration of technologies necessary to make them work together smoothly and efficiently, both within individual petascale systems and between different systems. It seems clear that this completely uncoordinated development model will not provide the software needed to support the unprecedented parallelism required for peta/ exascale computation on millions of cores, or the flexibility required to exploit new hardware models and features, such as transactional memory, speculative execution, and graphics processing units. This report describes the work of the community to prepare for the challenges of exascale computing, ultimately combing their efforts in a coordinated International Exascale Software Project.

Systems survey of endocytosis by multiparametric image analysis

Abstract: integrated with other cellular processes requires a comprehensive analysis of its molecular constituents and general design principles. Here, we developed a new strategy to phenotypically profile the human genome with respect to transferrin (TF) and epidermal growth factor (EGF) endocytosis by combining RNA interference, automated high-resolution confocal microscopy, quantitative multiparametric image analysis and high-performance computing. We identified several novel components of endocytic trafficking, including genes implicated in human diseases. We found that signalling pathways such as Wnt,integrin/cell adhesion, transforming growth factor(TGF)-band Notchregulatetheendocyticsystem, andidentified new genes involved in cargo sorting to a subset of signalling endosomes. A systems analysis by Bayesian networks further showed that the number, size, concentration of cargo and intracellular position of endosomes are not determined randomly but are subject to specific regulation, thus uncovering novel properties of the endocytic system.

Openmp Shared Memory Parallel Programming

Abstract: The Intel® Thread Checker is the second incarnation of projection based dynamic analysis technology first introduced with Assure that greatly simplifies application development with OpenMP. The ability to dynamically analyze multiple sibling OpenMP teams enhances the previous Assure support and complements previous work on static analysis. In addition, binary instrumentation capabilities allow detection of thread-safety violations in system and third party libraries that most applications use.

Performance evaluation of supercomputers using HPCC and IMB benchmarks

Abstract: The HPC Challenge (HPCC) benchmark suite and the Intel MPI Benchmark (IMB) are used to compare and evaluate the combined performance of processor, memory subsystem and interconnect fabric of five leading supercomputers - SGI Altix BX2, Cray X1, Cray Opteron Cluster, Dell Xeon cluster, and NEC SX-8. These five systems use five different networks (SGI NUMALINK4, Cray network, Myrinet, InfiniBand, and NEC IXS). The complete set of HPCC benchmarks are run on each of these systems. Additionally, we present Intel MPI Benchmarks (IMB) results to study the performance of 11 MPI communication functions on these systems.

Fiji: an open-source platform for biological-image analysis

Abstract: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Endosome maturation: Endosome maturation

Abstract: Being deeply connected to signalling, cell dynamics, growth, regulation, and defence, endocytic processes are linked to almost all aspects of cell life and disease. In this review, we focus on endosomes in the classical endocytic pathway, and on the programme of changes that lead to the formation and maturation of late endosomes/multivesicular bodies. The maturation programme entails a dramatic transformation of these dynamic organelles disconnecting them functionally and spatially from early endosomes and preparing them for their unidirectional role as a feeder pathway to lysosomes.

How to… home page

Abstract: Home PURPOSE OF THE CENTER: To develop the center to address state-of-the-art research, create innovating educational programs, and support technology transfers using commercially viable results to assist the Army Research Laboratory to develop the next generation Future Combat System in the telecommunications sector that assures prevention of perceived threats, and Non Line of Sight/Beyond Line of Sight lethal support.

Digital Twin: Values, Challenges and Enablers From a Modeling Perspective

Abstract: Digital twin can be defined as a virtual representation of a physical asset enabled through data and simulators for real-time prediction, optimization, monitoring, controlling, and improved decision making. Recent advances in computational pipelines, multiphysics solvers, artificial intelligence, big data cybernetics, data processing and management tools bring the promise of digital twins and their impact on society closer to reality. Digital twinning is now an important and emerging trend in many applications. Also referred to as a computational megamodel, device shadow, mirrored system, avatar or a synchronized virtual prototype, there can be no doubt that a digital twin plays a transformative role not only in how we design and operate cyber-physical intelligent systems, but also in how we advance the modularity of multi-disciplinary systems to tackle fundamental barriers not addressed by the current, evolutionary modeling practices. In this work, we review the recent status of methodologies and techniques related to the construction of digital twins mostly from a modeling perspective. Our aim is to provide a detailed coverage of the current challenges and enabling technologies along with recommendations and reflections for various stakeholders.

Efficiency of siRNA delivery by lipid nanoparticles is limited by endocytic recycling

Abstract: Despite substantial efforts to understand the interactions between nanoparticles and cells, the cellular processes that determine the efficiency of intracellular drug delivery remain largely unclear. Here we examined cellular uptake of siRNA delivered in lipid nanoparticles (LNPs) using cellular trafficking probes in combination with automated high-throughput confocal microscopy as well as defined perturbations of cellular pathways paired with systems biology approaches to uncover protein-protein and protein-small molecule interactions. We show that multiple cell signaling effectors are required for initial cellular entry of LNPs through macropinocytosis, including proton pumps, mTOR, and cathepsins. SiRNA delivery is substantially reduced as ≅70% of the internalized siRNA undergoes exocytosis through egress of LNPs from late endosomes/lysosomes. Niemann Pick type C1 (NPC1) is shown to be an important regulator of the major recycling pathways of LNP-delivered siRNAs. NPC1-deficient cells show enhanced cellular retention of LNPs inside late endosomes/lysosomes and increased gene silencing of the target gene. Our data suggests that siRNA delivery efficiency might be improved by designing delivery vehicles that can escape the recycling pathways.