| 11. |
- Kohnke, B, et al.
(författare)
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Gromex : A scalable and versatile fast multipole method for biomolecular simulation
- 2020
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Ingår i: Lecture Notes in Computational Science and Engineering. - Cham : Springer. ; , s. 517-543
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Atomistic simulations of large biomolecular systems with chemical variability such as constant pH dynamic protonation offer multiple challenges in high performance computing. One of them is the correct treatment of the involved electrostatics in an efficient and highly scalable way. Here we review and assess two of the main building blocks that will permit such simulations: (1) An electrostatics library based on the Fast Multipole Method (FMM) that treats local alternative charge distributions with minimal overhead, and (2) A λ-dynamics module working in tandem with the FMM that enables various types of chemical transitions during the simulation. Our λ-dynamics and FMM implementations do not rely on third-party libraries but are exclusively using C++ language features and they are tailored to the specific requirements of molecular dynamics simulation suites such as GROMACS. The FMM library supports fractional tree depths and allows for rigorous error control and automatic performance optimization at runtime. Near-optimal performance is achieved on various SIMD architectures and on GPUs using CUDA. For exascale systems, we expect our approach to outperform current implementations based on Particle Mesh Ewald (PME) electrostatics, because FMM avoids the communication bottlenecks caused by the parallel fast Fourier transformations needed for PME.
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| 12. |
- Popovic, Marko B., et al.
(författare)
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Practice Problems
- 2019
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Ingår i: Biomechatronics. ; , s. 567-604
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Selected practice problems in the format of numerical problems, concept questions, and case studies are presented in this chapter. Each problem is labeled with an estimated level of difficulty and list of most relevant chapters. Solutions and hints for about half of these problems are provided in the following chapter.
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| 13. |
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| 14. |
- Schotten, U., et al.
(författare)
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Current controversies in determining the main mechanisms of atrial fibrillation
- 2016
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Ingår i: Journal of Internal Medicine. - : Wiley. - 0954-6820. ; 279:5, s. 428-438
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Tidskriftsartikel (refereegranskat)abstract
- Despite considerable basic research into the mechanisms of atrial fibrillation (AF), not much progress has been made in the prognosis of patients with AF. With the exception of anticoagulant therapy, current treatments for AF still do not improve major cardiovascular outcomes. This may be due partly to the diverse aetiology of AF with increasingly more factors found to contribute to the arrhythmia. In addition, a strong increase has been seen in the technological complexity of the methods used to quantify the main pathophysiological alterations underlying the initiation and progression of AF. Because of the lack of standardization of the technological approaches currently used, the perception of basic mechanisms of AF varies widely in the scientific community. Areas of debate include the role of Ca2+-handling alterations associated with AF, the contribution and noninvasive assessment of the degree of atrial fibrosis, and the best techniques to identify electrophysiological drivers of AF. In this review, we will summarize the state of the art of these controversial topics and describe the diverse approaches to investigating and the scientific opinions on leading AF mechanisms. Finally, we will highlight the need for transparency in scientific reporting and standardization of terminology, assumptions, algorithms and experimental conditions used for the development of better AF therapies. Content List - Read more articles from the symposium: Atrial fibrillation - from atrial extrasystoles to atrial cardiomyopathy. What have we learned from basic science and interventional procedures.
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| 15. |
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| 16. |
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