23 papers · ranked by Valyu relevance
Alfons G. Hoekstra, Bastien Chopard, David Coster, Simon Portegies Zwart + 1 more
'Simon Portegies Zwart' 'Peter V. Coveney'] In this position paper, we discuss two relevant topics: (i) generic multiscale computing on emerging exascale high-performing computing environments, and (ii) the scaling of such applications towards the exascale. We will introduce the different phases when developing a…
Derek Groen, Jaroslaw Knap, Philipp Neumann, Diana Suleimenova + 2 more
In the last few decades, multiscale modelling has emerged as one of the dominant modelling paradigms in many areas of science and engineering. Its rise to dominance is primarily driven by advancements in computing power and the need to model systems of increasing complexity. The multiscale modelling paradigm is now…
Saad Alowayyed, Derek Groen, Peter V. Coveney, Alfons G. Hoekstra
- 1 Computational Science Lab, Institute for Informatics, University of Amsterdam, The Netherlands - 2 King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia - 3 Department of Computer Science, Brunel University London, United Kingdom - 4 Centre for Computational Science, University College…
Joris Borgdorff, Mariusz Mamoński, Bartosz Bosak, Krzysztof Kurowski + 5 more
'Mohamed Ben Belgacem' 'Bastien Chopard' 'Derek Groen' 'Peter V. Coveney' 'Alfons G. Hoekstra'] We present the Multiscale Coupling Library and Environment: MUSCLE 2. This multiscale componentbased execution environment has a simple to use Java, C++, C, Python and Fortran API, compatible with MPI, OpenMP and threading…
Matteo Capone, Marco Romanelli, Davide Castaldo, Giovanni Parolin + 3 more
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first…
Derek Groen, Stefan J. Zasada, Peter V. Coveney
—Multiscale and multiphysics applications are now commonplace, and many researchers focus on combining existing models to construct combined multiscale models. Here we present a concise review of multiscale applications and their source communities. We investigate the prevalence of multiscale projects in the EU and the…
Jacob Merson, Catalin R. Picu, Mark S. Shephard
This article presents MuMFiM, an open source application for multiscale modeling of fibrous materials on massively parallel computers. MuMFiM uses two scales to represent fibrous materials such as biological network materials (extracellular matrix, connective tissue, etc.). It is designed to make use of multiple levels…
Pariksheet Nanda, Maral Budak, Christian T. Michael, Kathryn Krupinsky + 1 more
Although infectious disease dynamics are often analyzed at the macro-scale, increasing numbers of drug-resistant infections highlight the importance of within-host modeling that simultaneously solves across multiple scales to effectively respond to epidemics. We review multiscale modeling approaches for complex…
Lionel Kusch, Sandra Diaz, Wouter Klijn, Kim Sontheimer + 3 more
Integration of information across heterogeneous sources creates added scientific value. It is, however, a challenge to progress, often a barrier, to interoperate data, tools and models across spatial and temporal scales. Here we present a design template for coupling simulators operating at different scales and…
Manik Kuchroo, Jessie Huang, Patrick Wong, Jean-Christophe Grenier + 23 more
The biomedical community is producing increasingly high dimensional datasets, integrated from hundreds of patient samples, which current computational techniques struggle to explore. To uncover biological meaning from these complex datasets, we present an approach called Multiscale PHATE, which learns abstracted…
E. Abreu, Paola Ferraz, Arthur Espírito Santo, F. Pereira + 2 more
'L. G. C. Santos' 'Fabrício S. Sousa'] Multiscale methods for second order elliptic equations based on non-overlapping domain decomposition schemes have great potential to take advantage of multi-core, state-of-the-art parallel computers. These methods typically involve solving local boundary value problems followed by…
Ondrej Krejcar, Hamidreza Namazi
The brain’s complex organization spans from molecular-level processes within neurons to large-scale networks, making it essential to understand this multiscale structure to uncover brain functions and address neurological disorders. Multiscale brain modeling has emerged as a transformative approach, integrating…
Sonata Kvedaravičiūtė, Andrej Antalík, Olivier Adjoua, Thomas Plé + 4 more
In this work, we present the development of a fully-polarizable KS-DFT/AMOEBA embedding scheme for delocalized basis sets such as plane-waves and real-space grids. The augmented problem of electron spill-out inherent to a polarizable QM/MM implementation with plane-wave basis sets is addressed and the periodicity for…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Authors not listed
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…
Lin Chen, Yuhan Chen, Ziqi Cheng, Jing Guo + 20 more
MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit…
Martin Werner
This paper provides an abstract analysis of parallel processing strategies for spatial and spatio-temporal data. It isolates aspects such as data locality and computational locality as well as redundancy and locally sequential access as central elements of parallel algorithm design for spatial data. Furthermore, the…
Marc P. Armstrong
The pace of improvement in the performance of conventional computer hardware has slowed significantly during the past decade, largely as a consequence of reaching the physical limits of manufacturing processes. To offset this slowdown, new approaches to HPC are now undergoing rapid development. This chapter describes…
Authors not listed
Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously we have developed the Spherical Grid and Treecode (SGT) and Gauss-Legendre-Spherical-t (GLST) algorithms for…
Maxim Lippeveld, Daniel Peralta, Andrew Filby, Yvan Saeys
Due to high resolution and throughput of modern image cytometry platforms, morphologically profiling generated datasets poses a significant computational challenge. Here, we present Scalable Cytometry Image Processing (SCIP), an image processing software aimed at running on distributed high performance computing…
Yongchun Lü, Xiangrui Zeng, Xinhui Tian, Xiao Shi + 6 more
'Xiaohui Zheng' 'Xiaodong Liu' 'Xiaofang Zhao' 'Xin Gao' 'Min Xu'] Background Resolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the 3D resolution for reconstructed…
Tim Marshall, Robert Raddi, Vincent Voelz
All-atom molecular dynamics (MD) simulations can provide detailed insight into a molecule's conformational ensemble in solution. While molecular force fields are parameterized to accurately model a protein's potential energy surface, it remains challenging in practice to evaluate how well force fields can capture…
Yingqi Tian, Zhaoxuan Xie, Zhen Luo, Haibo Ma
Using the mixed precision strategy to optimize quantum chemistry codes has been proved promising in saving computational cost and maintaining chemical accuracy. Here, an efficient mixed-precision density matrix renormalization group (DMRG) scheme, containing a two-level mixed-precision hierarchy, is developed and…