Tensor algebra operations such as contractions in computational chemistry consume a significant fraction of the computing time on large-scale computing platforms. The widespread use of tensor contractions between large multi-dimensional tensors in describing electronic structure theory has motivated the development of multiple tensor algebra frameworks targeting heterogeneous computing platforms. In this paper, we present Tensor Algebra for Many-body Methods (TAMM), a framework for productive and performance-portable development of scalable computational chemistry methods. TAMM decouples the specification of the computation from the execution of these operations on available high-performance computing systems. With this design choice, the scientific application developers (domain scientists) can focus on the algorithmic requirements using the tensor algebra interface provided by TAMM, whereas high-performance computing developers can direct their attention to various optimizations on the underlying constructs, such as efficient data distribution, optimized scheduling algorithms, and efficient use of intra-node resources (e.g., graphics processing units). The modular structure of TAMM allows it to support different hardware architectures and incorporate new algorithmic advances. We describe the TAMM framework and our approach to the sustainable development of scalable ground- and excited-state electronic structure methods. We present case studies highlighting the ease of use, including the performance and productivity gains compared to other frameworks.
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Sci Rep
December 2024
Department of Applied Mathematics, University of Washington, Seattle, 98195, WA, US.
This research investigates detectability of a class of mix-valued logical control networks through the application of a Luenberger-like observer. First, three concepts of detectability: detectability, strong detectability, and weak detectability are defined for the mix-valued logical control networks. Subsequently, the equivalent algebraic form of the control networks is obtained to deal with the three kinds of detectability.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Division of Scientific Computing, Department of Information Technology, Uppsala University, Box 337, SE-751 05 Uppsala, Sweden.
Density matrix perturbation theory based on recursive Fermi-operator expansions provides a computationally efficient framework for time-independent response calculations in quantum chemistry and materials science. From a perturbation in the Hamiltonian, we can calculate the first-order perturbation in the density matrix, which then gives us the linear response in the expectation values for some chosen set of observables. We present an alternative, dual formulation, where we instead calculate the static susceptibility of an observable, which then gives us the linear response in the expectation values for any number of different Hamiltonian perturbations.
View Article and Find Full Text PDFPac Symp Biocomput
December 2024
Department of Computer Science and Engineering, University of North Texas, TX, USA.
Alzheimer's disease (AD) is a neurocognitive disorder that deteriorates memory and impairs cognitive functions. Mild Cognitive Impairment (MCI) is generally considered as an intermediate phase between normal cognitive aging and more severe conditions such as AD. Although not all individuals with MCI will develop AD, they are at an increased risk of developing AD.
View Article and Find Full Text PDFActa Biotheor
November 2024
Amazon Web Services, 7 W34th Street, New York, NY, 10001, USA.
Coarse-grain models are essential to understand the biological function of DNA molecules because the length and time scales of the sequence-dependent physical properties of DNA are often beyond the reach of experimental and all-atom computational methods. Simulating coarse-grain models of DNA, e.g.
View Article and Find Full Text PDFSensors (Basel)
October 2024
Integrated Movement Studies, Alfred University, Alfred, NY 14802, USA.
This study introduces an innovative integration of Laban Movement Analysis (LMA) with biomechanical principles to examine the golf swing dynamics from an ecological perspective. Traditionally, LMA focuses on the qualitative aspects of movement, often isolated from external influences. This research bridges that gap by investigating how golfers manage and adapt to the inertial forces of the club throughout the swing.
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