Article
Chemistry, Physical
Giuseppe M. J. Barca, Melisa Alkan, Jorge L. Galvez-Vallejo, David L. Poole, Alistair P. Rendell, Mark S. Gordon
Summary: The novel implementation of the self-consistent field (SCF) procedure is specifically designed for high-performance execution on multiple graphics processing units (GPUs), showing remarkable speedups for various test molecules and basis sets compared to existing GPU codes. Strong scaling calculations demonstrate nearly ideal scalability up to 8 GPUs while maintaining high parallel efficiency for up to 18 GPUs.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Yingqi Tian, Zhaoxuan Xie, Zhen Luo, Haibo Ma
Summary: Mixed-precision optimization is an effective technique for improving computational performance while maintaining accuracy in quantum chemistry methods. In this study, a two-level mixed-precision implementation for the density matrix renormalization group (DMRG) method is developed. Benchmark results show that the proposed implementation achieves both improved performance and preserved accuracy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Melisa Alkan, Buu Q. Q. Pham, Jeff R. R. Hammond, Mark S. S. Gordon
Summary: The performance of Fortran 2008 DO CONCURRENT (DC) is compared with OpenACC and OpenMP target offloading (OTO) for the GAMESS quantum chemistry application. The study focuses on offloading the Fock build, a computational bottleneck in quantum chemistry codes, to GPUs using DC and OTO. The results show that DC can achieve a 3.0x speedup compared to OTO, making it a compelling programming model for offloading Fortran applications to GPUs.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Andrey Asadchev, Edward F. Valeev
Summary: In order to improve the efficiency of Gaussian integral evaluation on modern accelerated architectures, FLOP-efficient Obara-Saika-based recursive evaluation schemes are optimized to reduce memory usage. The use of multiquantal recurrences is shown to save significant memory for evaluating 3-center 2-particle integrals. Other innovations include leveraging register memory and compile-time features of modern C++/CUDA. The performance of the proposed schemes is demonstrated for various types of integrals and the implementation is available in the open-source LibintX library.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Computer Science, Software Engineering
Mariia Myronova, William Neveu, Mikhail Bessmeltsev
Summary: A vector sketch is a popular and natural geometry representation of a 2D shape, and the positive and negative spaces are key elements that define the shape. However, the notion of positive or negative space is mathematically ambiguous in vector sketches. In this study, a robust algorithm called Alpha Contours is proposed to construct a conservative estimate of the sketch shape, enabling the application of classical methods on vector sketches.
ACM TRANSACTIONS ON GRAPHICS
(2023)
Article
Mechanics
Bohao Zhou, Xudong Huang, Ke Zhang, Dianfang Bi, Ming Zhou
Summary: This paper proposes a block data-parallel lower-upper relaxation (BDPLUR) scheme based on Jacobi iteration and Roe's flux scheme and implements it on a GPU. Numerical experiments show that the BDPLUR scheme, especially when implemented on a GPU, is more than ten times faster than the original data-parallel lower-upper relaxation scheme.
Article
Chemistry, Multidisciplinary
Nobuki Inoue, Takahito Nakajima
Summary: A recursive scheme was proposed to calculate frequency-dependent Breit interactions in electronic structure calculations. The authors derived explicit expressions and asymptotic formulas for the generalized molecular incomplete gamma function corresponding to the Gaunt and gauge potentials. The numerical calculations showed significant variations in the shape of the generalized molecular incomplete gamma functions with increasing energy.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Computer Science, Information Systems
Cihangir Tezcan
Summary: This work focuses on the performance of the AES algorithm on GPUs, achieving significant breakthroughs in optimization to provide higher encryption throughput and surpassing CPU performance with hardware instructions and traditional FPGA clusters. Transitioning from AES-128 to AES-256 on GPUs has been proven to offer increased security without sacrificing performance.
Article
Neurosciences
Rin Kuriyama, Claudia Casellato, Egidio D'Angelo, Tadashi Yamazaki
Summary: This study focuses on large-scale simulation of detailed computational models of neuronal microcircuits using a scaffolding approach, which involves replacing simulation modules to improve computational speed. The research demonstrates that the scaffolding method can accelerate real-time simulation significantly, reducing computational time without affecting experimental results.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Chemistry, Physical
Ji Qi, Yingfeng Zhang, Minghui Yang
Summary: The calculation of two-electron repulsion integrals (ERIs) is crucial in Hartree-Fock calculations. A hybrid CPU/GPU method has been proposed to accelerate the computation and improve efficiency, especially for ERIs with varying angular momentum.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Computer Science, Information Systems
Muhammad Kashif Hanif, Karl-Heinz Zimmermann, Asad Anees
Summary: Bipartite graphs are commonly used in biological and physical sciences, and finding shortest paths in these graphs can be efficiently solved using dynamic programming algorithms. This study introduces parallel versions of Floyd-Warshall and Torgasin-Zimmermann algorithms, implemented on graphics processing unit using tropical matrix product. The performance of these algorithms is compared under different scenarios and parameters.
MULTIMEDIA TOOLS AND APPLICATIONS
(2022)
Article
Chemistry, Physical
Buu Q. Pham, Melisa Alkan, Mark S. Gordon
Summary: This paper discusses a framework for offloading four-index two-electron repulsion integrals to GPUs using OpenMP. The framework is applied to Fock build for low angular momentum s and p functions in both RHF and EFMO. Benchmark calculations show that the GPU code outperforms the existing CPU code in GAMESS, with a speedup ranging from 1.04 to 52x for clusters of water molecules. In addition, the parallel efficiency of the GPU code increases with system size in both RHF and EFMO.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Computer Science, Information Systems
Cosmin-Constantin Mihai, Ciprian Lupu
Summary: The research article demonstrates the use of video cards in multimodel adaptive robust control, showcasing the viability of utilizing graphics processing units in real time systems control through software simulation.
Article
Computer Science, Theory & Methods
Nhut-Minh Ho, Weng-Fai Wong
Summary: This article proposes Tensorox, a framework that utilizes the half-precision tensor cores on recent GPUs to accelerate non deep learning applications. By training shallow neural networks and running multiple instances in parallel using tensor operations on Nvidia GPUs, our approximation achieves higher accuracy than running the original single precision programs, while allowing for runtime adjustment of the degree of approximation.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2022)
Article
Computer Science, Hardware & Architecture
Yufei Ni, Yangdong Deng, Zonghui Li
Summary: This paper proposes a scheduling mechanism to unleash parallelism in the ray-tracing process on GPUs, which, when combined with a tile-based ray-tracing framework, significantly improves memory efficiency and outperforms traditional GPU architecture.
IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS
(2022)
Article
Chemistry, Medicinal
Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M. Merz
Summary: The new water models and ion parameter sets accurately reproduce experimental data, demonstrating improved performance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Medicinal
Gaurav Sharma, Lin Frank Song, Kenneth M. Merz
Summary: This study investigates the influence of the MLN-4760 inhibitor on ACE2 through molecular dynamics simulations. The presence of the inhibitor affects the conformational properties of ACE2 and its interaction with SARS-CoV-2.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Zhen Li, Kenneth M. Merz
Summary: Diffusion, as a fundamental property of fluids, plays a crucial role in both scientific research and everyday life. While the diffusion properties of many liquids, such as water, have been extensively studied, there has been a lack of theoretical research on transition metal ions. In this study, a workflow called ISAIAH was developed to accurately simulate the diffusion coefficients of 15 monoatomic ions in water. The results showed good agreement with experimental data, which allowed for the theoretical prediction of the diffusion coefficient of 239Pu4+ ion. The use of an augmented 12-6-4 Lennard-Jones potential parameter set showed better results compared to some other parameter sets, indicating that both hydration free energy and ion-oxygen distance play important roles in diffusion.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Gaurav Sharma, Kenneth M. Merz
Summary: Zinc is an essential transition metal ion that plays multiple roles in cellular function. This study used molecular dynamics simulations to explore the structure-function relationship of YiiP protein in a lipid bilayer and proposed a hypothesis on the zinc efflux mechanism. The study revealed the important role of zinc ions in restraining the protein's transmembrane domains and suggested the guiding role of amino acid H153 in transporting zinc ions. Understanding the zinc transport process can provide insights into treating diseases such as diabetes and cancer.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemical Research Methods
Susanta Das, Kiyoto Aramis Tanemura, Laleh Dinpazhoh, Mithony Keng, Christina Schumm, Lydia Leahy, Carter K. Asef, Markace Rainey, Arthur S. Edison, Facundo M. Fernandez, Kenneth M. Merz
Summary: In this study, an efficient CCS computational workflow was developed to accurately predict unknown structures using a machine learning model and standard DFT methods. TWIMS experiments were performed to validate the experimental values and assess uncertainties. The workflow yielded accurate structural predictions and provided unique insights into preferred conformations.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Madushanka Manathunga, Andreas W. Gotz, Kenneth M. Merz
Summary: Quantum chemistry allows for the study of systems with high accuracy, but its computational expense limits its application to a few atoms. To optimize performance, methods such as implementing quantum mechanical methods on modern hardware and using multiscale approaches have been developed. Simplified QM methods, including the use of machine learning, have also been created to enhance the speed and accuracy of calculations.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Physical
Ali Rahnamoun, Kurt A. O'Hearn, Mehmet Cagri Kaymak, Zhen Li, Kenneth M. Merz, Hasan Metin Aktulga
Summary: A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is proposed for molecular dynamics simulations of ions in condensed phases. The model introduces polarization effects by the electronegativity equalization model (EEM) method, allowing charges on the metal ion and its dummy atoms to fluctuate in response to the environment. This model can be coupled with nonpolarizable or polarizable water models and enhances the original fixed charge CDA model by adapting to the local solvent structure.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Abhishek Thakur, Gaurav Sharma, Vishnu Nayak Badavath, Venkatesan Jayaprakash, Kenneth M. Merz, Galia Blum, Orlando Acevedo
Summary: The COVID-19 outbreak has caused massive devastation worldwide, with millions of infections and deaths reported. Using a combination of crystal structures and validated inhibitors, four rules for designing potent inhibitors of SARS-CoV-2 main protease have been proposed. Experimental examination identified a potential lead compound with higher potency than known inhibitors.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Editorial Material
Chemistry, Medicinal
Guo-Wei Wei, Feng Zhu, Kenneth M. Merz
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Gotz, Jr Kenneth M. Merz
Summary: The researchers have ported and optimized the GPU-accelerated QUICK and AMBER-based QM/MM implementation on AMD GPUs. This includes the entire Fock matrix build and force calculation in QUICK, along with general performance improvements to the QUICK GPU code. Benchmark tests on NVIDIA V100 and AMD MI100 cards show similar performance for standalone HF/DFT calculations and QM/MM molecular dynamics simulations with QUICK and QUICK/AMBER. In addition, significant speedups are observed for QM/MM molecular dynamics simulations compared to the previous release version.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Editorial Material
Chemistry, Medicinal
Kenneth M. Merz, Guo-Wei Wei, Feng Zhu
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Zhen Li, Lin Frank Song, Gaurav Sharma, Basak Koca Findik, Kenneth M. Merz
Summary: Modeling the interaction between metal ions and small molecules is crucial in bridging the gap between two types of simulations. The 12-6-4 LJ nonbonded model has been successful in simulating metal ion systems and can accurately describe the three-component interactions by tuning the polarizability of the chelating atom. The transferability of this model has also been tested.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Hsu-Chun Tsai, Tai-Sung Lee, Abir Ganguly, Timothy J. Giese, Maximilian C. C. J. C. Ebert, Paul Labute, Kenneth M. Merz, Darrin M. York
Summary: We propose a framework for optimized alchemical transformation pathways in free energy simulations using nonlinear mixing and a new functional form for softcore potentials. The framework is implemented and tested in the GPU-accelerated AMBER software suite. The optimized pathways integrate important features such as smoothstep functions, power scaling of interactions, LJ pairwise form, and smoothing of the potential at the nonbonded cutoff boundary. The pathways demonstrate superior numerical stability and minimal variance of free energy estimates compared to traditional methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Madelyn Smith, Zhen Li, Luke Landry, Kenneth M. Merz, Pengfei Li
Summary: Atomic radii are important in scientific research and can be derived from crystal structures. However, determining the van der Waals (VDW) radii of ions is a challenge due to the combination of VDW and electrostatic interactions in crystal structures. In this study, VDW radii were determined based on a wavefunction analysis, showing excellent agreement with experimentally determined VDW radii of noble-gas atoms.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemical Research Methods
Susanta Das, Kiyoto Aramis Tanemura, Laleh Dinpazhoh, Mithony Keng, Christina Schumm, Lydia Leahy, Carter K. Asef, Markace Rainey, Arthur S. Edison, Facundo M. Fernandez, Kenneth M. Merz
Summary: This study developed an efficient CCS computational workflow using a machine learning model and standard DFT methods, and validated the workflow through Traveling Wave IM-MS experiments. It provided accurate structural predictions and insights into the preferred conformation of metabolites analyzed using IM-MS experiments. The workflow is significant for computing CCS values of conformationally flexible metabolites with complex molecular structures.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
