Search Results - "Van Dam, Hubertus"

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape by Kowalski, Karol, Bair, Raymond, Bauman, Nicholas P, Boschen, Jeffery S, Bylaska, Eric J, Daily, Jeff, de Jong, Wibe A, Dunning, Thom, Govind, Niranjan, Harrison, Robert J, Keçeli, Murat, Keipert, Kristopher, Krishnamoorthy, Sriram, Kumar, Suraj, Mutlu, Erdal, Palmer, Bruce, Panyala, Ajay, Peng, Bo, Richard, Ryan M, Straatsma, T. P, Sushko, Peter, Valeev, Edward F, Valiev, Marat, van Dam, Hubertus J. J, Waldrop, Jonathan M, Williams-Young, David B, Yang, Chao, Zalewski, Marcin, Windus, Theresa L

“…Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the…”
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Simulating One-Photon Absorption and Resonance Raman Scattering Spectra Using Analytical Excited State Energy Gradients within Time-Dependent Density Functional Theory by Silverstein, Daniel W, Govind, Niranjan, van Dam, Hubertus J. J, Jensen, Lasse

“…A parallel implementation of analytical time-dependent density functional theory gradients is presented for the quantum chemistry program NWChem. The…”
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A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria by Grosjean, Nicolas, Yee, Estella F., Kumaran, Desigan, Chopra, Kriti, Abernathy, Macon, Biswas, Sandeep, Byrnes, James, Kreitler, Dale F., Cheng, Jan-Fang, Ghosh, Agnidipta, Almo, Steven C., Iwai, Masakazu, Niyogi, Krishna K., Pakrasi, Himadri B., Sarangi, Ritimukta, van Dam, Hubertus, Yang, Lin, Blaby, Ian K., Blaby-Haas, Crysten E.

“…Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and…”
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Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis by Zhang, Lifang, Braynen, Janeen, Fahey, Audrey, Chopra, Kriti, Cifani, Paolo, Tadesse, Dimiru, Regulski, Michael, Hu, Fangle, van Dam, Hubertus J J, Xie, Meng, Ware, Doreen, Blaby-Haas, Crysten E

“…Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein…”
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Memorial Viewpoint for Joop van Lenthe by Balint-Kurti, Gabriel G., Broer, Ria, Budzelaar, Peter H. M., van Dam, Hubertus J. J., Dijkstra, Fokke, Eshuis, Henk, Groenenboom, Gerrit C., Guest, Martyn F., Havenith, Remco W. A., Meijer, Anthony J. H. M., van Mourik, Tanja, Rashid, Zahid

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Describing Excited State Relaxation and Localization in TiO2 Nanoparticles Using TD-DFT by Berardo, Enrico, Hu, Han-Shi, van Dam, Hubertus J. J, Shevlin, Stephen A, Woodley, Scott M, Kowalski, Karol, Zwijnenburg, Martijn A

“…We have investigated the description of excited state relaxation in naked and hydrated TiO2 nanoparticles using Time-Dependent Density Functional Theory…”
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Noniterative Multireference Coupled Cluster Methods on Heterogeneous CPU–GPU Systems by Bhaskaran-Nair, Kiran, Ma, Wenjing, Krishnamoorthy, Sriram, Villa, Oreste, van Dam, Hubertus J. J, Aprà, Edoardo, Kowalski, Karol

“…A novel parallel algorithm for noniterative multireference coupled cluster (MRCC) theories, which merges recently introduced reference-level parallelism (RLP)…”
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Theoretical studies of the global minima and polarizabilities of small lithium clusters by Hu, Han-Shi, Zhao, Ya-Fan, Hammond, Jeff R., Bylaska, Eric J., Aprà, Edoardo, van Dam, Hubertus J.J., Li, Jun, Govind, Niranjan, Kowalski, Karol

“…⿢Theoretical searching of the global minima structures of Li1⿿20 clusters.⿢State-of-the-art calculation of the polarizabilities (α) of Li1⿿20 clusters.⿢A…”
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On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters by Williams-Young, David B, de Jong, Wibe A, van Dam, Hubertus J J, Yang, Chao

“…The predominance of Kohn-Sham density functional theory (KS-DFT) for the theoretical treatment of large experimentally relevant systems in molecular chemistry…”
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A Case for Soft Error Detection and Correction in Computational Chemistry by van Dam, Hubertus J. J, Vishnu, Abhinav, de Jong, Wibe A

“…High performance computing platforms are expected to deliver 1018 floating operations per second by the year 2022 through the deployment of millions of cores…”
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Parallel Implementation of Multireference Coupled-Cluster Theories Based on the Reference-Level Parallelism by Brabec, Jiří, Pittner, Jiří, van Dam, Hubertus J. J, Aprà, Edoardo, Kowalski, Karol

“…A novel algorithm for implementing a general type of multireference coupled-cluster (MRCC) theory based on the Jeziorski–Monkhorst exponential ansatz…”
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Towards large-scale calculations with State-Specific Multireference Coupled Cluster methods: Studies on dodecane, naphthynes, and polycarbenes by Brabec, Jiří, Bhaskaran-Nair, Kiran, Kowalski, Karol, Pittner, Jiří, van Dam, Hubertus J.J.

“…[Display omitted] ► We investigate the potential of MRCC for studying molecules of non-trivial sizes. ► We find that MRCC is successful for dodecane,…”
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Designing a Scalable Fault Tolerance Model for High Performance Computational Chemistry: A Case Study with Coupled Cluster Perturbative Triples by van Dam, Hubertus J. J, Vishnu, Abhinav, de Jong, Wibe A

“…In the past couple of decades, the massive computational power provided by the most modern supercomputers has resulted in simulation of higher-order…”
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Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats by Chen, Wei, Ren, Yihui, Kagawa, Ai, Carbone, Matthew R., Chen, Samuel Yen-Chi, Qu, Xiaohui, Yoo, Shinjae, Clyde, Austin, Ramanathan, Arvind, Stevens, Rick L., van Dam, Hubertus J. J., Lu, Deyu

“…Fast screening of drug molecules based on the ligand binding affinity is an important step in the drug discovery pipeline. Graph neural fingerprint is a…”
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High-Throughput Virtual Screening and Validation of a SARS-CoV‑2 Main Protease Noncovalent Inhibitor by Clyde, Austin, Galanie, Stephanie, Kneller, Daniel W, Ma, Heng, Babuji, Yadu, Blaiszik, Ben, Brace, Alexander, Brettin, Thomas, Chard, Kyle, Chard, Ryan, Coates, Leighton, Foster, Ian, Hauner, Darin, Kertesz, Vilmos, Kumar, Neeraj, Lee, Hyungro, Li, Zhuozhao, Merzky, Andre, Schmidt, Jurgen G, Tan, Li, Titov, Mikhail, Trifan, Anda, Turilli, Matteo, Van Dam, Hubertus, Chennubhotla, Srinivas C, Jha, Shantenu, Kovalevsky, Andrey, Ramanathan, Arvind, Head, Martha S, Stevens, Rick

“…Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has…”
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On the suitability of MPI as a PGAS runtime by Daily, Jeff, Vishnu, Abhinav, Palmer, Bruce, van Dam, Hubertus, Kerbyson, Darren

“…Partitioned Global Address Space (PGAS) models are emerging as a popular alternative to MPI models for designing scalable applications. At the same time, MPI…”
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Achieving performance portability in Gaussian basis set density functional theory on accelerator based architectures in NWChemEx by Williams-Young, David B., Bagusetty, Abhishek, de Jong, Wibe A., Doerfler, Douglas, van Dam, Hubertus J.J., Vázquez-Mayagoitia, Álvaro, Windus, Theresa L., Yang, Chao

“…The numerical integration of the exchange–correlation (XC) potential is one of the primary computational bottlenecks in Gaussian basis set Kohn–Sham density…”
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Online data analysis and reduction: An important Co-design motif for extreme-scale computers by Foster, Ian, Ainsworth, Mark, Bessac, Julie, Cappello, Franck, Choi, Jong, Di, Sheng, Di, Zichao, Gok, Ali M, Guo, Hanqi, Huck, Kevin A, Kelly, Christopher, Klasky, Scott, Kleese van Dam, Kerstin, Liang, Xin, Mehta, Kshitij, Parashar, Manish, Peterka, Tom, Pouchard, Line, Shu, Tong, Tugluk, Ozan, van Dam, Hubertus, Wan, Lipeng, Wolf, Matthew, Wozniak, Justin M, Xu, Wei, Yakushin, Igor, Yoo, Shinjae, Munson, Todd

“…A growing disparity between supercomputer computation speeds and I/O rates means that it is rapidly becoming infeasible to analyze supercomputer application…”
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In situ Synchrotron X-ray Metrology Boosted by Automated Data Analysis for Real-time Monitoring of Cathode Calcination by Dongol, Ruhil, Mukherjee, Arpan, Bai, Jianming, van Dam, Hubertus J J, Carbone, Matthew R, Abell, E Frits, Zhong, Hui, Tayal, Akhil, Ma, Lu, Kahvecioglu, Ozgenur, Pupek, Krzysztof Z, Lu, Deyu, Rajan, Krishna, Wang, Feng

“…Synchrotron X-ray-based in situ metrology is advantageous for monitoring the synthesis of battery materials, offering high throughput, high spatial and…”
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Massively parallel implementation of the multireference Brillouin–Wigner CCSD method by Brabec, Jiří, Krishnamoorthy, Sriram, van Dam, Hubertus J.J., Kowalski, Karol, Pittner, Jiří

“…[Display omitted] ► We show scalability up to 1000 cores of our MR BWCCSD code for molecules with hundreds of orbitals. ► We show further speed-up by task…”
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