Bert de Jong

Wibe Albert (Bert) de Jong

Sr. Scientist, Group Lead, Dept. Head

Computational Science Department

Applied Computing for Scientific Discovery

WAdeJong@lbl.gov

Phone: +1 510 486 4589

Mobile: +1 509 430 4411

Biographical Sketch

Bert de Jong leads the Applied Computing for Scientific Discovery Group, which advances scientific computing by developing and enhancing applications in key disciplines, as well as developing tools and libraries for addressing general problems in computational science.

He currently serves as the Interim Department Head for Computational Sciences.

de Jong is the deputy director of the Quantum Systems Accelerator, which is part of the National Quantum Initiative. In addition,de Jong is the team director of the Accelerated Research for Quantum Computing (ARQC) Team AIDE-QC, funded by DOE ASCR, focused on developing software stacks, algorithms, and computer science and applied mathematics solutions for chemical sciences and other fields on near-term quantum computing devices. He is also a co-PI on the ARQC team FAR-QC (led out of Sandia). He is also part of LBNL’s quantum testbed, developing superconducting qubits. He is the LBNL lead for the BES QIS project (led out of PNNL), where he is focusing on new approaches for encoding wave functions and embedding quantum systems. Prior to this, de Jong was the director of the LBNL Quantum Algorithms Team QAT4Chem.

de Jong is a co-PI within the DOE ASCR Exascale Computing Project (ECP) as the LBNL lead for the NWChemEx effort, contributing to the development of an exascale computational chemistry code. He is the LBNL lead for the Basic Energy Sciences SPEC Computational Chemistry Center (led out of PNNL), where he is working on reduced scaling MCSCF and beyond GW approaches for molecules. He is also a co-PI on the BES Rare Earth Project, where he focuses on using machine learning and computational chemistry to discover new materials for rare earth separation.

He leads an effort on machine learning for chemical sciences, focused on developing deep learning networks (GANs and autoencoders) for the prediction of structure-function relationships and is developing approaches for inverse design. As part of this effort, his team developed the ML4Chem Python package.

In 2020 de Jong was elected as a Fellow of the AAAS.

de Jong publication record, citations and H-index can be found on Google Scholar or Publons. He is the Founding Editor-in-Chief for the IOP journal Electronic Structure, and a Specialist Editor for Computer Physics Communications.

Prior to joining Berkeley Lab, de Jong was with the Pacific Northwest National Laboratory (PNNL). There he led the High-Performance Software Development Group responsible for NWChem at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility providing integrated experimental and computational resources for environmental molecular science research. de Jong earned his doctorate in theoretical chemistry in 1998 from the University of Groningen in the Netherlands. He earned his master’s in chemistry from the University of Groningen in 1993 and his bachelor’s degree in chemical engineering from the Technical College of Leeuwarden, the Netherlands, in 1990. He was a postdoctoral fellow at PNNL before transitioning to a staff member in 2000.

Journal Articles

Karol Kowalski, Raymond Bair, Nicholas P. Bauman, Jeffery S. Boschen, Eric J. Bylaska, Jeff Daily, Wibe A. de Jong, Thom Dunning, Niranjan Govind, Robert J. Harrison, Murat Keceli, Kristopher Keipert, Sriram Krishnamoorthy, Suraj Kumar, Erdal Mutlu, Bruce Palmer, Ajay Panyala, Bo Peng, Ryan M. Richard, T. P. Straatsma, Peter Sushko, Edward F. Valeev, Marat Valiev, Hubertus J. J. van Dam, Jonathan M. Waldrop, David B. Williams-Young, Chao Yang, Marcin Zalewski, Theresa L. Windus, "From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape", Chemical Reviews, March 31, 2021, doi: 10.1021/acs.chemrev.0c00998

Benjamin Nachman, Miroslav Urbanek, Wibe A. de Jong, Christian W. Bauer, "Unfolding quantum computer readout noise", npj Quantum Information, 2020, 6:84, doi: 10.1038/s41534-020-00309-7

Miroslav Urbanek, Benjamin Nachman, Wibe A. de Jong, "Error detection on quantum computers improving the accuracy of chemical calculations", Physical Review A, 2020, 102:022427, doi: 10.1103/PhysRevA.102.022427

Miroslav Urbanek, Daan Camps, Roel Van Beeumen, Wibe A. de Jong, "Chemistry on quantum computers with virtual quantum subspace expansion", Journal of Chemical Theory and Computation, 2020, 16:5425–5431, doi: 10.1021/acs.jctc.0c00447

Muammar El Khatib, Wibe A de Jong, "ML4Chem: A Machine Learning Package for Chemistry and Materials Science", March 9, 2020, doi: 10.26434/chemrxiv.11952516.v1

Yu-Hang Tang, Wibe A. de Jong, "Prediction of atomization energy using graph kernel and active learning", The Journal of Chemical Physics, January 25, 2019, 150:044107, doi: 10.1063/1.5078640

Carter KP, Jian J, Pyrch MM, Forbes TZ, Eaton TM, Abergel RJ, De Jong WA, Gibson JK, "Reductive activation of neptunyl and plutonyl oxo species with a hydroxypyridinone chelating ligand", Chemical Communications, August 30, 2018, 54:10698-1070, doi: 10.1039/C8CC05626A

RM Richard, C Bertoni, JS Boschen, K Keipert, B Pritchard, EF Valeev, RJ Harrison, WA De Jong, TL Windus, "Developing a Computational Chemistry Framework for the Exascale Era", Computing in Science and Engineering, 2018, doi: 10.1109/MCSE.2018.2884921

JI Colless, VV Ramasesh, D Dahlen, MS Blok, ME Kimchi-Schwartz, JR McClean, J Carter, WA De Jong, I Siddiqi, "Computation of Molecular Spectra on a Quantum Processor with an Error-Resilient Algorithm", Physical Review X, 2018, 8, doi: 10.1103/PhysRevX.8.011021

JK Gibson, WA de Jong, MJ van Stipdonk, J Martens, G Berden, J Oomens, "Equatorial coordination of uranyl: Correlating ligand charge donation with the O<inf>yl</inf>-U-O<inf>yl</inf> asymmetric stretch frequency", Journal of Organometallic Chemistry, 2018, 857:94--100, doi: 10.1016/j.jorganchem.2017.10.010

JK Gibson, WA De Jong, PD Dau, Y Gong, "Heptavalent Actinide Tetroxides NpO<inf>4</inf>-and PuO<inf>4</inf>-: Oxidation of Pu(V) to Pu(VII) by Adding an Electron to PuO<inf>4</inf>", Journal of Physical Chemistry A, 2017, 121:9156--9162, doi: 10.1021/acs.jpca.7b09721

KD Vogiatzis, D Ma, J Olsen, L Gagliardi, WA De Jong, "Pushing configuration-interaction to the limit: Towards massively parallel MCSCF calculations", Journal of Chemical Physics, 2017, 147, doi: 10.1063/1.4989858

MD Hanwell, WA De Jong, CJ Harris, "Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application", Journal of Cheminformatics, 2017, 9, doi: 10.1186/s13321-017-0241-z

RJ Abergel, WA De Jong, GJP Deblonde, PD Dau, I Captain, TM Eaton, J Jian, MJ Van Stipdonk, J Martens, G Berden, J Oomens, JK Gibson, "Cleaving off Uranyl Oxygens through Chelation: A Mechanistic Study in the Gas Phase", Inorganic Chemistry, 2017, 56:12930--129, doi: 10.1021/acs.inorgchem.7b01720

GJP Deblonde, M Sturzbecher-Hoehne, PB Rupert, DD An, MC Illy, CY Ralston, J Brabec, WA De Jong, RK Strong, RJ Abergel, "Chelation and stabilization of berkelium in oxidation state+IV", Nature Chemistry, 2017, 9:843--849, doi: 10.1038/nchem.2759

JR McClean, ME Kimchi-Schwartz, J Carter, WA De Jong, "Hybrid quantum-classical hierarchy for mitigation of decoherence and determination of excited states", Physical Review A, 2017, 95, doi: 10.1103/PhysRevA.95.042308

WA De Jong, PD Dau, RE Wilson, J Marçalo, MJ Van Stipdonk, TA Corcovilos, G Berden, J Martens, J Oomens, JK Gibson, "Revealing Disparate Chemistries of Protactinium and Uranium. Synthesis of the Molecular Uranium Tetroxide Anion, UO<inf>4</inf>-", Inorganic Chemistry, 2017, 56:3686--3694, doi: 10.1021/acs.inorgchem.7b00144

TY Takeshita, WA De Jong, D Neuhauser, R Baer, E Rabani, "Stochastic Formulation of the Resolution of Identity: Application to Second Order Møller-Plesset Perturbation Theory", Journal of Chemical Theory and Computation, 2017, 13:4605--4610, doi: 10.1021/acs.jctc.7b00343

R. Atta-Fynn, E.J. Bylaska, W.A. de Jong, "Strengthening of the Coordination Shell by Counter Ions in Aqueous Th4+ Solutions", J. Phys. Chem. A, December 1, 2016, 120:10216–1022, doi: 10.1021/acs.jpca.6b09878

R.M. Cox, P.B. Armentrout, W.A. de Jong, "Reactions of Th+ + H2, D2, and HD Studied by Guided Ion Beam Tandem Mass Spectrometry and Quantum Chemical Calculations", J. Phys. Chem. B – Bruce Garrett Festschrift, February 1, 2016, 120:1601, doi: 10.1021/acs.jpcb.5b08008

DML Brown, H Cho, WA De Jong, "Bridging experiment and theory: A template for unifying NMR data and electronic structure calculations", Journal of Cheminformatics, January 1, 2016, 8, doi: 10.1186/s13321-016-0120-z

RM Cox, PB Armentrout, WA De Jong, "Reactions of Th+ + H<inf>2</inf>, D<inf>2</inf>, and HD Studied by Guided Ion Beam Tandem Mass Spectrometry and Quantum Chemical Calculations", Journal of Physical Chemistry B, 2016, 120:1601--1614, doi: 10.1021/acs.jpcb.5b08008

R Atta-Fynn, EJ Bylaska, WA De Jong, "Strengthening of the Coordination Shell by Counter Ions in Aqueous Th4+ Solutions", Journal of Physical Chemistry A, 2016, 120:10216--102, doi: 10.1021/acs.jpca.6b09878

R.M. Cox, P.B. Armentrout, W.A. de Jong, "Activation of CH4 by Th+ as Studied by Guided Ion Beam Mass Spectrometry and Quantum Chemistry", Inorganic Chemistry, March 13, 2015, 54:3584, doi: 10.1021/acs.inorgchem.5b00137

Y Gong, WA De Jong, JK Gibson, "Gas Phase Uranyl Activation: Formation of a Uranium Nitrosyl Complex from Uranyl Azide", Journal of the American Chemical Society, January 1, 2015, 137:5911--5915, doi: 10.1021/jacs.5b02420

Niranjan Govind, Wibe A. de Jong, "Simulating Cl K-edge X-ray absorption spectroscopy in MCl6 (2-) (M U, Np, Pu) complexes and UOCl5 (-) using time-dependent density functional theory", Theoretical Chemistry Accounts, 2014, 133, doi: 10.1007/s00214-014-1463-z

U Lourderaj, R Sun, SC Kohale, GL Barnes, WA De Jong, TL Windus, WL Hase, "The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory", Computer Physics Communications, 2014, 185:1074--1080, doi: 10.1016/j.cpc.2013.11.011

Samuel O. Odoh, Niranjan Govind, Georg Schreckenbach, Wibe A. de Jong, "Cation-Cation Interactions in [(UO2)(2)(OH)(n)](4-n) Complexes", Inorganic Chemistry, 2013, 52:11269-1127, doi: 10.1021/ic4015338

Pawel Tecmer, Niranjan Govind, Karol Kowalski, Wibe A de Jong, Lucas Visscher, "Reliable modeling of the electronic spectra of realistic uranium complexes.", The Journal of Chemical Physics, 2013, 139:034301, doi: 10.1063/1.4812360

Jochen Mikosch, Jiaxu Zhang, Sebastian Trippel, Christoph Eichhorn, Rico Otto, Rui Sun, Wibe A de Jong, Matthias Weidemuller, William L Hase, Roland Wester, "Indirect dynamics in a highly exoergic substitution reaction.", Journal of the American Chemical Society, 2013, 135:4250-9, doi: 10.1021/ja308042v

SO Odoh, EJ Bylaska, WA De Jong, "Coordination and hydrolysis of plutonium ions in aqueous solution using car-parrinello molecular dynamics free energy simulations", Journal of Physical Chemistry A, 2013, 117:12256--122, doi: 10.1021/jp4096248

R Atta-Fynn, EJ Bylaska, WA De Jong, "Importance of counteranions on the hydration structure of the curium ion", Journal of Physical Chemistry Letters, 2013, 4:2166--2170, doi: 10.1021/jz400887a

DF Johnson, K Bhaskaran-Nair, EJ Bylaska, WA De Jong, "Thermodynamics of tetravalent thorium and uranium complexes from first-principles calculations", Journal of Physical Chemistry A, 2013, 117:4988--4995, doi: 10.1021/jp404656y

WA De Jong, AM Walker, MD Hanwell, "From data to analysis: Linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language", Journal of Cheminformatics, 2013, 5, doi: 10.1186/1758-2946-5-25

HJJ Van Dam, A Vishnu, WA De Jong, "A case for soft error detection and correction in computational chemistry", Journal of Chemical Theory and Computation, 2013, 9:3995--4005, doi: 10.1021/ct400489c

Rui Sun, Kyoyeon Park, Wibe A. de Jong, Hans Lischka, Theresa L. Windus, William L. Hase, "Direct dynamics simulation of dioxetane formation and decomposition via the singlet center dot O-O-CH2-CH2 center dot biradical: Non-RRKM dynamics", Journal of Chemical Physics, 2012, 137, doi: 10.1063/1.4736843

R Atta-Fynn, DF Johnson, EJ Bylaska, ES Ilton, GK Schenter, WA De Jong, "Structure and hydrolysis of the U(IV), U(V), and U(VI) aqua ions from Ab initio molecular simulations", Inorganic Chemistry, 2012, 51:3016--3024, doi: 10.1021/ic202338z

D Rios, G Schoendorff, MJ Van Stipdonk, MS Gordon, TL Windus, JK Gibson, WA De Jong, "Roles of acetone and diacetone alcohol in coordination and dissociation reactions of uranyl complexes", Inorganic Chemistry, 2012, 51:12768--127, doi: 10.1021/ic3015964

Matthew R. Siebert, Adelia J. A. Aquino, Wibe A. de Jong, Giovanni Granucci, William L. Hase, "Potential energy surface for C2H4I2+center dot dissociation including spin-orbit effects", Molecular Physics, 2012, 110:2599-2609, doi: 10.1080/00268976.2012.725137

R Sun, K Park, WA de Jong, H Lischka, TL Windus, WL Hase, "Direct dynamics simulation of dioxetane formation and decomposition via the singlet ·O–O–CH<inf>2</inf>–CH<inf>2</inf>· biradical: Non-RRKM dynamics", Journal of Chemical Physics, 2012, 137:242--483, doi: 10.1063/1.4736843

Gary S. Groenewold, Michael J. van Stipdonk, Jos Oomens, Wibe A. de Jong, Michael E. McIlwain, "The gas-phase bis-uranyl nitrate complex [(UO2)(2)(NO3)(5)](-): Infrared spectrum and structure", International Journal of Mass Spectrometry, 2011, 308:175-180, doi: 10.1016/j.ijms.2011.06.002

George Schoendorff, Wibe A. de Jong, Michael J. Van Stipdonk, John K. Gibson, Daniel Rios, Mark S. Gordon, Theresa L. Windus, "On the Formation of Hypercoordinated Uranyl Complexes (vol 50, pg 8490, 2011)", Inorganic Chemistry, 2011, 50:11846-1184, doi: 10.1021/ic202173r

L Yang, R Taylor, WA de Jong, WL Hase, "A Model DMMP/TiO2 (110) Intermolecular Potential Energy Function Developed from ab Initio Calculations", Journal of Physical Chemistry C, 2011, 115:12403-1241, doi: 10.1021/jp1112137

VA Glezakou, WA deJong, "Cluster-Models for Uranyl(VI) Adsorption on alpha-Alumina", Journal of Physical Chemistry A, 2011, 115:1257-1263, doi: 10.1021/jp1092509

R Atta-Fynn, EJ Bylaska, GK Schenter, WA De Jong, "Hydration shell structure and dynamics of curium(III) in aqueous solution: First principles and empirical studies", Journal of Physical Chemistry A, 2011, 115:4665--4677, doi: 10.1021/jp201043f

G Schoendorff, WA De Jong, MJ Van Stipdonk, JK Gibson, D Rios, MS Gordon, TL Windus, "On the formation of hypercoordinated uranyl complexes", Inorganic Chemistry, 2011, 50:8490--8493, doi: 10.1021/ic201080z

M Srebro, N Govind, WA De Jong, J Autschbach, "Optical rotation calculated with time-dependent density functional theory: The OR45 Benchmark", Journal of Physical Chemistry A, 2011, 115:10930--109, doi: 10.1021/jp2055409

HJJ Van Dam, WA De Jong, E Bylaska, N Govind, K Kowalski, TP Straatsma, M Valiev, "NWChem: Scalable parallel computational chemistry", Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011, 1:888--894, doi: 10.1002/wcms.62

HJJ Van Dam, A Vishnu, WA De Jong, "Designing a scalable fault tolerance model for high performance computational chemistry: A case study with coupled cluster perturbative triples", Journal of Chemical Theory and Computation, 2011, 7:66--75, doi: 10.1021/ct100439u

GS Groenewold, MJ Van Stipdonk, J Oomens, WA De Jong, ME McIlwain, "The gas-phase bis-uranyl nitrate complex [(UO<inf>2</inf>)<inf>2</inf>(NO<inf>3</inf>)<inf>5</inf>]-: Infrared spectrum and structure", International Journal of Mass Spectrometry, 2011, 308:175--180, doi: 10.1016/j.ijms.2011.06.002

G Schoendorff, WA De Jong, MJ Van Stipdonk, JK Gibson, D Rios, MS Gordon, TL Windus, "Erratum: On the formation of hypercoordinated uranyl complexes (Inorganic Chemistry (2011) 50 (8490-8493) DOI: 10.1021/ic201080z)", Inorganic Chemistry, 2011, 50:11846, doi: 10.1021/ic202173r

TP Straatsma, EJ Bylaska, HJJ van Dam, N Govind, WA de Jong, K Kowalski, M Valiev, "Advances in Scalable Computational Chemistry. NWChem", Annual Reports in Computational Chemistry, 2011, 7:151--177, doi: 10.1016/B978-0-444-53835-2.00007-9

L Yang, R Taylor, WA De Jong, WL Hase, "A model DMMP/TiO<inf>2</inf>(110) intermolecular potential energy function developed from ab initio calculations", Journal of Physical Chemistry C, 2011, 115:12403--124, doi: 10.1021/jp1112137

GS Groenewold, MJ van Stipdonk, J Oomens, WA de Jong, GL Gresham, ME McIlwain, "Vibrational spectra of discrete UO22+ halide complexes in the gas phase", International Journal of Mass Spectrometry, 2010, 297:67-75, doi: 10.1016/j.ijms.2010.06.013

G Schoendorff, WA de Jong, MS Gordon, TL Windus, "Gas Phase Computational Studies on the Competition between Nitrite and Water Ligands in Uranyl Complexes", Journal of Physical Chemistry A, 2010, 114:8902-8912, doi: 10.1021/jp103227x

H Cho, WA De Jong, AP Sattelberger, F Poineau, KR Czerwinski, "Comprehensive solid-state NMR characterization of electronic structure in ditechnetium heptoxide", Journal of the American Chemical Society, 2010, 132:13138--131, doi: 10.1021/ja105687j

H Cho, WA de Jong, CZ Soderquist, "Probing the oxygen environment in UO22+ by solid-state O-17 nuclear magnetic resonance spectroscopy and relativistic density functional calculations", Journal of Chemical Physics, 2010, 132, doi: 10.1063/1.3308499

GS Groenewold, WA de Jong, J Oomens, MJ Van Stipdonk, "Variable Denticity in Carboxylate Binding to the Uranyl Coordination Complexes", Journal of the American Society for Mass Spectrometry, 2010, 21:719--727, doi: 10.1016/j.jasms.2010.01.021

WA De Jong, E Bylaska, N Govind, CL Janssen, K Kowalski, T Müller, IMB Nielsen, HJJ Van Dam, V Veryazov, R Lindh, "Utilizing high performance computing for chemistry: Parallel computational chemistry", Physical Chemistry Chemical Physics, 2010, 12:6896--6920, doi: 10.1039/c002859b

M Valiev, EJ Bylaska, N Govind, K Kowalski, TP Straatsma, HJJ Van Dam, D Wang, J Nieplocha, E Apra, TL Windus, WA De Jong, "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations", Computer Physics Communications, 2010, 181:1477--1489, doi: 10.1016/j.cpc.2010.04.018

GS Groenewold, MJ van Stipdonk, J Oomens, WA de Jong, GL Gresham, ME McIlwain, "Vibrational spectra of discrete UO<inf>2</inf>2+ halide complexes in the gas phase", International Journal of Mass Spectrometry, 2010, 297:67--75, doi: 10.1016/j.ijms.2010.06.013

AS LIPTON, RW HECK, WA DE JONG, AR GAO, XJ WU, A ROEHRICH, GS HARBISON, PD ELLIS, "Low Temperature Cu-65 NMR Spectroscopy of the Cu+ Site in Azurin", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2009, 131:13992-1399, doi: 10.1021/ja901308v

G SCHOENDORFF, TL WINDUS, WA DE JONG, "Density Functional Studies on the Complexation and Spectroscopy of Uranyl Ligated with Acetonitrile and Acetone Derivatives", JOURNAL OF PHYSICAL CHEMISTRY A, 2009, 113:12525-1253, doi: 10.1021/jp9038623

CM LEAVITT, VS BRYANTSEV, WA DE JONG, MS DIALLO, WA GODDARD, GS GROENEWOLD, MJ VAN STIPDONK, "Addition of H2O and O-2 to Acetone and Dimethylsulfoxide Ligated Uranyl(V) Dioxocations", JOURNAL OF PHYSICAL CHEMISTRY A, 2009, 113:2350-2358, doi: 10.1021/jp807651c

F Aubriet, JJ Gaumet, WA De Jong, GS Groenewold, AK Gianotto, ME McIlwain, MJ Van Stipdonk, CM Leavitt, "Cerium oxyhydroxide clusters: Formation, structure, and reactivity", Journal of Physical Chemistry A, 2009, 113:6239--6252, doi: 10.1021/jp9015432

P Nichols, N Govind, EJ Bylaska, WA De Jong, "Gaussian basis set and planewave relativistic spin-orbit methods in NWChem", Journal of Chemical Theory and Computation, 2009, 5:491--499, doi: 10.1021/ct8002892

JX ZHANG, U LOURDERAJ, SV ADDEPALLI, WA DE JONG, WL HASE, "Quantum Chemical Calculations of the Cl- + CH3I -> CH3Cl + I- Potential Energy Surface", JOURNAL OF PHYSICAL CHEMISTRY A, 2009, 113:1976-1984, doi: 10.1021/jp808146c

GS GROENEWOLD, J OOMENS, WA DE JONG, GL GRESHAM, ME MCILWAIN, MJ VAN STIPDONK, "Vibrational spectroscopy of anionic nitrate complexes of UO22+ and Eu3+ isolated in the gas phase", PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2008, 10:1192-1202, doi: 10.1039/b715337f

K KOWALSKI, JR HAMMOND, WA DE JONG, AJ SADLEJ, "Coupled cluster calculations for static and dynamic polarizabilities of C-60", JOURNAL OF CHEMICAL PHYSICS, 2008, 129, doi: 10.1063/1.3028541

VS BRYANTSEV, WA DE JONG, KC COSSEL, MS DIALLO, WA GODDARD, GS GROENEWOLD, W CHIEN, MJ VAN STIPDONK, "Two-electron three-centered bond in side-on (eta(2)) uranyl(V) superoxo complexes", JOURNAL OF PHYSICAL CHEMISTRY A, 2008, 112:5777-5780, doi: 10.1021/jp804202q

AS LIPTON, RW HECK, GR STAEHELI, M VALIEV, WA DE JONG, PD ELLIS, "A QM/MM approach to interpreting Zn-67 solid-state NMR data in zinc proteins", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2008, 130:6224-6230, doi: 10.1021/ja711240t

Patrick Nichols, Eric J. Bylaska, Gregory K. Schenter, Wibe de Jong, "Equatorial and apical solvent shells of the UO(2)(2+) ion", Journal of Chemical Physics, 2008, 128, doi: 10.1063/1.2884861

VE JACKSON, R CRACIUN, DA DIXON, KA PETERSON, WA DE JONG, "Prediction of vibrational frequencies of UO22+ at the CCSD(T) level", JOURNAL OF PHYSICAL CHEMISTRY A, 2008, 112:4095-4099, doi: 10.1021/jp710334b

LGM De Macedo, WA De Jong, "Fully relativistic calculations on the potential energy surfaces of the lowest 23 states of molecular chlorine", Journal of Chemical Physics, 2008, 128, doi: 10.1063/1.2827457

GS Groenewold, AK Gianotto, ME McIlwain, MJ Van Stipdonk, M Kullman, DT Moore, N Polfer, J Oomens, I Infante, L Visscher, B Siboulet, WA De Jong, "Infrared spectroscopy of discrete uranyl anion complexes", Journal of Physical Chemistry A, 2008, 112:508--521, doi: 10.1021/jp077309q

GS Groenewold, MJ Van Stipdonk, WA De Jong, J Oomens, GL Gresham, ME McIlwain, D Gao, B Siboulet, L Visscher, M Kullman, N Polfer, "Infrared spectroscopy of dioxouranium(V) complexes with solvent molecules: Effect of reduction", ChemPhysChem, 2008, 9:1278--1285, doi: 10.1002/cphc.200800034

JR Hammond, WA De Jong, K Kowalski, "Coupled-cluster dynamic polarizabilities including triple excitations", Journal of Chemical Physics, 2008, 128, doi: 10.1063/1.2929840

JR Hammond, K Kowalski, WA Dejong, "Dynamic polarizabilities of polyaromatic hydrocarbons using coupled-cluster linear response theory", Journal of Chemical Physics, 2007, 127, doi: 10.1063/1.2772853

JR Hammond, M Valiev, WA DeJong, K Kowalski, "Calculations of molecular properties in hybrid coupled-cluster and molecular mechanics approach", Journal of Physical Chemistry A, 2007, 111:5492--5498, doi: 10.1021/jp070553x

K Kowalski, JR Hammond, WA De Jong, "Linear response coupled cluster singles and doubles approach with modified spectral resolution of the similarity transformed Hamiltonian", Journal of Chemical Physics, 2007, 127, doi: 10.1063/1.2795708

K Kowalski, WA de Jong, "Noniterative inclusion of the triply and quadruply excited clusters: The locally renormalized perspective", Journal of Molecular Structure: THEOCHEM, 2006, 768:45--52, doi: 10.1016/j.theochem.2006.04.049

L POLLACK, TL WINDUS, WA DE JONG, et al., "Thermodynamic properties of the C-5, C-6, and C-8 n-alkanes from ab initio electronic structure theory", JOURNAL OF PHYSICAL CHEMISTRY A, 2005, 109:6934-6938, doi: 10.1021/jp044564r

DA DIXON, WA DE JONG, KA PETERSON, et al., "Heats of formation of xenon fluorides and the fluxionality of XeF6 from high level electronic structure calculations", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2005, 127:8627-8634, doi: 10.1021/ja0423116

LS CHEN, WA DE JONG, J YE, "Characterization of the molecular iodine electronic wave functions and potential energy curves through hyperfine interactions in the B0(u)(+)((IIu)-I-3) state", JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, 2005, 22:951-961, doi: 10.1364/JOSAB.22.000951

GS FANOURGAKIS, E APRA, WA DE JONG, SS Xantheas, "High-level ab initio calculations for the four low-lying families of minima of(H2O)(20). II. Spectroscopic signatures of the dodecahedron, fused cubes, face-sharing pentagonal prisms, and edge-sharing pentagonal prisms hydrogen bonding networks", JOURNAL OF CHEMICAL PHYSICS, 2005, 122:-, doi: 10.1063/1.1864892

WA De Jong, E Aprà, TL Windus, JA Nichols, RJ Harrison, KE Gutowski, DA Dixon, "Complexation of the carbonate, nitrate, and acetate anions with the uranyl dication: Density functional studies with relativistic effective core potentials", Journal of Physical Chemistry A, 2005, 109:11568--115, doi: 10.1021/jp0541462

DA Dixon, WA De Jong, KA Peterson, TB McMahon, "Methyl cation affinities of rare gases and nitrogen and the heat of formation of diazomethane", Journal of Physical Chemistry A, 2005, 109:4073--4080, doi: 10.1021/jp044561e

HM Cho, WA de Jong, BK McNamara, BM Rapko, IE Burgeson, "Temperature and isotope substitution effects on the structure and NMR properties of the pertechnetate ion in water", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2004, 126:11583--115, doi: 10.1021/ja047447i

S Hirata, T Yanai, WA de Jong, T Nakajima, K Hirao, "Third-order Douglas-Kroll relativistic coupled-cluster theory through connected single, double, triple, and quadruple substitutions: Applications to diatomic and triatomic hydrides", JOURNAL OF CHEMICAL PHYSICS, 2004, 120:3297--3310, doi: 10.1063/1.1639361

D Feller, KA Peterson, WA de Jong, DA Dixon, "Performance of coupled cluster theory in thermochemical calculations of small halogenated compounds", JOURNAL OF CHEMICAL PHYSICS, 2003, 118:3510--3522, doi: 10.1063/1.1532314

ES Ilton, WA deJong, PS Bagus, "Intra-atomic many-body effects in p-shell photoelectron spectra of Cr3+ ions", PHYSICAL REVIEW B, 2003, 68, doi: 10.1103/PhysRevB.68.125106

WA DE JONG, RJ HARRISON, JA NICHOLS, et al., "Fully relativistic correlated benchmark results for uranyl and a critical look at relativistic effective core potentials for uranium (vol 107, pg 22, 2001)", THEORETICAL CHEMISTRY ACCOUNTS, 2002, 107:318-318, doi: 10.1007/s00214-002-0328-z

DA DIXON, WA DE JONG, KA PETERSON, JS FRANCISCO, "Heats of formation of CBr, CHBr, and CBr2 from ab initio quantum chemistry", JOURNAL OF PHYSICAL CHEMISTRY A, 2002, 106:4725-4728, doi: 10.1021/jp0147067

WA DE JONG, L VISSCHER, WC NIEUWPOORT, "On the bonding and the electric field gradient of the uranyl ion (vol 458, pg 41, 1999)", JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 2002, 581:259-259, doi: PII S0166-1280(02)00057-X

PS Bagus, R Broer, WA de Jong, WC Nieuwpoort, F Parmigiani, L Sangaletti, "Comment on Atomic many-body effects for the p-shell photoelectron spectra of transition metals - Reply", PHYSICAL REVIEW LETTERS, 2001, 86:3693--3693, doi: 10.1103/PhysRevLett.86.3693

WA de Jong, RJ Harrison, DA Dixon, "Parallel Douglas-Kroll energy and gradients in NWChem: Estimating scalar relativistic effects using Douglas-Kroll contracted basis sets", JOURNAL OF CHEMICAL PHYSICS, 2001, 114:48--53, doi: 10.1063/1.1329891

WA de Jong, RJ Harrison, JA Nichols, DA Dixon, "Fully relativistic correlated benchmark results for uranyl and a critical look at relativistic effective core potentials for uranium", THEORETICAL CHEMISTRY ACCOUNTS, 2001, 107:22--26, doi: 10.1007/s002140100293

PS Bagus, R Broer, WA de Jong, WC Nieuwpoort, F Parmigiani, L Sangaletti, "Atomic many-body effects for the p-shell photoelectron spectra of transition metals", PHYSICAL REVIEW LETTERS, 2000, 84:2259--2262, doi: 10.1103/PhysRevLett.84.2259

M Pernpointner, L Visscher, WA De Jong, R Broer, "Parallelization of four-component calculations. I. Integral generation, SCF, and four-index transformation in the Dirac-Fock package MOLFDIR", JOURNAL OF COMPUTATIONAL CHEMISTRY, 2000, 21:1176--1186, doi: 10.1002/1096-987X(200010)21:13<1176::AID-JCC6>3.0.CO;2-E

WA de Jong, L Visscher, WC Nieuwpoort, "On the bonding and the electric field gradient of the uranyl ion", JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 1999, 458:41--52,

D Feller, ED Glendening, WA de Jong, "Structures and binding enthalpies of M+ (H2O)(n) clusters, MCu, Ag, Au", JOURNAL OF CHEMICAL PHYSICS, 1999, 110:1475--1491, doi: 10.1063/1.477814

C de Graaf, WA de Jong, R Broer, WC Nieuwpoort, "Theoretical study of the crystal field excitations in CoO", CHEMICAL PHYSICS, 1998, 237:59--65, doi: 10.1016/S0301-0104(98)00241-9

WA de Jong, J Styszynski, L Visscher, WC Nieuwpoort, "Relativistic and correlation effects on molecular properties: The interhalogens ClF, BrF, BrCl, IF, ICl, and IBr", JOURNAL OF CHEMICAL PHYSICS, 1998, 108:5177--5184, doi: 10.1063/1.476314

WA deJong, L Visscher, WC Nieuwpoort, "Relativistic and correlated calculations on the ground, excited, and ionized states of iodine", JOURNAL OF CHEMICAL PHYSICS, 1997, 107:9046--9058, doi: 10.1063/1.475194

C Sousa, WA DeJong, R Broer, WC Nieuwpoort, "Charge transfer and relativistic effects in the low-lying electronic states of CuCl, CuBr and CuI", MOLECULAR PHYSICS, 1997, 92:677--686, doi: 10.1080/002689797169952

C Sousa, WA deJong, R Broer, WC Nieuwpoort, "Theoretical characterization of the low-lying excited states of the CuCl molecule", JOURNAL OF CHEMICAL PHYSICS, 1997, 106:7162--7169, doi: 10.1063/1.473161

WA deJong, WC Nieuwpoort, "Relativity and the chemistry of UF6: A molecular Dirac-Hartree-Fock-CI study", INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1996, 58:203--216, doi: 10.1002/(SICI)1097-461X(1996)58:2<203::AID-QUA9>3.0.CO;2-1

F DIJKSTRA, WA DEJONG, WC NIEUWPOORT, "ELECTRON CORRELATION-EFFECTS ON THE F(6)-MANIFOLD OF THE EU3+ IMPURITY IN BA2GDNBO6", INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1995, 609--613,

Conference Papers

D. Jones, J. Bopaiah, F. Alghamedy, M. Jacobs, H.L. Weiss, W.A. de Jong, S.R. Ellingson, "Polypharmacology Within the Full Kinome: a Machine Learning Approach", AMIA Jt Summits Transl Sci Proc, May 18, 2018, 2017:98-107,

E.J. Bylaska, J. Hammond, M. Jacquelin, W.A. de Jong, M. Klemm, "Performance Evaluation of NWChem Ab-Initio Molecular Dynamics (AIMD) Simulations on the Intel® Xeon Phi© Processor", High Performance Computing. ISC High Performance 2017. Lecture Notes in Computer Science, Springer, Cham, October 21, 2017, 404-418, doi: 10.1007/978-3-319-67630-2_30

X. Zhang, A. Kucharski, S.R. Ellingson, W.A. de Jong, "Towards a better understanding of on and off target effects of the lymphocyte-specific kinase LCK for the development of novel and safer pharmaceuticals", Procedia Computer Science, June 9, 2017, 108:1222-1231, doi: 10.1016/j.procs.2017.05.268

Mathias Jacquelin, Wibe De Jong, Eric Bylaska, "Towards highly scalable Ab initio molecular dynamics (AIMD) simulations on the Intel knights landing manycore processor", Parallel and Distributed Processing Symposium (IPDPS), 2017 IEEE International, January 1, 2017, 234--243,

W.A. de Jong, M. Jacquelin, E.J. Bylaska, "Advancing Algorithms to Increase Performance of Correlated and Dynamical Electronic Structure Simulation", CMMSE 2016: Proceedings of the 16th International Conference on Mathematical Methods in Science and Engineering, September 1, 2016, 5:1342-1346,

D Ozog, A Kamil, Y Zheng, P Hargrove, JR Hammond, A Malony, WD Jong, K Yelick, "A Hartree-Fock Application Using UPC++ and the New DArray Library", 30th International Parallel and Distributed Processing Symposium (IPDPS), IEEE, May 23, 2016, 453--462, doi: 10.1109/IPDPS.2016.108

The Hartree-Fock (HF) method is the fundamental first step for incorporating quantum mechanics into many-electron simulations of atoms and molecules, and it is an important component of computational chemistry toolkits like NWChem. The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front static partitioning of tasks, followed by work stealing whenever necessary. To enable innovations in algorithms and exploit next generation exascale systems, it is crucial to support quantum chemistry codes using expressive and convenient programming models and runtime systems that are also efficient and scalable. This paper presents an HF implementation similar to GTFock using UPC++, a partitioned global address space model that includes flexible communication, asynchronous remote computation, and a powerful multidimensional array library. UPC++ offers runtime features that are useful for HF such as active messages, a rich calculus for array operations, hardware-supported fetch-and-add, and functions for ensuring asynchronous runtime progress. We present a new distributed array abstraction, DArray, that is convenient for the kinds of random-access array updates and linear algebra operations on block-distributed arrays with irregular data ownership. We analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. Our optimized implementation of HF using UPC++ and the DArrays library shows up to 20% improvement over GTFock with Global Arrays at scales up to 24,000 cores.

Wim Lavrijsen, Costin Iancu, Wibe Albert de Jong, Xin Chen, Karsten Schwan, "Exploiting Variability for Energy Optimization of Load Balanced Parallel Programs", EuroSys 2016, February 5, 2016,

Download File: iancu-eurosys16.pdf (pdf: 2.6 MB)

Hongzhang Shan, Samuel Williams, Wibe de Jong, Leonid Oliker, "Thread-Level Parallelization and Optimization of NWChem for the Intel MIC Architecture", Programming Models and Applications for Multicores and Manycores (PMAM), February 2015,

Download File: pmam15nwchem.pdf (pdf: 1.1 MB)

M Chabbi, W Lavrijsen, W De Jong, K Sen, J Mellor-Crummey, C Iancu, "Barrier elision for production parallel programs", Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, January 1, 2015, 2015-Jan:109--119, doi: 10.1145/2688500.2688502

W.A. de Jong, L. Lin, H. Shan, C. Yang and L. Oliker, "Towards modelling complex mesoscale molecular environments", International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE), 2014,

Hongzhang Shan, Brian Austin, Wibe de Jong, Leonid Oliker, Nick Wright, Edoardo Apra, "Performance Tuning of Fock Matrix and Two Electron Integral Calculations for NWChem on Leading HPC Platforms", Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS), November 2013, doi: 10.1007/978-3-319-10214-6_13

R. Atta-Fynn, E.J. Bylaska, W.A. de Jong, "Free energies and mechanisms of water exchange around Uranyl from first principles molecular dynamics", MRS Proceedings 1383, January 1, 2012,

A. Vishnu, H.J.J. van Dam, W.A. de Jong, P. Balaji, S. Song, "Fault Tolerant Communication Runtime Support for Data Centric Programming Models", International Conference on High Performance Computing (HiPC), 2010, 2010,

E. Apra, R.J. Harrison, W.A. de Jong, A.P. Rendell, V. Tipparaju, S.S. Xantheas, "Liquid water: obtaining the right answer for the right reasons", 2009 SC Conference on High Performance Computing Networking, Storage and Analysis, 2009, 7 pp., doi: 10.1145/1654059.1654127

D.A. Dixon, M.S. Gutowski, L.A. Pollack, T.L. Windus, W.A. de Jong, "High Level Computational Approaches to the Prediction of the Thermodynamics of Chemical Hydrogen Storage Systems and Hydrocarbon Fuels", March 15, 2005,

W.A. de Jong, D.A. Dixon, G.I. Fann, R.J. Harrison, J.A. Nichols, J. Nieplocha, T.L. Windus, Z. Zhang, "Computational Chemistry for Nuclear Waste Characterization and Processing: Relativistic Quantum Chemistry of Actinides", Proceedings of the Fourth International Conference on Supercomputing in Nuclear Applications, October 1, 2000,

Book Chapters

E. J. Bylaska, E. Apra, K. Kowalski, M. Jacquelin, W.A. de Jong, A. Vishnu, B. Palmer, J. Daily, T.P. Straatsma, J.R. Hammond, M. Klemm, "Transitioning NWChem to the Next Generation of Many Core Machines", Exascale Scientific Applications Scalability and Performance Portability, edited by Tjerk P. Straatsma, Katerina B. Antypas, Timothy J. Williams, (Taylor & Francis: November 9, 2017)

J. Autschbach, N. Govind, R. Atta-Fynn, E.J. Bylaska, J.H. Weare, W.A. de Jong, "Computational tools for predictive modeling of properties in complex actinide systems", Computational Methods in Lanthanide and Actinide Chemistry, pp. 299-342, ed. M. Dolg, Wiley-Blackwell, ( October 1, 2014)

T.P. Straatsma, E.J. Bylaska, H.J.J van Dam, N. Govind, W.A. de Jong, K. Kowalski, M. Valiev, "Advances in Scalable Computational Chemistry: NWChem", Annual Reports in Computational Chemistry, Volume 7, pp. 151-177, ed. R. Wheeler, D. Spellmeyer, Elsevier, ( October 12, 2011)

N. Govind, E.J. Bylaska, W.A. de Jong, K. Kowalski, T.P. Straatsma, M. Valiev, H.J.J. van Dam, "NWChem", Encyclopedia of Parallel Computing, pp. 1345-1350, ed. D. Padua, Springer, ( May 1, 2011)

K. Kowalski, J.R. Hammond, W.A. de Jong, P.D. Fan, M. Valiev, D. Wang, N. Govind, "Coupled Cluster Calculations for Large Molecular and Extended Systems", “Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology, ed. J.R. Reimers, ( 2011)

L. Visscher, W.A. de Jong, O. Visser, P.J.C. Aerts, H. Merenga, W.C. Nieuwpoort, "Relativistic Quantum Chemistry. The MOLFDIR Program Package", Methods and Techniques in Computational Chemistry: METECC-95, ed. E. Clementi and G. Corongiu, Cagliari, ( 1995)

W.A. de Jong, L. Visscher, O. Visser, P.J.C. Aerts, W.C. Nieuwpoort, "MOLFDIR: A Program Package for Molecular Dirac-Fock-CI Calculations", New Challenges in Computational Quantum Chemistry", ed. R. Broer, P.J.C. Aerts and P. Bagus, University of Groningen, ( January 1, 1993)

Reports

Hongzhang Shan, Samuel Williams, Wibe de Jong, Leonid Oliker, "Thread-Level Parallelization and Optimization of NWChem for the Intel MIC Architecture", LBNL Technical Report, October 2014, LBNL 6806E,

Download File: rpt83549.PDF (PDF: 615 KB)