Center for Functional Nanomaterials Theory and Computation Group

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The Theory and Computation Group supports an open community of staff, partners and users where theory interacts vigorously with experiment to achieve fundamental advances in nanoscience, emphasizing opportunities for impact on future energy needs.

As part of the CFN user facility, our computing facility has now transitioned to the BNL Institutional Cluster. We continue to provide our expertise and a suite of advanced scientific software for our users. Feel free to browse, look through some frequently asked questions, or contact one of the group members.

Details of the computer cluster

  • InfinitiBand EDR connectivity and GPFS distributed storage. CFN’s share of the storage is 200TB, evenly divided into two filesystems of ‘home’ and ‘work’.
  • Shared access: 216 GPU-loaded IC nodes. Each node is equipped with two 2.10 GHz 18-core Intel processors and 256 GB of RAM, and two Nvidia K80 or P100 GPUs. CFN owns 70 such nodes, or about 7.4 million CPU hours per cycle.
  • Exclusively for CFN users: 100 gen04 nodes (two 2.40 GHz hex core Intel processors and 48 GB of RAM), providing in total 3.5 million CPU hours per cycle.

Group expertise and computational tools

  • Deep learning framewoks. (Keras, TensorFlow, and Pytorch)
  • Solid-state techniques based on density functional theory. (VASP, Quantum Espresso, WIEN2k, CP2K)
  • Excited state techniques based on many-body perturbation theory. (Abinit, Yambo, Quantum Espresso, VASP, WIEN2k, local)
  • Tools to simulate X-ray core level spectroscopy (FEFF, XSpectra, OCEAN and VASP)
  • Quantum chemistry techniques including DFT based approaches as well as MP2, CASSCF, and coupled-cluster methods. (Gaussian 09 and 16, Q-Chem 4.2 and 5.0, ORCA, and local NWChem)
  • Classical molecular dynamics simulations with empirical potentials. (CHARMM, LAMMPS, Gromacs, local hybrid Brownian dynamics with Monte Carlo)
  • General purpose scientific computing and data analysis (latest Intel and PGI compilers and tools, Matlab DCS, RSoft)

Group Members

Group Leader

Sara E. Mason

Scientific Staff

  • Deyu Lu: Electronic structure methods; dispersion interactions; optical properties of nanostructures.
  • Xiaohui Qu: Deep learning and artificial intelligence; data science in materials and chemistry; electrochemical phenomena and mechanisms.
  • Alexei Tkachenko: Soft matter theory and statistical physics; polymer theory; theory of directed assembly.
  • Qin Wu: Density functional theory and quantum chemistry methods; electronic processes in organic materials and catalysis.

Postdoctoral Research Associates

Research Highlights

Here are some recent highlights from our facility. You can also see more examples on our highlights page.


Listed below are some recent publications (co)authored by our group members. You can also see the complete list of staff publications. Meanwhile, there are also many user-only publications that acknowledge our facility.

  1. N. Akter, M. Wang, J.-Q. Zhong, Z. Liu, T. Kim, D. Lu, J.A. Boscoboinik, and D.J. Stacchiola, "Stabilization of Oxidized Copper Nanoclusters in Confined Spaces," Topics in Catalysis 61(5-6), 419-427 (2018).
  2. C.N. Lininger, C.A. Cama, K.J. Takeuchi, A.C. Marschilok, E.S. Takeuchi, A.C. West, and M.S. Hybertsen, "Energetics of Lithium Insertion into Magnetite, Defective Magnetite, and Maghemite," Chemistry of Materials, 30(21), 7922-7937 (2018).
  3. H. Fei, J. Dong, Y. Feng, C.S. Allen, C. Wan, B. Volosskiy, M. Li, Z. Zhao, Y. Wang, H. Sun, P. An, W. Chen, Z. Guo, C. Lee, D. Chen, I. Shakir, M. Liu, T. Hu, Y. Li, A.I. Kirkland, X. Duan, and Y. Huang, "General Synthesis and Definitive Structural Identification of MN4C4 Single-Atom Catalysts with Tunable Electrocatalytic Activities," Nature Catalysis, 1(1), 63-72 (2018).
  4. J.H. Hu, K. Xu, L. Shen, Q. Wu, G.Y. He, J.Y. Wang, J. Pei, J.L. Xia, and M.Y. Sfeir, "New Insights into the Design of Conjugated Polymers for Intramolecular Singlet Fission," Nature Communications, 9, 2999 (2018).
  5. X. Hu, J. Huang, L. Wu, M. Kaltak, M.V. Fernandez-Serra, Q. Meng, L. Wang, A.C. Marschilok, E.S. Takeuchi, K.J. Takeuchi, M.S. Hybertsen, and Y. Zhu, "Atomic Scale Account of the Surface Effect on Ionic Transport in Silver Hollandite," Chemistry of Materials, 30(17), 6124-6133 (2018).
  6. J.J. Li, K. Sun, J. Li, Q.P. Meng, X.W. Fu, W.G. Yin, D.Y. Lu, Y. Li, M. Babzien, M. Fedurin, C. Swinson, R. Malone, M. Palmer, L. Mathurin, R. Mason, J.Y. Chen, R.M. Konik, R.J. Cava, Y.M. Zhu, and J. Tao, "Probing the Pathway of an Ultrafast Structural Phase Transition to Illuminate the Transition Mechanism in Cu2S," Applied Physics Letters, 113(4), 041904 (2018).
  7. Y. Lin, Y.Z. Li, J.T. Sadowski, W.C. Jin, J.I. Dadap, M.S. Hybertsen, and R.M. Osgood, "Excitation and Characterization of Image Potential State Electrons on Quasi-Free-Standing Graphene," Phys. Rev. B, 97(16), 9 (2018).
  8. J.A. Logan, and A.V. Tkachenko, "Compact Interaction Potential for van der Waals Nanorods," Physical Review E, 98(3), 032609 (2018)
  9. N. Patra, and A.V. Tkachenko, "Programmable Self-Assembly of Diamond Polymorphs from Chromatic Patchy Particles," Physical Review E, 98(3), 6 (2018).
  10. B. Ravel, A.J. Kropf, D.L. Yang, M.E. Wang, M. Topsakal, D.Y. Lu, M.C. Stennett, and N.C. Hyatt, "Nonresonant Valence-to-Core X-Ray Emission Spectroscopy of Niobium," Phys. Rev. B, 97(12), 7 (2018).
  11. H. Singh, M. Topsakal, K. Attenkofer, T. Wolf, M. Leskes, Y.D. Duan, F. Wang, J. Vinson, D.Y. Lu, and A.I. Frenkel, "Identification of Dopant Site and its Effect on Electrochemical Activity in Mn-Doped Lithium Titanate," Physical Review Materials, 2(12), 125403 (2018).
  12. K. Sun, Q. Wu, and H. Gan, "Molecular Insights into Ether-Based Electrolytes for Li-FeS2 Batteries," Energy Storage Materials, 12, 85-93 (2018).
  13. K. Sun, Q. Wu, X. Tong, and H. Gan, "Electrolyte with Low Polysulfide Solubility for Li-S Batteries," ACS Applied Energy Materials 1(6), 2608-2618, (2018).
  14. A.V. Tkachenko, and S. Maslov, "Onset of Natural Selection in Populations of Autocatalytic Heteropolymers," Journal of Chemical Physics, 149(13), 9 (2018).
  15. C.H. Zhang, S.Z. Yang, J.J. Wu, M.J. Liu, S. Yazdi, M.Q. Ren, J.W. Sha, J. Zhong, K.Q. Nie, A.S. Jalilov, Z.Y. Li, H.M. Li, B.I. Yakobson, Q. Wu, E.L. Ringe, H. Xu, P.M. Ajayan, and J.M. Tour, "Electrochemical CO2 Reduction with Atomic Iron-Dispersed on Nitrogen-Doped Graphene," Advanced Energy Materials, 8(19), 9 (2018).
  16. Y. Zhang, F. Lu, S. Liu, D. Lu, D. Su, M. Liu, Y. Zhang, P. Liu, J.X. Wang, and R.R. Adzic, "Oxygen Reduction on Gold Nanocrystal Surfaces in Alkaline Electrolyte: Evidence for Surface Proton Transfer Effects," ECS Transactions, 85(12), 93-110 (2018).
  17. J.-Q. Zhong, M. Wang, W.H. Hoffmann, M.A.v. Spronsen, D. Lu, and J.A. Boscoboinik, "Synchrotron-Based Ambient Pressure X-ray Photoelectron Spectroscopy of Hydrogen and Helium," Appl. Phys. Lett., 112(9), 091602 (2018).