Publications


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Peer-Reviewed Publications


2018

  • Freedman, R.J., Valles, D. (2018) A Communication Benchmark Tailored to Intel Broadwell Nodes and Tuned to the DEAC Cluster.  Proceedings of The 2018 IEEE 8th Annual Computing and Communication Workshop and Conference (CCWC). (2018)

2016

  • Freedman, R.J., Valles, D. “A Modeling Approach to Hardware Analysis of the Heterogeneous DEAC Cluster.” In Proceedings of The 2016 International Conf. on Computational Science and Computational Intelligence (CSCI). DOI 10.1109/CSCI.2016.271
  • Jason Howard and N.A.W. Holzwarth, “First principles simulations of the porous layered calcogenides Li2+xSnO3 and Li2+xSnS3“, ,Phys. Rev. B 94, 064198 (2016) Local copy
  • Ahmad Al-Qawasmeh and N.A.W. Holzwarth, ” Computational Study of Li Ion Electrolytes Composed of Li3AsS4 Alloyed with Li4GeS4“, Journal of the Electrochemical Society 163, A2079-A2088 (2016)Local copy
  • Larry E. Rush Jr. and N.A.W. Holzwarth, “First principles investigation of the Structural and electrolyte properties of Na4P2S6 and Li4P2S6“, , Solid State Ionics 286, 45-50 (2016) Local copy

2015

  • K. Berland, V.R. Cooper, K. Lee, E. Schröder, T. Thonhauser, P. Hyldgaard, and B.I. “Lundqvist van der Waals forces in density functional theory: a review of the vdW-DF method” Rep. Prog. Phys. 78, 066501 (2015).
  • Jacilynn A. Brant, Danielle M. Massi, N. A. W. Holzwarth, Joseph H. MacNeil, Alexios P. Douvalis, Thomas Bakas, Steve W. Martin, Michael D. Gross, and Jennifer A. Aitken, “Fast Lithium Ion Conduction in Li2SnS3: Synthesis, Physicochemical Characterization, and Electronic Structure”Chemistry of Materials 27, 189-196 (2015)
  • P. Canepa, K. Tan, Y. Du, H. Lu, Y.J. Chabal, and T. Thonhauser “Structural, elastic, thermal, and electronic responses of small-molecule-loaded metal-organic framework materials” J. Mater. Chem. A 3, 986 (2015).
  • Godwin R, Gmeiner W, Salsbury FR Jr. Importance of long-time simulations for rare event sampling in zinc finger proteins. J Biomol Struct Dyn. 2016;34(1):125-34. doi: 10.1080/07391102.2015.1015168. Epub 2015 Apr 9. PubMed PMID: 25734227; PubMed Central PMCID: PMC4600012.
  • Godwin, R., Gmeiner, W., Salsbury, F., “Importance of Long-Time Simulations for Rare Event Sampling in Zinc Finger Proteins”, Journal of Biomolecular Structure and Dynamics, In Press March 2015
  • K. Tan, N. Nijem, Y. Gao, S. Zuluaga, J. Li, T. Thonhauser, and Y.J. Chabal “Water interactions in metal organic frameworks” Cryst. Eng. Comm. 17, 247 (2015).
  • K. Tan, S. Zuluaga, Q. Gong, Y. Gao, N. Nijem, J. Li, T. Thonhauser, and Y.J. Chabal “Competitive coadsorption of CO2 with H2O, NH3, SO2, NO, NO2, N2, O2, and CH4 in M-MOF-74 (M = Mg, Co, Ni): The role of hydrogen bonding” Chem. Mater. 27, 2203 (2015).
  • Lu Y, Salsbury FR. Recapturing the Correlated Motions of Protein Using Coarse-Grained Models. Protein Pept Lett. 2015;22(7):654-9. PubMed PMID: 26100687; PubMed Central PMCID: PMC4706082.
  • Lu Y, Salsbury FR Jr. Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations. AIP Adv. 2015 Jan 22;5(1):017130. eCollection 2015 Jan. PubMed PMID: 25874157; PubMed Central PMCID: PMC4387600.
  • S. Zuluaga, L.-H. Liu, N. Shafiq, S.M. Rupich, J.-F. Veyan, Y.J. Chabal, and T. Thonhauser “Structural band-gap tuning in g-C3N4” Phys. Chem. Chem. Phys. 17, 957 (2015).

2014

2013

  • AbdelHafez EM, Diamanduros A, Negureanu L, Luy Y, Bean JH, Zielke K, Crowe B, Vasilyeva A, Clodfelter JE, Aly OM, Abuo-Rahma GE, Scarpinato KD, Salsbury FR Jr, King SB. Computational and synthetic studies towards improving rescinnamine as an inducer of MSH2-dependent apoptosis in cancer treatment. Mol Cancer Biol. 2013;1(1). pii: 44. PubMed PMID: 25485184; PubMed Central PMCID: PMC4254817.
  • P. Canepa, C.A. Arter, E.M. Conwill, D.H. Johnson, B.A. Shoemaker, K.Z. Soliman, and T. Thonhauser “High-throughput screening of small-molecule adsorption in MOF” J. Mater. Chem. A 1, 13597 (2013).
  • P. Canepa, Y.J. Chabal, and T. Thonhauser “When metal organic frameworks turn into linear magnets” Phys. Rev. B 87, 094407 (2013).
  • P. Canepa, N. Nijem, Y.J. Chabal, and T. Thonhauser “Diffusion of small molecules in metal organic framework materials” Phys. Rev. Lett. 110, 026102 (2013).
  • Ghosh S, Salsbury FR Jr, Horita DA, Gmeiner WH. Cooperative stabilization of Zn(2+):DNA complexes through netropsin binding in the minor groove of FdU-substituted DNA. J Biomol Struct Dyn. 2013;31(11):1301-10. doi: 10.1080/07391102.2012.732343. Epub 2012 Nov 16. PubMed PMID: 23153072; PubMed Central PMCID: PMC3825453.
  • B. Kolb, M. Kertesz, and T. Thonhauser “Binding interactions in dimers of phenalenyl and closed-shell analogues” J. Phys. Chem. A 117, 3642 (2013).
  • Nicholas Lepley, Yaojun A. Du, and N. A. W. Holzwarth, “Structures, Li+ mobilities, and interfacial properties of solid electrolytes Li3PS4 and Li3PO4 from first principles” Phys. Rev. B 88, 104103 (2013)
  • M.G. Lopez, P. Canepa, and T. Thonhauser “NMR study of small molecule adsorption in MOF-74-Mg” J. Chem. Phys. 138, 154704 (2013).
  • Negureanu L, Salsbury FR Jr. Destabilization of the MutSα’s protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations. J Mol Model. 2013 Nov;19(11):4969-89. doi: 10.1007/s00894-013-1998-2. Epub 2013 Sep 24. PubMed PMID: 24061854; PubMed Central PMCID: PMC3880575.
  • Negureanu L, Salsbury FR Jr. Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex. J Biomol Struct Dyn. 2014;32(6):969-92. doi: 10.1080/07391102.2013.799437. Epub 2013 Jun 25. PubMed PMID: 23799640; PubMed Central PMCID: PMC3884054.
  • N. Nijem, P. Canepa, U. Kaipa, K. Tan, K. Roodenko, S. Tekarli, J. Halbert, I.W.H. Oswald, R.K. Arvapally, C. Yang, T. Thonhauser, M.A. Omary, and Y.J. Chabal “Water cluster confinement and methane adsorption in the hydrophobic cavities of a fluorinated metal-organic framework” J. Am. Chem. Soc. 135, 12615 (2013).
  • S. W. Paine and A. Salam, “Computational Study of Tautomerism and Aromaticity in Mono- and Dithio-Substituted Tropolone”, Int. J. Quant. Chem. 113, 1245-1252 (2013).
  • Keerthi Senevirathne, Cynthia S. Day, Michael D. Gross, Abdessadek Lachgar, and N. A. W. Holzwarth,“A new crystalline LiPON electrolyte: Synthesis, properties, and electronic structure” Solid State Ionics 233, 95-101 (2013)
  • K. Tan, P. Canepa, Q. Gong, J. Liu, D.H. Johnson, A. Dyevoich, P.K. Thallapally, T. Thonhauser, J. Li, and Y.J. Chabal “Mechanism of preferential adsorption of SO2 into two microporous paddle wheel frameworks M(bdc)(ted)0.5” Chem. Mater. 25, 4653 (2013).

2012

  • B. Kolb and T. Thonhauser “Molecular biology at the quantum level: Can modern DFT forge the path? Nano LIFE 2, 1230006 (2012).
  • K. Lee, B. Kolb, T. Thonhauser, D. Vanderbilt, and D.C. Langreth “Structure and energetics of a ferroelectric organic crystal of phenazine and chloranilic acid” Phys. Rev. B 86, 104102 (2012).
  • N. D. Lepley and N. A. W. Holzwarth, “Computer Modeling of Crystalline Electrolytes — Lithium Thiophosphates and Phosphates” J. Electrochem. Soc. 159, A538-A547 (2012)
  • Q. Li and T. Thonhauser “A theoretical study of the hydrogen-storage potential of (H2)4CH4 in metal organic framework materials and carbon nanotubes” J. Phys.: Condens. Matter 24, 424204 (2012).
  • Y. Lin, H. Ma, C.W. Matthews, B. Kolb, S. Sinogeikin, T. Thonhauser, and W.L. Mao “Experimental and theoretical studies on a high pressure monoclinic phase of ammonia borane” J. Phys. Chem. C 116, 2172 (2012).
  • M.G. Lopez, D. Vanderbilt, T. Thonhauser, and I. Souza “Wannier-based calculation of the orbital magnetization in crystals” Phys. Rev. B 85, 014435 (2012).
  • Negureanu L, Salsbury FR Jr. The molecular origin of the MMR-dependent apoptosis pathway from dynamics analysis of MutSα-DNA complexes. J Biomol Struct Dyn. 2012;30(3):347-61. doi: 10.1080/07391102.2012.680034. Epub 2012 Jun 18. PubMed PMID: 22712459; PubMed Central PMCID: PMC3389999.
  • Negureanu L, Salsbury FR. Insights into protein – DNA interactions, stability and allosteric communications: a computational study of mutSα-DNA recognition complexes. J Biomol Struct Dyn. 2012;29(4):757-76. PubMed PMID: 22208277; PubMed Central PMCID: PMC3547537.
  • N. Nijem, P. Canepa, L. Kong, H. Wu, J. Li, T. Thonhauser, and Y.J. Chabal “Spectroscopic characterization of van der Waals interactions in a metal organic framework with unsaturated metal centers: MOF-74-Mg” J. Phys.: Condens. Matter 24, 424203 (2012).
  • N. Nijem, H. Wu, P. Canepa, A. Marti, K.J. Balkus Jr., T. Thonhauser, J. Li, and Y.J. Chabal “Tuning the gate opening pressure of metal-organic frameworks (MOFs) for the selective separation of hydrocarbon” J. Am. Chem. Soc. 134, 15201 (2012).
  • R. Sabatini, E. Kucukbenli, B. Kolb, T. Thonhauser, and S. de Gironcoli “Structural evolution of amino acid crystals under stress from a non-empirical density functional” J. Phys.: Condens. Matter 24, 424209 (2012).
  • Salsbury FR Jr, Poole LB, Fetrow JS. Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model. Proteins. 2012 Nov;80(11):2583-91. doi: 10.1002/prot.24142. Epub 2012 Aug 21. PubMed PMID: 22777874; PubMed Central PMCID: PMC3826958.
  • Salsbury FR Jr, Yuan Y, Knaggs MH, Poole LB, Fetrow JS. Structural and electrostatic asymmetry at the active site in typical and atypical peroxiredoxin dimers. J Phys Chem B. 2012 Jun 14;116(23):6832-43. doi: 10.1021/jp212606k. Epub 2012 Apr 4. PubMed PMID: 22401569; PubMed Central PMCID: PMC3383837.
  • K. Tan, N. Nijem, P. Canepa, Q. Gong, J. Li, T. Thonhauser, and Y.J. Chabal “Stability and hydrolyzation of metal organic frameworks with paddle-wheel SBUs upon hydration” Chem. Mater. 24, 3153 (2012).
  • Y. Yao, N. Nijem, J. Li, Y.J. Chabal, D.C. Langreth, and T. Thonhauser “Analyzing the frequency shift of physiadsorbed CO2 in metal organic framework materials” Phys. Rev. B 85, 064302 (2012).

2011

2010

2009

  • D.C. Langreth, B.I. Lundqvist, S.D. Chakarova-Käck, V.R. Cooper, M. Dion, P. Hyldgaard, A. Kelkkanen, J. Kleis, L. Kong, S. Li, P.G. Moses, E. Murray, A. Puzder, H. Rydberg, E. Schröder, and T. Thonhauser “A density functional for sparse matter” J. Phys.: Condens. Matter 21, 084203 (2009).
  • S. Li, V.R. Cooper, T. Thonhauser, B.I. Lundqvist, and D.C. Langreth “Stacking interactions and DNA intercalation” J. Phys. Chem. B 113, 11166 (2009).
  • T. Thonhauser, D. Ceresoli, and N. Marzari “NMR shifts for polycyclic aromatic hydrocarbons from first-principles” Int. J. Quantum Chem. 109, 3336 (2009).
  • T. Thonhauser, D. Ceresoli, A.A. Mostofi, N. Marzari, R. Resta, and D. Vanderbilt “A converse approach to the calculation of NMR shielding tensors” J. Chem. Phys. 131, 101101 (2009).
  • Salsbury FR Jr, Crowder MW, Kingsmore SF, Huntley JJ. Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor. J Mol Model. 2009 Feb;15(2):133-45. doi: 10.1007/s00894-008-0410-0. Epub 2008 Nov 28. PubMed PMID:19039608.
  • Vasilyeva A, Clodfelter JE, Rector B, Hollis T, Scarpinato KD, Salsbury FR Jr. Small molecule induction of MSH2-dependent cell death suggests a vital role of mismatch repair proteins in cell death. DNA Repair (Amst). 2009 Jan 1;8(1):103-13. doi: 10.1016/j.dnarep.2008.09.008. Epub 2008 Nov 12. PubMed PMID:18955167; PubMed Central PMCID: PMC3391744.

2008

2007

2006

  • E.E. Allen, J.S. Fetrow, L.W. Daniel, S.J. Thomas, D.J. John. Algebraic dependency models of protein signal transduction networks from time-series data. J. Theor. Biol. 238 (2): 317-330 JAN 21 2006
  • F. R. Salsbury Jr. An analysis of errors in Stil’s equation for macromolecular electrostatic solvation energies. Molecular Physics, April 20, 104, 1311 (2006)
  • J.S. Fetrow, S.T. Knutson, and M.H. Edgell. Mutations in α-helical solvent exposed sites of eglin c have long-range effects: evidence from molecular dynamics simulations. Proteins, May 1, 63, 356-72 (2006).
  • Yonas Abraham and N. A. W. Holzwarth, “A method for calculating electronic structures near surfaces of semi-infinite crystals “, Phys. Rev. B 73, 035412 (2006).
  • Y. Ma and A. Salam, On chiral selectivity of enantiomers using a circularly polarized pulsed laser under resonant and off-resonant conditions. Chem Phys 324, 367-375 (2006).
  • Y. Ma and A. Salam, Calculation of electronic circular dichroism spectra by rotating wave approximation. Chem Phys 324, 622-630 (2006).
  • F. R. Salsbury Jr., J. Clodfelter, M. Gentry, T. Hollis and K. D. Scarpinato, The molecular mechanism of DNA damage recognition by MutS homologs and its distinction from mismatch binding”, Nucleic Acids Research 2006 34(8):2173-2185
  • S. W. Paine and A. Salam, “Computational Study of Keto-Enol Equilibria of Tropolone in Gas and Aqueous Solution Phase”, Chem. Phys. 331, 61-66 (2006)
  • Y. Ma and A. Salam, “Controlling State Populations of Enantiomers of Real Chiral Molecules by Using a Circularly Polarized Pulsed Laser”, Chem. Phys. Lett. 431, 247-252 (2006).
  • M. Caudill, G.B. Cook, J.D. Grigsby, and H.P. Pfeiffer, “Circular orbits and spin in black-hole initial data,” Phys. Rev. D 74 064011 (2006).

2005

2004

2003

2002

2001

  • Yonas B. Abraham, N. A. W. Holzwarth, R. T. Williams, G. Eric. Matthews, and Alan R. Tackett, “The electronic structure of oxygen related defects in PbWO4 and CaMoO4 crystals” Phys. Rev. B64, 245109 (2001)
  • A. R. Tackett, N. A. W. Holzwarth, and G. E. Matthews, “A Projector Augmented Wave (PAW) code for electronic structure calculations, Part I: atompaw for generating atom-centered functions and PartII: pwpaw for periodic solids in a plane wave basis.” Computer physics Communications 135 329-347, 348-376 (2001)

2000