
PeerReviewed Publications
2010
 Y. A. Du and
N. A. W. Holzwarth, "First principles simulations of Li
ion migration in materials related to LiPON electrolytes", ECS
Transactions 25(36) 2536 (2010).

Y. A. Du and N. A. W. Holzwarth, "Firstprinciples study of LiPON
and related solid electrolytes", Phys. Rev. B 81 184106 (15pp) (2010).

X. Xu and N. A. W. Holzwarth, "A projector augmented wave (PAW)
formulation of HartreeFock calculations of electronic structure",
Phys. Rev. B 81 245105 (14pp) (2010).
2008
 F. R. Salsbury, S. T. Knutson, L. B. Poole and J. S. Fetrow, "Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid," Protein Science 17 299312(2008).
 J.D. Grigsby and G.B. Cook, "Measuring eccentricity in binary blackhole initial data," Phys. Rev. D 77 044011 (2008).
2007
 M. Boyle, D.A. Brown, L.E. Kidder, A.H. Mroue, H.P. Pfeiffer, M.A. Scheel, G.B. Cook and S.A. Teukilsky, "Highaccuracy comparison of numerical relativity simulations with postNewtonian expansions," Phys. Rev. D 76, 124038 (2007).
 M. H. Knaggs, F. R. Salsbury, M. H. Edgell, J. S. Fetrow. Insights into CheY relaxation and relaxation derived from molecular dynamics simulations. Biophys J .20622079 Mar 15 2007
 S. W. Paine and A. Salam. "A Computational Study of the KetoEnol Equilibria of Sulphur Substituted Analogues of Hydroxycyclopropenone", J. Mol. Struct. (THEOCHEM) 814, 105112 (2007).
 G.B. Cook and B.F. Whiting, "Approximate Killing Vectors on S^{2}," Phys. Rev. D 76, 041501(R) (2007).
 Yaojun A. Du and N. A. W. Holzwarth, "Li Ion Diffusion Mechanisms in the Crystalline Electrolyte γLi_{3}PO_{4}", Journal of the Electrochemical Society 154, A999A1004 (2007).
 Ping Tang, N. A. W. Holzwarth, and Yaojun A. Du, "Comparison of the electronic structures of four crystalline phases of FePO_{4}", Phys. Rev. B 76, 174118 (2007)
 Yaojun A. Du and N. A. W. Holzwarth, "Mechanisms of Li^{+} diffusion in crystalline Li_{3}PO_{4} electrolytes from first principles", Phys. Rev. B 76, 174302 (2007)
 Budiman, M.E., Knaggs, M.H., Fetrow, J.S., and Alexander, R.W. (2007) Using molecular dynamics to map interaction networks in an aminoacyltRNA synthetase. Proteins: Structure, Function, and Bioinformatics 68: 670689.
 Paul R. Anderson, Emil Mottola, and Ruslan Vaulin, Stress tensor from the trace anomaly in ReissnerNordström spacetimes, Physical Review D 76, 124028 (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 timeseries data. J. Theor. Biol. 238 (2): 317330 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 αhelical solvent exposed sites of eglin c have longrange effects: evidence from molecular dynamics simulations. Proteins, May 1, 63, 35672 (2006).
 Yonas Abraham and N. A. W. Holzwarth, "A method for calculating electronic structures near surfaces of semiinfinite 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 offresonant conditions. Chem Phys 324, 367375 (2006).
 Y. Ma and A. Salam, Calculation of electronic circular dichroism spectra by rotating wave approximation. Chem Phys 324, 622630 (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):21732185
 S. W. Paine and A. Salam, “Computational Study of KetoEnol Equilibria of Tropolone in Gas and Aqueous Solution Phase”, Chem. Phys. 331, 6166 (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, 247252 (2006).
 M. Caudill, G.B. Cook, J.D. Grigsby, and H.P. Pfeiffer, "Circular orbits and spin in blackhole initial data," Phys. Rev. D 74 064011 (2006).
2005
 E.E. Allen, J.S. Fetrow, L.W. Daniel, S.J. Thomas, D.J. John. Algebraic dependency models of protein signal transduction networks from timeseries data. J. Theor. Biol. 2005 Jul 4. Epub ahead of print.
 Huff RG, Bayram E, Tan H, Knutson ST, Knaggs MH, Richon AB, Santago P, Fetrow JS Chemical and structural diversity in cyclooxygenase protein active sites CHEMISTRY & BIODIVERSITY 2 (11): 15331552 2005
 M. J. Rave and W. C. Kerr. Berry's Phase for an Electron in a Periodic Potential without Inversion Symmetry. Euro. Phys. Jour. B, 45, 473 (2005)
 W. C. Kerr, M. J. Rave and L. A. Turski. The Phase Space Dynamics of SemiClassical Spin1/2 Bloch Electrons. Physical Review Letters 94, 176403 (2005)
 Paul R. Anderson, R. Balbinot, and A. Fabbri. Cutoff Anti de SitterSpace/ConformalFieldTheory Duality and the Quest for Braneworld Black Holes. Phys. Rev. Lett. 94, 061301
 S. W. Paine, A. J. Kresge, and A. Salam, An ab initio and density functional theory study of ketoenol equilibria of hydroxycyclopropenone in gas and aqueous solution phase. J. Phys. Chem. A 109, 4149 (2005).
2004
 K. Drotschmann, R. P. Topping, J. E. Clodfelter, and F. R. Salsbury, Jr. Mutations in the Nucleotidebinding Domain of MutS Homologs Uncouple Cell Death from Cell Survival. DNA Repair, 3 (7):729742
 L. R. Thomas, A. Henson, J. C. Reed, F. R. Salsbury, Jr., and A. Thorburn. Direct Binding of FADD to the TRAIL Receptor DR5 is Regulated by the Death Effector Domain of FADD. J. Bio. Chem. 279, 31
 M. S. Lee, F. R. Salsbury, Jr., and C. L. Brooks, III. Constant pHmolecular Dynamics using Continuous Titration Coordinate, Proteins: Structure, Function and Bioinformatics. Proteins: Struct Funct Bioinform 56 (4):738752
 M.S. Lee, F. R. Salsbury, Jr., and M. A. Olson. An Efficient Hybrid Implicit/Explicit Solvent Method for Biomolecular Simulations that Uses A Generalized Born Reaction Field and Multigrid Enhancements. J. Comp. Chem. 25:19677198
 E. Bayram, P. Santago II, R. Harris, Y. Xiao, A.J. Clauset, and J.D. Schmitt. Genetic Algorithms and SelfOrganizing Maps: A Powerful Combination for Modeling Complex QSAR and QSPR Problems. Journal of ComputerAided Molecular Design. 18:483493
 G.B. Cook and H.P. Pfeiffer, "Excision boundary conditions for black hole initial data," Phys. Rev. D 70, 104016 (2004).
 W. C. Kerr and A. J. Graham. Nucleation Rate of Critical Droplets on an Elastic String in a \phi^6 Potential. Phys. Rev. E 70, 066103
2003
 Ping Tang and N. A. W. Holzwarth. Electronic structures of FePO_4, LiFePO_4, and related materials. Physical Review B 68, 165107 (2003)
2002
 Jason D. Weibel, Charles F. Jackels, and Robert L. Swofford, "Experimental and ab initio investigation of the OH overtone vibration in ethanol" J. Chem. Phys. 117, 42454254 (2002)
 Harald P. Pfeiffer, Gregory B. Cook, and Saul A. Teukolsky, "Comparing initialdata sets for binary black holes," Phys. Rev. D 66 024047 (2002).
 A J Graham and W C Kerr, "Solution of Kramers' problem for a moderately to heavily damped elastic string", Phys Rev E 65, 016106
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 atomcentered functions and PartII: pwpaw for periodic solids in a plane wave basis." Computer physics Communications 135 329347, 348376 (2001)
2000
 Harald P. Pfeiffer, Saul A. Teukolsky, and Gregory B. Cook, "Quasicircular orbits for spinning binary black holes," Phys. Rev. D 62 104018 (2000).
 Lawrence E. Kidder, Mark A. Scheel, Saul A. Teukolsky, Eric D. Carlson and Gregory B. Cook, "Black hole evolution by spectral methods," Phys. Rev. D 62 084032 (2000).
 Y. Abraham, N. A. W. Holzwarth, and R. T. Williams, "Electronic Structure and Optical Properties of CdMoO_4 and CdWO_4 ", Phys. Rev. B 62, 17331741 (2000)
