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Faeder Lab

Publications

 

  1. A. L. Cooksy, S. Drucker, J. Faeder, and W. Klemperer. “High resolution spectrum of the n=1 P state of ArHCN.” J. Chem. Phys., 95, 3017, 1991. (pdf)
  2. J. Faeder. “A distributed Gaussian approach to the vibrational dynamics of Ar-benzene.” J. Chem. Phys., 99, 7664, 1993. (pdf)
  3. P. E. Maslen, J. M. Papanikolas, J. Faeder, R. Parson, and S. V. ONeil. “Solvation of electronically excited I2-.” J. Chem. Phys., 101, 5731, 1994. (pdf)
  4. W. C. Lineberger, M. Nadal, P. Campagnola, V. Vorsa, P. D. Kleiber, J. M. Papanikolas, P. E. Maslen, J. Faeder, R. Parson, and O. E. Poplawski. “Time-resolved dynamics in large cluster ions.” In Proceedings of the Robert A. Welch Foundation 38th Conference on Chemical Research: Chemical Dynamics of Transient Species, Houston, Texas, 1994. R. A. Welch Foundation.
  5. P. E. Maslen, J. Faeder, and R. Parson. “Ab initio calculations of the ground and excited states of I2- and ICl-.” Chem. Phys. Lett., 263, 63-72, 1996. (pdf)
  6. J. Faeder, N. Delaney, P. Maslen, and R. Parson. “Charge flow and solvent dynamics in the photodissociation of cluster ions: A nonadiabatic molecular dynamics study of I2-· Arn.” Chem. Phys. Lett., 270, 196-205, 1997. (pdf)
  7. N. Delaney, J. Faeder, P. E. Maslen, and R. Parson. “Photodissociation, recombination and electron transfer in cluster ions: A nonadiabatic molecular dynamics study of I2-(CO2)n.” J. Phys. Chem. A, 101, 8147-8151, 1997. (pdf)
  8. R. Parson and J. Faeder. “Ultrafast reaction dynamics in molecular cluster ions.” Science, 276, 1660, 1997. (link)
  9. J. Faeder and R. Parson. “Ultrafast reaction dynamics in cluster ions: Simulation of the transient photoelectron spectrum of I2-Arn photodissociation.” J. Chem. Phys., 108, 3909-3914, 1998. (pdf)
  10. S. Nandi, A. Sanov, N. Delaney, J. Faeder, R. Parson, and W. C. Lineberger. “Photodissociation of I2-·(OCS)n cluster ions: Structural implications.” J. Phys. Chem. A, 102, 8827-8835, 1998. (pdf)
  11. P. E. Maslen, J. Faeder, and R. Parson. “An effective Hamiltonian for an electronically excited solute in a polarizable molecular solvent.” Mol. Phys., 94, 693-706, 1998. (pdf)
  12. J. Faeder, N. Delaney, P. E. Maslen, and R. Parson. “Modeling structure and dynamics of solvated molecular ions: Photodissociation and recombination in I2-·(CO2)n.” Chem. Phys., 239, 525-547, 1998. (pdf)
  13. J. Faeder. The X2- files: Modeling photodissociation of molecular ions in clusters. PhD thesis, University of Colorado at Boulder, 1998. (pdf | GZippedPS)
  14. N. Delaney, J. Faeder, and R. Parson. “Photodissociation and recombination of solvated I2-: What causes the transient absorption peak?” J. Chem. Phys., 111, 452-455, 1999. (pdf)
  15. N. Delaney, J. Faeder, and R. Parson. “Simulation of UV photodissociation of I2-·(CO2)n: Spin-orbit quenching via solvent mediated electron transfer.” J. Chem. Phys., 111, 651-663, 1999. (pdf)
  16. A. Sanov, J. Faeder, R. Parson, and W. C. Lineberger. “Spin-orbit coupling in I·CO2 and I·OCS van der Waals complexes: beyond the pseudo-diatomic approximation.” Chem. Phys. Lett., 313, 812-819, 1999. (pdf)
  17. J. Faeder and B. M. Ladanyi. “Molecular dynamics simulations of the interior of aqueous reverse micelles.” J. Phys. Chem. B, 104, 1033-1046, 2000. (pdf)
  18. R. Parson, J. Faeder, and N. Delaney. “Charge flow and solvent dynamics in the photodissociation of solvated molecular ions” (Feature Article). J. Phys. Chem. A, 104, 9653-9665, 2000. (pdf)
  19. J. Faeder and B. M. Ladanyi. “Solvation dynamics in aqueous reverse micelles: A computer simulation study.” J. Phys. Chem. B, 105, 11148-11158, 2001. (pdf)
  20. J. Faeder, I. Pinkas, G. Knopp, Y. Prior, and D. J. Tannor. “Vibrational polarization beats in femtosecond CARS: A signature of dissociative pump-dump-pump wavepacket dynamics.” J. Chem. Phys., 115, 8440-8454, 2001. (pdf)
  21. B. Goldstein, J. R. Faeder, W. S. Hlavacek, M. L. Blinov, A. Redondo, and C. Wofsy. “Modeling the early signaling events mediated by aggregation of FceRI.” Mol. Immunol., 38, 1213-1219 (2002). (pdf)
  22. J. Faeder, M. V. Albert, and B. M. Ladanyi.  “Molecular dynamics simulations of the interior of aqueous reverse micelles.  II.  A comparison between sodium and potassium counterions.”  Langmuir, 19, 2514-2520, 2003. (pdf)
  23. J. R. Faeder, W. S. Hlavacek, I. Reischl, M. L. Blinov, H. Metzger, A. Redondo, C. Wofsy, and B. Goldstein. “Investigation of early events in FceRI-mediated signaling using a detailed mathematical model.” J. Immunol., 170, 3769-3781, 2003. (pdf)
  24. W. S. Hlavacek, J. R. Faeder, M. L. Blinov, A. S. Perelson, B. Goldstein. “The complexity of complexes in signal transduction.” Biotechnol. Bioeng. 84, 783-794, 2003. (pdf)
  25. B. Goldstein, J. R. Faeder, and W. S. Hlavacek. “Mathematical and computational models of immune-receptor signalling.” Nat. Rev. Immunol., 4, 445-456, 2004. (pdf)
  26. M. L. Blinov, J. R. Faeder, B. Goldstein, and W. S. Hlavacek. “BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.”  Bioinformatics, 20, 3289-3292, 2004. (pdf)
  27. J. R. Faeder, M. L. Blinov and W. S. Hlavacek. “Graphical rule-based representation of signal-transduction networks.” In Proc. ACM Symp. Appl. Computing, Ed. L. M. Liebrock,, ACM press, pp. 133-140, 2005. (pdf)
  28. J. R. Faeder, M. L. Blinov, B. Goldstein and W. S. Hlavacek. “Rule-based modeling of biochemical networks.” Complexity, 10, 22-41, 2005. (pdf)
  29. J. R. Faeder, M. L. Blinov, B. Goldstein, and W. S. Hlavacek.  “Combinatorial complexity and dynamical restriction of network flows in signal transduction.”  IEE Syst. Biol., 2, 5-15, 2005. (pdf)
  30. J. Faeder and B. M. Ladanyi. “Solvation dynamics in reverse micelles: The role of headgroup-solute interactions.” J. Phys. Chem. B, 109, 6732-6740, 2005. (pdf)
  31. M. L. Blinov, J. R. Faeder, J. Yang, B. Goldstein, and W. S. Hlavacek. “‘On-the-fly’ or ‘generate-first’ modeling?” Nat. Biotechnol., 23, 1344-1345, 2005. (pdf)
  32. M. L. Blinov, J. Yang, J. R. Faeder and W. S. Hlavacek. “Graph theory for rule-based modeling of biochemical networks.” Lect. Notes Comput. Sci. 4230, 89-106, 2006. (pdf)
  33. M. L. Blinov, J. R. Faeder, B. Goldstein, and W. S. Hlavacek. “A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity.” Biosystems, 83, 136-151, 2006. (pdf)
  34. M. L. Blinov, J. Yang, J. R. Faeder, and W. S. Hlavacek. “Depicting signaling cascades.” Nat. Biotechnol., 24, 137-138, 2006. (pdf)
  35. W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka, and W. Fontana. “Rules for modeling signal-transduction systems.” Sci. STKE., 2006, re6, 2006. (pdf)
  36. D. Barua, J. R. Faeder, and J. M. Haugh. “Structure-based kinetic models of modular signaling protein function: Focus on Shp2.” Biophys. J., 92, 2290-2300, 2007. (pdf)
  37. C. Torigoe, J. R. Faeder, J. M. Oliver, and B. Goldstein. “Kinetic proofreading of ligand-FcεRI interactions may persist beyond LAT phosphorylation.”  J. Immunol., 178,  3530-3535, 2007. (pdf)
  38. B. Goldstein, D. Coombs, J. R. Faeder and W. S. Hlavacek. “Kinetic proofreading model.” In Multichain Immune Recognition Receptor Signaling: From Spatiotemporal Organization to Human Disease, Ed. A. B. Sigalov. Landes Bioscience, in press.
  39. G. An, J. Faeder, and Y. Vodovotz. “Translational systems biology:  Introduction of an engineering approach to the pathophysiology of the burn patient.” J. Burn Care Res., in press.
  40. F. Mu, R. F. Williams, P. J. Unkefer, C. J. Unkefer, J. R. Faeder, and W. S. Hlavacek. “Carbon fate maps for metabolic reactions.” Bioinformatics, 23, 3193-3199, 2007. (pdf)
  41. J. S. Edwards, J. R. Faeder, W. S. Hlavacek Y. Jiang, I. Nemenman, and M. E. Wall.  “Q-bio 2007: a watershed moment in modern biology.” Mol. Syst. Biol., 3, 148, 2007. (pdf)
  42. D. Barua, J. R. Faeder, J. M. Haugh, “Computational models of tandem Src homology 2 domain interactions and application to phosphoinositide 3-kinase.” J. Biol. Chem., in press. (pdf) (supplement-pdf)
  43. J. Yang, M. I. Monine, James R. Faeder, and W. S. Hlavacek. “Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical Networks.” arxiv:0712.3773.
  44. T. Lipniacki, B, Hat, J.R. Faeder, and W. S. Hlavacek. “Stochastic effects and bistability in T cell receptor signaling.” Submitted.
  45. N. M. Borisov, A. S. Chistopolsky, J. R. Faeder, and B. N. Kholodenko. “Domain-Oriented Reduction of Rule-Based Network models.” Submitted.

 

 

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