Abdallah Sayyed-Ahmad
Assistant Professor, Theoretical and Computational Biophysics
Email: asayyeda@birzeit.edu Phone: 2982149 ext. 2507 Science Building Room 225


  • PhD, Indiana University, Bloomington, Indiana, USA, 2005
  • B.Sc., Bethlehem University, Bethlehem, Palestine, 1999

Research Interests

  • Mathematical methods for biology, biochemistry and biophysics.
  • Structure and dynamics of protein, nucleic acids, lipids and their complexes.
  • Molecular dynamics simulations and binding free energy calculations.
  • Molecular modeling, QSAR, virtual screening and docking.
  • Electrostatic effects on macromolecules in electrolyte media.
  • Metabolic and gene regulatory network modeling.Microarray data analysis through transcription kinetic modeling and information theory.
  • Applications of information theory, regularization, linear and nonlinear optimization to calibration problems in biological sciences.
  • Large-scale/Multilevel finite element solution of elliptic problems


  1. Prakash P, Sayyed-Ahmad A, Zhou Y, Volk DE, Gorenstein DG, Dial E, Lichtenberger LM and Gorfe AA, Aggregation Behavior of Ibuprofen, cholic acid and dodecylphosphocholine micelles. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1818(12), 2012.
  2. Priyanka P, Sayyed-Ahmad A and  Gorfe AA, “The Role of Conserved Waters in Conformational Transitions of Q61H K-ras. PLoS computational biology, 8 (2) : e1002394. doi:10.1371/journal.pcbi.1002394, 2012.
  3. Sayyed-Ahmad A, Lichtenberger, LM and Gorfe AA, “Structure and dynamics of cholic acid and dodecylphosphocholine-cholic acid aggregates” Langmuir, 26(16):13407-14, 2010
  4. Sayyed-Ahmad A, Khandelia H and Kaznessis YN “Relative Binding Free Energy Calculations between Antimicrobial Peptides and SDS or DPC micelles” Molecular Simulation, 35(10-11):986-997, 2009.
  5. Sayyed-Ahmad A and Kaznessis YN “Determining the orientation of the Beta-hairpin antimicrobial peptide Protegrin-1 in a DLPC lipid bilayer using an implicit solvent-membrane model” . PLoS One ;4(3):e479, 2009
  6. Bolintineanu DS, Sayyed-Ahmad A, Davis HT and Kaznessis YN “Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore”. PLoS computational biology, 5 (1) : e1000277. doi:10.1371/journal.pcbi.1000277, 2009.
  7. Langham A, Sayyed-Ahmad A and Kaznessis YN "On the nature of antimicrobial activity: a model for Protegrin-1",  Journal of American Chemical Society, 130(13):4338-4346, 2008
  8. Sayyed-Ahmad A, Miao Y and Ortoleva P "Poisson-Boltzmann Theory of Bionanosystems" , Communications in Computational Physics, 3:1100-1116, 2008.
  9. Lee J, Sayyed-Ahmad A, Sheen D “Basin Model Inversion Using Information Theory and Seismic Data”, Geophysics 72:6, 2007
  10. Sayyed-Ahmad A, Tuncay K, and Ortoleva P "Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory", BMC Bioinformatics, 8:20, 2007. (Research highlights & Highly Accessed)
  11. Sayyed-Ahmad A, Tuncay K, and Ortoleva P “Efficient solution technique for solving Poisson Boltzmann equation”, Journal of Computational Chemistry, 25(8):1068-1074, 2004.
  12. Sayyed-Ahmad A, Tuncay K, and Ortoleva P “Toward Automated Cell Model Development through Information Theory”, Journal of Physical Chemistry A, 107(49):10554-10565, 2003
  13. Ortoleva P, Berry E, Fan J , Fontus M, Navid A, Sayyed-Ahmad A, Sharif Z, Stanley F, Tuncay K, Weitzke E, and Wu L ”Karyote physico-chemical genome, proteome, metabolome cell modeling system”, Omics: A Journal of Integrative Biology, 7(3):269-283(15), 2003.


Last modified:  Abdallah Sayyed-Ahmad 11/3/2012