An Integrated Multiscale Computational Modeling and Experimental Research Program

Multiscale Modeling in Biology and Biomechanics: Molecular to Continuum

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Biophysics, Biochemistry, Biology and Biomechanics


Select Publications

  1. Molecular insights into the effect of an apoptotic raft-like bilayer on the conformation and dynamics of calreticulin. Wang et al. Biochimica et Biophysica Acta (BBA) – Biomembranes. [In press, published online ahead of print, December 6, 2019].
  2. Neurodegenerative Disease–Associated Variants in TREM2 Destabilize the Apical Ligand-Binding Region of the Immunoglobulin Domain.Frontiers in Neurology- Dementia, Dean et al. Published on November 26, 2019. doi: 10.3389/fneur.2019.01252
  3. Multiscale Simulation of the Interaction of Calreticulin-Thrombospondin-1 Complex with a Model Membrane Microdomain. J Biomol Struct Dyn., Wang et al.  2019, 37(3):811-822. doi: 10.1080/07391102.2018.1433065.  
  4. Calmodulin antagonist enhances DR5-mediated apoptotic signaling in TRA-8 resistant triple negative breast cancer cells. J Cell Biochem. Fancy et al. published:16 April 2018, 
  5. Activation Mechanisms of αVβ3 Integrin by Binding to Fibronectin: A Computational Study. Protein Science, Wang et al. 2017, June; 26(6):1124-1137.  DOI:10.1002/pro.3163 
  6. Calmodulin Binding to Death Receptor 5-mediated Death-inducing Signaling Complex in Breast Cancer Cells.  J Cell Biochem. Fancy et al.  2017 Aug;118(8):2285-2294. doi: 10.1002/jcb.25882. Epub 2017 Apr 12.
  7. Characterization of the Interactions between Calmodulin and Death Receptor 5 in Triple-Negative and Estrogen Receptor Positive Breast Cancer Cells: An Integrated Experimental and Computational Study. J Biol Chem. Fancy et al,  2016, 291:12862-12870
  8. Structural insight for roles of DR5 death domain mutations on oligomerization of DR5 death domain – FADD complex in the death-inducing signaling complex formation: a computational study.  Journal of Molecular Modeling, Yang et al. 2016, 22 (4):89.
  9. Molecular insight for the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions. Biochemistry, Liu et al., 2014, 53(40):6309-22; 
  10. Characterization  of calmodulin and Fas death domain interaction: an integrated experimental and  computational study. Biochemistry, Fancy et al., 2014, 53 (16), 2680–2688; 
  11. Structural Insight for the Roles of Fas Death Domain Binding to FADD and  Oligomerization Degree of the Fas - FADD complex in the Death Inducing  Signaling Complex Formation: A Computational Study.Proteins: Structure, Function, and Bioinformatic, Yan et al., 2013, 81(3):377-85; 
  12.  Effects of altered  restraints in β1 integrin on the force-regulated interaction between the  glycosylated I-like domain of β1 integrin and fibronectin III9-10: a steered  molecular dynamic study.Molecular & Cellular Biomechanics, Pan et al., 2011, 8(3): 233-52;
  13. Trifluoperazine Regulation of Calmodulin Binding to Fas: A  Computational Study. Proteins: Structure, Function, and Bioinformatic, Pan et al., 2011, 79(8):2543-56;
  14. Cell Surface Engineering with Polyelectrolyte Multilayer Thin Films. J Am Chem Soc., Wilson et al., 2011,133(18):7054-64;
  15. Molecular and Structural Insight  for the Role of Key Residues of Thrombospondin-1 and Calreticulin in Thrombospondin-1-  Calreticulin Binding. Biochemistry, Yan et al., 2011, 50(4): 566-573;
  16. Role of Altered Sialylation of the  I-like Domain of β1 Integrin in the Binding of Fibronectin to β1 Integrin: Thermodynamics  and Conformational Analyses. Biophys J, Pan et al., 2010, 99 (1): 208-217;
  17. Structural Insight for the Role of  Thrombospondin-1 Binding to Calreticulin in Calreticulin-Induced Focal Adhesion  Disassembly. Biochemistry, Yan et al., 2010, 49(17): 3685-3694;
  18. Amiloride Docking to Acid-sensing Ion Channel-1. Journal of Biological Chemistry, Qadri et al., 2010, 285(13): 9627-9635.
  19. Psalmotoxin-1 docking to  human acid sensing ion channel-1. Journal of Biological Chemistry, Qadri et al., 2009, 284(26): 17625-17633;
  20. Conformation  and Free Energy Analyses of the Complex of Ca2+-Bound Calmodulin and the Fas  Death Domain. Biophys J, Suever et al., 2008, 95(12): 5913-5921;
  21. Effect  of Altered Glycosylation on the Structure of the I-like Domain of beta1  Integrin: A Molecular Dynamics Study. Proteins: Structure, Function, and Bioinformatic, Liu et al., 2008, 73(4): 989-1000;
  22. Breaking an Extracellular α−β Clasp Activates β3 Integrins.Biochemistry, Vomund et al. , 2008, 47 (44): 11616-11624;
  23. Molecular  dynamics simulations of asymmetric NaCl and KCl solutions separated by  phosphatidylcholine bilayers: potential drops and structural changes induced by  strong Na+-lipid interactions and finite size effects. Biophys J, Lee et al.,2008, 94(9): 3565-3576;
  24. D-Periodic Collagen-Mimetic Microfibers. J Am Chem Soc., Rele et al., 2007, 129(47): 14780-14787;
  25. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J, Cheng et al., 2007, 92(10): 3397-406;
  26. Molecular dynamics simulation of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer.Biochemistry, Song et al., 2005, 44(41), 13425-13438;
  27. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state smoluchowski equation using finite element methods.Biophys. J, Zhang et al., 2005, 88(3):1659-1665;
  28. Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis.Biophys. J, Song et al., 2004, 87(3):1558-1566;
  29. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys. J, Song et al., 2004, 86(4):2017-2029;
  30. Three Dimensional Finite Element Model of the Human Anterior Cruciate Ligament - A Computational Analysis with Experimental Validation. J Biomech., Song et al., 2004, 37(3):383-390
Last Update: 12/16/2016

   Department of Biomedical Engineering           The University of Alabama at Birmingham

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