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 insight for the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions. Biochemistry, Liu et al., 2014, 53(40):6309-22; 
Characterization  of calmodulin and Fas death domain interaction: an integrated experimental and  computational study. Biochemistry, Fancy et al.,, 2014, 53 (16), pp 2680–2688; 

3. 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; 
4. 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., Mol Cell Biomech, 2011, 8(3): 233-52;
5.  Trifluoperazine Regulation of Calmodulin Binding to Fas: A  Computational Study. Proteins: Structure, Function, and Bioinformatic, Pan et al., 2011, 79(8):2543-56;

6. Cell Surface Engineering with Polyelectrolyte Multilayer Thin Films. J Am Chem Soc., Wilson et al., 2011,133(18):7054-64;
7. 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;
8. 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;
9. 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;
10. Amiloride Docking to Acid-sensing Ion Channel-1. Journal of Biological Chemistry, Qadri et al., 2010, 285(13): 9627-9635.
11. Psalmotoxin-1 docking to  human acid sensing ion channel-1. Journal of Biological Chemistry, Qadri et al., 2009, 284(26): 17625-17633;
12. 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;
13. 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;
14. Breaking an Extracellular α−β Clasp Activates β3 Integrins.Biochemistry, Vomund et al. , 2008, 47 (44): 11616-11624;
15. 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;
16. D-Periodic Collagen-Mimetic Microfibers. J Am Chem Soc., Rele et al., 2007, 129(47): 14780-14787;
17. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J, Cheng et al., 2007, 92(10): 3397-406;
18. 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;
19. 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;
20. 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;
21. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys. J, Song et al., 2004, 86(4):2017-2029;
22. 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:  August 19, 2015

   Department of Biomedical Engineering                       The University of Alabama at Birmingham

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