Medical Scientist Training Program    Back to Main

Faculty Detail    
Campus Address SHEL 803 Zip 2182
Phone  (205) 996-6939
Other websites

Graduate  Harbin Institute of Technology, Harbin, China    1998  PhD 
Fellowship  Tsinghua University, Beijing, China    2001  PhD 
Fellowship  University of Pittsburgh, Pittsburgh, PA    2002  PhD 

Faculty Appointment(s)
Appointment Type Department Division Rank
Center  Comp Arthritis, MSK, Bone & Autoimmunity Ctr  Comp Arthritis, MSK, Bone & Autoimmunity Ctr Professor
Center  Comprehensive Cancer Center  Comprehensive Cancer Center Professor
Center  Ctr for Clinical & Translational Sci  Ctr for Clinical & Translational Sci Professor
Center  Ctr Neurodegeneration & Exp Ther (CNET)  Ctr Neurodegeneration & Exp Ther (CNET) Professor
Primary  Biomedical Engineering  Biomedical Engineering Professor

Graduate Biomedical Sciences Affiliations
Biochemistry and Structural Biology 
Biochemistry and Structural Biology 
Cancer Biology 
Medical Scientist Training Program 
Pathobiology and Molecular Medicine 

Biographical Sketch 
Positions and Employment: 2002-2005 Research Associate, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, School of Medicine 2005-2006 Research Instructor, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, School of Medicine 2006-2012 Assistant Professor, Dept of Biomedical Eng, University of Alabama at Birmingham (UAB) 2012-current Associate Professor (with tenure), Dept of Biomedical Eng, UAB

Society Memberships
Organization Name Position Held Org Link
American Association for Cancer Research     
American Chemical Society     
Biomedical Engineering Society     
Biophysical Society     

Research/Clinical Interest
An integrated multi-scale computational modeling and biological experimental research program to study apoptosis, cell adhesion and biomaterial design
Yuhua Song group is using integrated computational modeling and molecular and cellular biological experimental approaches to investigate the fundamental structural and functional mechanisms of the protein interactions underlying the death receptor-mediated apoptosis and to identify molecular targets to overcome the drug resistance in breast cancer. Multiscale modeling of the protein complexes in regulating cell adhesion and collagen expression in tissue remodeling is another focus of the group. Song group am also interested in the optimized design of biomaterials and small molecules/drugs for cell-based therapeutics, including the applications in immunoisolation nanotechnology. Methodology development for multiscale modeling of complex biological systems continues to be a focus of Song research group. The research outcomes could contribute to multiscale computational bioengineering, biomolecular engineering, cancer, regenerative medicine, and biomechanics research fields.

Selected Publications 
Publication PUBMEDID
1. Lingyun Wang, Joanne E, Murphy-Ullrich, Yuhua Song*. Molecular insight for the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions. Biochemistry, 2014, 53 (40), pp 6309–6322.
2. Romone Fancy, Lingyun Wang, Tiara Napier, Jiabei Lin, Gu Jing, Aaron Lucius, Jay M McDonald, Tong Zhou, Yuhua Song*. Characterization of calmodulin and Fas death domain interaction: an integrated experimental and computational study. Biochemistry, 2014, 53 (16), pp 2680–2688
3. Qi Yan, Jay M McDonald, Tong Zhou, Yuhua Song*. 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 Bioinformatics, 2013, 81(3):377-85. PMID: 23042204.
4. Di Pan, Yuhua Song*. 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. Mol Cell Biomech, 2011, 8(3): 233-52. PMID: 21977518.
5. Di Pan, Qi Yan, Yabing Chen, Jay M McDonald, Yuhua Song*. Trifluoperazine Regulation of Calmodulin Binding to Fas: A Computational Study. Proteins: Structure, Function, and Bioinformatics, 2011, 79(8): 2543-2556. PMID: 21656570 (Impact Factor: 3.181)
6. John T. Wilson, Wanxing Cui, Veronika Kozlovskaya, Eugenia Kharlampieva, Di Pan, Zheng Qu, Venkata R. Krishnamurthy, Joseph Mets1, Vivek Kumar1, Jing Wen, Yuhua Song, Vladimir V. Tsukruk, and Elliot L. Chaikof. Cell Surface Engineering with Polyelectrolyte Multilayer Thin Films. J Am Chem Soc, 2011, 133(18): 7054-7064. PMID: 21491937 (Impact Factor: 8.981)
7. Qi Yan, Joanne E. Murphy-Ullrich, Yuhua Song*. Molecular and Structural Insight for the Role of Key Residues of Thrombospondin-1 and Calreticulin in Thrombospondin-1- Calreticulin Binding. Biochemistry, 2011, 50(4): 566-573. PMID: 21142150 (Impact Factor: 3.150)
8. Di Pan, Yuhua Song*. 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, 2010, 99 (1): 208-217. PMID: 20655849 (Impact Factor: 4.692)
9. Qi Yan, Joanne E. Murphy-Ullrich, Yuhua Song*. Structural Insight for the Role of Thrombospondin-1 Binding to Calreticulin in Calreticulin-Induced Focal Adhesion Disassembly. Biochemistry, 2010, 49(17): 3685-3694. PMID: 20337411 (Impact Factor: 3.150)
10. Yawar J. Qadri, Yuhua Song, Catherine M. Fuller and Dale J. Benos. Amiloride Docking to Acid-sensing Ion Channel-1. J Biol Chem, 2010, 285(13): 9627-9635. PMID: 20048170 (Impact Factor: 5.498)
11. Yawar J. Qadri, Bakhrom K. Berdiev, Yuhua Song, Howard L. Lippton, Catherine M. Fuller, and Dale J. Benos. Psalmotoxin-1 docking to human acid sensing ion channel-1. Journal of Biological Chemistry, 2009, 284(26): 17625-17633. PMID: 19395383 (Impact Factor: 5.498)
12. Anthony N. Vomund, Sarah Stuhlsatz-Krouper, Yuhua Song and William A. Frazier. Breaking an Extracellular - Clasp Activates 3 Integrins. Biochemistry, 2008, 47 (44): 11616-11624. PMID: 18841997 (Impact Factor: 3.150)
13. Jonathan Suever, Yabing Chen, Jay M McDonald, Yuhua Song*. Conformation and Free Energy Analyses of the Complex of Ca2+-Bound Calmodulin and the Fas Death Domain. Biophys. J. 2008, 95(12): 5913-5921. PMID: 18820240 (Impact Factor: 4.692)
14. Yuemin Liu, Di Pan, Susan L. Bellis, Yuhua Song*. Effect of Altered Glycosylation on the Structure of the I-like Domain of beta1 Integrin: A Molecular Dynamics Study. Proteins: Structure, Function, and Bioinformatics, 2008, 73(4): 989-1000. PMID: 18536010 (Impact Factor: 3.181)
15. Sun Joo Lee, Yuhua Song, Nathan A. Baker. 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. 2008, 94(9): 3565-3576. PMID: 18222999 (Impact Factor: 4.692)
16. Shyam Rele, Yuhua Song, Robert P. Apkarian, Zheng Qu, Vincent P. Conticello and Elliot L. Chaikof. D-Periodic Collagen-Mimetic Microfibers. J Am Chem Soc. 2007, 129(47): 14780-14787. PMID: 17985903 (Impact Factor: 8.981)
17. Yuhui Cheng, Jason K. Suen, Deqiang Zhang, Stephen D. Bond, Yongjie Zhang, Yuhua Song, Nathan A. Baker, Chandrajit L. Bajaj, Michael J. Holst and J. Andrew McCammon. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J, 2007, 92(10): 3397-406. PMID: 17307827 (Impact Factor: 4.692)
18. Yuhua Song, Victor Guallar, Nathan A. Baker. Molecular dynamics simulation of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer. Biochemistry, 2005, 44(41), 13425-13438. PMID: 16216066 (Impact Factor: 3.150)
19. Deqiang Zhang, Jason Suen, Yongjie Zhang, Yuhua Song, Zoran Radic, Palmer Taylor, Michael J. Holst, Chandrajit Bajaj, Nathan A. Baker, J. Andrew McCammon. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state smoluchowski equation using finite element methods. Biophys J, 2005, 88(3):1659-1665. PMID: 15626705 (Impact Factor: 4.692)
20. Yuhua Song, Yongjie Zhang, Chandrajit L. Bajaj, Nathan A. Baker. Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis. Biophys J. 2004, 87(3):1558-1566. PMID: 15345536 (Impact Factor: 4.692)
21. Yuhua Song , Yongjie Zhang , Tongye Shen , Chandrajit L. Bajaj , J. Andrew McCammon and Nathan A. Baker. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J. 2004, 86(4):2017-2029. PMID: 15041644 (Impact Factor: 4.692)
22. Yuhua Song, Richard E. Debski, Volker Musahl, Maribeth Thomas, Savio L-Y. Woo. A three dimensional finite element model of the human anterior cruciate ligament – a computational analysis with experimental validation. J Biomech. 2004, 37(3):383-390. PMID: 14757458 (Impact Factor: 3.252)
23. Yuhua Song, Yongnian Yan, Renji Zhang etc. Manufacture of the die of auto-mobile deck part based on rapid prototyping and rapid tooling technology. Journal of Materials Processing Technology, 2002, 20(1-3):237-242 (Impact Factor: 1.726)
24. Yuhua Song, Yongnian Yan, Renji Zhang etc. Boundary model between casting and matrix and its influence on the dimensional accuracy analysis of rapid tooling. Proceeding of the institution of mechanical engineers Part B - Journal of Engineering Manufacture, 2002, 216 (8):1123-1134 (Impact Factor: 0.699)
25. Yuhua Song, Yongnian Yan, Renji Zhang Qingping Lu etc. 3-D non-linear cou-pled thermomechanical finite element analysis of the dimensional accuracy for aasting dies in rapid tooling. Finite Elements in Analysis and Design, 2001, 38 (1):79-91. (Impact Factor: 1.346)
26. Yuhua Song, Kaifing Zhang, Zhongren Wang, Faxi Dao, Yongnian Yan, etc. Coupled thermo-mechanical analysis of plastics thermoforming. Polymer Engineering and Science, 2000, 40(8):1736-1746. (Impact Factor: 1.296)
27. Yuhua Song, Kaifing Zhang, Zhongren Wang, Faxi Diao. 3-D FEM analysis of temperature field and thermal stress for plastics thermoforming. Journal of Materials Processing Technology, 2000, 97(1):35-43. (Impact Factor: 1.726)
28. Yuhua Song, Kaifeng Zhang, Zhongren Wang, Faxi Diao. Study on the warpage of plastics vacuum- forming process. Journal of Reinforced Plastics and Composites, 1999, 18(10): 931-941. (Impact Factor: 0.823)
29. Yuhua Song, Yongnian Yan, Zhang Renji. Coupled thermo-mechanical FEM aanalysis of laminated object manufacturing. China Mechanical Engineering. 2000, 11(Suppl):37-40.
30. Yuhua Song, Kaifeng Zhang, Zhongren Wang. 3-D FEM analysis of temperature field for plastic sheet thermoforming. Journal of Plasticity Engineering, 1998, 5(4):33-41
31. Kaifeng Zhang, Yuhua Song, Zhongren Wang. Study of latent heat disposal during FEM analysis of 3-D temperature field of plastic thermoforming. Material Science and Tech, 1998, 6(2):83-87
32. Yuhua Song, Shanzhi Ren, Fengyu Qing. The experimental research and realization on computer about 3-Dimensional shrinkage prediction of ductile iron casting. Materials Science & Technology, 1997, 5(1):114-116
33. Kaifeng Zhang, Yuhua Song. Analysis of thickness distribution control process of vacuum forming part by rigid visco-plastic shell FEM. Journal of Plasticity Engineering, 1997, 4(3):38-42 

Computational Biology/Biomechanics, Mechanotransduction, Protein/Biomembrane structure and function, death receptor-mediated apoptosis, Cell adhesion, Biomaterials