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Faculty Detail    
Campus Address SHEL 803 Zip 2182
Phone 205-996-6939
E-mail yhsong@uab.edu
Other websites http://www.eng.uab.edu/yhsong

Faculty Appointment(s)
Appointment Type Department Division Rank
Primary  Biomedical Engineering  Biomedical Engineering Associate Professor
Center  Biomedical Engineering  Biomatrix Eng Regen Med (BERM) Ctr Associate Professor
Center  Center for Metabolic Bone Disease  Center for Metabolic Bone Disease Associate Professor
Center  Comprehensive Cancer Center  Comprehensive Cancer Center Associate 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 
Before joining UAB, Dr. Yuhua Song was a research instructor in the Department of Biochemistry and Molecular Biophysics at Washington University in St. Louis School of Medicine. During her working and training in the Center for Computational Biology at Washington University, Dr. Song combined the strengths of different computational methods: quantum mechanics, molecular dynamics and continuum finite element methods to study the complex biological phenomena to understand the function the biological systems with a multi-scale modeling approach. Before joining Washington University, Dr. Song was a post-doctoral fellow in the Musculoskeletal Research Center at the University of Pittsburgh where she developed computational models for soft tissue biomechanics and orthopedic biomechanics applications. Since 2009, with the support of a “Mentored Quantitative Research Development Award” from NIH and Biomedical Engineering Department at The University of Alabama at Birmingham, Dr. Song has also established a molecular and cell biology experimental component in her group. Dr. Song’s work has been published in Biophysical Journal, Journal of Biological Chemistry, J Am Chem Soc., Proteins: Structure, Function, and Bioinformatic, Biochemistry, and Journal of Biomechanics.

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
Our research goals are to understand the molecular mechanisms and structural basis of biomolecular interactions underlying the signaling pathways of apoptosis and cell adhesion in cancer, cardiovascular and orthopedic diseases, and to design the optimized peptide/copolymers to obtain functional biomaterials for biomedical applications, using an integrated computational and experimental approach. The specific group research projects are described as below. 1. Protein interactions underlying death receptor-mediated death induced signaling complex formation to mediate apopotosis 2. Molecular regulatory mechanisms for glycosylated integrin-mediated signaling in cell adhesion and calreticulin-modulated signaling in focal adhesion disassembly 3. Novel biomaterial designs for biomedical applications 4. Methodology development for multiscale modeling

Selected Publications 
Publication PUBMEDID
1. Di Pan, Yuhua Song*. Effects of altered restraints in beta1 integrin on the force-regulated interaction between the glycosylated I-like domain of beta1 integrin and fibronectin III9-10: a steered molecular dynamic study. Mol Cell Biomech, 2011, 8(3): 233-52.
2. 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.
3. 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):7054-64
4. 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, 566–573
5. 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 doi:10.1016/j.bpj.2010.03.063
6. 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), pp 3685–3694
7. Yawar J. Qadri, Yuhua Song, Catherine M. Fuller and Dale J. Benos. Amiloride Docking to Acid-sensing Ion Channel-1. J Biol Chem. 2010 Mar 26;285(13):9627-35. Epub 2010 Jan 4.
8. 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, 284(26), 17625-17633, 2009
9. 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
10. 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
11. 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
12. 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 3565-3576
13. 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 Nov 28;129(47):14780-14787
14. Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J, 92, 3397-406, 2007.
15. 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
16. 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 March 88(3):1659-1665
17. 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 Sep.; 87(3):1558-1566.
18. 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 Apr; 86(4):2017-29.
19. 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 Mar; 37(3):383-90.

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