Publications-Center for the Mechanics and Engineering of Cellular Systems - Carnegie Mellon University

Selected Publications

2014 

Kim, Y.T., M. Hazar, D. Vijayraghavan, J. Song, W. C. Messner, L.A. Davidson, P,R, LeDuc (2014). Mechanochemical Actuators of Embryonic Epithelial Contractility. Proceedings of the National Academy of Sciences (in press)

Sae-Ueng, U., D. Li, X. Zuo, J.B. Huffman, F.L. Homa, D. Rau, and A. Evilevitch (2014) Solid-to-fluid DNA transition inside HSV-1 capsid close to the temperature of infection. Nature chemical biology.

Spagnol S.T., K.N. Dahl (2014). Active cytoskeletal force and chromatin condensation independently modulate intranuclear network fluctuations. Integrative Biology, vol. 6, iss. 5, pp. 523-31.

Palchesko R.N., J.M. Szymanksi  A. Sahu, and A.W. Feinberg (2014). Shrink Wrapping Cells in a Defined Extracellular Matrix to Modulate the Chemo-Mechanical Microenvironment. Cellular and Molecular Bioengineering, vol. 7, iss. 3, pp. 355-368.

Yang G. (2014) Image-based computational tracking and analysis of spindle protein dynamics, in Mitosis: Methods and Protocols. Methods in Molecular Biology, vol. 1136

Komori H., Q. Xiao, B.M. McCartney (2014). Brain tumor specifies intermediate progenitor cell identity by attenuating beta-catenin/Armadillo activity. Development, vol. 141, iss. 1, pp.51-62.

Tao L., G. Xu, Y.J. Zhang (2014). Structure-Aligned Guidance Estimation in Surface Parameterization Using Eigenfunction-based Cross Field. Graphical Models.

G.R. Smith, L. Xie, B. Lee, and R. Schwartz.  Applying cellular crowding models to simulations of capsid assembly in vitro.  Biophysical Journal, vol. 106, iss.1, pp. 310-320.

Fahrenkopf M.A, B.E. Ydstie, T. Mukherjee, and J.W. Schneider (2014). Modeling and Global Optimization of DNA Separation. Comp. Chem. Engr., vol. 64, pp.63-70.

Vistein R, Puthenveedu MA. Src Regulates Sequence-Dependent Beta-2 Adrenergic Receptor Recycling via Cortactin Phosphorylation. Traffic. 2014 Jul 31. in press

Murphy R.F. (2014). A new era in bioimage informatics. Bioinformatics, vol. 30, iss. 10, pp. 1353.

Gozen B. A., A. Tabatabai, O.B. Ozdoganlar (2014). High-Density Soft-Matter Electronics with Micron-Scale Line Width Advanced Materials, vol. 26, iss. 30, pp. 5211-5216.

Tasoglu S, E Diller, S Guven, M Sitti, U Demirci. Untethered micro-robotic coding of three-dimensional material composition. Nature communications, vol.  5, pp. 3124.

Liu, T., U. Sae-Ueng, D. Li, X. Zuo, G. Lander, B. Jonsson, D. Rau, I. Shefer, and A. Evilevitch (2014) Solid-to-Fluid like DNA Transition in Viruses Facilitates Infection. P Natl Acad Sci USA (in press).

2013

Vistein R., M.A. Puthenveedu (2013). Reprogramming of G protein-coupled receptor recycling and signaling by a kinase switch. Proc Natl Acad Sci U S A, vol. 110, iss. 38, pp.15289-94.

Kalinowski A., Z. Qin, K. Coffey, R. Kodali, M.J. Buehler, M. Lösche, K.N. Dahl (2013). Calcium causes a conformational change in lamin A tail domain that promotes farnesyl-mediated membrane association. Biophysics Journal, vol. 104, iss. 10, pp. 2246-53.

Sun Y., R. Duffy, A. Lee, and A.W. Feinberg (2013). Optimizing the Structure and Contractility of Skeletal Muscle Thin Films. Acta Biomaterialia, vol. 9, iss. 8, pp. 7885-7894.

Gunawardena S., G. Yang, and L.S.B. Goldstein (2013). Presenilin controls kinesin-1 and dynein function during AP vesicle transport in vivo, Human Molecular Genetics, vol. 22, pp. 3838-3843.

Tan L., A. Acharya, K. Dayal (2013). Coarse variables of autonomous ODE systems and their evolution. Computer Methods in Applied Mechanics And Engineering, vol. 253, pp. 199-218.

Chowdhury S.A., S. E. Shackney, K. Heselmeyer-Haddad, T. Ried, A. A. Schäffer, R. Schwartz (2013).   Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. Bioinformatics, vol. 29, iss. 13, pp. i189-i198.

Goldman J.M., L.A. Zhang, B.A. Armitage, D.H. Lee, and J.W. Schneider (2013). High Affinity γPNA Sandwich Hybridization Assay for Rapid Detection of Short Nucleic Acid Targets with Single Mismatch Discrimination. Biomacromolecules, vol. 14, iss. 7, pp. 2253-2261.

Horn M., K. Matyjaszewski (2013). Solvent Effects on the Activation Rate Constant in Atom Transfer Radical Polymerization. Macromolecules, vol. 46, iss. 9, pp. 3350-3357.

Anandan K., O.B. Ozdoganlar (2013). An LDV-based methodology for measuring axial and radial error motions when using miniature ultra-high-speed (UHS) micromachining spindles. 

Precision Engineering-Journal of the International Societies for Precision Engineering and Nanotechnology, vol. 37, iss. 1, pp.172-186. 

Edwards, M.R, R. W. Carlsen, M. Sitti (2013). Near and far-wall effects on the three-dimensional motion of bacteria-driven microbeads. Applied Physics Letters, vol. 102, iss. 14.

Tan, C., S. Saurabh, M. Bruchez, R. Schwartz, P.R. LeDuc (2013). Molecular Crowding Shapes Gene Expression in Synthetic Cellular Nanosystems. Nature Nanotechnology, vol. 8, pp. 602–608.

2012

Booth-Gauthier E. A., Alcoser T. A., Yang G., and Dahl K. N. (2012) Force-induced changes in subnuclear movement and rheology, Biophysical Journal, vol. 103, pp. 2423-2431.

B.H. Cho, I. Cao-Berg, J.A. Bakal, and  R.F. Murphy (2012) OMERO.searcher: Content-based image search for microscope images. Nature Methods 9:633-634.

Palchesko RN, Zhang L, Sun Y and Feinberg AW. (2012) Development of Polydimethylsiloxane Substrates with Tunable Elastic  Modulus to Study Cell Mechanobiology in Muscle and Nerve PLoS ONE, 7(12), e51499, pp 1-13.  

Elmar Nurmemmedov, Martin Castelnovo, Elisabeth Medina, Carlos E Catalano, Alex Evilevitch, (2012)"Challenging packaging limits and infectivity of phage lambda", Journal of Molecular Biology,13 January 2012, Vol. 415, Issue 2, pp 263-273 .  

Gable A., Qiu M., Titus J., Balchand S., Ferenz N. F., Ma N., Fagerstrom C., Ross R. L., Yang G., and Wadsworth P. (2012) Dynamic reorganization of Eg5 in the mammalian spindle throughout mitosis requires dynein and TPX2, Molecular Biology of the Cell, vol. 23, pp. 1254-1266.  

Grover, A., Schmidt, B. F., Salter, R. D., Watkins, S. C., Waggoner, A. S., & Bruchez, M. P. (2012). Genetically Encoded pH Sensor for Tracking Surface Proteins through Endocytosis. Angewandte Chemie (International Ed in English), 51(20), 4838–4842. doi:10.1002/anie.201108107.

Ribeiro AJS, Tottey S, Taylor RWE, Bise R, Kanade T, Badylak SF, Dahl KN (2012) Mechanical characterization of adult stem cells from bone marrow and perivascular niches. Journal of Biomechanics 45(7):1280-7.

Paredes, E. & Das, S. R. (2012) Optimization of acetonitrile co-solvent and copper stoichiometry for pseudo-ligandless click chemistry with nucleic acids.  Bioorg Med Chem Lett 22, 5313-5316, doi:10.1016/j.bmcl.2012.06.027   

Y. Zhang, X. Liang, J. Ma, Y. Jing, M. J. Gonzales, C. Villongco, A.  Krishnamurthy, L. R. Frank, P. Stark, S. M. Narayan, A. McCulloch. (2012) An  Atlas-Based Geometry Pipeline for Cardiac Hermite Model Construction and  Diffusion Tensor Reorientation. /Medical Image Analysis/,  16(6):1130-1141.  

Ruder, W.C., Pratt, E.D., Bakhru, S., Sitti. M., Zappe, S., Cheng, C.M., Antaki, J.A., & LeDuc, P.R. (2012).Three-Dimensional Microfiber Devices that Mimic Physiological Environments to Probe Cell Mechanics and Signaling. Lab Chip, 12, 1775-1779.

L. Xie, G. Smith, X. Feng, and R. Schwartz. (2012) Surveying capsid assembly pathways through simulation-based data fitting. Biophysical Journal, 103:1545-1554,. 

Nawroth J, Lee H, Feinberg AW, McCain M, Grosberg A, Dabiri JO and  Parker KK. (2012) A Tissue-Engineered Jellyfish with Biomimetic Propulsion Nature Biotechnology, 30(8), pp 792-797.  

Ruder, W.C., LeDuc, P.R. (2012) Cells Gain Traction in 3D. Proceedings of the National Academy of Sciences 109, 11060-11061.

Siegwart, D. J., Oh, J. K., Matyjaszewski, K. (2012) ATRP in the design of functional materials for biomedical applications, Prog. Polym. Sci. 37, 18–37.

2011

Rape, A.D., W.H. Guo, and Y.L. Wang. (2011) The regulation of traction force in relation to cell shape and focal adhesions. Biomaterials 32(8):2043-51. Epub 2010 Dec 15.

Weinger J., M. Qiu, G. Yang, and T. Kapoor. (2011) A nonmotor microtubule binding site in kinesin-5 is required for filament crosslinking and sliding, Current Biology, 21:1-7.

Finkel, J. S., and A. P. Mitchell. (2011) Genetic control of Candida  albicans biofilm development. Nature Review Microbiology 9:109-118. 

Zhou, M-N, E. Kunttas-Tatli, S. Zimmerman, F. Zhouzheng, and B.M. McCartney. (2011) Cortical localization of APC2 plays a role in actin organization but not in Wnt signaling in Drosophila. Journal of Cell Science, 124(Pt 9): p. 1589-600.

Chou, S., Cheng, C.-M., Lin, Y. W., Chen, C.-C., & LeDuc, P. R. (2011) Localized Neurite Outgrowth Sensing through Micro-patterned Elastic Substrates. Soft Matter, 21, 9871-9877.

Averick, S., Paredes, E., Li, W., Matyjaszewski, K. & Das, S. R. (2011). Direct DNA conjugation to star polymers for controlled reversible assemblies.  Bioconjug Chem 22, 2030-2037, doi:10.1021/bc200240q  

Steward, R. L., Cheng, C. M., Ye, J. D., Bellin, R. M., & LeDuc, P. R. (2011) Mechanical stretch and shear flow induced reorganization and recruitment of fibronectin in fibroblasts. Scientific Reports (Nature Publishing Group), 1(147), 1-12. 

Stadler, A., Delos Santos,J., Stensrud, E., Dembska A.,  Kunttas-Tatli E. ,Liu S., Silva, G., Sobers, J. Shank, N.,Gramlich, P., Carell, T., Peteanu, L.,  McCartney, B., Armitage B., (2011) Fluorescent DNA Nanotags Featuring Covalently Attached Intercalating Dyes: Synthesis, Antibody Conjugation and Intracellular Imaging. Bioconjugate Chemistry 22(8):1491-1502

Ruder, W.C. and P.R. LeDuc. (2011) Bioinspirations: Cell-Inspired Small-Scale Systems for Enabling Studies in Experimental Biomechanics. Integrative and Comparative Biology (Former journal name: American Zoologist) 51(1):128-132.

Arabagi V., Behkam B., Cheung E., and Sitti M. (2011)Modeling of Stochastic Motion of Bacteria Propelled Spherical Microbeads,” Journal of Applied Physics, vol. 109, p. 114702.

Matyjaszewski, K., (2011) Architecturally complex polymers with controlled heterogeneity, Science. 2011, 333, 1104–1105.

Murphy RF. An active role for machine learning in drug development. Nature Chemical Biology 7:327-330.

2010

Goodman B., W. Channels, M. Qiu, P. Iglesias, G Yang, and Y. Zheng. (2010) Lamin B counteracts the kinesin Eg5 to restrain spindle pole separation during spindle assembly, Journal of Biological Chemistry, 285:35238-35244.

Holt, B.D., P.A. Short, A.D. Rape, Y.L. Wang, M.F. Islam, and K.N. Dahl. (2010) Carbon nanotubes reorganize actin structures in cells and ex vivo. ACS Nano 4(8):4872-8.

Lin, Y.W., R.M. Bellin, C.M. Cheng, R. Steward, Y.R. Cheng, P.R. LeDuc, and C.C. Chen. (2010) Probing Localized Neural Mechanotransduction through Surface-Modified Elastomeric Matrices and Electrophysiology. Nature Protocols 714, 5(4): 714-724.

Zimmerman, S.G., L. M. Thorpe, V. R. Medrano, C. A. Mallozzi, and B. M. McCartney. (2010) Apical constriction and invagination downstream of the canonical Wnt signaling pathway requires Rho1 and Myosin II. Developmental Biology 340:54-66.

2009

Domian, I.J., M. Chiravuri, P. van der Meer, A.W. Feinberg, X. Shi, Y. Shao, S.M. Wu, K.K. Parker, and K.R. Chien. (2009) Generation of functional ventricular heart muscle from mouse ventricular progenitor cells. Science 326(5951):426-9.

Frey, M.T. and Y.L. Wang. (2009) A photo-modulatable material for probing cellular responses to substrate rigidity. Soft Matter 5:1918-1924.

Webb, R.L., O. Rozov, S. Watkins, and B.M. McCartney. (2009) Using Total Internal Reflection Fluorescence (TIRF) microscopy to visualize cortical microtubules in the Drosophila syncytial embryo. Developmental Dynamics 238(10): 2622-2632.

Bellin, R.M., J.D. Kubicek, M.J. Frigault, A.J. Kamien, R. Steward, H.M. Barnes, M.B. DiGiacomo, L.J. Duncan, C.K. Edgerly, E.M. Morse, C.Y. Park, J.J. Fredberg, C.M. Cheng, and P.R. LeDuc. (2009) Defining the Role of Syndecan-4 in Mechanotransduction using Surface-Modification Approaches. Proceedings of the National Academy of Sciences 106(52): 22102-22107.

Webb, R.L., M-N Zhou, and B.M. McCartney. (2009) An APC2-Diaphanous complex organizes actin  in the Drosophila syncytial embryo. Development 136(8):1283-1293.