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

Selected Publications


Spagnol S.T., K.N. Dahl (2016). Spatially resolved quantification of chromatin condensation through differential local rheology in cell nuclei fluorescence lifetime imaging. PLoS One, 11(1):e0146244.

Duffy R.M., Sun Y., Feinberg A.W. (2016). Understanding the Role of ECM Protein Composition and Geometric Micropatterning for Engineering Human Skeletal Muscle. Annals of Biomedical Engineering, 44(6):2076-2089.

He J., Y. Wang, M.A. Missinato, E. Onuoha, L.A. Perkins, S.C. Watkins, C.M. St Croix, M. Tsang, M.P. Bruchez (2016). A genetically targetable near-infrared photosensitizer. Nat Methods, 13(3):263–8.

Lutz J.F., J.M. Lehn, E.W. Meijer, K. Matyjaszewski (2016). From precision polymers to complex materials and systems. NATURE REVIEWS MATERIALS, 1(5).

Mataev E., S.K. Rastogi, A. Madhusudan, J. Bone, N. Lamprinakos, Y. Picard, T. Cohen-Karni (2016). Synthesis of Group IV Nanowires on Graphene: The Case of Ge Nanocrawlers. Nano Lett., 16(8):5267-5272

Yu Y., H.-C. Lee, K.-C. Chen, J. Suhan, M. Qiu, Q. Ba and G. Yang (2016) Inner membrane fusion mediates spatial distribution of axonal mitochondria. Scientific Reports, doi:10.1038/srep18981.

Kim H. Y., T.R. Jackson, and L.A. Davidson (2016). On the role of mechanics in driving mesenchymal-to-epithelial transitions. Seminars in Cell and Developmental Biology.

Roman T., L. Xie, and R. Schwartz (2016). Medoidshift clustering applied to genomic bulk tumor data. BMC Genomics, 17(S1):6.

McGarvey, J.C. et al. Actin-Sorting Nexin 27 (SNX27)-Retromer Complex Mediates Rapid Parathyroid Hormone Receptor Recycling. JOURNAL OF BIOLOGICAL CHEMISTRY, 291(21):10986-11002.

Pawar, Y. Zhang, Y. Jia, X. Wei, T. Rabczuk, C. L. Chan, C. Anitescu (2016). Adaptive FEM-based Nonrigid Image Registration Using Truncated Hierarchical B-splines. A Special Issue of FEF 2015 in Computers and Mathematics with Applications, 72:2028-2040.

Deseri L. , P. Pollaci, M. Zingales, K. Dayal (2016). Fractional hereditariness of lipid membranes: Instabilities and linearized evolution. JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS, 58:11-27.

Abdullah A.M., P.V. Braun, K.J. Hsia (2016). Programmable shape transformation of elastic spherical domes. SOFT MATTER, 12(29):6184-6195.

Warren K.M., M.M. Islam, P.R. LeDuc, R. Steward (2016). 2D and 3D Mechanobiology in Human and Nonhuman Systems. ACS APPLIED MATERIALS & INTERFACES, 8(34):21869-21882.

Mitchell A.P. (2016). MICROBIOLOGY Fungus produces a toxic surprise. NATURE, 532(7597):41-42.

Roybal K.T., T.E. Buck, X.T. Ruan, B.H. Cho, D.J. Clark, R. Ambler, H.M. Tunbridge, J.W. Zhang, P. Verkade, C. Wulfing, R.F. Murphy (2016). Computational spatiotemporal analysis identifies WAVE2 and cofilin as joint regulators of costimulation-mediated T cell actin dynamics. SCIENCE SIGNALING, 9(424).


Sun Y., Q. Jallerat, J.M. Szymanksi, A.W. Feinberg (2015). Conformal Nanopatterning of Extracellular Matrix Proteins onto Topographically Complex Surfaces. Nature Methods, 2(12):134-6.

Ganesh S., Z. Qin, S.T. Spagnol, M.T. Biegler, K.A. Coffey, A. Kalinowski, M.J. Buehler, K.N. Dahl (2015). The Tail Domain of Lamin B1 is More Strongly Modulated by Divalent Cations than Lamin A. Nucleus, 6(3):203-11.

Bowman S.L., M.A. Puthenveedu (2015). Postendocytic Sorting of Adrenergic and Opioid Receptors: New Mechanisms and Functions. Progress in Molecular Biology and Translational Science, 132:189-206.

Mitchell K. F., R. Zarnowski, H. Sanchez, J.A. Edward, E. L. Reinicke, J. E. Nett, A. P. Mitchell, D.R. Andes (2015). Community Participation in Biofilm Matrix Assembly and Function. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 12(13):4092-7.

Magenau A.J.D., S. Saurabh, S.K. Andreko, C.A. Telmer, B.F. Schmidt, A.S. Waggoner, M.P. Bruchez (2015). Genetically Targeted Fluorogenic Macromolecules for Subcellular Imaging and Cellular Perturbation. Biomaterials, 66:1-8.

Liao T., G. Xu, Y. Zhang (2015). Atom Simplification and Quality T-mesh Generation for Multi-resolution Biomolecular Surfaces. IGAA Special Issue in Lecture Notes in Computational Sciences and Engineering (accepted).

M. Temerinac-Ott, A.W. Naik, R.F. Murphy (2015). Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions. BMC Bioinformatics, 16:213.

Fraldi M., A. Cugno, L. Deseri, K. Dayal, N. Pugno (2015). A Frequency-Based Hypothesis for Mechanically Targeting and Selectively Attacking Cancer Cells. Journal of the Royal Society Interface, 12:111.

Weaver L. N., S.C. Ems-McClung, S.H. Chen, G. Yang, S.L. Shaw, C.E. Walczak (2015). The Ran-GTP Gradient Spatially Regulates XCTK2 in the Spindle. Current Biology, 25:1506-14.

Xu W., N.V. Solis, R.L. Ehrlich, C.A. Woolford, S.G. Filler, A.P. Mitchell (2015). Activation and Alliance of Regulatory Pathways in C. Albicans during Mammalian Infection. Public Library of Science Biology (PLoS Biol), 13(2).

Egan P., R. Sinko, P.R. LeDuc, S. Keten (2015). The Role of Mechanics in Biological and Bio-Inspired Systems. Nature Communications, 6:7418.


Sae-Ueng U, Li D, Zuo X, Huffman JB, Homa FL, Rau D, Evilevitch A (2014). Solid-to-fluid DNA transition inside HSV-1 capsid close to the temperature of infection. Nat Chem Biol. 2014 Oct;10(10):861-7. doi: 10.1038/nchembio.1628.

Zhang, J., Guo, W.-H., and Wang, Y.-L. (2014) Microtubules stabilize cell polarity by localizing rear signals. Proc. Natl. Acad. Sci. USA, 111:16383-16388.

Kim, Y.T., Hazar, M., Vijayraghavan, D., Song, J., Messner, W.C., Davidson, L.A., LeDuc, P.R. (2014). Mechanochemical Actuators of Embryonic Epithelial Contractility. Proceedings of the National Academy of Sciences 111, 14366–14371

A. Kumar, A. Rao, S. Bhavani, J.Y. Newberg, and R. F. Murphy (2014). Automated Analysis of Immunohistochemical Images Identifies Candidate Location Biomarkers for Cancers. Proc. Natl. Acad. Sci. U.S.A. 111:18249.

Palchesko RN, Szymanksi JM, Sahu A and Feinberg AW (2014). Shrink Wrapping Cells in a Defined Extracellular Matrix to Modulate the Chemo-Mechanical Microenvironment Cellular and Molecular Bioengineering, 7(3):355-368.

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

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

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

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

T. Liao, G. Xu, Y. Zhang (2014). Structure-Aligned Guidance Estimation in Surface Parameterization Using Eigenfunction-based Cross Field. Graphical Models, 76(6):691-705.

Tan X, Wang Y, Armitage BA, Bruchez MP (2014). Label-free Molecular Beacons for Biomolecular Detection. Analytical chemistry.

Warren, K.M., Mpagazehe, J.N., LeDuc, P.R., Higgs, C.F (2014). Probing the Elastic Response of Microalga Scenedesmus Dimorphus in Dry and Aqueous Environments through Atomic Force Microscopy. Applied Physics Letters 105, 163701.

Chin Ming Hui, Joanna Pietrasik, Michael Schmitt, Clare Mahoney, Jihoon Choi, Michael R. Bockstaller and Krzysztof Matyjaszewski (2014). Surface-Initiated Polymerization as Enabling Tool for Multifunctional (Nano) Engineered Hybrid Materials. Chem. Mat., 26, 745−762.

Saadyah E. Averick, Sourav K. Dey, Debasish Grahacharya, Krzysztof Matyjaszewski, and Subha R. Das, Angew (2014). Solid Phase Incorporation of an ATRP Initiator onto Nucleic Acids and Small Molecules for Direct and Facile Access to Polymer Biohybrids. Chem, 53, 2739–2744

Smith GR, Xie L, Lee B, Schwartz R (2014). Applying molecular crowding models to simulations of virus capsid assembly in vitro. Biophys J. 06(1):310-20.

Chung D, Barker BM, Carey CC, Merriman B, Werner ER, Lechner BE, Dhingra S, Cheng C, Xu W, Blosser SJ, Morohashi K, Mazurie A, Mitchell TK, Haas H, Mitchell AP, Cramer RA. (2014) ChIP-seq and In Vivo Transcriptome Analyses of the Aspergillus fumigatus SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence. PLoS Pathog. 6;10(11):e1004487. PMID: 25375670

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

Tasoglu S, E Diller, S Guven, M Sitti, U Demirci (2014). Untethered micro-robotic coding of three-dimensional material composition. Nature communications, 5:3124.

Wong, S., Guo, W.-H., and Wang, Y.-L. (2014) Fibroblasts probe substrate rigidity with filopodia extensions before occupying an area. Proc. Natl. Acad. Sci. USA, 111:17176-17181.

Liu T, Sae-Ueng U, Li D, Lander GC, Zuo X, Jönsson B, Rau D, Shefer I, Evilevitch (2014). A. Solid-to-fluid-like DNA transition in viruses facilitates infection. Proc Natl Acad Sci U S A. 111(41):14675-80. doi: 10.1073/pnas.1321637111. 


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.


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.


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.


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.


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.