Preprints, submitted manuscripts
- Peter Morse, Merlijn van Deen, Sven Wijtmans, Martin Van Hecke, M. L. Manning, “Two classes of events in sheared particulate matter,” submitted, arXiv:1907.10198 (2020).
- Steffen Grosser,Jürgen Lippoldt, Linda Oswald, Matthias Merkel, Daniel M. Sussman, Frederic Renner, Erik W. Morawetz, Steve Pawlizak, Anatol Fritsch, Lars Christian Horn, Bahriye Aktas, M. Lisa Manning, and Josef A. Käs. “Elongated cells fluidize malignant tissues,” submitted (2020).
- Xun Wang*, Matthias Merkel*, Leo B. Sutter*, Gonca Erdemci-Tandogan, M. Lisa Manning, Karen E. Kasza. “A solid-to-fluid transition is predicted by cell shape and alignment in an anisotropic tissue of the developing fly embryo”, submitted, on BioRXiv https://doi.org/10.1101/781492 (2020).
D. Richard, M. Ozawa, S. Patinet, E. Stanifer, B. Shang, S. Ridout, B. Xu, G. Zhang, P. Morse, J.-L. Barrat, L. Berthier, M.L. Falk, P. Guan, A. Liu, K. Martens, S. Sastry, D. Vandembroucq, E. Lerner, and M.L. Manning. Predicting plasticity in disordered solids from structural indicators. in preparation (2020).
- Preeti Sahu, Daniel M. Sussman, Matthias Rübsam, Aaron F. Mertz, Valerie Horsley, Eric R. Dufresne, Carien M. Niessen, M. Cristina Marchetti, M. Lisa Manning, J. M. Schwarz. Small-scale demixing in confluent biological tissues. accepted in Soft Matter. arXiv:1905.00657 (2020).
- Rathbun L, Colicino E, Coyne S, Reilly N, Erdemci-Tandogan G, Garrastegui A, Freshour J, Santra P, Manning ML, Amack J, Hehnly H. “Cytokinetic bridge triggers de novo lumen formation in vivo,” accepted in Nature Communications (2020).
- Preeti Sahu*, Janice Kang*, Gonca Erdemci-Tandogan, M. Lisa Manning. Linear and nonlinear mechanical responses can be quite different in models for biological tissues. Soft Matter, DOI: 10.1039/C9SM01068H. arXiv:1905.12714 (2020).
- Michael Czajkowski, Daniel M. Sussman, M. Cristina Marchetti, M. Lisa Manning. Glassy Dynamics in Models of Confluent Tissue with Mitosis and Apoptosis. Soft Matter, arXiv:1905.01603, DOI: 10.1039/C9SM00916G (2019).
- Matthias Merkel, Karsten Baumgarten, Brian P. Tighe, M. Lisa Manning. A minimal-length approach unifies rigidity in underconstrained materials. arXiv:1809.01586, PNAS (2019). https://doi.org/10.1073/pnas.1815436116 Funding: Simons Foundation #446222, the Alfred P. Sloan Foundation, the Gordon and Betty Moore Foundation, the Research Corporation for Scientific Advancement though the Cottrell Scholars program, and computational support through NSF ACI-1541396. MLM also acknowledges support from the Simons Foundation under grant number 454947, and NSF-DMR-1352184 and NSF-PHY-1607416
- M.E. Brasch*, G. Passucci*, A. Gulvady, C. E. Turner, M. L. Manning, J. H. Henderson, “Nuclear position relative to the Golgi body and nuclear orientation are differentially responsive indicators of cell polarized motility,” PLOS ONE, https://doi.org/10.1371/journal.pone.0211408, (2019). *authors contributed equally Funding: NSF-CMMI-1334611, NSF-DMR-1352184, Simons MMLS (Award #446222).
- G. Passucci, M.E. Brasch, J. H. Henderson, M. L. Manning, “Identifying the mechanisms that generate super-diffusivity in mouse fibroblast trajectories on 2D substrates”, PLOS Comp Bio https://doi.org/10.1371/journal.pcbi.1006732, arxiv:1712.05049 (2019).
Associated software download: https://github.com/Manning-Research-Group/superdiffusive_spp_modelingFunding: NSF-BMMB-1334493, NSF-DMR-1352184, RSCA, Sloan.
- Tristan Sharp, Matthias Merkel, M. Lisa Manning, Andrea J. Liu, “Statistical properties of 3D cell geometry from 2D slices”, arXiv:1802.09131 PLOS ONE, https://doi.org/10.1371/journal.pone.0209892 (2019). Funding: Sloan, Gordon and Betty Moore, RSCA, NSF DMR-1352184, NSF-PHY-1607416, Simons MMLS (Award #446222). Computational support provided through NSF ACI-1541396.
- Gonca Erdemci-Tandogan, Madeline Clark, Jeff Amack, M. L. Manning. “Tissue flow induces shape change during morphogenesis”, arxiv:1804.02252, Biophysical Journal https://doi.org/10.1016/j.bpj.2018.10.028 (2018). Funding: NIH R01GM117598, Simons MMLS (Award #446222). Computing infrastructure support provided through NSF ACI-1541396.
- E M Stanifer, P K Morse, A A Middleton, M L Manning. “Simple random matrix model for the vibrational spectrum of jammed packings.” arXiv:1804.04074, Phys Rev E 98, 042908 DOI: 10.1103/PhysRevE.98.042908 (2018). Funding: Simons Glass (Award #454947), NSF DMR-1352184. Computational resources provided by Syracuse University and NSF ACI-1541396.
- M. Czajkowski, Dapeng Bi, M. L. Manning, M. C. Marchetti, “Hydrodynamics of shape-driven rigidity transitions in motile tissues”, Soft Matter 27, arxiv.org/abs/1710.09405 DOI: 10.1039/C8SM00446C (2018).Funding: Simons MMLS (Award #446222), Simons Glass (Award #454947), the Syracuse Soft & Living Matter Program, NSF DMR-1352184, NIH R01GM117598-02.
- Fabio Giavazzi, Matteo Paoluzzi, Marta Macchi, Dapeng Bi, Giorgio Scita, M. Lisa Manning, Roberto Cerbino, M. Cristina Marchetti. “Flocking Transition in Confluent Tissues” Soft Matter 18, arXiv:1706.01113 doi:10.1039/C8SM00126J (2018) . Funding: Syracuse Soft Matter Program, Simons Glass (Award #454947), Simons MMLS (Award #446222), NSF DMR-1352184, NIH R01GM117598-02. Computing support from NSF ACI-1541396.
- Daniel M. Sussman, M. Paoluzzi, M. Cristina Marchetti, M. Lisa Manning, “Anomalous glassy dynamics in simple models of dense biological tissue” Euro. Phys. Lett. 121 36001, arxiv:1712.05758 doi: 10.1209/0295-5075/121/36001 (2018). Funding: NSF POLS-1607416, Simons MMLS (Award #446222), NSF DMR-1352184, Cottrell. Computing support through NSF ACI-1541396.
- Agnik Dasgupta, Matthias Merkel, Andrew E. Jacob, Jonathan Dawson, M. Lisa Manning and Jeffrey D. Amack, “Asymmetric cell volume changes regulate epithelial remodeling of the left-right organizer”, eLife 7 e30963 DOI: 10.7554/eLife.30963 (2018). Funding: NIH R01GM117598, Simons MMLS (#446222), Cottrell, Gordon and Betty Moore Foundation. Computing infrastructure support through NSF ACI-1541396.
- Daniel Sussman, Jennifer Schwarz, M. Cristina Marchetti, M. Lisa Manning. “Soft yet sharp interfaces in vertex-based models for confluent tissues”. Physical Review Letters 120, 058001, arXiv:1710.00708 DOI: 10.1103/PhysRevLett.120.058001 (2018)Funding: NSF-POLS1607416, Simons MMSL (#446222), NSF DMR-1352184, Cottrell, Syracuse University Soft Matter Program. Computing support through NSF ACI-1541396.
- Matthias Merkel and Lisa Manning. “A geometrically controlled rigidity transition in a model for confluent 3D tissues”, FastTrack communication, New Journal of Physics 20 022002, arXiv:1706.02656 DOI:10.1088/1367-2630/aaaa13 (2018). Funding: Sloan, Gordon and Betty Moore, Cottrell, Simons MMLS (446222) and Glass (454947), NSF-DMR-1352184, and NSF-PHY-1607416. Computational support through NSF ACI-1541396.
- X. Yang, Dapeng Bi, M. Czajkowski, M. Merkel, M. L. Manning, M. C. Marchetti, “Correlating Cell Shape and Cellular Stress in Motile Confluent Tissues”, PNAS 114 (48) 12663-12668, arXiv:1704.05951 DOI: 10.1073/pnas.1705921114 (2017) .Funding: Syracuse University Soft Matter Program, Simons MMLS (#446222), NSF DMR-1352184, NIH R01GM117598-02. Computational resources provided by Syracuse University and through NSF Grant ACI-1541396.
- Sven Wijtmans, M. L. Manning, “Disentangling sound modes and defects in disordered solids,” Cover article in Soft Matter 13 5649-5655, arXiv:1502.00685 DOI: 10.1039/C7SM00792B (2017). NSF-DMR-1352184, Sloan, Simons Glass (#45494). Computing resources provided by Syracuse University and NSF-ACI-1541396.
- M. Merkel and M. L. Manning. “Using cell deformation and motion to predict forces and collective behavior in morphogenesis.” Invited review, Seminars in Cell and Developmental Biology 67, 161-169, DOI: 10.1016/j.semcdb.2016.07.029 (2017). Funding: Sloan, NSF-BMMB-1334611, NSF-DMR-1352184, NIH-1R01GM117598-01, Gordon and Betty Moore Foundation, Cottrell, the Syracuse University HTC Campus Grid, NSF award ACI-1541396 and the Soft Matter Program at Syracuse University.
- Dapeng Bi, X. Yang, M. C. Marchetti, M. L. Manning, “Motility-driven glass transitions in biological tissues,” Phys. Rev X 6 021011, arXiv:1509.06578 DOI: 10.1103/PhysRevX.6.021011 (2016). Funding: Sloan, NSF-BMMB-1334611, NSF-DMR-1352184, NIH R01GM117598-02, Gordon and Betty Moore Foundation, Cottrell, Syracuse University HTC Campus Grid, and the Soft Matter Program at Syracuse University.
- Dapeng Bi, J. Lopez, J. Schwarz, M. L. Manning, “A density-independent rigidity transition in biological tissues,” Nature Physics 11 1074-1079, arXiv:1409.0593 DOI: 10.1038/nphys3471 (2015). Funding:Sloan, NSF CMMI-1334611, NSF DMR-1352184.recommended in F1000Prime as being of special significance in its field by F1000 Faculty Member Xavier Trepat. http://f1000.com/prime/726043939?subscriptioncode=b0d58b25-d44e-4cfb-915c-7bfb1c97695f
- Steve Pawlizak, Anatol Fritsch, Steffen Grosser, Dave Ahrens, Tobias Thalheim, Stefanie Riedel, Tobias Kießling, Mareike Zink, M. Lisa Manning, and Josef A. Käs, “Testing the differential adhesion hypothesis across the epithelial−mesenchymal transition”, New Journal of Physics 17, 24 August, DOI: 10.1088/1367-2630/17/8/083049 (2015).
highlighted in a “Perspective” article in the new journal of physics by Dr. Fredberg and Tambe: http://iopscience.iop.org/article/10.1088/1367-2630/17/9/091001Funding: NSF BMMB-1334611, NSF DMR-1352184,
- Jin-Ah Park, Jae Hun Kim, Dapeng Bi, Jennifer A. Mitchel, Nader Taheri Qazvini, Kelan Tantisira, ChanYoung Park, Maureen McGill, Sae-Hoon Kim, Robert Steward, Jr., Stephanie Burger, Weiliang Qiu, Scott H. Randell, Alvin Kho, Dhananjay Tambe, Corey Hardin, Stephanie A. Shore, Elliot Israel, David A. Weitz, Daniel J. Tschumperlin, Scott T. Weiss, Elizabeth P. Henske, M. Lisa Manning, James P. Butler, Jeffrey M. Drazen, Jeffrey J. Fredberg, “Unjamming and cell shape in the asthmatic airway epithelium,” Nature Materials 14 1040–1048, DOI:10.1038/nmat4357 (2015). Funding: Sloan, NSF BMMB-1334611, NSF DMR-1352184.highlighted in a news and views article in Nature Materials by Dr. Swartz: http://www.nature.com/nmat/journal/v14/n10/full/nmat4434.html
- [pdf] Danielle S. Bassett, Eli T. Owens, Mason A. Porter, M. Lisa Manning, Karen E. Daniels. “Practical Methods for the Examination of Force Chain Network Architecture in Granular Materials” Soft Matter, arXiv:1408.3841 DOI: 10.1039/C4SM01821D (2015). (Cover article) Funding:Sloan Foundation, NSF BMMB-1334611, NSF DMR-1352184
- [pdf] M. L. Manning and A. J. Liu, “A random matrix definition of the boson peak,” Europhysics Letters, 109 36002 arXiv:1307.5904 DOI: 10.1209/0295-5075/109/36002 (2015). Funding: NSF DMR-1352184
- Craig Fox, M. L. Manning and J. D. Amack. Quantitative description of fluid flows produced by left–right cilia in zebrafish. Methods in Cell Biology. 127, 175-187 https://doi.org/10.1016/bs.mcb.2014.12.010 (2015) (Cover image). Funding: NSF-BMMB-1334611 and NSF-DMR-1352184.
- [pdf] Xingbo Yang, M. Lisa Manning and M. Cristina Marchetti, “Aggregation and Segre- gation of confined active particles,” Soft Matter 10 (34), 6477 – 6484 DOI:10.1039/C4SM00927D (2014). Recommended with a commentary in the Journal Club for Condensed Matter. Funding: NSF BMMB-1334611, NSF DMR-1352184
- [pdf] R. M. Baker, M. E. Brasch, M. L. Manning, J. H. Henderson, “Automated, contour- based tracking and analysis of cell behavior over long timescales in environments of varying complexity and cell density,” J. Roy. Soc. Interface 11(97), 20140386, DOI: 10.1098/rsif.2014.0386 (2014). Funding: NSF BMMB-1334611
- [pdf] Dapeng Bi, J. Lopez, J. Schwarz, M. L. Manning, “Energy barriers and cell migration in densely packed tissues,” Soft Matter 10 1885-1890, arXiv:1308.3891 DOI:10.1039/C3SM52893F (2014). Recommended with a commentary in the Journal Club for Condensed Matter. Funding: NSF BMMB-1334611, Syracuse University Chancellor’s Fund, Dean of the College of Arts & Sciences.
- [pdf] T. Idema, J. O. Dubuis, L. Kang, M. L. Manning, P. C. Nelson, T. C. Lubensky, and A. J. Liu, “The syncytial Drosophila embryo as a mechanically excitable medium,” PLOS ONE 8(10): e77216. arXiv:1304.4025 DOI: 10.1371/journal.pone.0077216 (2013). No MLM funding
- [pdf] E-.M. Schoetz, M. Lanio, J. Talbot, and M. L. Manning, “Glassy dynamics in three dimensional embryonic tissues,” J. R. Soc. Interface 10(89): 20130726 arXiv:1307.4454 DOI: 10.1098/rsif.2013.0726 (2013). Funding: Syracuse University College of Arts and Sciences. Computational support from the Princeton Center for Theoretical Science.
- [pdf] JD Amack, ML Manning. . Science 338 (6104), 212-215 DOI: 10.1126/science.1223953 (2012). Funding: Syracuse University College of Arts & Sciences
- [pdf] Guangliang Wang, M. Lisa Manning, Jeffrey D Amack. Regional Cell Shape Changes Control Form and Function of Kupffer’s Vesicle in the Zebrafish Embryo. Developmental Biology. Volume 370, Issue 1, 1 October 2012, Pages 52–62. DOI: 10.1016/j.ydbio.2012.07.019 (2012). Funding: No MLM funding.
- [pdf] M. L. Manning and A.J. Liu. Vibrational modes identify soft spots in a sheared disordered packing. Phys. Rev. Lett. 107 108302 arXiv:1012.4822 DOI: 10.1103/PhysRevLett.107.108302 (2011). No MLM funding
- [pdf] K. Chen, M. L. Manning, P. J. Yunker, W. G. Ellenbroek, Z. Zhang, A. J. Liu, and A. G. Yodh. Measurement of Correlations between Low-Frequency Vibrational Modes and Particle Rearrangements in Quasi-Two-Dimensional Colloidal Glasses. Phys. Rev. Lett.107 108301 arXiv:1103.2352 DOI: 10.1103/PhysRevLett.107.108301 (2011). No MLM funding
- [pdf] (Supp. Info) M. L. Manning, R. A. Foty, M. S. Steinberg, and E.-M. Schoetz, “Coaction of intercellular adhesion and cortical tension specifies tissue surface tension,” Proc. Nat. Acad. Sci. 107, 28 12517-12522, DOI: 10.1073/pnas.1003743107 (2010). Funding: No MLM funding.
- [pdf] “Pulse-like, crack-like and supershear earthquake ruptures with shear strain localization,” E. G. Daub, M. L. Manning and J. M. Carlson, J. Geophys. Res. 115, B05311 DOI: 10.1029/2009JB006388 (2010) NSF DMR‐0606092, NSF/USGS Southern California Earthquake Center
- [pdf] M. L. Manning, E. G. Daub, J. S. Langer and J. M. Carlson. Rate dependent shear bands in a shear transformation zone model of amorphous solids. Phys. Rev. E 79, 016110, DOI: 10.1103/PhysRevE.79.016110 (2009) Funding: NSF Graduate research fellowship
- [pdf] E. G. Daub, M. L. Manning and J. M. Carlson. Dynamic weakening due to strain localization in a constitutive model for fault gouge. Geophys. Res. Lett. 35, L12310, DOI: 10.1029/2008GL033835 (2008). Funding: McDonnell, Packard Foundation, NSF DMR-0606092, NSF/USGS Southern California Earthquake Center
- [pdf] J. S. Langer and M. L. Manning. Steady-state, effective-temperature dynamics in a glassy material.Phys. Rev. E 76 056107, arXiv:0709.3329 DOI: 10.1103/PhysRevE.76.056107 (2007). Funding: NSF, McDonnell, Packard Foundation, NSF DMR-0606092
- [pdf] M. L. Manning, J. S. Langer, and J. M. Carlson. Strain localization in a shear transformation zone model for amorphous solids. Phys. Rev. E 76 056106, arXiv:0706.1078 DOI: 10.1103/PhysRevE.76.056106 (2007). Funding: McDonnell, Packard, NSF DMR-0606092,
- [pdf] M. Manning, J. M. Carlson, and J. Doyle. Highly Optimized Tolerance in dense and sparse resource regimes. Phys. Rev. E 72 056106, DOI: 10.1103/PhysRevE.72.016108 (2005). Funding:NSF, Packard, NSF DMR-9813752, McDonnell, Institute for Collaborative Biotechnologies through ARO DAAD19-03-D-0004.
- Manning, M. L. & Eva-Maria Schoetz, C. “Focus on physical models in biology: multicellularity and active matter”, Editorial in New Journal of Physics 17, 040201, (2015).
- [pdf] M. L. Manning, R. A. Foty, M. S. Steinberg, and E.-M. Schoetz, “Reply to Krens et al: Cell stretching may initiate cell differentiation,” Proc. Nat. Acad. Sci. 108, 3, E11, DOI: 10.1073/pnas.1011542108 (2011).
- [pdf] M. L. Manning, Effective temperature and strain localization in amorphous solids. Ph. D. Thesis. September 2008.