Vavylonis Group

Department of Physics


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News/Views/Opinion Articles

Book Chapters

Peer Reviewed Journal Articles

Peer Reviewed Conference Proceedings

NEWS/VIEWS/OPINION ARTICLES

  1. T. Kim and D. Vavylonis, "A special issue on discrete modeling of the cytoskeleton," Cytoskeleton, 76:493–494 (2019).
  2. D. Vavylonis and B. G. Horan, "Cell Biology: Capturing Formin’s Mechano-Inhibition," CURRENT BIOLOGY, 27:R1078–R1080 (2017).
  3. "How Will Kinetics and Thermodynamics Inform Our Future Efforts to Understand and Build Biological Systems?" CELL SYSTEMS 4:144-146 (2017).
  4. "Actin Biophysics in the tradition of Fumio Oosawa: a Special Issue with Contributions from Participants at the 2016 "Now in Actin" meeting in Nagoya", CYTOSKELETON 74:445 (2017).

BOOK CHAPTERS

  1. D. Holz, L. M. McMillen, G. L. Ryan, and D. Vavylonis, "Lamellipodia in Stationary and Fluctuating Steady States," Springer volume "Cell movement: Modeling and Applications," pages 211-258 (2018) https://doi.org/10.1007/978-3-319-96842-1_8.
  2. T. Drake, E. Yusuf and D. Vavylonis, "A Systems-Biology Approach to Yeast Actin Cables", in "Advances in Systems Biology", Springer series Advances in Experimental Medicine and Biology, 736:325-35 (2012).

JOURNAL ARTICLES

  1. D. M. Rutkowski, V. Vincenzetti, D. Vavylonis, S. G. Martin, "Cdc42 mobility and membrane flows regulate fission yeast cell shape and survival," bioRxiv https://doi.org/10.1101/2023.07.21.550042 (2023)
  2. A. R. Hall, Y. K. Choi, W. Im, D. Vavylonis, "Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study," Structure 32:1-11 (2024)
  3. S. Yamashiro, D. Rutkowski, K. A. Lynch, D. Vavylonis, N. Watanabe "Force transmission by retrograde actin flow-induced dynamic molecular stretching of Talin," Nature Communications 14:8468 (2023)
  4. H. Opalko, S. Geng, A. R. Hall, D. Vavylonis, J. B. Moseley, "Design principles of Cdr2 node patterns in fission yeast cells," Mol. Biol. Cell 34:br18, 1–10 (2023)
  5. Y. Li, O. Kučera, D. Cuvelier, D. M. Rutkowski, M. Deygas, D. Rai, T. Pavlovič, F. N. Vicente, M. Piel, G. Giannone, D. Vavylonis, A. Akhmanova, L. Blanchoin, M. Théry, "Compressive forces stabilise microtubules in living cells," Nature Materials 22 : 913-924 (2023)
  6. R. Bhattacharjee, A. R. Hall, M. C. Mangione, M. G. Igarashi, R. H. Roberts-Galbraith, J.-S. Chen, D. Vavylonis, K. L. Gould, "Multiple polarity kinases inhibit phase separation of F-BAR protein Cdc15 and antagonize cytokinetic ring assembly in fission yeast," eLife 12 :e83062 (2023)
  7. S. Zhang and D. Vavylonis, "Steps of actin filament branch formation by Arp2/3 complex investigated with coarse-grained molecular dynamics", Front. Cell Dev. Biol. 11:1071977 (2023). Special Issue "Shedding Light on Asymmetric Cellular Machinery"
  8. D. Holz, A. R. Hall, E. Usukura, S. Yamashiro, N. Watanabe and D. Vavylonis, "A mechanism with severing near barbed ends and annealing explains structure and dynamics of dendritic actin networks," eLife 11:e69031(2022)
  9. D. Rutkowski and D. Vavylonis, "Discrete mechanical model of lamellipodial actin network implements molecular clutch mechanism and generates arcs and microspikes," PLOS Comp. Biol. 17: e1009506 (2021)
  10. V. Gerganova, I. Lamas, D. M. Rutkowski, A. Vještica, D. G. Castro, V. Vincenzetti, D. Vavylonis, S. G. Martin, "Cell patterning by secretion-induced plasma membrane flows," Science Advances 7:eabg6718 (2021)
  11. M. Rodriguez Pino, I. Nuñez, C. Chen, M. E. Das, D. J. Wiley, G. D’Urso, P. Buchwald, D. Vavylonis, F. Verde, "Cdc42 GTPase Activating Proteins (GAPs) Maintain Generational Inheritance of Cell Polarity and Cell Shape in Fission Yeast," Mol. Biol. Cell 32:ar14, 1-17 (2021)
  12. T. Litschel, C. F. Kelley, D. Holz, M. Adeli Koudehi, S. Kenjiro Vogel, L. Burbaum, N. Mizuno, D. Vavylonis, P. Schwille, "Reconstitution of Contractile Actomyosin Rings in Vesicles," Nature Communications 12: 2254 (2021)
  13. H. Smith, N. Pinkerton, D. B. Heisler, E. Kudryashova, A. R. Hall, K. R. Karch, V. Wysocki, M. Sotomayor, E. Reisler, D. Vavylonis, D. S. Kudryashov, “Rounding out the understanding of ACD toxicity with the discovery of cyclic forms of actin oligomers,” Int. J. Mol. Sci. 22: 718 (2021), for special issue "Cytoskeletoxins: Bacterial and Viral Effector Proteins Targeting the Cytoskeleton”.
  14. B. Khalili, H. Lovelace, D. M. Rutkowski, D. Holz, D. Vavylonis, "Fission Yeast Polarization: Modeling Cdc42 Oscillations, Symmetry Breaking, and Zones of Activation and Inhibition," Cells 9:1769 (2020)
  15. B. G. Horan, A. R. Hall and D. Vavylonis, "Insights into actin polymerization and nucleation using a coarse grained model," Biophys. J. 119:553-566 (2020)
  16. M. Adeli Koudehi, D. M. Rutkowski and D. Vavylonis, "Organization of Associating or Crosslinked Actin Filaments in Confinement," Cytoskeleton 76:532-548 (2019)
  17. K. Koseki, D. Taniguchi, S. Yamashiro, H. Mizuno, D. Vavylonis and N. Watanabe, "Lamellipodium tip actin barbed ends serve as a force sensor," Genes to Cells 24:705-718 (2019)
  18. T. Zhang, H. Tang, D. Vavylonis, and D. J. Cosgrove, "Disentangling loosening from softening: insights into primary cell wall structure," The Plant Journal 100:1101-1117 (2019).
  19. T. Xu, C. Langouras, M. Adeli Koudehi, B. E. Vos, N. Wang, G. H. Koenderink, X. Huang, and D. Vavylonis, "Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX," Scientific Reports, 9:1717 (2019)
  20. S. Yamashiro, D. Taniguchi, S. Tanaka, T. Kiuchi, D. Vavylonis, N. Watanabe, "Convection-Induced Biased Distribution of Actin Probes in Live Cells," Biophys. J. 116:142-150 (2019).
  21. D. Holz and D. Vavylonis, "Building a dendritic actin filament network branch by branch: models of filament orientation pattern and force generation in lamellipodia," Biophys. Rev. 10:1577–1585 (2018).
  22. B. Khalili, L. Merlini, V. Vincenzetti, S. G. Martin, and D. Vavylonis, "Exploration and Stabilization of Ras1 Mating Zone: a Mechanism with Positive and Negative Feedbacks" PLOS Comp. Biol., 2018, 14:e1006317. (Recommended in Faculty of 1000)
  23. Yamashiro S., Tanaka S., McMillen L.M., Taniguchi D., Vavylonis D., Watanabe N. "Myosin-dependent actin stabilization as revealed by single-molecule imaging of actin turnover," Mol. Biol. Cell 29:1917-2025 (2018). (Recommended in Faculty of 1000)
  24. B. G. Horan, G. Zerze, Y. C, Kim, D. Vavylonis, and J. Mittal, "Computational modeling highlights the role of the disordered Formin Homology 1 domain in profilin-actin transfer," FEBS Lett. 592:1804-1816 (2018).
  25. Kudryashova E, Heisler D.B., Williams B., Harker A., Shafer K., Quinlan M.E., Kovar D.R., Vavylonis D., Kudryashov D.S. "Actin-cross-linking Toxin is a Universal Inhibitor of Tandem-organized and Oligomeric G-actin-binding Proteins," Current Biology 28:1536-1547 (2018).
  26. G. L. Ryan, D. Holz, S. Yamashiro, D. Taniguchi, N. Watanabe, D. Vavylonis, "Cell protrusion and retraction driven by fluctuations in actin polymerization: A two-dimensional model," CYTOSKELETON 74:490-503 (2017).
  27. T. Zhang, D. Vavylonis, D. M. Durachko, D. J. Cosgrove, "Nanoscale Movements of Cellulose Microfibrils in Primary Cell Walls," NATURE PLANTS 3:17056 (2017). (Recommened in Faculty of 1000).
  28. L. M. McMillen and D. Vavylonis, "Model of turnover kinetics in the lamellipodium: implications of slow- and fast- diffusing capping protein and Arp2/3 complex," PHYSICAL BIOLOGY 13:066009 (2016).
  29. L. Merlini, B. Khalili, F. O. Bendezú, D. Hurwitz, V. Vincenzetti, D. Vavylonis, S. M. Martin, "Local pheromone release from dynamic polarity sites underlies cell-cell pairing during yeast mating," CURRENT BIOLOGY 26:1117-1125 (2016).
  30. D. Zhang, T. C. Bidone, D. Vavylonis, "ER-PM contacts define actomyosin kinetics for proper contractile ring assembly," CURRENT BIOLOGY 26:647-653 (2016).
  31. H. Tang, T. C. Bidone, D. Vavylonis, "Computational model of polarized actin cables and contractile actin ring formation in budding yeast," CYTOSKELETON, 72: 517-533 (2015).
  32. D. B. Heisler, E. Kudryashova, D. O. Grinevich, C. Suarez, J. D. Winkelman, K. G. Birukov, S. R. Kotha, N. L. Parinandi, D. Vavylonis, D. R. Kovar, D. S. Kudryashov, "ACD toxin-produced actin oligomers poison formin-controlled actin polymerization," SCIENCE, 49:535-539 (2015).
  33. T. Xu, D. Vavylonis, F.-C. Tsai, G. H. Koenderink, W. Nie, E. Yusuf, I-J. Lee, J.-Q. Wu, X. Huang, "SOAX: A software for quantification of 3D biopolymer networks," SCIENTIFIC REPORTS, 5:9081 (2015).
  34. E. Vitriol, L. M. McMillen, M. Kapustina, S. Gomez, D. Vavylonis, and J. Q. Zheng, "Two Functionally Distinct Sources of Actin Monomers Supply the Leading Edge of Lamellipodia," CELL REPORTS  11:433-445 (2015).
  35. F. O. Bendezú, V. Vincenzetti, D. Vavylonis, R. Wyss, H. Vogel, and S. G. Martin, "Spontaneous Cdc42 Polarization Independent of GDI-mediated Extraction and Actin-based Trafficking," PLOS BIOLOGY, 13:e1002097 (2015).
  36. W. Nie, M.-T. Wei, D. H. Ou Yang, S. S. Jedlicka, D. Vavylonis, "Formation of contractile networks and fibers in the medial cell cortex through myosin-II turnover, contraction, and stress-stabilization," CYTOSKELETON 72:29-46 (2015).
  37. T. C. Bidone, H. Tang, D. Vavylonis, "Dynamic Network Morphology and Tension Buildup in 3D Model of Cytokinetic Ring Assembly," BIOPHYS. J. 107:2618-2628 (2014).
  38. H. Tang, D. Laporte and D. Vavylonis, "Actin cable distribution and dynamics arising from cross-linking, motor-pulling and filament turnover," MOL. BIOL. CELL 25:3006-3016 (2014). (Recommended in Faculty of 1000)
  39. S. Yamashiro, H. Mizuno, M. B. Smith, G. L. Ryan, T. Kiuchi, D. Vavylonis, N. Watanabe, "New single-molecule speckle microscopy reveals modification of the retrograde actin flow by focal adhesions at nanometer scales," MOL. BIOL. CELL 25:1010-1024 (2014).
  40. T. Xu, D. Vavylonis and X. Huang, "3D Actin Network Centerline Extraction with Multiple Active Contours," MEDICAL IMAGE ANALYSIS 18:272-284 (2014).
  41. T. Drake and D. Vavylonis, "Model of fission yeast cell shape driven by membrane-bound growth factors and the cytoskeleton," PLOS COMPUTATIONAL BIOLOGY, 9:e1003287 (2013).
  42. N. Watanabe, Y. Sawako, D. Vavylonis and T. Kiuchi, "Molecular viewing of actin polymerizing actions and beyond: combination analysis of SiMS microscopy with modeling, FRAP and s-FDAP," DEVELOPMENT, GROWTH AND DIFFERENTIATION, 55:508-514 (2013).
  43. M. B. Smith, T. Kiuchi, N. Watanabe and D. Vavylonis, "Distributed Actin Turnover in the Lamellipodium and FRAP Kinetics," BIOPHYS. J. 104:247-257 (2013).
  44. G. L. Ryan, N. Watanabe and D. Vavylonis, "Image Analysis Tools to Quantify Cell Shape and Protein Dynamics near the Leading Edge," CELL STRUCTURE AND FUNCTION, 19:1-7 (2013).
  45. D. Laporte, N. Ojkic, D. Vavylonis and J.-Q. Wu, "alpha-Actinin and fimbrin cooperate with myosin-II to organize actomyosin bundles during contractile-ring assembly," MOL. BIOL. CELL, 23:3094-3110 (2012).
  46. M. Das, T. Drake, D. Wiley, P. Buchwald, D. Vavylonis and F. Verde, "Oscillatory dynamics of Cdc42 GTPase in the control of polarized growth," SCIENCE 337:239-243 (2012).
  47. G. L. Ryan, N. Watanabe and D. Vavylonis, "A review of models of fluctuating protrusion and retraction patterns at the leading edge of motile cells," CYTOSKELETON 69:195-206 (2012) .
  48. G. L. Ryan, H. Petroccia, N. Watanabe and D. Vavylonis, "Excitable actin dynamics in lamellipodial protrusion and retraction," BIOPHYS. J. 102:1493-1502 (2012).
  49. M. B. Smith, E. Karatekin, A. Gohlke, H. Mizuno, N. Watanabe and D. Vavylonis, "Interactive, computer-assisted tracking of speckle trajectories in fluorescence microscopy: application to actin polymerization and membrane fusion," BIOPHYS. J., 101:1794-1804 (2011). (Recommended in Faculty of 1000)
  50. N. Ojkic, J.-Q. Wu and D. Vavylonis, "Model of Myosin Node Aggregation into a Contractile Ring: the Effect of Local Alignment," J. PHYS.: CONDENS. MATTER special issue on Cooperative Dynamics in Cells, 23, 374103 (2011).
  51. M. B. Smith, H. Li, T. Shen, X. Huang, E. Yusuf, and D. Vavylonis, "Segmentation and Tracking of Cytoskeletal Filaments using Open Active Contours," CYTOSKELETON, 67 693-705 (2010).
  52. N. Ojkic and D. Vavylonis, "Kinetics of Myosin Node Aggregation into a Contractile Ring," PHYS. REV. LETT., 105 048102 (2010).
  53. T. Drake and D. Vavylonis, "Cytoskeletal Dynamics in Fission Yeast: A Review of Models for Polarization and Division," HFSP J., 4 122-130 (2010).
  54. H. Wang and D. Vavylonis, "Model of For3p-mediated actin cable assembly in fission yeast," PLOS ONE, 3 e4078 (2008).
  55. D. Vavylonis, J.-Q. Wu, S. Hao, B. O'Shaughnessy, and T. D. Pollard, "Assembly Mechanism of the Contractile Ring for Cytokinesis by Fission Yeast," SCIENCE, 319 97-100 (2008). (Recommended in Faculty of 1000)
  56. I. Fujiwara, D. Vavylonis, and T. D. Pollard, "Polymerization kinetics of ADP- and ADP-Pi-actin determined by TIRF microscopy," PROC. NATL. ACAD. SCI. USA, 104 8827-8832 (2007).
  57. D. Vavylonis, D. R. Kovar, B. O'Shaughnessy, and T. D. Pollard, "Model of Formin-Associated Actin Filament Elongation," MOLECULAR CELL, 39 455-466 (2006).
  58. D. Vavylonis, Q. Yang, and B. O'Shaughnessy, "Actin Polymerization Kinetics, Cap Structure, and Fluctuations", PROC. NATL. ACAD. SCI. USA 102, 8543-8548 (2005). (Recommended in Faculty of 1000).
  59. B. O'Shaughnessy and D. Vavylonis, "Non-Equilibrium in Adsorbed Polymer Layers", J. PHYS.: CONDENS. MATTER 17, R63-R99 (2005).
  60. B. O'Shaughnessy and D. Vavylonis, "Dynamics of Living Polymers", EUR. PHYS. J. E 12, 481-496 (2003).
  61. B. O'Shaughnessy and D. Vavylonis, "The Slowly Formed Guiselin Brush", EUROPHYS. LETT. 63, 895-901 (2003).
  62. B. O'Shaughnessy and D. Vavylonis, "Irreversible Adsorption from Dilute Polymer Solutions", EUR. PHYS. J. E 11, 213-230 (2003).
  63. B. O'Shaughnessy and D. Vavylonis, "Pulsed Laser Polymerization at Low Conversions: Broadening and Chain Transfer Effects", MACROMOL. THEORY SIMUL. 12, 401-412 (2003). (Featured on cover).
  64. B. O'Shaughnessy and D. Vavylonis, "The Ultrasensitivity of Living Polymers", PHYS. REV. LETT. 90, 118301 (2003).
  65. B. O'Shaughnessy and D. Vavylonis, "Irreversibility and Polymer Adsorption", PHYS. REV. LETT. 90, 056103 (2003).
  66. B. O'Shaughnessy and D. Vavylonis, "Interfacial Reactions: Mixed Order Kinetics and Segregation Effects", PHYS. REV. LETT. 84, 3193-3196 (2000).
  67. B. O'Shaughnessy and D. Vavylonis, "Interfacial Reaction Kinetics", EUR. PHYS. J. E 1, 159-177 (2000).
  68. B. O'Shaughnessy and D. Vavylonis, "Reactive Polymer Interfaces: How Reaction Kinetics Depend on Reactivity and Density of Chemical Groups", MACROMOLECULES 32, 1785-1796 (1999).
  69. B. O'Shaughnessy and D. Vavylonis, "Reactions at Polymer Interfaces: Transitions from Chemical to Diffusion-Control and Mixed Order Kinetics", EUROPHYS. LETT. 45, 638-644 (1999).
  70. B. O'Shaughnessy and D. Vavylonis, "Kinetic Regimes and Cross-Over Times in Many-Particle Reacting Systems", EUROPHYS. LETT. 45, 653-658 (1999).
  71. B. O'Shaughnessy and D. Vavylonis, "Reaction Kinetics in Polymer Melts", EUR. PHYS. J. B 6, 363-372 (1998).

PUBLICATIONS IN PEER REVIEWED CONFERENCE PROCEEDINGS

  1. T. C. Bidone, H. Tang and D. Vavylonis, "Insights into the mechanics of cytokinetic ring assembly using 3D modeling," Int. Mech. Eng. Congress Expo. 2014;9. pii: V009T12A090
  2. T. Xu, H. Li, T. Shen, N. Ojkic, D. Vavylonis, X. Huang "Extraction and analysis of actin networks based on open active contour models," Proc IEEE Int. Symp. Biomed. Imaging. 2011:1334-1340 (2011).
  3. H. Li, T. Shen, D. Vavylonis, X. Huang, "Actin Filament Segmentation Using Spatiotemporal Active-Surface and Active-Contour Models," Med. Image Comput. Comput. Assist. Interv. 13:86-94 (2010) .
  4. H. Li, T. Shen, D. Vavylonis, X. Huang, "Actin Filament Tracking Based on Particle Filters and Stretching Open Active Contour Models," Med. Image Comput. Comput. Assist. Interv. 12:673-681 (2009)
  5. H. Li, T. Shen, M. B. Smith, I. Fujiwara, D. Vavylonis, and X. Huang, "Automated Actin Filament Segmentation, Tracking, and Tip Elongation Measurements based on Open Active Contour Models," Proc IEEE Int. Symp. Biomed Imaging. 2009:1302-1305 (2009) .