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Publications of Joshua E. S. Socolar    :chronological  alphabetical  combined  bibtex listing:

Papers Published

  1. M. Sun, X. Cheng, and J. E. S. Socolar, Regulatory logic and pattern formation in the early sea urchin embryo, Journal of Theoretical Biology (August, 2014), ISSN 0022-5193 [S0022519314004354], [doi]  [abs]
  2. Marcoux, Catherine and Byington, Travis W. and Qian, Zongjin and Charbonneau, Patrick and Socolar, Joshua E. S., Emergence of limit-periodic order in tiling models, Phys. Rev. E, vol. 90 (July, 2014), pp. 012136, American Physical Society [PhysRevE.90.012136], [doi]
  3. X. Cheng, D. C. Lyons, J. E. S. Socolar, and D. R. McClay, Delayed transition to new cell fates during cellular reprogramming, Developmental Biology, vol. 391 no. 2 (April, 2014), pp. 147-157 [S001216061400222X], [doi]  [abs]
  4. M. Sun, X. Cheng, and J.E.S. Socolar, Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors, Chaos, vol. 23 (June, 2013), pp. 025104 [doi]  [abs]
  5. X. Cheng, M. Sun and J. E. S. Socolar, Autonomous Boolean modelling of developmental gene regulatory networks, J. Royal Soc. Interface (January, 2013) [doi]  [abs]
  6. J.E.S. Socolar and J.M. Taylor, Forcing nonperiodicity with a single tile, The Mathematical Intelligencer, vol. 34 no. 1 (Spring, 2012) [doi]  [abs]
  7. T. Byington and J. E. S. Socolar, Hierarchical freezing in a lattice model, Physical Review Letters, vol. 108 (January, 2012), pp. 045701 [doi]  [abs]
  8. R. Durrett, J. P. Gleeson, A. Lloyd, P. J. Mucha, F. Shi, D. Sivakoff, J. E. S. Socolar, C. Varghese, Graph fission in an evolving voter model, Proc. Nat. Acad. Sci., vol. 109 no. 10 (2012), pp. 3682-3687 [doi]  [abs]
  9. X. Gong and J. E. S. Socolar, Quantifying the complexity of random Boolean networks, Physical Review E, vol. 85 (2012), pp. 066107 [doi]  [abs]
  10. Karim S. Khalil, Amanda Sagastegui, Yu Li, Mukarram A. Tahir, Joshua E. S. Socolar, Benjamin J. Wiley, Benjamin B. Yellen, Binary colloidal structures assembled through Ising interactions, Nature Communications, vol. 3 (2012), pp. 794 [html], [doi]  [abs]
  11. Socolar, Joshua E. S. and Taylor, Joan M., An aperiodic hexagonal tile, J. Comb. Theory Ser. A, vol. 118 (November, 2011), pp. 2207--2231, Academic Press, Inc., Orlando, FL, USA, ISSN 0097-3165 [doi]
  12. J. E. S. Socolar, Local action, global impact: Forcing nonperiodicity with a single structural unit, Chaos, vol. 21 (2011), pp. 041106 [doi]  [abs]
  13. H. L. D. de S. Cavalcante, D. J. Gauthier, J. E. S. Socolar, R. Zhang, On the origin of chaos in autonomous Boolean networks, Phil. Trans. R. Soc. A, vol. 368 (January, 2010), pp. 495-513 [doi]  [abs]
  14. V. Sevim, X. Gong and J.E.S. Socolar, Reliability of transcriptional cycles and the yeast cell-cycle oscillator, PLoS Computational Biology, vol. 6 no. 7 (2010), pp. e1000842 [doi]  [abs]
  15. R. Zhang, H. L. D. de S.Cavalcante, Z. Gao, D. J. Gauthier, J. E. S. Socolar, M. M. Adams and D. P. Lathrop, Boolean chaos, Physical Review E (Rapid Communications), vol. 80 (2009), pp. 045202(R) [doi]  [abs]
  16. J. Norrell and J.E.S. Socolar, Boolean modeling of collective effects in complex networks, Physical Review E, vol. 79 (2009), pp. 061908 [doi]  [abs]
  17. D.A. Orlando, C.Y. Lin, A. Bernard, J.Y. Wang, J.E.S. Socolar, E.S. Iversen, A.J. Hartemink, and S.B. Haase, Global control of cell-cycle transcription by coupled CDK and network oscillators, Nature (May 7, 2008) [doi]
  18. A.S. Ribeiro, S.A. Kauffman, J. Lloyd-Price, B. Samuelsson, J.E.S. Socolar, Mutual information in random Boolean models of regulatory networks, Physical Review E, vol. 77 (2008), pp. 011901 [doi]  [abs]
  19. B.P. Tighe and J.E.S. Socolar, Nonlinear elastic stress response in granular packings, Physical Review E, vol. 77 (2008), pp. 031303 [doi]  [abs]
  20. J.E.S. Socolar, Time-delay control for discrete maps, in Handbook of Chaos Control, edited by E. Scholl and H. G. Schuster (December, 2007), Wiley-VCH Verlag GmbH [html]  [abs]
  21. A. Shreim, P. Grassberger, W. Nadler, B. Samuelsson, J.E.S. Socolar, and M. Paczuski, Network Analysis of the State Space of Discrete Dynamical Systems, Physical Review Letters, vol. 98 (2007), pp. 198701 [e198701]  [abs]
  22. J. Norrell, B. Samuelsson, and J.E.S. Socolar, Attractors in continuous and Boolean networks, Physical Review E, vol. 76 (2007), pp. 046122 [e046122]  [abs]
  23. C.M. Berger, J.W. Cain, J.E.S. Socolar, and D.J. Gauthier, Control of electrical alternans in simulations of paced myocardium using extended time-delay autosynchronization, Physical Review E, vol. 76 (2007), pp. 041917 (Selected for Virtual Journal of Biological Physics Research.) [GetabsServlet]  [abs]
  24. J.E.S. Socolar, The hexagonal parquet tiling: k-isohedral monotiles with arbitrarily large k, Mathematical Intelligencer, vol. 29 (2007), pp. 33-38 [pdf]  [abs] [author's comments]
  25. J.E.S. Socolar, Nonlinear Dynamical Systems, in Complex Systems Science and Biomedicine, edited by Deisboeck and Kresh (February, 2006), Kluwer  [author's comments]
  26. B. Samuelsson and J.E.S. Socolar, Exhaustive percolation on random networks, Physical Review E, vol. 74 (2006), pp. 031912 [e036113]  [abs]
  27. D. V. Foster, S. A. Kauffman, and J. E. S. Socolar, Network growth models and genetic regulatory networks, Physical Review E, vol. 73 (2006), pp. 031912 [e031912]  [abs]
  28. B.P. Tighe, J.E.S. Socolar, D.G. Schaeffer, W.G. Mitchener, and M.L. Huber, Force distributions in a triangular lattice of rigid bars, Phys. Rev. E, vol. 72 (2005), pp. 031306  [abs]
  29. S. Dealy, S.A. Kauffman and J.E.S. Socolar, Modeling pathways of differentiation in genetic regulatory networks with Boolean networks, Complexity, vol. 11 no. 1 (2005), pp. 52-60  [abs]
  30. I. Harrington and J.E.S Socolar, Design and robustness of delayed feedback controllers for discrete systems, Phys. Rev. E, vol. 69 (2004), pp. 56207
  31. J.E.S. Socolar, Discrete models of force chain networks, Discrete and Continuous Dynamical Systems, vol. 3 (November, 2003), pp. 601-18 [0212162]
  32. M. Otto, J.-P. Bouchaud, P. Claudin, and J.E.S. Socolar, Anisotropy in granular media: classical elasticity and directed force chain network, Phys. Rev. E, vol. 67 no. 3 (March, 2003), pp. 031302 [0211015]
  33. P. Hoevel and J.E.S. Socolar, Stability domains for time-delay feedback control with latency, Physical Review E, vol. 68 (2003), pp. 036206 [0302033]
  34. J.E.S. Socolar and S.A. Kauffman, Scaling in ordered and critical random Boolean networks, Physical Review Letters, vol. 90 (February, 2003), pp. 068702 [0212306]
  35. J.E.S. Socolar, P. Claudin, and D.G. Schaeffer, Directed force chain models and stress response in static granular materials, European Physics Journal, vol. 7 (December, 2002), pp. 353-70 [0201242]
  36. O. Beck, A. Amann, E. Schoell, and J.E.S. Socolar, `Comparison of time-delayed feedback schemes for spatio-temporal control of chaos, Phys. Rev. E, vol. 66 (2002), pp. 016213
  37. J.E.S Socolar, Chaos, in Encyclopedia of Physical Science and Technology, 3rd Edition, edited by R. Meyers (2001), Academic Press (revision of article by R. Jensen.)
  38. I. Harrington and J.E.S. Socolar, Limitation on stabilizing plane waves via time-delay feedback, Phys. Rev. E, vol. 64 (2001), pp. 056206
  39. J.E.S. Socolar, S. Richards, and W. Wilson, Evolution in a spatially structured population subject to rare epidemics, Phys. Rev. E, vol. 63 (2001), pp. 041908
  40. M. Bleich and J.E.S. Socolar, Delay feedback control of a paced excitable oscillator, International Journal of Bifurcations and Chaos, vol. 10 (2000), pp. 603
  41. M. Sexton, J.E.S. Socolar, and D.G. Schaeffer, Force distribution in a scalar model for noncohesive granular material, Phys. Rev. E, vol. 60 (January, 1999), pp. 1999 [9810392]
  42. S. Richards, W. Wilson, and J.E.S. Socolar, Selection for intermediate mortality and reproduction rates in a spatially structured population, Proceedings of the Royal Society of London B, vol. 266 (1999)
  43. J.E.S. Socolar and D.J. Gauthier, Analysis and comparison of multiple-delay schemes for controlling unstable fixed points of discrete maps, Phys. Rev. E, vol. 57 (1998), pp. 6589
  44. D.A. Egolf and J.E.S. Socolar, Failure of linear control in noisy coupled map lattices, Phys. Rev. E, vol. 57 (1998), pp. 5271
  45. J.E.S. Socolar, Average stresses and force fluctuations in noncohesive granular materials, Phys. Rev. E, vol. 57 (1998), pp. 3204 [9710089]
  46. D.J. Gauthier and J.E.S Socolar, Comment on Dynamic Control of Cardiac Alternans, Physical Review Letters, vol. 79 (1997), pp. 4938
  47. M.E. Bleich, D. Hochheiser, J.V. Moloney, and J.E.S. Socolar, Controlling extended systems with spatially filtered, time-delayed feedback, Phys. Rev. E, vol. 55 (1997), pp. 2119
  48. D.W. Sukow, M.E. Bleich, D.J. Gauthier, and J.E.S. Socolar, Controlling chaos in a fast diode resonator using extended time-delay autosynchronization: experimental observations and theoretical analysis, Chaos, vol. 7 (1997), pp. 560
  49. M.E. Bleich and J.E.S. Socolar, Controlling spatiotemporal dynamics with time-delay feedback, Phys. Rev. E, vol. 54 (1996), pp. R17
  50. M.E. Bleich and J.E.S. Socolar, Stability of Periodic Orbits Controlled by Time-delay Feedback, Phys. Lett. A, vol. 210 (1995), pp. 87
  51. J.E.S. Socolar, D.W. Sukow, and D.J. Gauthier, Stabilizing Unstable Periodic Orbits in Fast Dynamical Systems, Phys. Rev. E, vol. 50 (1994), pp. 3245
  52. D.J. Gauthier, D.W. Sukow, H.M. Concannon, and J.E.S. Socolar, Stabilizing Unstable Periodic Orbits in a Fast Diode Resonator Using Continuous Time-delay Auto-synchronization, Phys. Rev. E, vol. 50 (1994), pp. 2343
  53. G. Grinstein, C. Jayaprakash and J.E.S. Socolar, Scale Invariance of Nonconserved Quantities in Driven Systems, Phys. Rev. E, vol. 48 (1993), pp. R643
  54. J.E.S. Socolar, G. Grinstein and C. Jayaprakash, On Self-organized Criticality in Nonconserving Systems, Phys. Rev. E, vol. 47 (1993), pp. 2366
  55. J. Krug, J.E.S. Socolar, and G. Grinstein, Surface Fluctuations and Criticality in a Class of 1D Sandpile Models, Phys. Rev. A (RC), vol. 46 (1992), pp. 4479
  56. J. Krug and J.E.S. Socolar, Comment on "Scalings of Growing Self-Organized Surfaces", Phys. Rev. Lett., vol. 68 (1992), pp. 722
  57. J.E.S. Socolar, Theory of Packings of Identical Hard Disks Generated by Ballistic Deposition, Europhys. Lett., vol. 18 (1992), pp. 39
  58. J.E.S. Socolar, Growth Rules for Quasicrystals, in Quasicrystals: The State of the Art, edited by D. DiVincenzo and P. Steinhardt (1991), World Scientific, Singapore
  59. J.E.S. Socolar, The Alternation Condition and 2D Quasicrystals, in Quasicrystals, Springer Series in Solid-State Sciences, edited by T. Fujiwara and T. Ogawa, vol. 93 (1990), Springer-Verlag, Berlin
  60. J.E.S. Socolar, Weak Matching Rules for Quasicrystals, Communications in Mathematical Physics, vol. 129 (1990), pp. 599-619
  61. J.E.S. Socolar, Locality Constraints and 2D Quasicrystals, in Quasicrystals - Adriatico Anniversary Research Conference, edited by M.V. Jaric and S. Lundqvist (1989), World Scientific, Singapore
  62. J.E.S. Socolar, Simple Octagonal and Dodecagonal Quasicrystals, Phys. Rev. B, vol. 39 (1989), pp. 10519-51
  63. G.Y. Onoda, P.J. Steinhardt, D.P. DiVincenzo, and J.E.S. Socolar, Reply to Comment on PRL, Phys. Rev. Lett., vol. 62 (1989), pp. 1210
  64. G.Y. Onoda, P.J. Steinhardt, D.P. DiVincenzo, and J.E.S. Socolar, Growing Perfect Quasicrystals, Phys. Rev. Lett., vol. 60 (1988), pp. 2653-56
  65. J.E.S. Socolar and D.C. Wright, Explanation of Peak Shapes Observed in Diffraction from Icosahedral Quasicrystals, Phys. Rev. Lett., vol. 59 (1987), pp. 221-224
  66. J.E.S. Socolar, Phason Strain in Quasicrystals, Journal de Physique, vol. C3 (1986), pp. 217-27
  67. T.C. Lubensky, J.E.S. Socolar, P.J. Steinhardt, P.A. Bancel, and P.A. Heiney, Distortion and Peak Broadening in Quasicrystal Diffraction Patterns, Phys. Rev. Lett., vol. 57 (1986), pp. 1440-43
  68. J.E.S. Socolar, T.C. Lubensky, and P.J. Steinhardt, Phonons, Phasons and Dislocations in Quasicrystals, Phys. Rev. B, vol. 34 (1986), pp. 3345-60
  69. J.E.S. Socolar and P.J. Steinhardt, Quasicrystals II: Unit Cell Structures, Phys. Rev. B, vol. 34 (1986), pp. 617-47
  70. J.E.S. Socolar, P.J. Steinhardt, and D. Levine, Quasicrystals with Arbitrary Orientational Symmetry, Rapid Communication, Phys. Rev. B, vol. 32 (1985), pp. 5547-50
  71. E.J. Mele and J. Socolar, Numerical Integration of the Time Evolution Operator: Excited-State Dynamics in Conjugated Molecules, Quantum Chemistry Symposium, International Journal of Quantum Chemistry, vol. 18 (1984), pp. 347-58
  72. J.P. Gollub, E.J. Romer and J.E. Socolar, Trajectory Divergence for Coupled Relaxation Oscillators: Measurements and Models, Journal of Statistical Physics, vol. 23 no. 3 (1980), pp. 321-333
  73. M. Sun, X. Cheng, and J. E. S. Socolar, Regulatory logic and pattern formation in the early sea urchin embryo, Journal of Theoretical Biology , ISSN 0022-5193 [S0022519314004354], [doi]

Papers Submitted

  1. M. Sun, X. Cheng, and J.E.S. Socolar, Regulatory Logic and Pattern Formation in the Early Sea Urchin Embryo, Journal of Theoretical Biology (October, 2013)  [abs]
  2. X. Cheng, J.E.S. Socolar, and D. McClay, Emergence of competence for cell fate reprogramming, Developmental Biology (2013)  [abs]