Publications of Joshua E. S. Socolar    :recent first  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) [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. [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, 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] .
  25. J.E.S. Socolar, Nonlinear Dynamical Systems, in Complex Systems Science and Biomedicine, edited by Deisboeck and Kresh (February, 2006), Kluwer .
  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 (March, 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 (December, 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 [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] .