
Papers Published

 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]
.
 Marcoux, Catherine and Byington, Travis W. and Qian, Zongjin and Charbonneau, Patrick and Socolar, Joshua E. S., Emergence of limitperiodic order in tiling models,
Phys. Rev. E, vol. 90
(July, 2014),
pp. 012136, American Physical Society [PhysRevE.90.012136], [doi] .
 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. 147157 [S001216061400222X], [doi] [abs]
.
 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]
.
 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]
.
 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]
.
 T. Byington and J. E. S. Socolar, Hierarchical freezing in a lattice model,
Physical Review Letters, vol. 108
(January, 2012),
pp. 045701 [doi] [abs]
.
 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. 36823687 [doi] [abs]
.
 X. Gong and J. E. S. Socolar, Quantifying the complexity of random Boolean networks,
Physical Review E, vol. 85
(2012),
pp. 066107 [doi] [abs]
.
 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]
.
 Socolar, Joshua E. S. and Taylor, Joan M., An aperiodic hexagonal tile,
J. Comb. Theory Ser. A, vol. 118
(November, 2011),
pp. 22072231, Academic Press, Inc. [doi] .
 J. E. S. Socolar, Local action, global impact: Forcing nonperiodicity with a single structural unit,
Chaos, vol. 21
(2011),
pp. 041106 [doi] [abs]
.
 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. 495513 [doi] [abs]
.
 V. Sevim, X. Gong and J.E.S. Socolar, Reliability of transcriptional cycles and the yeast cellcycle oscillator,
PLoS Computational Biology, vol. 6 no. 7
(2010),
pp. e1000842 [doi] [abs]
.
 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]
.
 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]
.
 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 cellcycle transcription by coupled CDK and network oscillators,
Nature
(May, 2008) [doi] .
 A.S. Ribeiro, S.A. Kauffman, J. LloydPrice, 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]
.
 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]
.
 J.E.S. Socolar, Timedelay control for discrete maps,
in Handbook of Chaos Control, edited by E. Scholl and H. G. Schuster
(December, 2007), WileyVCH Verlag GmbH [html] [abs]
.
 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]
.
 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]
.
 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 timedelay autosynchronization,
Physical Review E, vol. 76
(2007),
pp. 041917(Selected for Virtual Journal of Biological Physics Research.)
[GetabsServlet] [abs]
.
 J.E.S. Socolar, The hexagonal parquet tiling: kisohedral monotiles with arbitrarily large k,
Mathematical Intelligencer, vol. 29
(2007),
pp. 3338 [pdf] [abs]
.
 J.E.S. Socolar, Nonlinear Dynamical Systems,
in Complex Systems Science and Biomedicine, edited by Deisboeck and Kresh
(February, 2006), Kluwer .
 B. Samuelsson and J.E.S. Socolar, Exhaustive percolation on random networks,
Physical Review E, vol. 74
(2006),
pp. 031912 [e036113] [abs]
.
 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]
.
 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]
.
 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. 5260 [abs]
.
 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 .
 J.E.S. Socolar, Discrete models of force chain networks,
Discrete and Continuous Dynamical Systems, vol. 3
(November, 2003),
pp. 60118 [0212162] .
 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] .
 P. Hoevel and J.E.S. Socolar, Stability domains for timedelay feedback control with latency,
Physical Review E, vol. 68
(March, 2003),
pp. 036206 [0302033] .
 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] .
 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. 35370 [0201242] .
 O. Beck, A. Amann, E. Schoell, and J.E.S. Socolar, `Comparison of timedelayed feedback schemes for spatiotemporal control of chaos,
Phys. Rev. E, vol. 66
(December, 2002),
pp. 016213 .
 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.)
.
 I. Harrington and J.E.S. Socolar, Limitation on stabilizing plane waves via timedelay feedback,
Phys. Rev. E, vol. 64
(2001),
pp. 056206 .
 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 .
 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 .
 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] .
 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) .
 J.E.S. Socolar and D.J. Gauthier, Analysis and comparison of multipledelay schemes for controlling unstable fixed points of discrete maps,
Phys. Rev. E, vol. 57
(1998),
pp. 6589 .
 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 .
 J.E.S. Socolar, Average stresses and force fluctuations in noncohesive granular materials,
Phys. Rev. E, vol. 57
(1998),
pp. 3204 [9710089] .
 D.J. Gauthier and J.E.S Socolar, Comment on Dynamic Control of Cardiac Alternans,
Physical Review Letters, vol. 79
(1997),
pp. 4938 .
 M.E. Bleich, D. Hochheiser, J.V. Moloney, and J.E.S. Socolar, Controlling extended systems with spatially filtered, timedelayed feedback,
Phys. Rev. E, vol. 55
(1997),
pp. 2119 .
 D.W. Sukow, M.E. Bleich, D.J. Gauthier, and J.E.S. Socolar, Controlling chaos in a fast diode resonator using extended timedelay autosynchronization: experimental observations and theoretical analysis,
Chaos, vol. 7
(1997),
pp. 560 .
 M.E. Bleich and J.E.S. Socolar, Controlling spatiotemporal dynamics with timedelay feedback,
Phys. Rev. E, vol. 54
(1996),
pp. R17 .
 M.E. Bleich and J.E.S. Socolar, Stability of Periodic Orbits Controlled by Timedelay Feedback,
Phys. Lett. A, vol. 210
(1995),
pp. 87 .
 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 .
 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 Timedelay Autosynchronization,
Phys. Rev. E, vol. 50
(1994),
pp. 2343 .
 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 .
 J.E.S. Socolar, G. Grinstein and C. Jayaprakash, On Selforganized Criticality in Nonconserving Systems,
Phys. Rev. E, vol. 47
(1993),
pp. 2366 .
 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 .
 J. Krug and J.E.S. Socolar, Comment on "Scalings of Growing SelfOrganized Surfaces",
Phys. Rev. Lett., vol. 68
(1992),
pp. 722 .
 J.E.S. Socolar, Theory of Packings of Identical Hard Disks Generated by Ballistic Deposition,
Europhys. Lett., vol. 18
(1992),
pp. 39 .
 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 .
 J.E.S. Socolar, The Alternation Condition and 2D Quasicrystals,
in Quasicrystals, Springer Series in SolidState Sciences, edited by T. Fujiwara and T. Ogawa, vol. 93
(1990), SpringerVerlag, Berlin .
 J.E.S. Socolar, Weak Matching Rules for Quasicrystals,
Communications in Mathematical Physics, vol. 129
(1990),
pp. 599619 .
 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 .
 J.E.S. Socolar, Simple Octagonal and Dodecagonal Quasicrystals,
Phys. Rev. B, vol. 39
(1989),
pp. 1051951 .
 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 .
 G.Y. Onoda, P.J. Steinhardt, D.P. DiVincenzo, and J.E.S. Socolar, Growing Perfect Quasicrystals,
Phys. Rev. Lett., vol. 60
(1988),
pp. 265356 .
 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. 221224 .
 J.E.S. Socolar, Phason Strain in Quasicrystals,
Journal de Physique, vol. C3
(1986),
pp. 21727 .
 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. 144043 .
 J.E.S. Socolar, T.C. Lubensky, and P.J. Steinhardt, Phonons, Phasons and Dislocations in Quasicrystals,
Phys. Rev. B, vol. 34
(1986),
pp. 334560 .
 J.E.S. Socolar and P.J. Steinhardt, Quasicrystals II: Unit Cell Structures,
Phys. Rev. B, vol. 34
(1986),
pp. 61747 .
 J.E.S. Socolar, P.J. Steinhardt, and D. Levine, Quasicrystals with Arbitrary Orientational Symmetry, Rapid Communication,
Phys. Rev. B, vol. 32
(1985),
pp. 554750 .
 E.J. Mele and J. Socolar, Numerical Integration of the Time Evolution Operator: ExcitedState Dynamics in Conjugated Molecules, Quantum Chemistry Symposium,
International Journal of Quantum Chemistry, vol. 18
(1984),
pp. 34758 .
 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. 321333 .
 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

 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]
.
 X. Cheng, J.E.S. Socolar, and D. McClay, Emergence of competence for cell fate reprogramming,
Developmental Biology
(2013) [abs]
.