Publications
2023
Scholarly publications
Liu, Z., Panja, D., & Barkema, G. (2023). Domain growth in polycrystalline graphene. Nanomaterials, 13(24), Article 3127. https://doi.org/10.3390/nano13243127
Staniczenko, P. P. A., & Panja, D. (2023). Temporal origin of nestedness in interaction networks. PNAS Nexus, 2(12), 1-9. Article pgad412. https://doi.org/10.1093/pnasnexus/pgad412
Dekker, M. M., Coffeng, L. E., Pijpers, F. P., Panja, D., & de Vlas, S. J. (2023). Reducing societal impacts of SARS-CoV-2 interventions through subnational implementation. eLife, 12, Article e80819. https://doi.org/10.7554/eLife.80819
2022
Scholarly publications
Ou, J., Buskens, V., van de Rijt, A., & Panja, D. (2022). Influence maximization under limited network information: Seeding high-degree neighbors. Journal of Physics: Complexity, 3(4), Article 045004. https://doi.org/10.1088/2632-072X/ac9444
Dekker, M., Schram, R., Ou, J., & Panja, D. (2022). Hidden dependence of spreading vulnerability on topological complexity. Physical Review. E, Statistical, nonlinear, and soft matter physics, 105(5), 1-13. Article 054301. https://doi.org/10.1103/PhysRevE.105.054301
Liu, Z., Panja, D., & Barkema, G. (2022). Structural dynamics of polycrystalline graphene. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 105(4), 1-7. Article 044116. https://doi.org/10.1103/PhysRevE.105.044116
Dekker, M., Blanken, T., Dablander, F., Ou, J., Borsboom, D., & Panja, D. (2022). Quantifying agent impacts on contact sequences in social interactions. Scientific Reports, 12(1), Article 3483. https://doi.org/10.1038/s41598-022-07384-0
Jong, K. D., Panja, D., Karssenberg, D., & Kreveld, M. V. (2022). Scalability and composability of flow accumulation algorithms based on asynchronous many-tasks. Computers & Geosciences, 162, 1-12. Article 105083. https://doi.org/10.1016/j.cageo.2022.105083
Dekker, M. M., van Lieshout, R. N., Ball, R. C., Bouman, P. M., Dekker, S. C., Dijkstra, H. A., Goverde, R. M. P., Huisman, D., Panja, D., Schaafsma, A. A. M., & van den Akker, J. M. (2022). A next step in disruption management: combining operations research and complexity science. Public Transport, 14(1), 5-26. https://doi.org/10.1007/s12469-021-00261-5
2021
Scholarly publications
Petersik, P. J., Panja, D., & Dijkstra, H. (2021). One-parametric bifurcation analysis of data-driven car-following models. Physica D: Nonlinear Phenomena, 427, Article 133016. https://doi.org/10.1016/j.physd.2021.133016
Dekker, M., Franca, A., Panja, D., & Cohen, M. (2021). Characterizing neural phase-space trajectories via Principal Louvain Clustering. Journal of Neuroscience Methods, 362, 1-10. Article 109313. https://doi.org/10.1016/j.jneumeth.2021.109313
Jong, K. D., Kreveld, M. V., Panja, D., Schmitz, O., & Karssenberg, D. (2021). Global scale hydrological modelling at 100 m, 1 h resolution, in Python. https://doi.org/10.5194/egusphere-egu21-7154
de Jong, K., Panja, D., van Kreveld, M., & Karssenberg, D. (2021). An environmental modelling framework based on asynchronous many-tasks: Scalability and usability. Environmental Modelling and Software, 139, Article 104998. https://doi.org/10.1016/j.envsoft.2021.104998
Dekker, M. M., & Panja, D. (2021). Cascading dominates large-scale disruptions in transport over complex networks. PLoS One, 16(1), Article e0246077. https://doi.org/10.1371/journal.pone.0246077
Popularising publications
Panja, D., & Dekker, M. M. (2021). Het modelleren van infectieziekten vanuit het perspectief van statistische fysica. Nederlands Tijdschrift voor Natuurkunde, 87(1), 18-22.
https://dspace.library.uu.nl/bitstream/handle/1874/411082/Het_modelleren_van_infectieziekten_def.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/411082/Het_modelleren_van_infectieziekten_def.pdf?sequence=1
2020
Scholarly publications
Jong, K. D., Karssenberg, D., Panja, D., & Kreveld, M. V. (2020, Mar 23). Towards a scalable framework for earth science simulation models, using asynchronous many-tasks. EGU. https://doi.org/10.5194/egusphere-egu2020-18749
Zhong, W., Barkema, G. T., & Panja, D. (2020). Super slowing down in the bond-diluted Ising model. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 102(2), Article 022132. https://doi.org/10.1103/PhysRevE.102.022132
2019
Scholarly publications
Zhong, W., Panja, D., & Barkema, G. T. (2019). Approximate dynamical eigenmodes of the Ising model with local spin-exchange moves. Physical Review. E, Statistical, nonlinear, and soft matter physics, 100(1), Article 012132. https://doi.org/10.1103/PhysRevE.100.012132
Dekker, M. M., & Panja, D. (2019). A reduced phase-space approach to analyse railway dynamics. In IFAC-PapersOnLine (Vol. 52, pp. 1-6) https://doi.org/10.1016/j.ifacol.2019.06.001
Dekker, M. M., Panja, D., Dijkstra, H., & Dekker, S. C. (2019). Predicting transitions across macroscopic states for railway systems. PLoS One, 14(6), Article e0217710. https://doi.org/10.1371/journal.pone.0217710
2018
Scholarly publications
Panja, D., Barkema, G. T., Zhong, W., & Ball, R. C. (2018). Critical dynamical exponent of the two-dimensional scalar ϕ4 model with local moves. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 98(6), Article 062128. https://doi.org/10.1103/PhysRevE.98.062128
Panja, D., Barkema, G. T., Zhong, W., & Ball, R. (2018). Generalized Langevin equation formulation for anomalous diffusion in the Ising model at the critical temperature. Physical Review. E, Statistical, nonlinear, and soft matter physics, 98(1), Article 012124. https://doi.org/10.1103/PhysRevE.98.012124
Dekker, M. M., van Lieshout, R. N., Ball, R. C., Bouman, P. M., Dekker, S. C., Dijkstra, H. A., Goverde, R. M. P., Huisman, D., Panja, D., Schaafsma, A. A. M., & van den Akker, J. M. (2018). A Next Step in Disruption Management: Combining Operations Research and Complexity Science. In Conference on Advanced Systems in Public Transport (CASPT) 2018
https://dspace.library.uu.nl/bitstream/handle/1874/372764/dekker2.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/372764/dekker2.pdf?sequence=1
2015
Scholarly publications
Panja, D., Barkema, G. T., & Ball, R. C. (2015). Complex Interactions with the Surroundings Dictate a Tagged Chain's Dynamics in Unentangled Polymer Melts. Macromolecules, 48(5), 1442-1453. https://doi.org/10.1021/ma502523p
Panja, D., Barkema, G. T., & van Leeuwen, J. M. J. (2015). Efficient simulation of semiflexible polymers. Physical Review. E, Statistical, nonlinear, and soft matter physics, 92(3), Article 032603. https://doi.org/10.1103/PhysRevE.92.032603
2014
Scholarly publications
Barkema, G. T., Panja, D., & van Leeuwen, J. M. J. (2014). Semiflexible polymer dynamics with a bead-spring model. Journal of Statistical Mechanics: Theory and Experiment, 2014, Article P11008. https://doi.org/10.1088/1742-5468/2014/11/P11008, https://doi.org/10.1088/1742-5468/2014/11/P11008
Furtado, F., Damron, J., Trutschel, M-L., Franz, C., Schröter, K., Ball, R. C., Saalwächter, K., & Panja, D. (2014). NMR Observations of Entangled Polymer Dynamics: Focus on Tagged Chain Rotational Dynamics and Confirmation from a Simulation Model. Macromolecules, 47, 256-268. https://doi.org/10.1021/ma4021938
2013
Scholarly publications
Keesman, R., Barkema, G. T., & Panja, D. (2013). Dynamical eigenmodes of star and tadpole polymers. Journal of Statistical Mechanics: Theory and Experiment, 2013, P02021/1-P02021/21. Article P02021. https://doi.org/10.1088/1742-5468/2013/02/P02021
Keesman, R., Barkema, G. T., & Panja, D. (2013). Dynamical eigenmodes of a polymerized membrane. Journal of Statistical Mechanics: Theory and Experiment, 2013, P04009/1-P04009/17. Article P04009. https://doi.org/10.1088/1742-5468/2013/04/P04009
Panja, D., Barkema, G. T., & Kolomeisky, A. B. (2013). Through the eye of the needle: recent advances in understanding biopolymer translocation. Journal of physics. Condensed matter, 25(41), 413101 /1-413101 /15. Article 413101. https://doi.org/10.1088/0953-8984/25/41/413101
Molineux, I. J., & Panja, D. (2013). Popping the cork: mechanisms of phage genome ejection. Nature Reviews. Microbiology, 11, 194-204. https://doi.org/10.1038/nrmicro2988
Lemay, S. G., Panja, D., & Molineux, I. J. (2013). Role of osmotic and hydrostatic pressures in bacteriophage genome ejection. Physical Review. E, Statistical, nonlinear, and soft matter physics, 87(2), 022714/1-022714/5. Article 022714. https://doi.org/10.1103/PhysRevE.87.022714
2011
Scholarly publications
Panja, D. (2011). Probabilistic Phase Space Trajectory Description for Anomalous Polymer Dynamics. Journal of physics. Condensed matter, 23(10), Article 105103. https://doi.org/10.1088/0953-8984/23/10/105103
Barkema, G. T., Panja, D., & van Leeuwen, J. M. J. (2011). Structural modes of a polymer in the repton model. Journal of Chemical Physics, 134(15), Article 154901. https://doi.org/10.1063/1.3580287, https://doi.org/10.1063/1.3580287
Hatlo, M. M., Panja, D., & van Roij, R. H. H. G. (2011). Translocation of DNA Molecules through Nanopores with Salt Gradients: The Role of Osmotic Flow. Physical Review Letters, 107(6), 068101. https://doi.org/10.1103/PhysRevLett.107.068101
2010
Scholarly publications
Panja, D. (2010). Generalized Langevin Equation Formulation for Anomalous Polymer Dynamics. Journal of Statistical Mechanics: Theory and Experiment, 2010, Article L02001. https://doi.org/10.1088/1742-5468/2010/02/L02001
Panja, D. (2010). Anomalous Polymer Dynamics Is Non-Markovian: Memory Effects and The Generalized Langevin Equation Formulation. Journal of Statistical Mechanics: Theory and Experiment, 2010, Article P06011. https://doi.org/10.1088/1742-5468/2010/06/P06011
Panja, D., & Molineux, I. J. (2010). Dynamics of Bacteriophage Genome Ejection In Vitro and In Vivo. Physical Biology, 7(4), Article 045006. https://doi.org/10.1088/1478-3975/7/4/045006
Panja, D., & Barkema, G. T. (2010). Simulations of two-dimensional unbiased polymer translocation using the bond fluctuation model. Journal of Chemical Physics, 132(1), 014902/1-014902/10. https://doi.org/10.1063/1.3281641
https://dspace.library.uu.nl/bitstream/handle/1874/199349/JCP.132.014902.2010.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/199349/JCP.132.014902.2010.pdf?sequence=1
Baiesi, M., Barkema, G. T., Carlon, E., & Panja, D. (2010). Unwinding dynamics of double-stranded polymers. Journal of Chemical Physics, 133(15), 154907/1-154907/4. https://doi.org/10.1063/1.3505551
https://dspace.library.uu.nl/bitstream/handle/1874/199341/jcp10-unwind.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/199341/jcp10-unwind.pdf?sequence=1
2009
Scholarly publications
Panja, D., Barkema, G. T., & Kolomeisky, A. B. (2009). Non-equilibrium dynamics of single polymer adsorption to solid surfaces. Journal of Physics: Condensed Matter, 21(24), 242101/1-242101/6.
Panja, D., & Barkema, G. T. (2009). Rouse modes of self-avoiding flexible polymers. Journal of Chemical Physics, 131(15), 154903/1-154903/7.
https://dspace.library.uu.nl/bitstream/handle/1874/42607/GetPDFServlet.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/42607/GetPDFServlet.pdf?sequence=1
Vocks, H., Panja, D., & Barkema, G. T. (2009). Amplitude and frequency spectra of thermal fluctuations of a translocating RNA molecule. Journal of Physics: Condensed Matter, 21(37), 375105/-375105/7.
Panja, D., Barkema, G. T., & Ball, R. C. (2009). Reply to the comment on ‘Anomalous dynamics of unbiased polymer translocation through a narrow pore’ and other recent papers by D Panja, G Barkema and R Ball. Journal of Physics: Condensed Matter, 21, 098002/1-098002/3.
2008
Scholarly publications
Panja, D., Barkema, G. T., & Ball, R. C. (2008). Polymer translocation out of planar confinements. Journal of physics. Condensed matter, 20, 075101.
Panja, D., & Barkema, G. T. (2008). Passage Times for Polymer Translocation Pulled through a Narrow Pore. Biophysical Journal, 94(5), 1630-1637. https://doi.org/10.1529/biophysj.107.116434
Vocks, H., Panja, D., Barkema, G. T., & Ball, R. C. (2008). Pore-blockade times for field-driven polymer translocation. Journal of physics. Condensed matter, 20, 095224.
2007
Scholarly publications
Panja, D., & Selten, F. M. (2007). Extreme Associated Functions: Optimally Linking Local Extremes to Large-scale Atmospheric Circulation Structures. Atmospheric Chemistry and Physics Discussions, 7, 14433-14460. https://doi.org/10.5194/acpd-7-14433-2007
2006
Scholarly publications
Panja, D., van Beijeren, H., & Kruis, H. V. (2006). Systematic Density Expansion of the Lyapunov Exponents for a Two-dimensional Random Lorentz Gas. Journal of Statistical Physics, 124(2-4), 823-842. https://doi.org/10.1007/s10955-005-9001-y
Panja, D., & Ostojic, S. (2006). Elasticity from the Force Network Ensemble in Granular Media. Physical Review Letters, 97(20), Article 208001. https://doi.org/10.1103/PhysRevLett.97.208001
Wolterink, JK., Barkema, GT., & Panja, D. (2006). Passage times for unbiased polymer translocation through a narrow pore. Physical Review Letters, 96(20), Article 208301. https://doi.org/10.1103/PhysRevLett.96.208301
2005
Scholarly publications
Panja, D., & Ostojic, S. (2005). Response of a Hexagonal Granular Packing under a Localized Overload: Effects of Pressure. In Proceedings Powders and Grains 2005 (pp. 81-85). A.A. Balkema.
Panja, D., & Ostojic, S. (2005). Response of a Hexagonal Granular Packing under a Localized External Force. Europhysics Letters, 71(1), 70-76. https://doi.org/10.1209/epl/i2004-10530-9
Panja, D., & Ostojic, S. (2005). Response of a Hexagonal Granular Packing under a Localized External Force: Exact Solutions. Journal of Statistical Mechanics: Theory and Experiment, 2005, Article P01011. https://doi.org/10.1088/1742-5468/2005/01/P01011
2004
Scholarly publications
Panja, D. (2004). Effects of Fluctuations on Propagating Fronts. Physics Reports, 393, 87-174. https://doi.org/:10.1016/j.physrep.2003.12.001
Panja, D., Ostojic, S., & Nienhuis, B. (2004). Clustering in a One-dimensional Inelastic Lattice Gas. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 69(4), Article 041301. https://doi.org/10.1103/PhysRevE.69.041301
Panja, D. (2004). Fluctuating Fronts as Correlated Extreme Value Problems: An Example of Gaussian Statistics. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 70(3), Article 036101. https://doi.org/10.1103/PhysRevE.70.036101
2003
Scholarly publications
Panja, D. (2003). Surprising Aspects of Fluctuating ``Pulled'' Fronts. In Proceedings for 3rd International Conference Unsolved Problems of Noise (UPoN) and fluctuations in physics, biology and high technology 2002 (1 ed., Vol. 665, pp. 539-550). American Institute of Physics. https://doi.org/10.1063/1.1584931
Panja, D., Tripathy, G., & van Saarloos, W. (2003). Front Propagation and Diffusion in the A <--> A + A Hard-core Reaction on a Chain. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 67( 046206), Article 046206. https://doi.org/10.1103/PhysRevE.67.046206
Panja, D. (2003). Asymptotic Scaling of the Diffusion Coefficient of Fluctuating ``Pulled'' Fronts. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 68(6), Article 065202(R). https://doi.org/10.1103/PhysRevE.68.065202
2002
Scholarly publications
Panja, D. (2002). An Elementary Proof of Lyapunov Exponent Pairing for Hard-Sphere Systems at Constant Kinetic Energy. Journal of Statistical Physics, 109(3-4), 705-727.
Panja, D., & van Saarloos, W. (2002). Fluctuating ``Pulled'' Fronts: the Origin and the Effects of a Finite Particle Cutoff. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 66(3), Article 036206. https://doi.org/10.1103/PhysRevE.66.036206
Panja, D., & van Saarloos, W. (2002). The Weakly Pushed Nature of ``Pulled'' Fronts with a Cutoff. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 65(5), Article 057202. https://doi.org/10.1103/PhysRevE.65.057202
Panja, D., & van Zon, R. (2002). Lyapunov Exponent Pairing for a Thermostatted Hard-Sphere Gas under Shear in the Thermodynamic Limit. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 65(6), Article 060102(R). https://doi.org/10.1103/PhysRevE.65.060102
Panja, D., & van Zon, R. (2002). Pairing of Lyapunov Exponents for a Hard-Sphere Gas under Shear in the Thermodynamic Limit. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 66(2), Article 021101. https://doi.org/10.1103/PhysRevE.66.021101
Panja, D., & van Saarloos, W. (2002). Fronts with a Growth Cutoff but Speed Higher than the Linear Spreading Speed. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 66(1), Article 015206(R). https://doi.org/10.1103/PhysRevE.66.015206
2001
Scholarly publications
Dellago, C., van Beijeren, H., Panja, D., & Dorfman, J. R. (2001). Field dependent collision frequency of the two-dimensional driven random Lorentz gas. Physical Review. E, Statistical, nonlinear, and soft matter physics, 64, 036217.
https://dspace.library.uu.nl/bitstream/handle/1874/15223/dellago_01_field-dependent_collision.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/15223/dellago_01_field-dependent_collision.pdf?sequence=1
2000
Scholarly publications
Panja, D., van Beijeren, H., & Dorfman, J. R. (2000). Long-time-tail effects on Lyapunov exponents of a random two-dimensional field-driven Lorentz gas. Journal of Statistical Physics, 100(1-2), 279-311. https://doi.org/10.1023/A%3A1018604115227
https://dspace.library.uu.nl/bitstream/handle/1874/37438/0002132v1.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/37438/0002132v1.pdf?sequence=1