Publications
2026
Scholarly publications
Romeijnders, M., van Boven, M., & Panja, D. (2026). Risk mapping novel respiratory pathogens with large-scale dynamic contact networks. Communications Medicine, Article 229. [DOI]
2025
Scholarly publications
Morán, J., Pijpers, F. P., Weitzel, U., Jean-Philippe, B., & Panja, D. (2025). Critical fragility in sociotechnical systems. PNAS, 122(9), Article e2415139122. [DOI] [Repository]
2024
Scholarly publications
Liu, Z., Panja, D., & Barkema, G. T. (2024). Structural dynamics of a model of amorphous silicon. Physica A: Statistical Mechanics and its Applications, 650, Article 129978. [DOI] [Repository]
Morán, J., Romeijnders, M., Pierre, L. D., Pijpers, F., Weitzel, U., Panja, D., & Bouchaud, J.-P. (2024). Timeliness criticality in complex systems. Nature Physics, 20(8), 1352–1358. [DOI] [Repository]
2023
Scholarly publications
Liu, Z., Panja, D., & Barkema, G. (2023). Domain growth in polycrystalline graphene. Nanomaterials, 13(24), 1-13. Article 3127. [DOI] [Repository]
Staniczenko, P. P. A., & Panja, D. (2023). Temporal origin of nestedness in interaction networks. PNAS Nexus, 2(12), 1-9. Article pgad412. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
Dekker, M. M., & Panja, D. (2021). Cascading dominates large-scale disruptions in transport over complex networks. PLoS One, 16(1), Article e0246077. [DOI] [Repository]
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. [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
Dekker, M. M., & Panja, D. (2019). A reduced phase-space approach to analyse railway dynamics. In IFAC-PapersOnLine (Vol. 52, pp. 1-6) [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
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 [Repository]
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. [DOI] [Repository]
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. [DOI] [Repository]
2014
Scholarly publications
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. [DOI]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [DOI]
Molineux, I. J., & Panja, D. (2013). Popping the cork: mechanisms of phage genome ejection. Nature Reviews. Microbiology, 11, 194-204. [DOI]
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. [DOI] [Repository]
2011
Scholarly publications
Panja, D. (2011). Probabilistic Phase Space Trajectory Description for Anomalous Polymer Dynamics. Journal of physics. Condensed matter, 23(10), Article 105103. [DOI]
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. [DOI] [Repository]
2010
Scholarly publications
Panja, D. (2010). Generalized Langevin Equation Formulation for Anomalous Polymer Dynamics. Journal of Statistical Mechanics: Theory and Experiment, 2010, Article L02001. [DOI]
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. [DOI]
Panja, D., & Molineux, I. J. (2010). Dynamics of Bacteriophage Genome Ejection In Vitro and In Vivo. Physical Biology, 7(4), Article 045006. [DOI]
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. [DOI] [Repository]
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. [DOI] [Repository]
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. [Repository]
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. [DOI]
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. [DOI]
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. [DOI]
Panja, D., & Ostojic, S. (2006). Elasticity from the Force Network Ensemble in Granular Media. Physical Review Letters, 97(20), Article 208001. [DOI]
Wolterink, JK., Barkema, GT., & Panja, D. (2006). Passage times for unbiased polymer translocation through a narrow pore. Physical Review Letters, 96(20), Article 208301. [DOI]
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. [DOI]
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. [DOI]
2004
Scholarly publications
Panja, D. (2004). Effects of Fluctuations on Propagating Fronts. Physics Reports, 393, 87-174. [DOI]
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. [DOI]
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. [DOI]
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. [DOI]
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. [DOI]
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). [DOI]
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. [DOI]
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. [DOI]
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). [DOI]
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. [DOI]
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). [DOI]
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. [Repository]
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. [DOI] [Repository]