Grima Group

 

 

 

 

 

 

66. Smith S and Grima R. 2016. Fast simulation of Brownian dynamics in a crowded environment.

(submitted)

 

65. Smith S and Grima R. 2016. An exact solution to Brownian dynamics of a reversible bimolecular reaction. (submitted)

 

64. Grima R and Leier A. 2016. Exact product formation rates for stochastic enzyme kinetics. (submitted)

 

63. Smith S and Grima R. 2016. Bounds on intrinsic biochemical noise in spatial systems. (submitted)

 

62. Frohlich F, Thomas P, Kazeroonian A, Theis FJ, * Grima R and * Hasenauer J.. 2016. Inference for stochastic chemical kinetics using moment equations and system size expansion. PLoS Computational Biology 12(7):e1005030 PDF (* Joint corresponding authors)

 

61. Singh A and Grima R. 2016. The Linear-Noise Approximation and moment-closure approximations for stochastic chemical kinetics. (accepted for publication as a chapter in a book by MIT Press)

 

60. Voliotis M, Thomas P, Bowsher C and Grima R. 2016. The extra reaction algorithm for stochastic simulation of networks in fluctuating environments (accepted for publication as a chapter in a book by MIT Press)

 

59. Andreychenko A, Bortolussi L, Grima R, Thomas P and Wolf V. 2016. Distribution approximations for the chemical master equation: comparison of the method of moments and the system size expansion. (accepted for publication as a chapter in Springer book series) http://arxiv.org/abs/1509.09104

 

58. Voliotis M, Thomas P, * Grima R and * Bowsher C. 2016. Stochastic simulation of biomolecular networks in dynamic environments, PLoS Computational Biology 12(6):e1004923 PDF (* Joint corresponding authors)

 

57. Schnoerr D, Grima R and Sanguinetti G. 2016. Cox-process representation and inference for stochastic reaction-diffusion processes. Nature Communications 7:11729 PDF

 

56. Smith S, Cianci C and Grima R. 2016. Analytical approximations for spatial stochastic gene expression in single cells and tissues. J. R. Soc. Interface 13:20151051 PDF

 

55. Smith S and Grima R. 2016. Breakdown of the reaction-diffusion master equation with nonelementary rates. Physical Review E 93:052135 PDF

 

54. Cianci C, Smith S, and Grima R. 2016. Molecular finite-size effects in stochastic models of equilibrium chemical systems. Journal of Chemical Physics 144:084101 PDF

 

53. Smith S, Cianci C and Grima R. 2015. Model reduction for stochastic chemical systems with abundant species. Journal of Chemical Physics 143:214105 PDF

 

52. Schnoerr D, Sanguinetti G and Grima R. 2015. Comparison of different moment-closure approximations for stochastic chemical kinetics. Journal of Chemical Physics 143:185101 PDF

 

51. Grima R. 2015. The linear-noise approximation and the chemical master equation exactly agree up to second-order moments for a class of chemical systems. Physical Review E 92: 042124 arxiv.org/pdf/1509.00612v1.pdf

 

50. Thomas P and Grima R. 2015. Approximate distributions of the Master equation, Physical Review E 92:012120 PDF

 

49. Duncan A, Liao S, Vejchodsky T, Erban R and Grima R. 2015. Noise-induced multistability in chemical systems: Discrete vs Continuum modeling, Physical Review E 91:042111 PDF

 

48. Thomas P, Fleck C, Grima R and Popovic N. 2014. System size expansion of the master equation using Feynman rules and diagrams, Journal of Physics A: Mathematical and Theoretical 47:455007 PDF

 

47. Johansson H, Jones H. J, Foreman J, Hemsted J. R., Stewart K, Grima R and Halliday K. 2014. Arabidopsis cell expansion is controlled by a photothermal switch, Nature Communications 5:4848 PDF

 

46. Schnoerr D, Sanguinetti G and Grima R. 2014. Validity conditions and stability of moment closure approximations for stochastic chemical kinetics. Journal of Chemical Physics 141:084103 PDF

 

45. Schnoerr D, Sanguinetti G and Grima R. 2014. The complex chemical Langevin equation. Journal of Chemical Physics 141:024103 PDF

 

44. Middleton A, Fleck C and Grima R. 2014. A continuum approximation to an off-lattice, individual-cell based model of cell migration and adhesion. Journal of Theoretical Biology 359: 220 PDF (Recommended reading by Faculty of 1000)

 

43. Thomas P, Popovic N and Grima R. 2014. Phenotypic switching in gene regulatory networks. Proceedings of the National Academy of Sciences of the United States of America 111: 6994 PDF Supplementary PDF

 

42. Chew Y.H, Smith R.W, Jones H. J, Seaton D., Grima R and Halliday K. 2014. Mathematical models light up plant signaling. Plant Cell 26: 5 PDF

 

41. Grima R. 2014. Anomalous fluctuation scaling laws in stochastic enzyme kinetics: increase of noise strength with the mean concentration. Physical Review E. 89: 012710 PDF

 

40. Grima R, Nils W and Schnell S. 2014. Single molecule enzymology à la Michaelis-Menten. Febs Journal 281: 518 PDF

 

39. Toner DLK, and Grima R. 2013. Effects of bursty protein production on the noisy oscillatory properties of downstream pathways. Scientific Reports 3:2438 PDF

 

38. Thomas P, Straube A. V., Timmer J., Fleck C., Grima R. 2013. Signatures of nonlinearity in single cell noise-induced oscillations. Journal of Theoretical Biology 335:222 PDF

 

37. Basile R., Grima R. and Popovic N. 2013. A graph-based approach for the approximate solution of the chemical master equation. Bulletin of Mathematical Biology 75:1653 PDF

 

36. Thomas P, Matuschek H, Grima R. 2013. How reliable is the linear noise approximation of gene regulatory networks? BMC Genomics 14(Suppl 4):S5 PDF

 

35. Toner DLK, and Grima R. 2013. Molecular noise induces concentration oscillations in chemical systems with stable node steady states. Journal of Chemical Physics 138:055101 PDF

 

34. Grima R, and Kim J. 2012. Editorial: Modelling noise in biochemical reaction networks. 2012 IET Systems Biology 6:101 PDF

 

33. Ramaswamy R, Gonzalez-Segredo N, Sbalzarini IF, Grima R. 2012. Discreteness-induced concentration inversion in mesoscopic chemical systems. Nature Communications. 3:779. PDF Supplementary PDF


32. Thomas P, Matuschek H, Grima R. 2012. Computation of biochemical pathway fluctuations beyond the linear noise approximation using iNA. IEEE International Conference on Bioinformatics and Biomedicine. 10.1109/BIBM.2012.6392668 PDF


31. Thomas P, Matuschek H, Grima R. 2012. intrinsic Noise Analyzer: a software package for the exploration of stochastic biochemical kinetics using the system-size expansion. PLoS ONE. 7(6):e38518. PDF


30. Thomas P, Grima R, Straube AV. 2012. Rigorous elimination of fast stochastic variables from the linear-noise approximation using projection operators. Physical Review E. 86: 041110 PDF


29. Thomas P, Straube AV, Grima R. 2012. The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions. BMC Systems Biology. 6:39. PDF (Editor's Pick for 2012)


28. Wenden B, Toner DLK, Hodge SK, Grima R, Millar AJ. 2012. Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Proceedings of the National Academy of Sciences of the United States of America. 109:6757. PDF (Selected as "Must Read" by Faculty of 1000)


27. Grima R, Schmidt D, Newman TJ. 2012. Steady-state fluctuations of a genetic feedback loop: an exact solution. Journal of Chemical Physics. 137:035104. PDF


26. Grima R. 2012. A study of the accuracy of moment-closure approximations for stochastic chemical kinetics. Journal of Chemical Physics . 136:154105. PDF


25. Grima R. 2011. Construction and accuracy of partial differential equation approximations to the chemical master equation. Physical Review E. 84:056109. PDF


24. Thomas P, Straube AV, Grima R. 2011. Limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks. Journal of Chemical Physics. 135:181103. PDF Supplementary PDF


23. Grima R, Thomas P, Straube AV. 2011. How accurate are the chemical Langevin and Fokker-Planck equations? Journal of Chemical Physics. 135:084103. PDF (Editor's Choice for 2011)


22. Grima R, Yaliraki SN, Barahona M. 2010. Crowding-induced anisotropic transport modulates reaction kinetics in nanoscale porous media. Journal of Physical Chemistry B. 114:5380. PDF


21. Grima R. 2010. An effective rate equation approach to reaction kinetics in small volumes: theory and application to biochemical reactions in nonequilibrium steady-state conditions. Journal of Chemical Physics. 133:035101 PDF

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20. Grima R. 2010. Intrinsic biochemical noise in crowded intracellular conditions. Journal of Chemical Physics. 132:185102. PDF


19. Le Bihan T, Grima R, Martin S, Forster T, Le Bihan Y. 2010. Quantitative analysis of low abundance peptides in HeLa cell cytoplasm by targeted LC-MS and stable isotope dilution: Emphasizing the distinction between peptide detection and peptide identification. Rapid Communications in Mass Spectrometry. 24:1093. PDF


18. Thomas P, Straube AV, Grima R. 2010. Stochastic theory of large-scale enzyme-reaction networks: finite-copy number corrections to rate equation models. Journal of Chemical Physics. 133:195101. PDF


17. Grima R. 2009. Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments. BMC Systems Biology. 3:101. PDF


16. Grima R. 2009. Noise-induced breakdown of the Michaelis-Menten reaction in steady-state conditions. Physical Review Letters. 102:218103. PDF


15. Grima R, Schnell S. 2008. Modelling reaction kinetics inside cells. Essays in Biochemistry. 45:41. PDF


14. Grima R. 2008. Multiscale modeling of biological pattern formation. Current Topics in Developmental Biology. 81:435. PDF


13. Grima R, Yaliraki SN. 2007. Brownian motion of an asymmetrical particle in a potential field. Journal of Chemical Physics. 127:084511. PDF


12. Grima R, Schnell S. 2007. Can differential adhesion drive somite formation? Developmental Biology. 307:248. PDF


11. Grima R. 2007. Directed cell migration in the presence of obstacles. Theoretical Biology and Medical Modelling. 4:2. PDF


10. Grima R, DeGraffenreid J, Venables JA. 2007. Mean-field theory of nucleation on strained surfaces. Physical Review B. 76:233405. PDF


9. Grima R, Schnell S. 2007. A mesoscopic simulation approach for modelling intracellular reactions. Journal of Statistical Physics. 128:139. PDF

 

8. Schnell S, Grima R, Maini PK. 2007. Multiscale modelling in biology. American Scientist. 95:134. PDF


7. Grima R, Schnell S. 2006. How reaction kinetics with time-dependent rate coefficients differ from generalized mass action. ChemPhysChem. 7:1422. PDF


6. Grima R. 2006. Phase transitions and superuniversality in the dynamics of a self-driven particle. Physical Review E. 74:011125. PDF


5. Grima R, Schnell S. 2006. A systematic investigation of the rate laws valid in intracellular environments. Biophysical Chemistry. 124:1. PDF

 

4. Grima R. 2005. Strong coupling dynamics of a multi-cellular chemotactic system. Physical Review Letters. 95:128103. PDF


3. Grima R, Newman TJ. 2004. Accurate discretization of advection-diffusion equations. Physical Review E. 70:036703. PDF


2. Newman TJ, Grima R. 2004. Many-body theory of chemotactic interactions. Physical Review E. 70:051916. PDF

 

1. Grima R, Micallef A, Colls JJ. 2002. External contribution to urban air pollution. Environmental monitoring and assessment. 73:291. PDF

 


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