Simulation of reaction-diffusion processes in crowded systems

2016–

  • Blanco, P.M.; Garces, J.L.; Madurga, S.; Mas, F.    Macromolecular diffusion in crowded media beyond the hard-sphere model. Soft Matter, 14, 2018, 3105-3114.  https://doi.org/10.1039/C8SM00201K
  • Nedyalkova, M.; Donkova, B.; Romanova, J.; Tzvetkov, G.; Madurga, S.; Simeonov, V.  Iron oxide nanoparticles – In vivo/in vitro biomedical applications and in silico studies. Advances In Colloid And Interface Science, 249, 2017, 192-212.  https://doi.org/10.1016/j.cis.2017.05.003
  • Blanco, P.M.; Via, M.; Garcés, J.L.; Madurga, S.; Mas, F. Brownian Dynamics Computational Model of protein Diffusion in Crowded Media with Dextran Macromolecules as Obstacles. Entropy, 19(3), 105, 2017. doi: http://dx.doi.org/10.3390/e19030105
  • Pitulice, L.; Craciun, D.; Vilaseca, E.; Madurga, S.; Pastor, I.; Mas, F.; Isvoran, A. 2016. Fractal dimensions of the trajectoriy of a single particle diffusion in crowded media. Romanian Journal of Physics.

2011-2015

  • Balcells, C.; Pastor, I.; Pitulice, L.; Hernández, C.; Via, M.; Garcés, J.L.; Madurga, S.; Vilaseca, E.; Isvoran, A.; Cascante, M.; Mas, F. 2015. Macromolecular crowding upon in-vivo-like enzyme-kinetics: effect of enzyme-obstacle size ratio. New Frontiers in Chemistry succesor of Annals of West University of Timisoara, 24(1), 3.
  • Balcells, C.; Pastor, I.; Vilaseca, E.; Madurga, S.; Cascante, M.; Mas, F. 2014. Macromolecular crowding effect upon in vitro enzyme kinetics: Mixed activation-diffusion control of the oxidation of NADH by pyruvate catalyzed by lactate dehydrogenase. Journal of Physical Chemistry B, vol. 118, num. 15, p. 4062-4068. doi: http://dx.doi.org/10.1021/jp4118858
  • Galgoczy, R.; Pastor, I.; Colom, A.; Sunyer, R.; Giménez, A.; Mas, F.; Alcaraz, J. 2014. A spectrophotometer-based diffusivity assay reveals that diffusion hindrance of small molecules in extracellular matrix gels used in 3D cultures is dominated by viscous effects. Colloids and Surfaces B-Biointerfaces, 120, 200-207. doi: http://dx.doi.org/10.1016/j.colsurfb.2014.05.017
  • Pastor, I.; Balcells, C.; Pitulice, L.; Vilaseca, E.; Madurga, S.; Isvoran, A.; Cascante, M.; Mas, F. 2014. Effect of crowding by Dextrans in enzymatic reactions. Biophysical Chemistry, 185, 8-13. doi: http://dx.doi.org/10.1016/j.bpc.2013.10.006
  • Pitulice, L.; Vilaseca, E.; Pastor, I.; Madurga, S.; Garcés, J.L.; Isvoran, A.; Mas, F. 2014. Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size. Mathematical Biosciences, 251, 72-82. doi: http://dx.doi.org/10.1016/j.mbs.2014.03.012
  • Pitulice, L.; Pastor, I.; Vilaseca, E.; Madurga, S.; Isvoran, A.; Cascante, M.; Mas, F. 2013. Influence of macromolecular crowding on the oxidation of ABTS by hydrogen peroxide catalyzed by HRP. Journal of Biocatalysis & Biotransformation.
  • Pastor, I.; Vilaseca, E.; Madurga, S.; Garcés, J.L.; Cascante, M.; Mas, F. 2011. Effect of Cowding by Dextrans on the Hidrolysis of N-succinyl-L-phenyl-Ala-p-nitroanilide Catalyzed by alpha-Chymotrypsin upon Addition of Dextran with Different Concentrations and Sizes. Journal of Physical Chemistry B, vol. 115, num. 5, p. 1115-1121. doi: http://dx.doi.org/10.1021/jp105296
  • Pitulice, L.; Vilaseca, E.; Isvoran, A.; Garcés, J.L.; Mas, F. 2011. Aspects of fractal kinetics of enzymatic reactions by Monte Carlo simulations. Annals of West University of Timisoara. Series Chemistry, In 11 th National Conference of Biophysics (p. 77).
  • Vilaseca, E.; Pastor, I.; Isvoran, A.; Madurga, S.; Garcés, J.L.; Mas, F. 2011. Diffusion in macromolecular crowded media. Monte Carlo simulation of obstructed diffusion vs. FRAP experiments. Theoretical Chemistry Accounts Special Isue Computational Chemistry Spain, 128(4-6), 795-805.
  • Vilaseca, E.; Isvoran, A.; Madurga, S.; Pastor, I.; Garcés, J.L.; Mas, F. 2011. New insights into diffusion in 3D crowded media by Monte Carlo simulations: Effect of size, mobility and spatial distribution of obstacles. Physical Chemistry Chemical Physics, 13(16), 7396-7407. doi: http://dx.doi.org/10.1039/C0CP01218A

2006-2010

  • Pastor, I; E. Vilaseca; S. Madurga; J.L. Garcés; M. Cascante; F. Mas. 2010. Diffusion of alpha-Chymotrypsin in solution crowded media. A fluorescence recovery after photobleaching study. Journal of Physical Chemistry B 114(11):4028-4034 & Erratum ibid 114 (2010) 12182. doi: http://dx.doi.org/10.1021/jp1067796.
  • Isvoran, A.; E. Vilaseca; J.L. Garcés; L. Unipan; F. Mas. 2008. Non-classical kinetics for enzymatic reactions in two-dimensional media. Romanian Journal of Biophysics 18(4):283-291.
  • Isvoran, A.; E. Vilaseca; L. Unipan; J.L. Garcés; F. Mas. 2008. Computational study of diffusion in cellular two-dimensional crowded media modelled as a mixture of mobile and inmobile obstacles.  Revue Roumaine de Chimie 53(5):415-419.
  • Isvoran, A.; E. Vilaseca; L. Unipan; J.L. Garcés; F. Mas. 2007. Monte Carlo simulation of single-particle diffusion in two-dimensional and three-dimensional crowded media. Romanian J. Biophys. 17(1):21-32.
  • Isvoran, A.; E. Vilaseca; J.L. Garcés; L. Unipan; F. Mas. 2007. Simulation of diffusion in two-dimensional crowded media. AIP Conference Proceedings 899:469-470.
  • Ortega, F.; J.L. Garcés; F. Mas; B. Kholodenko; M. Cascante. 2006. Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements. FEBS Journal 273(17):3915-3926. doi: http://dx.doi.org/10.1111/j.1742-4658.2006.05394.x

  • Isvoran, A.; E. Vilaseca; F. Ortega; M. Cascante; F. Mas. 2006. About implementing a Monte Carlo simulation for enzymatic reactions in crowded media. J. Serbian Chem. Soc. 75:75-86.

 

2001-2005

  • Ortega, F.; M. Ehrenberg; L. Acerenza; H.V. Westerhoff; F. Mas; M. Cascante. 2002. Sensitivity analysis of metabolic cascades catalized by bifunctional enzymes. Molecular Biology Reports 29(1-2):211-215.

  • Ortega, F.; L. Acerenza; H.V. Westerhoff; F. Mas; M. Cascante. 2002. Product dependence and bifunctionality compromise the ultrasensitivity of signal transduction cascades. Proceedings of the National Academy of Sciences of the United States of America – PNAS 99:1170-1175. doi: http://dx.doi.org/10.1073/pnas.022267399