santiago-schnell Goto Github PK

concentration-sensing-crowded-environments

Quasi-reversible simulation wrapper for Interacting Particle Reaction Diffusion simulations.

error-estimates-for-mm-progress-curves

Python scripts for paper "On the estimation errors of K_M and V from time-course experiments using the Michaelis–Menten equation" [Biophysical Chemistry 219 (2016), 17-27]

estimation-lag-time-monomer-addition

Matlab code for kinetic model of paper "Estimation of the lag time in a subsequent monomer addition model for fibril elongation" [Phys.Chem.Chem.Phys. 18 (2016), 21259]

estimation-oscillations-period

Matlab code for estimate statistically significant periods of oscillations in time course data [PLoS One 9 (2014), e93826]

gui-method-to-infer-kinetics-and-network-architecture

Matlab code for "A Graphical User Interface for a Method to Infer Kinetics and Network Architecture (MIKANA)" [PLoS ONE 6(2011), e27534]

information-processing-er-stress-sensors

Python scripts used to model and quantify information capacity of ER stress for preprint "Information processing by endoplasmic reticulum stress sensors" [DOI: ]. All codes were run using Python, version 2.7.

lattice-off_lattice-enzyme-kinetics-crowded-environment

C++ code for models implemented in the paper "A systematic investigation of the rate laws valid in intracellular environments" [Biophys Chem 124 (2006) 1–10]

macroscopic-simulations-microtubule-dynamics

Matlab code for "Macroscopic simulations of microtubule dynamics predict two steady-state processes governing array morphology" [Comput Biol Chem 35 (2011), 269-281]

obstacles-impact-diffusion-kinetics-enzyme-reaction

C++ code for model implemented in the paper "Unravelling the impact of obstacles in diffusion and kinetics of an enzyme catalysed reaction" [Phys Chem Chem Phys 16 (2014), 4492]

pareto-upr-feedback-control

Python scripts used to simulate the model and calculate Pareto sets from paper "How to design an optimal sensor network for the unfolded protein response" [Mol Biol Cell 29 (2018), 3052-3062]. All codes were run using Python, version 2.7.

predicting-neuroblastoma-logic-based-model

Python code to reproduce results from the paper "Predicting neuroblastoma using developmental signals and a logic-based model" [Biophys Chem 238 (2018), 30-38]

square-lattice-reaction-kinetics-crowded-environments

Matlab code for simulations of paper "Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws" [Prog Biophys Mol Biol 85 (2004) 235–260]

ss-linear-noise-approximation