115 citations · 298 across the 6 of their papers we have counts for
6 papers
Computing stationary distributions in equilibrium and non-equilibrium systems with Forward Flux Sampling
Chantal Valeriani, Rosalind J. Allen, Marco J. Morelli +2
We present a method for computing stationary distributions for activated processes in equilibrium and non-equilibrium systems using Forward Flux Sampling (FFS). In this method, the…
DNA looping provides stability and robustness to the bacteriophage lambda switch
Marco J. Morelli, Pieter Rein ten Wolde, Rosalind J. Allen
The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. Despite extensiv…
Reaction Brownian Dynamics and the effect of spatial fluctuations on the gain of a push-pull network
Marco J. Morelli, Pieter Rein ten Wolde
Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-gr…
Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch
M. J. Morelli, R. J. Allen, S. Tanase-Nicola +1
In many stochastic simulations of biochemical reaction networks, it is desirable to ``coarse-grain'' the reaction set, removing fast reactions while retaining the correct system dy…
Reaction coordinates for the flipping of genetic switches
M. J. Morelli, S. Tanase-Nicola, R. J. Allen +1
We present a detailed analysis, based on the Forward Flux Sampling (FFS) simulation method, of the switching dynamics and stability of two models of genetic toggle switches, consis…
Diffusion of transcription factors can drastically enhance the noise in gene expression
Jeroen S. van Zon, Marco J. Morelli, Sorin Tanase-Nicola +1
We study by simulation the effect of the diffusive motion of repressor molecules on the noise in mRNA and protein levels in the case of a repressed gene. We find that spatial fluct…