134 citations · 192 across the 9 of their papers we have counts for
9 papers
Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation
O. Pulkkinen, R. Metzler
Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed…
Distance matters: the impact of gene proximity in bacterial gene regulation
Otto Pulkkinen, Ralf Metzler
Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product…
Finite-size effects in dynamics of zero-range processes
Janne Juntunen, Otto Pulkkinen, Juha Merikoski
The finite-size effects prominent in zero-range processes exhibiting a condensation transition are studied by using continuous-time Monte Carlo simulations. We observe that, well a…
State estimation of long-range correlated non-equilibrium systems: media estimation
Otto Pulkkinen
Non-equilibrium systems have long-ranged spatial correlations even far away from critical points. This implies that the likelihoods of spatial steady state profiles of physical obs…
Dynamics of gene expression under feedback
Otto Pulkkinen, Johannes Berg
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where…
Polymer dynamics in time-dependent periodic potentials
Janne Kauttonen, Juha Merikoski, Otto Pulkkinen
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanism…