Taking the reaction-diffusion master equation to the microscopic limit (2009)
Sjoberg, Paul, Berg, Otto G, Elf, Johan
The reaction-diffusion master equation (RDME) is commonly used to model processes where both the spatial and stochastic nature of chemical reactions need to be considered. We show that the RDME in...
Target Location by DNA-Binding Proteins: Effects of Roadblocks and DNA Looping (2008)
Li, Gene-Wei, Berg, Otto G., Elf, Johan
The model of facilitated diffusion describes how DNA-binding proteins, such as transcription factors (TFs), find their chromosomal targets by combining 3D diffusion through the cytoplasm and 1D...
Noise-Induced Min Phenotypes in E. coli (2006)
The spatiotemporal oscillations of the Escherichia coli proteins MinD and MinE direct cell division to the region between the chromosomes. Several quantitative models of the Min system have been...
Noise induced Min phenotypes in E. coli (2006)
The spatiotemporal oscillations of the E. coli proteins MinD and MinE direct cell division to the region between the chromosomes. Several quantitative models of the Min system have been suggested...
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation? (2005)
Ribosome-mediated transcriptional attenuation mechanisms are commonly used to control amino acid biosynthetic operons in bacteria. The mRNA leader of such an operon contains an open reading frame...
Supplementary information: ‘MesoRD User’s Guide ’ and other (2005)
Johan Hattne, David Fange, Johan Elf
Summary: MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method, which is an exact method to simulate the...
FOKKER-PLANCK APPROXIMATION OF THE MASTER EQUATION IN MOLECULAR BIOLOGY (2005)
Paul Sj, Öberg Per, L Ötstedt, Johan Elf
The master equation of chemical reactions is solved by first approximating it by the Fokker-Planck equation. Then this equation is discretized in the state space and time by a finite volume method....
Stochastic reaction-diffusion simulation with MesoRD (2005)
Hattne, Johan, Fange, David, Elf, Johan
Summary: MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method, which is an exact method to simulate the...
Stochastic reaction-diffusion simulation with MesoRD (2005)
Hattne, Johan, Fange, David, Elf, Johan
Summary: MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular, it is an implementation of the Next Subvolume Method, which is an exact method to simulate the...
Intracellular Flows and Fluctuations (2004)
Mathematical models are now gaining in importance for descriptions of biological processes. In this thesis, such models have been used to identify and analyze principles that govern bacterial protein...
Intracellular Flows and Fluctuations (2004)
Mathematical models are now gaining in importance for descriptions of biological processes. In this thesis, such models have been used to identify and analyze principles that govern bacterial protein...
Problems of high dimension in molecular biology (2003)
Johan Elf, Per Lötstedt, Paul Sjöberg
The deterministic reaction rate equations are not an accurate description of many systems in molecular biology where the number of molecules of each species often is small. The master equation of...
Systems Biology Is Taking Off (2003)
Ehrenberg, Måns, Elf, Johan, Aurell, Erik, Sandberg, Rickard, Tegnér, Jesper
Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation (2003)
Biochemical networks in single cells can display large fluctuations in molecule numbers, making mesoscopic approaches necessary for correct system descriptions. We present a general method that...
Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation
Biochemical networks in single cells can display large fluctuations in molecule numbers, making mesoscopic approaches necessary for correct system descriptions. We present a general method that...
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?
Ribosome-mediated transcriptional attenuation mechanisms are commonly used to control amino acid biosynthetic operons in bacteria. The mRNA leader of such an operon contains an open reading frame...
Ribosome bypassing at serine codons as a test of the model of selective transfer RNA charging
Lindsley, Dale, Bonthuis, Paul, Gallant, Jonathan, Tofoleanu, Teodora, Elf, Johan, Ehrenberg, Måns
Recently, a model of the flux of amino acids through transfer RNAs (tRNAs) and into protein has been developed. The model predicts that the charging level of different isoacceptors carrying the same...
Selective charging of tRNA isoacceptors induced by amino-acid starvation
Dittmar, Kimberly A, Sørensen, Michael A, Elf, Johan, Ehrenberg, Måns, Pan, Tao
Aminoacylated (charged) transfer RNA isoacceptors read different messenger RNA codons for the same amino acid. The concentration of an isoacceptor and its charged fraction are principal determinants...
Near-Critical Phenomena in Intracellular Metabolite Pools
Elf, Johan, Paulsson, Johan, Berg, Otto G., Ehrenberg, Måns
The supply and consumption of metabolites in living cells are catalyzed by enzymes. Here we consider two of the simplest schemes where one substrate is eliminated through Michaelis-Menten kinetics,...
Near-Critical Behavior of Aminoacyl-tRNA Pools in E. coli at Rate-Limiting Supply of Amino Acids
The rates of consumption of different amino acids in protein synthesis are in general stoichiometrically coupled with coefficients determined by codon usage frequencies on translating ribosomes. We...
Noise-Induced Min Phenotypes in E. coli
The spatiotemporal oscillations of the Escherichia coli proteins MinD and MinE direct cell division to the region between the chromosomes. Several quantitative models of the Min system have been...
Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation
Biochemical networks in single cells can display large fluctuations in molecule numbers, making mesoscopic approaches necessary for correct system descriptions. We present a general method that...
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?
Ribosome-mediated transcriptional attenuation mechanisms are commonly used to control amino acid biosynthetic operons in bacteria. The mRNA leader of such an operon contains an open reading frame...
Ribosome bypassing at serine codons as a test of the model of selective transfer RNA charging
Lindsley, Dale, Bonthuis, Paul, Gallant, Jonathan, Tofoleanu, Teodora, Elf, Johan, Ehrenberg, Måns
Recently, a model of the flux of amino acids through transfer RNAs (tRNAs) and into protein has been developed. The model predicts that the charging level of different isoacceptors carrying the same...
Selective charging of tRNA isoacceptors induced by amino-acid starvation
Dittmar, Kimberly A, Sørensen, Michael A, Elf, Johan, Ehrenberg, Måns, Pan, Tao
Aminoacylated (charged) transfer RNA isoacceptors read different messenger RNA codons for the same amino acid. The concentration of an isoacceptor and its charged fraction are principal determinants...
Near-Critical Phenomena in Intracellular Metabolite Pools
Elf, Johan, Paulsson, Johan, Berg, Otto G., Ehrenberg, Måns
The supply and consumption of metabolites in living cells are catalyzed by enzymes. Here we consider two of the simplest schemes where one substrate is eliminated through Michaelis-Menten kinetics,...
Near-Critical Behavior of Aminoacyl-tRNA Pools in E. coli at Rate-Limiting Supply of Amino Acids
The rates of consumption of different amino acids in protein synthesis are in general stoichiometrically coupled with coefficients determined by codon usage frequencies on translating ribosomes. We...
Noise-Induced Min Phenotypes in E. coli
The spatiotemporal oscillations of the Escherichia coli proteins MinD and MinE direct cell division to the region between the chromosomes. Several quantitative models of the Min system have been...