Drying-induced hydrophobic polymer collapse
Ten Wolde, Pieter Rein, Chandler, David
We have used computer simulation to study the collapse of a hydrophobic chain in water. We find that the mechanism of collapse is much like that of a first-order phase transition. The evaporation of...
Drying-induced hydrophobic polymer collapse
Ten Wolde, Pieter Rein, Chandler, David
We have used computer simulation to study the collapse of a hydrophobic chain in water. We find that the mechanism of collapse is much like that of a first-order phase transition. The evaporation of...
Transcriptional Regulation by Competing Transcription Factor Modules
Hermsen, Rutger, Tans, Sander, Ten Wolde, Pieter Rein
Gene regulatory networks lie at the heart of cellular computation. In these networks, intracellular and extracellular signals are integrated by transcription factors, which control the expression of...
Fundamental Limits to Position Determination by Concentration Gradients
Tostevin, Filipe, Ten Wolde, Pieter Rein, Howard, Martin
Position determination in biological systems is often achieved through protein concentration gradients. Measuring the local concentration of such a protein with a spatially varying distribution...
Enzyme Localization Can Drastically Affect Signal Amplification in Signal Transduction Pathways
Van Albada, Siebe B, Ten Wolde, Pieter Rein
Push–pull networks are ubiquitous in signal transduction pathways in both prokaryotic and eukaryotic cells. They allow cells to strongly amplify signals via the mechanism of zero-order...
An allosteric model of circadian KaiC phosphorylation
Van Zon, Jeroen S., Lubensky, David K., Altena, Pim R. H., Ten Wolde, Pieter Rein
In a recent series of ground-breaking experiments, Nakajima et al. [Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, Kondo T (2005) Science 308:414–415] showed that the three...
Diffusion of Transcription Factors Can Drastically Enhance the Noise in Gene Expression
Van Zon, Jeroen S., Morelli, Marco J., Tănase-Nicola, Sorin, Ten Wolde, Pieter Rein
We study by Green's Function Reaction Dynamics the effect of the diffusive motion of repressor molecules on the noise in mRNA and protein levels for a gene that is under the control of a repressor....
Regulatory Control and the Costs and Benefits of Biochemical Noise
Tănase-Nicola, Sorin, Ten Wolde, Pieter Rein
Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells is,...
Reaction Coordinates for the Flipping of Genetic Switches
Morelli, Marco J., Tănase-Nicola, Sorin, Allen, Rosalind J., Ten Wolde, Pieter Rein
We present a detailed analysis, based on the forward flux sampling simulation method, of the switching dynamics and stability of two models of genetic toggle switches, consisting of two mutually...
Differential Affinity and Catalytic Activity of CheZ in E. coli Chemotaxis
Van Albada, Siebe B., Ten Wolde, Pieter Rein
Push–pull networks, in which two antagonistic enzymes control the activity of a messenger protein, are ubiquitous in signal transduction pathways. A classical example is the chemotaxis system of...
DNA looping provides stability and robustness to the bacteriophage λ switch
Morelli, Marco J., Ten Wolde, Pieter Rein, Allen, Rosalind J.
The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage λ presents a unique challenge to quantitative modeling. Despite extensive characterization of...
The switching dynamics of the bacterial flagellar motor
Van Albada, Siebe B, Tănase-Nicola, Sorin, Ten Wolde, Pieter Rein
Many bacteria are propelled by flagellar motors that stochastically switch between the clockwise and counterclockwise rotation direction. Although the switching dynamics is one of their most...
Spatio-temporal correlations can drastically change the response of a MAPK pathway
Takahashi, Koichi, Tănase-Nicola, Sorin, Ten Wolde, Pieter Rein
Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade where, in each layer of the cascade, a...
Combinatorial Gene Regulation Using Auto-Regulation
Hermsen, Rutger, Ursem, Bas, Ten Wolde, Pieter Rein
As many as 59% of the transcription factors in Escherichia coli regulate the transcription rate of their own genes. This suggests that auto-regulation has one or more important functions. Here, one...