Related papers: Single molecule enzymology a la Michaelis-Menten
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…
The past decade has seen a revived interest in the unavoidable or intrinsic noise in biochemical and genetic networks arising from the finite copy number of the participating species. That is, rather than modeling regulatory networks in…
A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon,…
Current single-molecule imaging techniques are incapable of providing stochastic information of individual chemical reactions. We have developed an optical imaging method for stochastic analysis of individual electrochemical reactions. The…
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
Biomolecular condensates provide distinct chemical environments, which control various cellular processes. The diffusive dynamics and chemical kinetics inside phase-separated condensates can be studied experimentally by fluorescently…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
The celebrated Michaelis-Menten (MM) expression provides a fundamental relation between the rate of enzyme catalysis and substrate concentration. The validity of this classical expression is, however, restricted to macroscopic amounts of…
Recent fluorescence spectroscopy measurements of single-enzyme kinetics have shown that enzymatic turnovers form a renewal stochastic process in which the inverse of the mean waiting time between turnovers follows the Michaelis-Menten…
We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…
Within systems biology there is an increasing interest in the stochastic behavior of genetic and biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous…
We study a class of Stochastic Differential Equations (SDEs) with jumps modeling multistage Michaelis--Menten enzyme kinetics, in which a substrate is sequentially transformed into a product via a cascade of intermediate complexes. These…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize…
Two powerful and complementary experimental approaches are commonly used to study the cell cycle and cell biology: One class of experiments characterizes the statistics (or demographics) of an unsynchronized exponentially-growing…