Quantitative modeling of bacterial chemotaxis: signal amplification and accurate adaptation

Y Tu - Annual review of biophysics, 2013 - annualreviews.org
We review the recent developments in understanding the bacterial chemotaxis signaling
pathway by using quantitative modeling methods. The models developed are based on …

Chemotaxis: how bacteria use memory

N Vladimirov, V Sourjik - 2009 - degruyter.com
Bacterial chemotaxis represents one of the simplest and best studied examples of
unicellular behavior. Chemotaxis allows swimming bacterial cells to follow chemical …

[图书][B] Physical biology of the cell

R Phillips, J Kondev, J Theriot, H Garcia - 2012 - taylorfrancis.com
Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics
for undergraduate or graduate students. It maps the huge and complex landscape of cell …

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

MW Sneddon, JR Faeder, T Emonet - Nature methods, 2011 - nature.com
Managing the overwhelming numbers of molecular states and interactions is a fundamental
obstacle to building predictive models of biological systems. Here we introduce the Network …

Cooperative binding

MI Stefan, N Le Novère - PLoS computational biology, 2013 - journals.plos.org
Molecular binding is an interaction between molecules that results in a stable association
between those molecules. Cooperative binding occurs if the number of binding sites of a …

Modeling the chemotactic response of Escherichia coli to time-varying stimuli

Y Tu, TS Shimizu, HC Berg - Proceedings of the National …, 2008 - National Acad Sciences
In their natural environment, cells need to extract useful information from complex temporal
signals that vary over a wide range of intensities and time scales. Here, we study how such …

Logarithmic sensing in Escherichia coli bacterial chemotaxis

YV Kalinin, L Jiang, Y Tu, M Wu - Biophysical journal, 2009 - cell.com
We studied the response of swimming Escherichia coli (E. coli) bacteria in a comprehensive
set of well-controlled chemical concentration gradients using a newly developed microfluidic …

A modular gradient‐sensing network for chemotaxis in Escherichia coli revealed by responses to time‐varying stimuli

TS Shimizu, Y Tu, HC Berg - Molecular systems biology, 2010 - embopress.org
The Escherichia coli chemotaxis‐signaling pathway computes time derivatives of
chemoeffector concentrations. This network features modules for signal …

Bacterial strategies for chemotaxis response

A Celani, M Vergassola - Proceedings of the National …, 2010 - National Acad Sciences
Regular environmental conditions allow for the evolution of specifically adapted responses,
whereas complex environments usually lead to conflicting requirements upon the …

Accuracy of direct gradient sensing by single cells

RG Endres, NS Wingreen - Proceedings of the National …, 2008 - National Acad Sciences
Many types of cells are able to accurately sense shallow gradients of chemicals across their
diameters, allowing the cells to move toward or away from chemical sources. This …