Title |
In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics
|
---|---|
Published in |
PLoS Computational Biology, February 2014
|
DOI | 10.1371/journal.pcbi.1003456 |
Pubmed ID | |
Authors |
Pascal Carrivain, Maria Barbi, Jean-Marc Victor |
Abstract |
We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 2 | 40% |
Spain | 1 | 20% |
Norway | 1 | 20% |
Unknown | 1 | 20% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 2 | 40% |
Science communicators (journalists, bloggers, editors) | 2 | 40% |
Scientists | 1 | 20% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 1 | 4% |
India | 1 | 4% |
Germany | 1 | 4% |
Unknown | 22 | 88% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 9 | 36% |
Researcher | 5 | 20% |
Professor | 2 | 8% |
Student > Postgraduate | 2 | 8% |
Student > Master | 2 | 8% |
Other | 4 | 16% |
Unknown | 1 | 4% |
Readers by discipline | Count | As % |
---|---|---|
Physics and Astronomy | 5 | 20% |
Biochemistry, Genetics and Molecular Biology | 5 | 20% |
Engineering | 4 | 16% |
Agricultural and Biological Sciences | 3 | 12% |
Medicine and Dentistry | 2 | 8% |
Other | 5 | 20% |
Unknown | 1 | 4% |