@article {2019|2139,
	title = {Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions},
	journal = {J Phys Chem B},
	volume = {123},
	year = {2019},
	month = {Apr},
	pages = {3312-3324},
	abstract = {<p>Aqueous ionic solutions are ubiquitous in chemistry and in biology. Experiments show that ions affect water dynamics, but a full understanding of several questions remains needed: why some salts accelerate water dynamics while others slow it down, why the effect of a given salt can be concentration-dependent, whether the effect of ions is rather local or more global. Numerical simulations are particularly suited to disentangle these different effects, but current force fields suffer from limitations and often lead to a poor description of dynamics in several aqueous salt solutions. Here, we develop an improved classical force field for the description of alkali halides that yields dynamics in excellent agreement with experimental measurements for water reorientational and translational dynamics. These simulations are analyzed with an extended jump model, which allows to compare the effects of ions on local hydrogen-bond exchange dynamics and on more global properties like viscosity. Our results unambiguously show that the ion-induced changes in water dynamics are usually mostly due to a local effect on the hydrogen-bond exchange dynamics; in contrast, the change in viscosity leads to a smaller effect, which governs the retardation only for a minority of salts and at high concentrations. We finally show how the respective importance of these two effects can be directly determined from experimental measurements alone, thus providing guidelines for the selection of an electrolyte with specific dynamical properties.</p>
},
	doi = {10.1021/acs.jpcb.9b01053},
	author = {Laage, Damien and Guillaume Stirnemann}
}
@article {2015|1582,
	title = {The elastic free energy of a tandem modular protein under force.},
	journal = {Biochem. Biophys. Res. Comm.},
	year = {2015},
	pages = {1{\textendash}5},
	keywords = {free energy landscape, tandem modular protein},
	issn = {0006291X},
	doi = {10.1016/j.bbrc.2015.03.051},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0006291X15004866},
	author = {Valle-Orero, Jessica and Eckels, Edward and Guillaume Stirnemann and Popa, Ionel and Berkovich, Ronen and Fernandez, Julio M.}
}
@article {2013|1752,
	title = {Elasticity, structure, and relaxation of extended proteins under force.},
	journal = {Proc. Natl. Acad. Sci. U.s.a},
	volume = {110},
	year = {2013},
	pages = {3847{\textendash}52},
	abstract = {<p>Force spectroscopies have emerged as a powerful and unprecedented tool to study and manipulate biomolecules directly at a molecular level. Usually, protein and DNA behavior under force is described within the framework of the worm-like chain (WLC) model for polymer elasticity. Although it has been surprisingly successful for the interpretation of experimental data, especially at high forces, the WLC model lacks structural and dynamical molecular details associated with protein relaxation under force that are key to the understanding of how force affects protein flexibility and reactivity. We use molecular dynamics simulations of ubiquitin to provide a deeper understanding of protein relaxation under force. We find that the WLC model successfully describes the simulations of ubiquitin, especially at higher forces, and we show how protein flexibility and persistence length, probed in the force regime of the experiments, are related to how specific classes of backbone dihedral angles respond to applied force. Although the WLC model is an average, backbone model, we show how the protein side chains affect the persistence length. Finally, we find that the diffusion coefficient of the protein{\textquoteright}s end-to-end distance is on the order of 10(8) nm(2)/s, is position and side-chain dependent, but is independent of the length and independent of the applied force, in contrast with other descriptions.</p>},
	keywords = {Atomic Force, Biophysical Phenomena, Computer Simulation, Elasticity, Mechanical, Microscopy, Models, Molecular, Molecular Dynamics Simulation, Proteins, Proteins: chemistry, Stress, Ubiquitin, Ubiquitin: chemistry},
	issn = {1091-6490},
	url = {http://www.pnas.org/content/early/2013/02/13/1300596110.abstract},
	author = {Guillaume Stirnemann and Giganti, David and Fernandez, Julio M and Berne, B J}
}
