Molecular dynamics simulations of enhanced green fluorescent proteins: Effects of F64L, S65T and T203Y mutations on the ground-state proton equilibria

2003 ◽  
Vol 51 (3) ◽  
pp. 378-389 ◽  
Author(s):  
R. Nifosì ◽  
V. Tozzini
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Fluorescent Proteins ◽  
Green Fluorescent Proteins ◽  
Dynamics Simulations ◽  
Green Fluorescent

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations

2021 ◽  
Vol 23 (14) ◽  
pp. 8525-8540
Author(s):  
Mudong Feng ◽  
Michael K. Gilson
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Molecular Motors ◽  
Motor Performance ◽  
Molecular Simulations ◽  
Mechanistic Analysis ◽  
Dynamics Simulations ◽  
Shed Light

Ground-state and excited-state molecular dynamics simulations shed light on the rotation mechanism of small, light-driven molecular motors and predict motor performance. How fast can they rotate; how much torque and power can they generate?

Ab Initio Molecular Dynamics of Column IV Microclusters

1990 ◽  
Vol 193 ◽  
Author(s):  
David A. Drabold ◽  
Stefan Klemm ◽  
Otto F. Sankey
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Vibrational Spectra ◽  
Ground State ◽  
Spectral Estimation ◽  
Ab Initio Molecular Dynamics ◽  
Estimation Technique ◽  
Dynamics Simulations ◽  
Small Clusters

ABSTRACTWe report the results of ab-initio molecular dynamics simulations for small clusters of Si and C atoms. Ground-state geometries and vibrational spectra are presented. We also describe a Bayesian spectral estimation technique which we have found to be useful in analyzing molecular dynamics trajectories.

scholarly journals Cavity molecular dynamics simulations of liquid water under vibrational ultrastrong coupling

2020 ◽  
Vol 117 (31) ◽  
pp. 18324-18331 ◽  
Author(s):  
Tao E. Li ◽  
Joseph E. Subotnik ◽  
Abraham Nitzan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Liquid Water ◽  
Ground State ◽  
Cavity Mode ◽  
Translational Diffusion ◽  
Static Properties ◽  
Cavity Modes ◽  
Stretch Mode ◽  
Dynamics Simulations

We simulate vibrational strong coupling (VSC) and vibrational ultrastrong coupling (V-USC) for liquid water with classical molecular dynamics simulations. When the cavity modes are resonantly coupled to the O−H stretch mode of liquid water, the infrared spectrum shows asymmetric Rabi splitting. The lower polariton (LP) may be suppressed or enhanced relative to the upper polariton (UP) depending on the frequency of the cavity mode. Moreover, although the static properties and the translational diffusion of water are not changed under VSC or V-USC, we do find the modification of the orientational autocorrelation function of H2O molecules especially under V-USC, which could play a role in ground-state chemistry.

scholarly journals Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

Molecules ◽  
2019 ◽  
Vol 24 (9) ◽  
pp. 1653 ◽  
Author(s):  
Aurélien de la Lande ◽  
Aurelio Alvarez-Ibarra ◽  
Karim Hasnaoui ◽  
Fabien Cailliez ◽  
Xiaojing Wu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Density Functional ◽  
Molecular Simulations ◽  
High Energy ◽  
Umbrella Sampling ◽  
Visible Absorption ◽  
Dynamics Simulations

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.

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