scholarly journals Vibrational free energy and phase stability of paramagnetic and antiferromagnetic CrN fromab initiomolecular dynamics

2014 ◽  
Vol 89 (17) ◽  
Author(s):  
Nina Shulumba ◽  
Björn Alling ◽  
Olle Hellman ◽  
Elham Mozafari ◽  
Peter Steneteg ◽  
...  
Keyword(s):  
Free Energy ◽  
Phase Stability ◽  
Vibrational Free Energy

scholarly journals Dynamic allostery of protein alpha helical coiled-coils

2005 ◽  
Vol 3 (6) ◽  
pp. 125-138 ◽  
Author(s):  
Rhoda J Hawkins ◽  
Tom C.B McLeish
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Molecular Motor ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Coarse Grained ◽  
Static Structure ◽  
Change In The Mean ◽  
The Individual ◽  
Vibrational Free Energy

Alpha helical coiled-coils appear in many important allosteric proteins such as the dynein molecular motor and bacteria chemotaxis transmembrane receptors. As a mechanism for transmitting the information of ligand binding to a distant site across an allosteric protein, an alternative to conformational change in the mean static structure is an induced change in the pattern of the internal dynamics of the protein. We explore how ligand binding may change the intramolecular vibrational free energy of a coiled-coil, using parameterized coarse-grained models, treating the case of dynein in detail. The models predict that coupling of slide, bend and twist modes of the coiled-coil transmits an allosteric free energy of ∼2 k B T , consistent with experimental results. A further prediction is a quantitative increase in the effective stiffness of the coiled-coil without any change in inherent flexibility of the individual helices. The model provides a possible and experimentally testable mechanism for transmission of information through the alpha helical coiled-coil of dynein.

Reproducibility of vibrational free energy by different methods

2018 ◽  
Vol 150 ◽  
pp. 47-53 ◽  
Author(s):  
Pavel Korotaev ◽  
Maxim Belov ◽  
Aleksey Yanilkin
Keyword(s):  
Free Energy ◽  
Vibrational Free Energy

Free Energy Calculations of Precipitate Nucleation

2007 ◽  
Vol 539-543 ◽  
pp. 2395-2400 ◽  
Author(s):  
Shigeto R. Nishitani ◽  
Atsuto Seko ◽  
Koretaka Yuge ◽  
Isao Tanaka
Keyword(s):  
Free Energy ◽  
Energy Barrier ◽  
Harmonic Approximation ◽  
Free Energy Calculations ◽  
Free Energy Barrier ◽  
Initial State ◽  
Final State ◽  
The Matrix ◽  
Predicted Values ◽  
Vibrational Free Energy

Our recently proposed calculating method reliably predicts the nucleation free energy barrier of the homogeneous and coherent precipitations. Helmholtz free energy change is clearly defined and calculated by the purely enthalpic and entropic contributions between the initial state of the isolated solute atoms scattering around the matrix and the final state of the cluster of size n traveling around the matrix. The enthalpic term is calculated by the reliable first principles method and the entropic term is estimated by the ideal solution model. The vibrational free energy is also included by the quasi-harmonic approximation. The model calculation was performed on bcc Cu precipitations in the Fe-Cu system. The predicted values of the critical number of 12 atoms and the critical free energy barrier of 0.6eV show good agreement with the experimentally estimated ones for the annealing temperature of 773K and the initial concentration of 1.4at%Cu.

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