scholarly journals Removing External Degrees of Freedom from Transition-State Search Methods using Quaternions

2015 ◽  
Vol 11 (3) ◽  
pp. 1055-1062 ◽  
Author(s):  
Marko Melander ◽  
Kari Laasonen ◽  
Hannes Jónsson
Keyword(s):  
Transition State ◽  
Degrees Of Freedom ◽  
Search Methods ◽  
Transition State Search ◽  
External Degrees

Comparison of double-ended transition state search methods

2007 ◽  
Vol 127 (13) ◽  
pp. 134102 ◽  
Author(s):  
Elena F. Koslover ◽  
David J. Wales
Keyword(s):  
Transition State ◽  
Search Methods ◽  
Transition State Search

Entanglement between internal and external degrees of freedom of a driven trapped atom

2010 ◽  
Vol T140 ◽  
pp. 014034 ◽  
Author(s):  
Maryam Roghani ◽  
Hanspeter Helm ◽  
Heinz-Peter Breuer
Keyword(s):  
Degrees Of Freedom ◽  
External Degrees

Transition State Search Using a Guided Direct Inversion in the Iterative Subspace Method

2012 ◽  
Vol 8 (12) ◽  
pp. 5175-5179 ◽  
Author(s):  
Joseph W. May ◽  
Jeremy D. Lehner ◽  
Michael J. Frisch ◽  
Xiaosong Li
Keyword(s):  
Transition State ◽  
Subspace Method ◽  
Direct Inversion ◽  
Transition State Search

Gaussian Process Regression for Minimum Energy Path Optimization and Transition State Search

2019 ◽  
Vol 123 (44) ◽  
pp. 9600-9611 ◽  
Author(s):  
Alexander Denzel ◽  
Bernard Haasdonk ◽  
Johannes Kästner
Keyword(s):  
Transition State ◽  
Gaussian Process ◽  
Minimum Energy ◽  
Gaussian Process Regression ◽  
Path Optimization ◽  
Minimum Energy Path ◽  
Transition State Search

scholarly journals Transition mechanism for a periodic bar-and-joint framework with limited degrees of freedom controlled by uniaxial load and internal stiffness

2018 ◽  
Vol 5 (6) ◽  
pp. 180139 ◽  
Author(s):  
H. Tanaka ◽  
K. Hamada ◽  
Y. Shibutani
Keyword(s):  
Exact Solution ◽  
Transition State ◽  
Nonlinear Elasticity ◽  
External Force ◽  
Degrees Of Freedom ◽  
Critical Value ◽  
Uniaxial Load ◽  
Transition Mechanism ◽  
Two Systems ◽  
Load Displacement

A specific periodic bar-and-joint framework with limited degrees of freedom is shown to have a transition mechanism when subjected to an external force. The static nonlinear elasticity of this framework under a uniaxial load is modelled with the two angular variables specifying the rotation and distortion of the linked square components. Numerically exploring the equilibrium paths then reveals a transition state of the structure at a critical value of the internal stiffness. A simplified formulation of the model with weak nonlinear terms yields an exact solution of its transition state. Load–displacement behaviour and stability for the two systems with or without approximation are analysed and compared.

Density dependence of the external degrees of freedom: application to a simplified version of the perturbed hard chain theory

1988 ◽  
Vol 41 (1-2) ◽  
pp. 59-80 ◽  
Author(s):  
Giuseppe Ciocca ◽  
Isamu Nagata ◽  
Vincenzo Brandani
Keyword(s):  
Density Dependence ◽  
Degrees Of Freedom ◽  
Chain Theory ◽  
External Degrees

scholarly journals Exploration of Transition State Search in Physical Chemistry

Daxue Huaxue ◽  
2021 ◽  
Vol 0 (0) ◽  
pp. 2012018-0
Author(s):  
Xin Zhang ◽  
Peinan He
Keyword(s):  
Physical Chemistry ◽  
Transition State ◽  
Transition State Search

scholarly journals Unbiased Atomistic Insight in the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation

2018 ◽  
Author(s):  
Faidon Z. Brotzakis ◽  
Peter G. Bolhuis
Keyword(s):  
Transition State ◽  
Degrees Of Freedom ◽  
Process Analysis ◽  
Salt Bridge ◽  
Underlying Mechanism ◽  
Full Detail ◽  
Hydration Water ◽  
Native Contact ◽  
Reorientation Dynamics

Association and dissociation of proteins are fundamental processes in nature. While this process is simple to understand conceptually, the details of the underlying mechanism and role of the solvent are poorly understood. Here we investigate the mechanism and solvent role for the dissociation of the hydrophilic β-lactoglobulin dimer by employing transition path sampling. Analysis of the sampled path ensembles indicates that dissociation (and association) occurs via a variety of mechanisms: 1) a direct aligned dissociation 2) a hopping and rebinding transition followed by unbinding 3) a sliding transition before unbinding. Reaction coordinate and transition state analysis predicts that, besides native contact and vicinity salt-bridge interactions, solvent degrees of freedom play an important role in the dissociation process. Analysis of the structure and dynamics of the solvent molecules reveals that the dry native interface induces enhanced populations of both disordered hydration water and hydration water with higher tetrahedrality, mainly nearby hydrophobic residues. Bridging waters, hydrogen bonded to both proteins, support contacts, and exhibit a faster decay and reorientation dynamics in the transition state than in the native state interface, which renders the proteins more mobile and assists in rebinding. While not exhaustive, our sampling of rare un-biased reactive molecular dynamics trajectories shows in full detail how proteins can dissociate via complex pathways including (multiple) rebinding events. The atomistic insight obtained assists in further understanding and control of the dynamics of protein-protein interaction including the role of solvent.PACS numbers:

Application of numerical basis sets with a family of DFT methods to predict the transition states of Diels-Alder reactions: Assessing the accuracy through synchronous transit method

2017 ◽  
Author(s):  
Saurav Dutta ◽  
Bhabani S. Mallik
Keyword(s):  
Transition State ◽  
Alder Reaction ◽  
Diels Alder ◽  
Computational Method ◽  
Basis Set ◽  
Basis Sets ◽  
Gaussian Basis Sets ◽  
Dft Methods ◽  
Diels Alder Reaction ◽  
Transition State Search

<div> <table> <tr> <td> <p>Knowledge of the transition state is crucial in determining the mechanism in order to diversify the applicability of the reaction. The computational method is the most convenient way to locate the transition state in the absence any efficient experimental technique. We have applied the method of the transition state search on the Diels-Alder reaction computationally by means of combined linear synchronous transit and quadratic synchronous transit methods. Here we have shown that, of various methods adopted, BOP functional with numerical basis set provides a computationally economical alternative to the widely used B3LYP functional with higher Gaussian basis sets in the transition state search. It can reproduce the experimental parameters like activation energy of the Diels-Alder reaction, and the calculations are much faster than the corresponding other functional based calculations.</p> </td> </tr> </table> </div>

Sign in / Sign up

Export Citation Format

Share Document