منابع مشابه
Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning
Reaction coordinates are vital tools for qualitative and quantitative analysis of molecular processes. They provide a simple picture of reaction progress and essential input for calculations of free energies and rates. Iso-committor surfaces are considered the optimal reaction coordinate. We present an algorithm to compute efficiently a sequence of isocommittor surfaces. These surfaces are cons...
متن کاملReaction coordinates of biomolecular isomerization.
Transition path sampling has been applied to the molecular dynamics of the alanine dipeptide in vacuum and in aqueous solution. The analysis shows that more degrees of freedom than the traditional dihedral angles, phi and psi, are necessary to describe the reaction coordinates for isomerization of this molecule. In vacuum, an additional dihedral angle is identified as significant. In solution, ...
متن کاملEffective dynamics along given reaction coordinates, and reaction rate theory.
In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free ...
متن کاملComputing Hopf Bifurcations in Chemical Reaction Networks Using Reaction Coordinates
The analysis of dynamic of chemical reaction networks by computing Hopf bifurcation is a method to understand the qualitative behavior of the network due to its relation to the existence of oscillations. For low dimensional reaction systems without additional constraints Hopf bifurcation can be computed by reducing the question of its occurrence to quantifier elimination problems on real closed...
متن کاملGENERATING REACTION COORDINATES BY THE PAULlNG RELATION
RA-, =RA-&), R,-c = RB__c@) (5) These two parametric equations uniquely determine a trajectory which we shall call the BEBO RC. This we compare to the minimum energy path on the appropriate potential energy surface (PES). A good agreement is known to exist for H2 + H PES (see fig. 1 of ref. [3] and ref. [4]) and for H2 + F [4] where the PES of Bender et al. [5] has been used. The aim of this le...
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ژورنال
عنوان ژورنال: Wiley Interdisciplinary Reviews: Computational Molecular Science
سال: 2016
ISSN: 1759-0876
DOI: 10.1002/wcms.1276