Quadratic string method for determining the minimum-energy path based on multiobjective optimization

2006 ◽  
Vol 124 (5) ◽  
pp. 054109 ◽  
Author(s):  
Steven K. Burger ◽  
Weitao Yang
Keyword(s):  
Multiobjective Optimization ◽  
Minimum Energy ◽  
Minimum Energy Path ◽  
String Method

Optimization-Based String Method for Finding Minimum Energy Path

2013 ◽  
Vol 14 (2) ◽  
pp. 265-275 ◽  
Author(s):  
Amit Samanta ◽  
Weinan E
Keyword(s):  
Minimum Energy ◽  
Smooth Curve ◽  
Chem Phys ◽  
Descent Method ◽  
Method Phys ◽  
Steepest Descent Method ◽  
Minimum Energy Path ◽  
String Method ◽  
Constrained Minimization Problems ◽  
Minimization Algorithms

AbstractWe present an efficient algorithm for calculating the minimum energy path (MEP) and energy barriers between local minima on a multidimensional potential energy surface (PES). Such paths play a central role in the understanding of transition pathways between metastable states. Our method relies on the original formulation of the string method [Phys. Rev. B, 66,052301 (2002)], i.e. to evolve a smooth curve along a direction normal to the curve. The algorithm works by performing minimization steps on hyperplanes normal to the curve. Therefore the problem of finding MEP on the PES is remodeled as a set of constrained minimization problems. This provides the flexibility of using minimization algorithms faster than the steepest descent method used in the simplified string method [J. Chem. Phys., 126(16), 164103 (2007)]. At the same time, it provides a more direct analog of the finite temperature string method. The applicability of the algorithm is demonstrated using various examples.

scholarly journals Minimum-Energy Path for a U6 RNA Conformational Change Involving Protonation, Base-Pair Rearrangement and Base Flipping

2009 ◽  
Vol 391 (5) ◽  
pp. 894-905 ◽  
Author(s):  
Vincenzo Venditti ◽  
Lawrence Clos ◽  
Neri Niccolai ◽  
Samuel E. Butcher
Keyword(s):  
Conformational Change ◽  
Base Pair ◽  
Minimum Energy ◽  
Minimum Energy Path ◽  
Base Flipping ◽  
U6 Rna

scholarly journals On apparent barrier-free reactions

2020 ◽  
Vol 3 (1) ◽  
pp. 3-8
Author(s):  
Maikel Ballester
Keyword(s):  
Low Temperature ◽  
Chemical Reactions ◽  
Rate Constant ◽  
Kinetic Models ◽  
Rate Coefficient ◽  
Minimum Energy ◽  
Temperature Limit ◽  
Rate Coefficients ◽  
Minimum Energy Path ◽  
Full Dimension

Rate coefficients of bi-molecular chemical reactions are fundamental for kinetic models. The rate coefficient dependence on temperature is commonly extracted from the analyses of the reaction minimum energy path. However, a full dimension study of the same reaction may suggest a different asymptotic low-temperature limit in the rate constant than the obtained from the energetic profile.

Seemingly Anomalous Angular Distributions in H + D2 Reactive Scattering

Science ◽  
2012 ◽  
Vol 336 (6089) ◽  
pp. 1687-1690 ◽  
Author(s):  
Justin Jankunas ◽  
Richard N. Zare ◽  
Foudhil Bouakline ◽  
Stuart C. Althorpe ◽  
Diego Herráez-Aguilar ◽  
...  
Keyword(s):  
Cross Sections ◽  
Collision Energy ◽  
Minimum Energy ◽  
Angular Distributions ◽  
Quantum Mechanical ◽  
Minimum Energy Path ◽  
Reactive Scattering ◽  
Rotational Excitation ◽  
Reaction Products ◽  
Trajectory Calculations

When a hydrogen (H) atom approaches a deuterium (D2) molecule, the minimum-energy path is for the three nuclei to line up. Consequently, nearly collinear collisions cause HD reaction products to be backscattered with low rotational excitation, whereas more glancing collisions yield sideways-scattered HD products with higher rotational excitation. Here we report that measured cross sections for the H + D2 → HD(v′ = 4, j′) + D reaction at a collision energy of 1.97 electron volts contradict this behavior. The anomalous angular distributions match closely fully quantum mechanical calculations, and for the most part quasiclassical trajectory calculations. As the energy available in product recoil is reduced, a rotational barrier to reaction cuts off contributions from glancing collisions, causing high-j′ HD products to become backward scattered.

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