Ring polymer molecular dynamics in gas-surface reactions: tests on initial sampling and potential energy landscape

2021 ◽  
pp. e1941367
Author(s):  
Chen Li ◽  
Qinghua Liu ◽  
Liang Zhang ◽  
Yongle Li ◽  
Bin Jiang
2021 ◽  
Vol 23 (10) ◽  
pp. 6141-6153
Author(s):  
Jianwei Cao ◽  
Yanan Wu ◽  
Haitao Ma ◽  
Zhitao Shen ◽  
Wensheng Bian

Quantum dynamics and ring polymer molecular dynamics calculations reveal interesting dynamical and kinetic behaviors of an endothermic complex-forming reaction.


Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7250
Author(s):  
Yukinobu Takahashi ◽  
Yu Hashimoto ◽  
Kohei Saito ◽  
Toshiyuki Takayanagi

The dissociative photodetachment dynamics of the oxalate anion, C2O4H− + hν → CO2 + HOCO + e−, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron–photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO2 and HOCO fragments. This is because photodetachment of the parent anion leads to Franck–Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C2O4H− anion with closed- and open-form structures.


2020 ◽  
Vol 22 (1) ◽  
pp. 344-353 ◽  
Author(s):  
Yang Liu ◽  
Jun Li

Thermal rate coefficients for the Cl + CH4/CD4 reactions were studied on a new full-dimensional accurate potential energy surface with the spin–orbit corrections considered in the entrance channel.


2020 ◽  
Vol 22 (41) ◽  
pp. 23657-23664
Author(s):  
Yang Liu ◽  
Hongwei Song ◽  
Jun Li

The kinetics of the title reaction is studied by running the ring polymer molecular dynamics and quantum dynamics on an accurate potential energy surface.


2020 ◽  
Vol 117 (26) ◽  
pp. 14987-14995 ◽  
Author(s):  
Ratan Othayoth ◽  
George Thoms ◽  
Chen Li

Effective locomotion in nature happens by transitioning across multiple modes (e.g., walk, run, climb). Despite this, far more mechanistic understanding of terrestrial locomotion has been on how to generate and stabilize around near–steady-state movement in a single mode. We still know little about how locomotor transitions emerge from physical interaction with complex terrain. Consequently, robots largely rely on geometric maps to avoid obstacles, not traverse them. Recent studies revealed that locomotor transitions in complex three-dimensional (3D) terrain occur probabilistically via multiple pathways. Here, we show that an energy landscape approach elucidates the underlying physical principles. We discovered that locomotor transitions of animals and robots self-propelled through complex 3D terrain correspond to barrier-crossing transitions on a potential energy landscape. Locomotor modes are attracted to landscape basins separated by potential energy barriers. Kinetic energy fluctuation from oscillatory self-propulsion helps the system stochastically escape from one basin and reach another to make transitions. Escape is more likely toward lower barrier direction. These principles are surprisingly similar to those of near-equilibrium, microscopic systems. Analogous to free-energy landscapes for multipathway protein folding transitions, our energy landscape approach from first principles is the beginning of a statistical physics theory of multipathway locomotor transitions in complex terrain. This will not only help understand how the organization of animal behavior emerges from multiscale interactions between their neural and mechanical systems and the physical environment, but also guide robot design, control, and planning over the large, intractable locomotor-terrain parameter space to generate robust locomotor transitions through the real world.


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