Weighted least square analysis method for free energy calculations
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25580
Abstract: Free energy calculation is an efficient way for studying rare event dynamics. For a complex rare event dynamics, multiple reaction coordinates may be required to describe the transition path between equilibrium states. Theoretically, a one‐dimensional… read more here.
Keywords: analysis method; free energy; transition path; energy ... See more keywords
Ab initio-based investigation of phase transition path and magnetism of Ni–Mn–In alloys with excess Ni or Mn
Sign Up to like & getrecommendations! Published in 2020 at "Acta Materialia"
DOI: 10.1016/j.actamat.2020.05.049
Abstract: Abstract Herein, we have revealed the phase transition path and magnetic properties of Ni–Mn–In alloys with excess Ni or Mn (Ni24+xMn12In12-x, Ni24+xMn12-xIn12 and Ni24Mn12+xIn12-x) by using ab initio calculations. It is demonstrated that excess Ni… read more here.
Keywords: alloys excess; phase transition; phase; transition path ... See more keywords
ATESA: An Automated Aimless Shooting Workflow.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00543
Abstract: Transition path sampling methods are powerful tools for studying the dynamics of rare events in molecular simulations. However, these methods are generally restricted to experts with the knowledge and resources to properly set up and… read more here.
Keywords: automated aimless; aimless shooting; atesa automated; transition path ... See more keywords
Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting
Sign Up to like & getrecommendations! Published in 2019 at "Nature Communications"
DOI: 10.1038/s41467-019-09739-0
Abstract: Na+/H+ antiporters exchange sodium ions and protons on opposite sides of lipid membranes. The electroneutral Na+/H+ antiporter NhaP from archaea Pyrococcus abyssi (PaNhaP) is a functional homolog of the human Na+/H+ exchanger NHE1, which is… read more here.
Keywords: proton; panhap transition; transition; transition path ... See more keywords
An Optimal Control Method to Compute the Most Likely Transition Path for Stochastic Dynamical Systems with Jumps
Sign Up to like & getrecommendations! Published in 2022 at "Chaos"
DOI: 10.1063/5.0093924
Abstract: Many complex real world phenomena exhibit abrupt, intermittent, or jumping behaviors, which are more suitable to be described by stochastic differential equations under non-Gaussian Lévy noise. Among these complex phenomena, the most likely transition paths… read more here.
Keywords: likely transition; transition path; path stochastic; transition ... See more keywords