Ying-Chih Chiang

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Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed together with computationally expensive enhanced sampling methods. Here we show that this sampling inefficiency, which(More)
Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl-CoA and shikimate, yet it also exhibits broad substrate permissiveness in vitro. How do enzymes like HCT avoid functional derailment by cellular metabolites(More)
Single-step free energy perturbation (sFEP) has often been proposed as an efficient tool for a quick free energy scan due to its straightforward protocol and the ability to recycle an existing molecular dynamics trajectory for free energy calculations. Although sFEP is expected to fail when the sampling of a system is inefficient, it is often expected to(More)
The resonant Auger process is studied in intense x-ray laser fields. It is shown that the dressing of the initial and decaying states by the field leads to coupled complex potential surfaces which, even for diatomic molecules, possess intersections at which the nonadiabatic couplings are singular. HCl is studied as an explicit showcase example. The exact(More)
A time-dependent approach for the kinetic energy release (KER) spectrum is developed for a fragmentation of a diatomic molecule after an electronic decay process, e.g., Auger process. It allows one to simulate the time-resolved spectra and provides more insight into the molecular dynamics than the time-independent approach. Detailed analysis of the(More)
In an electronic decay process followed by fragmentation the kinetic energy release and electron spectra can be measured. Classically they are the mirror image of each other, a fact which is often used in practice. Quantum expressions are derived for both spectra and analyzed. It is demonstrated that these spectra carry complementary quantum information and(More)
We investigate the exact wavefunction as a single product of electronic and nuclear wavefunction for a model conical intersection system. Exact factorized spiky potentials and nodeless nuclear wavefunctions are found. The exact factorized potential preserves the symmetry breaking effect when the coupling mode is present. Additionally nodeless wavefunctions(More)
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