Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation

We review in this article our recent simulation works on modeling peptide T-jump and thermal unfolding Fourier transform infrared spectroscopy(FTIR) and two-dimensional infrared(2DIR) spectra. The theoretical and computational techniques used,including Markov state model(MSM), integrated tempering sampling(ITS) and nonlinear exciton propagation(NEP), are first briefly introduced. The protocols for simulating the thermal unfolding as well as T-jump unfolding are then summarized in details. The simulated spectral features, such as the intensity and ellipticity, are demonstrated to agree well with the experimental observations.