Chungwen Liang

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We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the transmembrane helices, which is changing during the opening(More)
We present the implementation of an approach to simulate the two-dimensional sum frequency generation response functions of systems with numerous coupled chromophores using a quantum-classical simulation scheme that was previously applied successfully to simulate two-dimensional infrared spectra. We apply the simulation to the amide I band of a(More)
We report the simulation results of the proton transport in a binary mixture of amphiphilic tetramethylurea (TMU) molecules and water. We identify different mechanisms that either facilitate or retard the proton transport. The efficiency of these mechanisms depends on the TMU concentration. The overall picture is more complicated than a recent suggestion(More)
For decades, the enigma of the hydrophobic force has captured the imagination of scientists. In particular, Frank and Evans' idea that the hydrophobic effect was mainly due to some kind of "iceberg" formation around a hydrophobic solute stimulated many experiments and molecular dynamics simulation studies. A better understanding of hydrophobic interactions(More)
We model the two-dimensional infrared (2DIR) spectrum of a proton channel to investigate its applicability as a spectroscopy tool to study the proton transport process in biological systems. Proton transport processes in proton channels are involved in numerous fundamental biochemical reactions. However, probing the proton transport process at the molecular(More)
We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental(More)
In this paper, we develop and test a new approximate propagation scheme for calculating two-dimensional infrared and visible spectra. The new scheme scales one order more efficiently with the system size than the existing schemes. A Trotter type of approximation is used for the matrix exponent that describes the time evolution of the quantum system. This is(More)
Second-harmonic scattering experiments of water and other bulk molecular liquids have long been assumed to be insensitive to interactions between the molecules. The measured intensity is generally thought to arise from incoherent scattering due to individual molecules. We introduce a method to compute the second-harmonic scattering pattern of molecular(More)
Electrolytes interact with water in many ways: changing dipole orientation, inducing charge transfer, and distorting the hydrogen-bond network in the bulk and at interfaces. Numerous experiments and computations have detected short-range perturbations that extend up to three hydration shells around individual ions. We report a multiscale investigation of(More)
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