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It has long been accepted that the multiple‐ion single‐file transport model is appropriate for many kinds of ion channels. However, most of the purely theoretical works in this field did not capture all of the important features of realistic systems. Nowadays, large‐scale atomic‐level simulations are more feasible. The discrepancy between theories, simulations, and experiments are getting obvious, enabling people to carefully examine the missing parts of the theoretical models and methods. In this work, it is attempted to find out the essential features that such kinds of models should possess, such that the physical properties of an ion channel be adequately reflected. [ABSTRACT FROM AUTHOR]

In the present work, we analyze the influence of the polarization effects taking place during the course of a 2DIR spectroscopy experiment performed on a molecular system undergoing an intermolecular vibrational energy transfer process. When both donor and acceptor molecules participating in the vibrational energy transfer are embedded in a host solvent, they face rotational diffusion that strongly distorts the resulting 2DIR spectra. It could be expected that the difference between rotational diffusion constants will be of particular interest. For this purpose, the polarization effects are discussed according to the different orderings of the laser‐molecule interactions. Next, we study the distortions of the spectra as a function of the rotational diffusion constants of the individual molecules. The knowledge of these polarization effects is relevant to the interpretation of the spectra. Finally, the conclusions reached in this work for a vibrational energy transfer are valid for any other type of third‐order optical process performed on the same molecular system. [ABSTRACT FROM AUTHOR]

In this work, we focused on the kinetics of a one‐dimensional Ising system (1DIS) with constant nearest‐neighbor interaction (NNI). The exact solution of both thermodynamics and kinetics of this system under quasi‐chemical approximation (QCA) had been shown in the literature, and the equilibrium solution was exact. In this work, it was discussed why QCA applied the best in the case of 1DIS with constant NNI. Furthermore, extension had been made to discuss that due to this special reason, perhaps the kinetics of the system under QCA is the correct steady‐state kinetics. Inspired by this observation, the activity and activity coefficients of the system was studied closely to re‐examine the form of the equation of motion under QCA. A novel concept—the instantaneous activities and the corresponding instantaneous activity coefficients—was introduced, and in terms of these quantities the kinetics seemed to be much simpler and physically more meaningful. The chevron plot of this system was also discussed and new way of looking at the rollover of chevron plots was presented. [ABSTRACT FROM AUTHOR]

The performance of an analytical expression for algorithmic decoherence time is investigated for non–Born–Oppenheimer molecular dynamics. There are two terms in the function that represents the dependence of the decoherence time on the system parameters; one represents decoherence due to the quantum time-energy uncertainty principle and the other represents a back reaction from the decoherent force on the classical trajectory. We particularly examine the question of whether the first term should dominate. Five one-dimensional two-state model systems that represent limits of multidimensional nonadiabatic dynamics are designed for testing mixed quantum-classical methods and for comparing semiclassical calculations with exact quantum calculations. Simulations are carried out with the semiclassical Ehrenfest method (SE), Tully’s fewest switch version (TFS) of the trajectory surface hopping method, and the decay-of-mixing method with natural switching, coherent switching (CSDM), and coherent switching with reinitiation (CSDM-D). The CSDM method is demonstrated to be the most accurate method, and it has several desirable features: (i) It behaves like the representation-independent SE method in the strong nonadiabatic coupling regions; (ii) it behaves physically like the TFS method in noninteractive region; and (iii) the trajectories are continuous with continuous momenta. The CSDM method is also demonstrated to balance coherence well with decoherence, and the results are nearly independent of whether one uses the adiabatic or diabatic representation. The present results provide new insight into the formulation of a physically correct decoherence time to be used with the CSDM method for non–Born–Oppenheimer molecular dynamic simulations. [ABSTRACT FROM AUTHOR]

In studying ultrafast electron transfer from a dye molecule to a nanosized semiconductor particle, pump-probe experiments are commonly used. In this system the electron transfer (ET) rate is faster than vibrational relaxation so that the ET rate should be described by a single-level rate constant and the probing signal (often in the form of time-resolved spectra) contains the contribution from the dynamics of both population and coherence (i.e., wave packet). In this paper, we shall present the theoretical treatments for femtosecond time-resolved pump-probe experiment and the dynamics of population and coherence by the density matrix method, and the calculation of single-level ET rate constant involved in a pump-probe experiment. As an application, we show the theoretical results using parameters extracted from experiments on a specific dye/semiconductor system. [ABSTRACT FROM AUTHOR]

A statistical-mechanical treatment of the solubilization in micelle is presented in combination with molecular simulation. The micellar solution is viewed as an inhomogeneous and partially finite, mixed solvent system, and the method of energy representation is employed to evaluate the free-energy change for insertion of a solute into the micelle inside with a realistic set of potential functions. Methane, benzene, and ethylbenzene are adopted as model hydrophobic solutes to analyze the solubilization in sodium dodecyl sulfate micelle. It is shown that these solutes are more favorably located within the micelle than in bulk water and that the affinity to the micelle inside is stronger for benzene and ethylbenzene than for methane. The micellar system is then divided into the hydrophobic core, the head-group region in contact with water, and the aqueous region outside the micelle to assess the relative importance of each region in the solubilization. In support of the pseudophase model, the aqueous region is found to be unimportant to determine the extent of solubilization. The contribution from the hydrophobic-core region is shown to be dominant for benzene and ethylbenzene, while an appreciable contribution from the head-group region is observed for methane. The methodology presented is not restricted to the binding of a molecule to micelle, and will be useful in treating the binding to such nanoscale structures as protein and membrane. [ABSTRACT FROM AUTHOR]

The evolution of gold nanoparticle (Au NP) clusters in living cells are studied by using sectional dark-field optical microscopy and chromatic analysis approach. During endocytosis, Au NP clusters undergo fantastic color changes, from green to yellow-orange due to the plasmonic coupling effect. Analysis of brightness/hue values of the dark-field images helps estimate the numbers of Au NPs in the clusters. The Au NP clusters were further categorized into four groups within the endocytosis. As the results, the late endosomes had increased number of large Au NP clusters with time, while clustered numbers in secondary and tertiary groups were first increased and then decreased due to the fusion and fission of the endocytic vesicles. The time constants and cluster numbers for different groups are fitted by using an integrated rate equation, and show a positive correlation with the size of the Au NP cluster. The efficiency of Au NP uptake is only about 50% for normal cells, while 75% for cancer cells. Compared to normal cells, cancer cells show a larger number in uptake, while faster rate in removal. The propose method helps the kinetic study of endocytosed nanoparticles in physiological conditions. [ABSTRACT FROM AUTHOR]

Abstract: K+ are selectively coordinated in the selectivity filter and concerted K+ and water movements in this region ensure high conduction rates in K+ channels. In channels with long pores many K+ binding sites are located intracellular to the selectivity filter (inner vestibule), but their contribution to permeation has not been well studied. We investigated this phenomenon by slowing the ion permeation process via blocking inwardly rectifying Kir2.1 channels with Ba2+ in the selectivity filter and observing the effect of K+ in the inner vestibule on Ba2+ exit. The dose–response effect of the intracellular K+ concentration ([K+]i) on Ba2+ exit was recorded with and without intracellular polyamines, which compete with K+ for binding sites. Ba2+ exit was facilitated by the cooperative binding of at least three K+. Site-directed mutagenesis studies suggest that K+ interacting with Ba2+ bound in the selectivity filter were located in the region between selectivity filter and cytoplasmic pore, i.e. the water cavity and G-loop. One of the K+ binding sites was located at residue D172 and another was possibly at M301. This study provides functional evidence for the three K+ binding sites in the inner vestibule previously identified by crystal structure study. [Copyright &y& Elsevier]