Microscopic Interactions of Melatonin, Serotonin and Tryptophan with Zwitterionic Phospholipid Membranes

The interactions at the atomic level between small molecules and the main components of cellular plasma membranes are crucial for elucidating the mechanisms allowing for the entrance of such small species inside the cell. We have performed molecular dynamics and metadynamics simulations of tryptophan, serotonin, and melatonin at the interface of zwitterionic phospholipid bilayers. In this work, we will review recent computer simulation developments and report microscopic properties, such as the area per lipid and thickness of the membranes, atomic radial distribution functions, angular orientations, and free energy landscapes of small molecule binding to the membrane. Cholesterol affects the behaviour of the small molecules, which are mainly buried in the interfacial regions. We have observed a competition between the binding of small molecules to phospholipids and cholesterol through lipidic hydrogen-bonds. Free energy barriers that are associated to translational and orientational changes of melatonin have been found to be between 10–20 kJ/mol for distances of 1 nm between melatonin and the center of the membrane. Corresponding barriers for tryptophan and serotonin that are obtained from reversible work methods are of the order of 10 kJ/mol and reveal strong hydrogen bonding between such species and specific phospholipid sites. The diffusion of tryptophan and melatonin is of the order of 10−7 cm2/s for the cholesterol-free and cholesterol-rich setups.

Optical and Structural Properties of α-Si1-xCx Films

In this paper, we reported experimental results about optical and structural properties of amorphous silicon carbide (α-Si1-xCx). The films of a-Si1-xCx) were grown by CVD on substrate of quartz glass. Optical constants (n-refractive index, a-absorption coefficient, Eg-optical energy band gap) of these films were determined by transmission spectra. The radial distribution functions (RDFs) of α- Sil−xCx) films were drawn out from the data of x-ray diffraction spectra. According to the RDFs, we imagined the statistic scene from which we could obtain the information of atomic radial distribution. The bond lengths and bond numbers of Si-Si, Si-C, and C-C could be also determined by RDFs. From the analysis of Raman spectra, we obtained the information of their vibration state density, and discerned the peaks of bond vibration, which agreed well with the results of α-Si1-xCx) RDF.

A Geometrical Model of the Structure of Liquid Silicon Incorporating the Local- and Medium-Range Orders

A new structure model of liquid silicon is tested by incorporating the local bond orientational order and the medium-range radial distribution. The shoulder observed on the high Q side of the principal peak in the structure factor of liquid silicon appears to be mainly caused by the atomic radial distribution in the range from 0.4 to 0.6 nm. On the other hand, a molecular dynamics simulation on liquid silicon shows that the angular distribution of neighboring atoms has tetrahedral-like features, similar to those in the β-tin type crystal structure with c/a = 0.7. With these facts in mind, a new geometrical model of liquid silicon is proposed which simultaneously satisfies the experimental density, radial distribution, calculated bond orientational order, and typical liquid nature of random orientation in the long range.