The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.

In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics manipulator (MD manipulator) is a controlled MDS type. As an example, the applicability of the developed algorithm for assembling peptide nanotubes (PNT) from linear phenylalanine (F or Phe) chains of different chirality is presented. The most adequate regimes for the formation of nanotubes of right chirality D from the initial L-F and nanotubes of left chirality L of their initial dipeptides D-F modes were determined. We use the method of a mixed (vector–scalar) product of the vectors of the sequence of dipole moments of phenylalanine molecules located along the nanotube helix to calculate the magnitude and sign of chirality of self-assembled helical phenylalanine nanotubes, which shows the validity of the proposed approach. As result, all data obtained correspond to the regularity of the chirality sign change of the molecular structures with a hierarchical complication of their organization.

In this study we consider the features of spatial-structure formation in proteins and their application in bioengineering. Methods for the quantitative assessment of the chirality of regular helical and irregular structures of proteins are presented. The features of self-assembly of phenylalanine (F) into peptide nanotubes (PNT), which form helices of different chirality, are also analyzed. A method is proposed for calculating the magnitude and sign of the chirality of helix-like peptide nanotubes using a sequence of vectors for the dipole moments of individual peptides.

A spatio-temporal model of megacity development that treats the megacity as an active medium is presented. From our point of view, it is advisable to consider the process of urban ecosystem development from the standpoint of the theory of autowave self-organization in active media. According to this concept, the urban ecosystem is considered as interacting with each other’s natural and anthropogenic subsystems with significant heterogeneity of areas affected by human intervention and urban geobiocoenoses. The model is based on the general principles of active medium dynamics; therefore, it is universal for any object to be considered an active medium. The only difference when using the model to predict the development of urban ecosystems in countries with different socio-economic and political prerequisites is the variety of parameters included in the model, i.e., the activation parameter, the autowave process inhibitors, and the characteristic scales of the activator and inhibitor. The model was tested on the example of Moscow expansion in the period of 1952–1968 and showed good agreement with the map data. By means of the model, a prediction of Shanghai and surrounding territory development until 2030 was made.

The concept of active media is used as a biophysical foundation for modeling spatiotemporal self organization in natural-anthropogenic ecosystems, appearing as establishment of regular dynamic structures with stable or unstable modes of development. Urban ecosystems are a hierarchy of interacting active media, with their nonlinearity being objectively formed owing to an extreme anthropogenic load, mismatch between the characteristic times and the evolutionary scales of the natural and anthropogenic components, as well as a complex system of positive and negative feedbacks between the constituent subsystems. The described model is purposefully simplified in order to use the Fitz-Hugh-Nagumo equation. The elaborated approach is of a general character and allows for a systematic description of spatiotemporal development of urban eco systems as distributed dissipative systems.