Mathematical Biology and Bioinformatics 

About: Mathematical Biology and Bioinformatics is an academic journal published by Institute of Mathematical Problems of Biology of RAS (IMPB RAS). The journal publishes majorly in the area(s): Biology & Genome. It has an ISSN identifier of 1994-6538. It is also open access. Over the lifetime, 454 publications have been published receiving 1257 citations. The journal is also known as: Mathematical biology and bioinformatics.

Formation of stationary electronic states in finite homogeneous molecular chains

Abstract: Evolution of an arbitrary initial distribution of a quantum-mechanical particle in a uniform molecular chain is simulated by a system of coupled quantum- classical dynamical equations with dissipation. Stability of a uniform distribution of the particle over the chain is studied. An asymptotical expression is obtained for the time in which a localized state is formed. The validity of the expression is checked by direct computational experiments. It is shown that the time of soliton and multisoliton type states formation depends strongly on the initial phase of the particle's wave function. It is shown that in multisoliton states objects with a fractional electron charge which can be observed experimentally are realized. The results obtained are applied to synthetic uniform polynucleotide molecular chains.

Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: Modeling of structure and properties

Abstract: The structure and properties of diphenylalanine peptide nanotubes based on phenylalanine were investigated by various molecular modeling methods. The main approaches were semi-empirical quantum-chemical methods (PM3 and AM1), and molecular mechanical ones. Both the model structures and the structures extracted from their experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by naturally-occurring self-assembly showed their important differences depending on D- and L-chirality. In both the cases, the effect of chirality on the results of self-assembly of diphenylalanine peptide nanotubes was established: peptide nanotubes based on the D-diphenylalanine (D-FF) has high condensation energy E0 in transverse direction and forms thicker and shorter peptide nanotubes bundles, than that based on L-diphenylalanine (L-FF). A topological difference was established: model peptide nanotubes were optimized into structures consisting of rings, while naturally self-assembled peptide nanotubes consisted of helical coils. The latter were different for the original L-FF and D-FF. They formed helix structures in which the chirality sign changes as the level of the macromolecule hierarchy raises. Total energy of the optimal distances between two units are deeper for L-FF (–1.014 eV) then for D-FF (–0.607 eV) for ring models, while for helix coil are approximately the same and have for L-FF (–6.18 eV) and for D-FF (–6.22 eV) by PM3 method; for molecular mechanical methods energy changes are of the order of 2–3 eV for both the cases. A topological transition between a ring and a helix coil of peptide nanotube structures is discussed: self-assembled natural helix structures are more stable and favourable, they have lower energy in optimal configuration as compared with ring models by a value of the order of 1 eV for molecular mechanical methods and 5 eV for PM3 method.