The heterogeneity of aqueous solutions: the current situation in the context of experiment and theory.

The advancement of experimental methods has provided new information about the structure and structural fluctuations of water. Despite the appearance of numerous models, which aim to describe a wide range of thermodynamic and electrical characteristics of water, there is a deficit in systemic understanding of structuring in aqueous solutions. A particular challenge is the fact that even pure water is a heterogeneous, multicomponent system composed of molecular and supramolecular structures.

Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules.

DFT (VASP) and semi-empirical (HyperChem) calculations for the L- and D-chiral diphenylalanine (L-FF and D-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. The results obtained show that after optimization, the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like-cluster obtained after optimization inside L-FF and D-FF PNT and total L-FF and D-FF PNT with embedded water/ice cluster are discussed.

Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis.

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT.

A model of autowave self-organization as a hierarchy of active media in the biological evolution.

Within the framework of the active media concept, we develop a biophysical model of autowave self-organization which is treated as a hierarchy of active media in the evolution of the biosphere. We also propose a mathematical model of the autowave process of speciation in a flow of mutations for the three main taxonometric groups (prokaryotes, unicellular and multicellular eukaryotes) with a naturally determined lower boundary of living matter (the appearance of prokaryotes) and an open upper boundary for the formation of new species. It is shown that the fluctuation-bifurcation description of the evolution for the formation of new taxonometric groups as a trajectory of transformation of small fluctuations into giant ones adequately reflects the process of self-organization during the formation of taxa.

Chirality Driven Twisting as a Driving Force of Primitive Folding in Binary Mixtures.

The N-trifluoroacetylated α-aminoalcohols (TFAAAs) are able to form quasi-one-dimensional supramolecular fibers (strings) when chirally pure, and isometric precipitates in the racemate. The strings' formation leads to the reversible gelation of the solution. The fresh gels occupy all the available volume, however during the incubation, they contract and concentrate in the central region of the tube.

A percolation model of natural selection.

A new approach has been proposed and developed: the selection of optimal variants in the evolutionary mutation flow is considered as an analogue of a percolation filter. Interaction of mutations in a series of generations and random processes of drift determine the collective behavior of nodes (individuals - carriers and converters of mutations) and bonds (mutations) in the space of percolation lattice. It is shown that the choice of the development trajectory at the population level depends on the spectrum of supporting and prohibiting mutations under the influence of conjugate deterministic and random factors.

Spontaneous Resolution and Super-coiling in Xerogels of the Products of Photo-Induced Formose Reaction.

This work addresses the supramolecular self-organization in the xerogels of formose reaction products. The UV-induced formose reaction was held in over-saturated formaldehyde solutions at 70C without a catalyst. The solutions of the obtained carbohydrates were dried on a glass slide, and the obtained xerogels demonstrated a prominent optical activity, while the initial solutions were optically inactive.

Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes.

The structure and properties of diphenylalanine (FF) peptide nanotubes (PNT) based on phenylalanine were investigated by various molecular modeling methods. The main approach employed semi-empirical quantum-chemical methods (PM3 and AM1). Ab initio, density functional theory methods and molecular mechanical approaches were also used.

[Influence of Storage Temperature and Cryopreservation Conditions on the Extent of Human Sperm DNA Fragmentation].

With the direct labeling procedure for detecting DNA fragmentation we explored the influence of the different storage temperature conditions as well as different methods of cryopreservation on the structure of DNA organization in the human sperm. 19 sperm samples obtained from healthy men with normozoospermia (according to the criteria of the World Health Organization) were used for investigation. A significant increase of human sperm DNA-fragmentation was observed after 8 hours of incubation at +39 degrees C (by 76.

[Gelation in Low Concentrated Solutions of Cholesterol and Ergosterol].

The molecular dynamics method has been applied to investigate the conformational behavior of biologically important chiral molecules of cholesterol and ergosterol. The formation of strings in the solution of cholesterol in methanol and the lack of strings in solutions of ergosterol in methanol has been experimentally detected. It was shown that the intermolecular dynamics in the molecule has a significant impact on the potential of structure formation.

[Experimental observation of synergetic regular change of chirality sign in the hierarchy of biomimetic structures].

Having investigated chiroptical characteristics of homochiral solutions of biomimetics the rule of changing a chirality sign in spontaneous formation of supramolecular helical structures was experimentally substantiated. This self-organization presents evidence of a fundamental synergetic law of changing the chirality sign during the transition to a higher hierarchical level, being of common for modular prebiotic homochiral systems and basic molecular biological systems.

["Microbiological aging" by Mechnikov. How to interpret these ideas today?].

I.I. Mechnikov's hypothesis that the key to prolongation of life lies in the introduction of useful microflora to the gut was not proved.

[Chirality as a primary switch of hierarchical levels in molecular biological systems].

A synergetic law, being of common physicochemical and biological sense, is formulated: any evolving system that possesses an excess of free energy and elements with chiral asymmetry, while being within one hierarchical level, is able to change the type of symmetry in the process of self-organization increasing its complexity but preserving the sign of a prevailing chirality (left - L or right - D twist). The same system tends to form spontaneously a sequence of hierarchical levels with alternating chirality signs of de novo formed structures and with an increase of the structures relative scales. In living systems, the hierarchy of conjugated levels of macromolecular structures that begins from the "lowest" asymmetric carbon serves as an anti-entropic factor as well as the structural basis of "selected mechanical degrees of freedom" in molecular machines.

Superspiralization of chiral strings.

A phenomenon of superspiralization was revealed in homochiral solutions of biomimetics with strings lengths from 10(2) nm to 10(2) μ and longer: strings of greater size spontaneously formed in solution are twined of the smaller strings, which also have a helical structure. The chiral pitch depends on the conditions of formation of a particular string and can vary by several times in different strings of the same specimen.

Metric similarity of dynamic commutation processes in situ and in vitro.

The dynamics of string growth was studied in model homochiral solutions of biomimetics, trifluoroacetylated amino alcohols (TFAAA) in heptane, water, and inverted heptane-water emulsion. In heptane and water, a thick (~1 μ in diameter) string had a crown of thin strings on its growing terminal and these thin strings effectively adsorbed dissolved TFAAA. In emulsion, the strings grew inside the water droplets, in which this TFAAA cannot be solved, presumably due to transport of TFAAA molecules from heptane into water in the surface layer surrounding the string.

Biological fluids as chiral anisometric media.

Molecules of dissolved substance in many homochiral solutions are arranged in linear associations forming chiral strings (with length to diameter proportion of 10(1)-10(5)), which leads to solidification of the solution into anisometric gel. This paper describes the formation of the string system in aqueous solution of amino acid phenylalanine, formation of individual strings, weaving of thin strings into thick ones, successive alteration of the solution chirality sign with transition to new levels of the association organization. It seems that biological media are anisometric fluids containing chiral molecular associations and strings, or anisometric gels.

[From symmetries to the laws of evolution. I. Chirality as a means of active media stratification].

Features of the hypothetical evolution of a hierarchy of chiral objects formed by active media are discussed. On the basis of experimental facts a new synergetic generalization is made: an evolving system can repeatedly broaden the spectrum of its symmetry types within one level of organization which increases its complexity and change the sign of chirality during transition to a higher level. Switching the chirality sign of macroscopic objects provides irreversibility of stratification.

[Native and chiral modified NMDA-receptor NR1-binding core ligands modeling].

Native and chiral modified (with non-enzymatic Asn racemization) NR1-binding core of NMDA-receptor was modelled by means of molecular dynamic ligand modelling. It was concluded that Gly, D-Ser, D-Asn and D-Thr are ligands of NR1-binding core native NMDA-receptor, whereas the chiral modified NR1-binding core is characterized by the aliphatic non-polar amino acids D-Ala, D-Leu, D-Ile and D-Pro as ligands. The latter amino acids can be considered as effective ligands of NMDA-receptor NR1-binding core in age-related pathology.

[Energy distribution and ionic selectivity of the bacterial potassium channel].

An explanation for the ionic selectivity of the bacterial potassium channel K(CS)A is offered, which is based on a comparison of energy interactions of lithium, sodium, and potassium cations with the atoms of the selective filter of an protein pore. Using quantum-chemical calculations, the presence of a deeper potential hole for potassium ions was discovered, which explains the energy preferableness in their permeability. It has been shown that the traditional methods of force field AMBER, CHARMM, OPLS in reference parametrization and also at their partial reparametrization give incorrect ratings of energy distribution of ions in the channel.

[Mixed monolayers of amphiphile-modified nucleic bases and diynoic acids. I. Phase states at air-water interface and in Langmuir-Blodgett films].

Monolayers of amphiphile-modified nucleic bases with diynoic acid were obtained and characterized. The synthesized nucleic bases contained in the monolayer complementarily bind the nucleotide molecules contained in the aqueous subphase, and the structure of the resulting monolayers can be fixed by the photopolymerization of diynoic acid. The resulting monolayer exemplifies a novel type of model systems for investigating molecular recognition at the surface of biological membranes.

[Chiral safety of the biosphere as a biophysical problem].

The biosphere with its inherent chiral asymmetry fixed in the process of biological evolution at the level of L-amino acids and D-hydrocarbons and some other biologically active compounds of biogenic origin is under strong pressure of chiral substances produced by chemical, pharmaceutical, and other branches of industry and agriculture. Effective use of enantiomers is accompanied by toxic and even mutagenic effects of their mirror-image enantiomorphs. Only small amounts of products are tested for chiral purity; there is no system of global biosphere monitoring as well as no common standards of permissible concenrations.

[On the methods of calculation of the electrostatic potential in a protein channel].

The profiles of the electrostatic potential along the axis of a gramicidin channel were calculated using two quantum chemistry methods (EHT and CNDO/2) and three methods of force fields (AMBER, CHARMM, and OPLS). The calculations were performed without taking into account the contribution of water. A comparative analysis of the calculated profiles indicated that the electrostatic field of point charges of the CHARMM force field is close to that obtained by the quantum chemistry methods.

[The school of Blumenfeld today].

A historical survey of the activity of the Chair of Biophysics of the Physical Faculty of the Moscow State University as a scientific school of L.A. Blumenfeld, its founder and head, is given.

[Permeabilization of cell membrane by programmed form of electrical pulses].

The role of the shape of electric pulses of cell permeabilization and lysis was studied using the newly developed DPS electroporator. The effects of bipolar pulses, steep rising and falling edges in the pulses, delays between pulses, and shapes of DC signals between the edges on the lysis of bovine oocytes and the permeabilization of their cell membranes were investigated. Comparing the permeabilization rates with the lysis rates revealed a number of correlations, which make it possible to optimize the pulse shapes for achieving maximum permeabilization rates while keeping the lysis rates low.