Vladimir Bystrov - Academia.edu (original) (raw)

Papers by Vladimir Bystrov

Mathematical Biology and Bioinformatics, Jun 30, 2023

Институт математических проблем биологии РАН-филиал ИПМ им. М.В. Келдыша РАН, Пущино, Россия Анно... more Институт математических проблем биологии РАН-филиал ИПМ им. М.В. Келдыша РАН, Пущино, Россия Аннотация. В работе развивается подход к моделированию процессов самосборки сложных молекулярных наноструктур методами молекулярной динамики с помощью молекулярно-динамического манипулятора. Ранее этот подход был рассмотрен на примере сборки фенилаланиновой спиральной нанотрубки из линейного набора цепочек молекул фенилаланина (F) различной хиральности: левых L-F и правых D-F. Теперь нами разработан алгоритм молекулярно-динамической самосборки спиральных структур типа пептидных нанотрубок из молекул дифенилаланина (FF) различной хиральности L-FF и D-FF. Процесс самосборки цепочек дипептидов в спиральные структуры нанотрубок представляет собой имитацию прикладывания определенных силовых воздействий к имеющейся начальной линейной структуре с целью получения конечной структуры того же химического состава, но с иной спиральной геометрией. В качестве основного программного обеспечения использован программный комплекс моделирования молекулярной динамики PUMA-CUDA. Используя этот инструмент, можно исследовать процесс формирования спиральных структур из линейной последовательности любых аминокислот. Был выполнен сравнительный анализ структур нанотрубок, полученных при сборке методами молекулярной динамики и при их экспериментальной самосборке, с применением метода визуально-дифференциального анализа. Установлено, что полученные данные соответствуют закону смены знака хиральности молекулярных спиральных структур при усложнении их иерархического уровня организации.

Aktualʹnye voprosy biologičeskoj fiziki i himii, May 27, 2024

Coupling between electrical and mechanical phenomena is very often in nature. Apparently, it unde... more Coupling between electrical and mechanical phenomena is very often in nature. Apparently, it underpins the functionality of materials and systems as diversified as ferroelectrics and multiferroics to electroactive molecules to biological materials. In ferroelectrics, electromechanical behavior is directly linked to polarization order parameter and hence can be used to study phenomena ranging from polarization reversal mechanisms, domain wall pinning, cross-coupled phenomena in multiferroics, to direct imaging of electron-lattice coupling. It may be said that electromechanical coupling is also a key component of many electrochemical transformations, in which changes in oxidation state are associated with the variation in molecular shape and bond geometry. Electromechanical energy conversion is an integral part of processes such as triboelectricity, cavitation, and sonoluminescence. It will not be an exaggeration to say that electromechanics, along with mechanics and transport, is one of the fundamental phenomena in nature. Therefore, it forms a basis for numerous device applications, and is thus directly relevant to virtually all existing and emerging aspects of materials and nanoscience. Recent years showed significant growth of interest towards nanoscale electromechanical phenomena originating independently in ferroelectric MEMS, biological, nano-and material science, and organic chemistry communities. The interest is stimulated both by development of nanoscience and necessity for efficient electromechanical motion and transformation at the nanoscale, and also recent emergence of scanning probe microscopy techniques capable of addressing electromechanical phenomena at a local level. As a relevant comparison, nanoscale properties are often accessible as a result of evolutionary development from macroscopic probes (e.g. interferometry or Berlincourt meter) to nanoscale, and corresponding macroscopic properties have been studied systematically since the dawn of industrial revolution. Electromechanical properties described by antisymmetric tensors averaged out in macroscopic systems and corresponding coupling coefficients are typically small (~100 pm/V), necessitating precise measurement tools even for macroscopic samples. These two factors resulted in limited quantitative and reproducible macroscopic studies of electromechanics even in single crystals and ceramics, recognized as important for applications (piezotransducers, SAW, sonar, ultrasonic imaging devices). Nanoscale offers a set of novel electromechanical phenomena induced by symmetry breaking at low dimensionality and by unique combination of high electric field and charge in nanovolumes that can lead to anomalous polarization reversal [1]. Ferroelectric materials are being intensively investigated due to their outstanding characteristics useful for various microelectronic devices ranging from nonvolatile ferroelectric random access (FeRAMs) memories to microelectromechanical systems (MEMS). For these applications, the nanoscale properties of ferroelectrics are of crucial importance. Since the feature size of potential devices is currently approaching to the submicron dimensions, local characterization techniques are becoming indispensable to meet the requirements of microelectronic industry. Local properties are expected to deviate from macroscopic ones due to confinement effects, lack of sufficient nucleation, and surface phenomena [2]. Piezoresponse Force Microscopy (PFM) has recently proved its usefulness for high-resolution domain imaging and local electromechanical characterization of ferroelectric materials [3].

Keldysh Institute Preprints, 2021

Mathematical Biology and Bioinformatics, Oct 2, 2009

The most principal methods of studying hydroxyapatite (HAP) nanostructures and proton transfer pe... more The most principal methods of studying hydroxyapatite (HAP) nanostructures and proton transfer peculiarities, its polarization properties are presented in this paper. HAP is one of the most widely used materials in medicine and biotechnology. The interaction between HAP biomaterials and living cells is improved, if the HAP surface is charged. The charge is inducible on HAP ceramics by the proton transport along the OH chains in columnar channels. These chains are formed by OH ions along c-axis and are surrounded by calcium triangles. The paper presents ab initio quantum-chemical calculations (with Gaussian98 code, HF, 6-31G(d)), which clarify the double-well asymmetric potential energy profile and were held to investigate the energy barriers for proton transport along the columnar channel. The calculated values of barriers can explain long storage of polarization charge, which is observed in experiments. The value of applied electric field could switch asymmetry of double-wall potential and made the proton transfer possible is of the order of 10 9 V/m, but proton tunneling is possible at 10 6 V/m. The estimated value of HAP surface polarization ~ 0.1 C/m 2 influences movement of living cells and leads to their adhesion on the charged HAP surface.

Proceedings of the International Conference "Mathematical Biology and Bioinformatics"

В работе проведено молекулярное моделирование и компьютерный анализ фотоэлектронных эффектов в ди... more В работе проведено молекулярное моделирование и компьютерный анализ фотоэлектронных эффектов в дифенилаланиновых (FF) пептидных нанотрубках (PNT) «левой» (L-FF) и «правой» (D-FF) хиральности, собранными в спиральную структуру, с использованием квантовохимических полуэмпирических методов из программных пакетов HyperChem (AM1, RM1) и MOPAC (PM3, PM7, PM6-D3H4) в разных приближениях Хартри-Фока. Результаты расчетов фотоэлектронных характеристик FF PNT (значения E_HOMO, E_LUMO и ширины запрещенной зоны Eg = E_LUMO-E_HOMO), и их изменения под влиянием электрического поля, анализируются также в сравнении со значениями внутреннего электрического поля, создаваемого собственной поляризацией вдоль оси нанотрубок суммарным дипольным моментом дипептидов FF. Полученные значения ширины запрещенной зоны Eg ~ 3.5-4.9 эВ лежат в области солнечно-слепого ультрафиолета (ССУФ) и находятся в хорошем согласии с экспериментальными данными, также как, и оценки эффектов фотолюминесценции. Создание электрического поля и его изменения возможно здесь также влиянием внедренных слоев полимерного сегнетоэлектрика ПВДФ/П(ВДФ-ТрФЭ). Благодаря объемному фотовольтаическому эффекту, эти композитные гетероструктуры могут быть использованы для автономного гибкого солнечно-слепого ультрафиолетового (ССУВ) фотоприемника.

Nanomaterials, 2021

The chirality quantification is of great importance in structural biology, where the differences ... more 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 differen...

Nanomaterials, 2021

In this study we consider the features of spatial-structure formation in proteins and their appli... more 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.

Minerals, 2021

High-temperature powder sintering is an integral part of the dense ceramic manufacturing process.... more High-temperature powder sintering is an integral part of the dense ceramic manufacturing process. In order to find the optimal conditions for producing a ceramic product, the information about its behavior at high temperatures is required. However, the data available in the literature are very contradictory. In this work, the thermal stability of hydroxyapatite prepared by a solid-state mechanochemical method and structural changes occurring during sintering were studied. Stoichiometric hydroxyapatite was found to remain as a single-phase apatite structure with the space group P63/m up to 1300 °C inclusively. A further increase in the sintering temperature leads to its partial decomposition, a decrease in the crystallite size of the apatite phase, and the appearance of significant structural strains. It was shown that small deviations from stoichiometry in the Ca/P ratio upward or downward during the hydroxyapatite synthesis lead to a significant decrease in the thermal stability of...

Nanomaterials, 2020

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral... more 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. Ferroelectric properties of tubular water/ice helix-like cluster, obtained after optimization inside L-FF and D-FF PNT, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed.

Crystal Growth & Design, 2019

To verify high purity of the used powders we have performed 1 H NMR and UHPLC-MS analyses to reve... more To verify high purity of the used powders we have performed 1 H NMR and UHPLC-MS analyses to reveal the impurities mentioned above. 1 H NMR measurements of powders dissolved in D 2 O in the presence of DCl and separately in DMSO-d6 did not reveal the presence of any impurities in both powders. Additional recrystallization of powders from H 2 O-HFIP mixture did not affect the purity of the samples according to 1 H NMR spectroscopy. However the sensitivity of the method does not exceed 3-5% and thus cannot undoubtedly confirm the identical purity of the dipeptides.

Journal of Molecular Modeling, 2019

The structure and properties of diphenylalanine (FF) peptide nanotubes (PNT) based on phenylalani... more 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. Both model structures and structures extracted from experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by natural self-assembly revealed important differences depending on chirality: D and L. In both the cases, the effect of chirality on the results of self-assembly of FF PNT was established: PNT based on the D-FF has large condensation energy E 0 in the transverse direction, and form thicker and shorter PNT bundles than those based on L-FF. A topological difference was established: model PNT were optimized into structures consisting of rings, while naturally self-assembled PNT consisted of helical turns. The latter nanotubes differed from the original L-FF and D-FF and formed helix structures of different chirality signs in accordance with the alternation rule of chirality due to macromolecule hierarchy. A topological transition between ring and helix turn PNT structures is discussed: self-assembled natural helix structures are favorable and their energy is lower by a value of the order of one to several eV.

Proceedings of the International Conference "Mathematical Biology and Bioinformatics", 2018

Proceedings of the International Conference "Mathematical Biology and Bioinformatics", 2018

Proceedings of the International Conference "Mathematical Biology and Bioinformatics", 2018

Proceedings of the 13th IEEE International Symposium on Applications of Ferroelectrics, 2002. ISAF 2002.

ABSTRACT The new experimental results and theoretical approaches in the bioferroelectricity field... more ABSTRACT The new experimental results and theoretical approaches in the bioferroelectricity field are analyzed and discussed. The earlier predicted Ferroelectric and Liquid-Crystal-Like Ferroelectric properties of a biological membrane (V. Bystrov, Ferr.Lett., 1992, v.13(6), p.127; 1997, v.27., p.87; 2000, v.27(5-6), p.147; R.Leuchtag&v.Bystrov, Ferroelectrics, 1999, v.220(3-4), p. 157), which was studied in the ion channels, now was experimentally observed in bacteriorhodopsin containing purple membrane films (I.Ermolina et al, J.Phys.Chem., 2001, v.105 (14), p. 2673). Recently bioferroelectric properties of biological objects had developed to the biomedical applications. One of this specific features is the nonlinear response on the weak actions (irradiation, external fields, various kind of nutrition etc.) in the vicinity of the critical for human organism (bifurcation) point, characterized biological object on various levels as on molecular, cell as on the whole organism level.

Journal of Applied Physics, 2015

Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid... more Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid (DNA). In the DNA molecule, thymine binds to adenine via two hydrogen bonds, thus stabilizing the nucleic acid structure and is involved in pairing and replication. Here, we show that synthetic thymine microcrystals grown from the solution exhibit local piezoelectricity and apparent ferroelectricity, as evidenced by nanoscale electromechanical measurements via Piezoresponse Force Microscopy. Our experimental results demonstrate significant electromechanical activity and polarization switchability of thymine, thus opening a pathway for piezoelectric and ferroelectric-based applications of thymine and, perhaps, of other DNA nucleobase materials. The results are supported by molecular modeling of polarization switching under an external electric field.

Математическая биология и биоинформатика, 2011

Electronic structure and self-polarization of P(VDF-TrFE) Langmuir-Blodgett nanofilms according t... more Electronic structure and self-polarization of P(VDF-TrFE) Langmuir-Blodgett nanofilms according to their thickness, composition and structural conformation under temperature phase transition were analyzed. Both thermostimulated exoelectron emission (TSEE) spectroscopy and computational simulation, including quantum-chemical calculations from first principles, were provided. PVDF and composite P(VDF-TrFE) (70:30) molecular chains as Trans and Gauche conformers as well as crystal cells were modeled for these agreedupon TSEE analyses. The quantum-chemical calculations and the computational simulation were based on the density functional theory (DFT) as well as semiempirical (PM3) methods. It was demonstrated that the energies of electron states as well as the total energies of the studied PVDF and P(VDFTrFE) molecular clusters during phase transformation influenced electron work function and electron affinity. The performed combined analysis of the TSEE experimental data as well as the computational data of the molecular models showed the effectiveness of that joined approach. TSEE for the first time was in use for contactless measurements of nanofilm polarization and characterizations of the phase transition. The proposed new method can be widely used in nanobiomedicine, particularly in development of new bone bio-implants, including built-in sensors (new smart nanotechnology).

Mathematical Biology and Bioinformatics, Jun 30, 2023

Институт математических проблем биологии РАН-филиал ИПМ им. М.В. Келдыша РАН, Пущино, Россия Анно... more Институт математических проблем биологии РАН-филиал ИПМ им. М.В. Келдыша РАН, Пущино, Россия Аннотация. В работе развивается подход к моделированию процессов самосборки сложных молекулярных наноструктур методами молекулярной динамики с помощью молекулярно-динамического манипулятора. Ранее этот подход был рассмотрен на примере сборки фенилаланиновой спиральной нанотрубки из линейного набора цепочек молекул фенилаланина (F) различной хиральности: левых L-F и правых D-F. Теперь нами разработан алгоритм молекулярно-динамической самосборки спиральных структур типа пептидных нанотрубок из молекул дифенилаланина (FF) различной хиральности L-FF и D-FF. Процесс самосборки цепочек дипептидов в спиральные структуры нанотрубок представляет собой имитацию прикладывания определенных силовых воздействий к имеющейся начальной линейной структуре с целью получения конечной структуры того же химического состава, но с иной спиральной геометрией. В качестве основного программного обеспечения использован программный комплекс моделирования молекулярной динамики PUMA-CUDA. Используя этот инструмент, можно исследовать процесс формирования спиральных структур из линейной последовательности любых аминокислот. Был выполнен сравнительный анализ структур нанотрубок, полученных при сборке методами молекулярной динамики и при их экспериментальной самосборке, с применением метода визуально-дифференциального анализа. Установлено, что полученные данные соответствуют закону смены знака хиральности молекулярных спиральных структур при усложнении их иерархического уровня организации.

Aktualʹnye voprosy biologičeskoj fiziki i himii, May 27, 2024

Coupling between electrical and mechanical phenomena is very often in nature. Apparently, it unde... more Coupling between electrical and mechanical phenomena is very often in nature. Apparently, it underpins the functionality of materials and systems as diversified as ferroelectrics and multiferroics to electroactive molecules to biological materials. In ferroelectrics, electromechanical behavior is directly linked to polarization order parameter and hence can be used to study phenomena ranging from polarization reversal mechanisms, domain wall pinning, cross-coupled phenomena in multiferroics, to direct imaging of electron-lattice coupling. It may be said that electromechanical coupling is also a key component of many electrochemical transformations, in which changes in oxidation state are associated with the variation in molecular shape and bond geometry. Electromechanical energy conversion is an integral part of processes such as triboelectricity, cavitation, and sonoluminescence. It will not be an exaggeration to say that electromechanics, along with mechanics and transport, is one of the fundamental phenomena in nature. Therefore, it forms a basis for numerous device applications, and is thus directly relevant to virtually all existing and emerging aspects of materials and nanoscience. Recent years showed significant growth of interest towards nanoscale electromechanical phenomena originating independently in ferroelectric MEMS, biological, nano-and material science, and organic chemistry communities. The interest is stimulated both by development of nanoscience and necessity for efficient electromechanical motion and transformation at the nanoscale, and also recent emergence of scanning probe microscopy techniques capable of addressing electromechanical phenomena at a local level. As a relevant comparison, nanoscale properties are often accessible as a result of evolutionary development from macroscopic probes (e.g. interferometry or Berlincourt meter) to nanoscale, and corresponding macroscopic properties have been studied systematically since the dawn of industrial revolution. Electromechanical properties described by antisymmetric tensors averaged out in macroscopic systems and corresponding coupling coefficients are typically small (~100 pm/V), necessitating precise measurement tools even for macroscopic samples. These two factors resulted in limited quantitative and reproducible macroscopic studies of electromechanics even in single crystals and ceramics, recognized as important for applications (piezotransducers, SAW, sonar, ultrasonic imaging devices). Nanoscale offers a set of novel electromechanical phenomena induced by symmetry breaking at low dimensionality and by unique combination of high electric field and charge in nanovolumes that can lead to anomalous polarization reversal [1]. Ferroelectric materials are being intensively investigated due to their outstanding characteristics useful for various microelectronic devices ranging from nonvolatile ferroelectric random access (FeRAMs) memories to microelectromechanical systems (MEMS). For these applications, the nanoscale properties of ferroelectrics are of crucial importance. Since the feature size of potential devices is currently approaching to the submicron dimensions, local characterization techniques are becoming indispensable to meet the requirements of microelectronic industry. Local properties are expected to deviate from macroscopic ones due to confinement effects, lack of sufficient nucleation, and surface phenomena [2]. Piezoresponse Force Microscopy (PFM) has recently proved its usefulness for high-resolution domain imaging and local electromechanical characterization of ferroelectric materials [3].

Keldysh Institute Preprints, 2021

Mathematical Biology and Bioinformatics, Oct 2, 2009

The most principal methods of studying hydroxyapatite (HAP) nanostructures and proton transfer pe... more The most principal methods of studying hydroxyapatite (HAP) nanostructures and proton transfer peculiarities, its polarization properties are presented in this paper. HAP is one of the most widely used materials in medicine and biotechnology. The interaction between HAP biomaterials and living cells is improved, if the HAP surface is charged. The charge is inducible on HAP ceramics by the proton transport along the OH chains in columnar channels. These chains are formed by OH ions along c-axis and are surrounded by calcium triangles. The paper presents ab initio quantum-chemical calculations (with Gaussian98 code, HF, 6-31G(d)), which clarify the double-well asymmetric potential energy profile and were held to investigate the energy barriers for proton transport along the columnar channel. The calculated values of barriers can explain long storage of polarization charge, which is observed in experiments. The value of applied electric field could switch asymmetry of double-wall potential and made the proton transfer possible is of the order of 10 9 V/m, but proton tunneling is possible at 10 6 V/m. The estimated value of HAP surface polarization ~ 0.1 C/m 2 influences movement of living cells and leads to their adhesion on the charged HAP surface.

Proceedings of the International Conference "Mathematical Biology and Bioinformatics"

В работе проведено молекулярное моделирование и компьютерный анализ фотоэлектронных эффектов в ди... more В работе проведено молекулярное моделирование и компьютерный анализ фотоэлектронных эффектов в дифенилаланиновых (FF) пептидных нанотрубках (PNT) «левой» (L-FF) и «правой» (D-FF) хиральности, собранными в спиральную структуру, с использованием квантовохимических полуэмпирических методов из программных пакетов HyperChem (AM1, RM1) и MOPAC (PM3, PM7, PM6-D3H4) в разных приближениях Хартри-Фока. Результаты расчетов фотоэлектронных характеристик FF PNT (значения E_HOMO, E_LUMO и ширины запрещенной зоны Eg = E_LUMO-E_HOMO), и их изменения под влиянием электрического поля, анализируются также в сравнении со значениями внутреннего электрического поля, создаваемого собственной поляризацией вдоль оси нанотрубок суммарным дипольным моментом дипептидов FF. Полученные значения ширины запрещенной зоны Eg ~ 3.5-4.9 эВ лежат в области солнечно-слепого ультрафиолета (ССУФ) и находятся в хорошем согласии с экспериментальными данными, также как, и оценки эффектов фотолюминесценции. Создание электрического поля и его изменения возможно здесь также влиянием внедренных слоев полимерного сегнетоэлектрика ПВДФ/П(ВДФ-ТрФЭ). Благодаря объемному фотовольтаическому эффекту, эти композитные гетероструктуры могут быть использованы для автономного гибкого солнечно-слепого ультрафиолетового (ССУВ) фотоприемника.

Nanomaterials, 2021

The chirality quantification is of great importance in structural biology, where the differences ... more 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 differen...

Nanomaterials, 2021

In this study we consider the features of spatial-structure formation in proteins and their appli... more 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.

Minerals, 2021

High-temperature powder sintering is an integral part of the dense ceramic manufacturing process.... more High-temperature powder sintering is an integral part of the dense ceramic manufacturing process. In order to find the optimal conditions for producing a ceramic product, the information about its behavior at high temperatures is required. However, the data available in the literature are very contradictory. In this work, the thermal stability of hydroxyapatite prepared by a solid-state mechanochemical method and structural changes occurring during sintering were studied. Stoichiometric hydroxyapatite was found to remain as a single-phase apatite structure with the space group P63/m up to 1300 °C inclusively. A further increase in the sintering temperature leads to its partial decomposition, a decrease in the crystallite size of the apatite phase, and the appearance of significant structural strains. It was shown that small deviations from stoichiometry in the Ca/P ratio upward or downward during the hydroxyapatite synthesis lead to a significant decrease in the thermal stability of...

Nanomaterials, 2020

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral... more 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. Ferroelectric properties of tubular water/ice helix-like cluster, obtained after optimization inside L-FF and D-FF PNT, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed.

Crystal Growth & Design, 2019

To verify high purity of the used powders we have performed 1 H NMR and UHPLC-MS analyses to reve... more To verify high purity of the used powders we have performed 1 H NMR and UHPLC-MS analyses to reveal the impurities mentioned above. 1 H NMR measurements of powders dissolved in D 2 O in the presence of DCl and separately in DMSO-d6 did not reveal the presence of any impurities in both powders. Additional recrystallization of powders from H 2 O-HFIP mixture did not affect the purity of the samples according to 1 H NMR spectroscopy. However the sensitivity of the method does not exceed 3-5% and thus cannot undoubtedly confirm the identical purity of the dipeptides.

Journal of Molecular Modeling, 2019

The structure and properties of diphenylalanine (FF) peptide nanotubes (PNT) based on phenylalani... more 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. Both model structures and structures extracted from experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by natural self-assembly revealed important differences depending on chirality: D and L. In both the cases, the effect of chirality on the results of self-assembly of FF PNT was established: PNT based on the D-FF has large condensation energy E 0 in the transverse direction, and form thicker and shorter PNT bundles than those based on L-FF. A topological difference was established: model PNT were optimized into structures consisting of rings, while naturally self-assembled PNT consisted of helical turns. The latter nanotubes differed from the original L-FF and D-FF and formed helix structures of different chirality signs in accordance with the alternation rule of chirality due to macromolecule hierarchy. A topological transition between ring and helix turn PNT structures is discussed: self-assembled natural helix structures are favorable and their energy is lower by a value of the order of one to several eV.

Proceedings of the International Conference "Mathematical Biology and Bioinformatics", 2018

Proceedings of the International Conference "Mathematical Biology and Bioinformatics", 2018

Proceedings of the International Conference "Mathematical Biology and Bioinformatics", 2018

Proceedings of the 13th IEEE International Symposium on Applications of Ferroelectrics, 2002. ISAF 2002.

ABSTRACT The new experimental results and theoretical approaches in the bioferroelectricity field... more ABSTRACT The new experimental results and theoretical approaches in the bioferroelectricity field are analyzed and discussed. The earlier predicted Ferroelectric and Liquid-Crystal-Like Ferroelectric properties of a biological membrane (V. Bystrov, Ferr.Lett., 1992, v.13(6), p.127; 1997, v.27., p.87; 2000, v.27(5-6), p.147; R.Leuchtag&v.Bystrov, Ferroelectrics, 1999, v.220(3-4), p. 157), which was studied in the ion channels, now was experimentally observed in bacteriorhodopsin containing purple membrane films (I.Ermolina et al, J.Phys.Chem., 2001, v.105 (14), p. 2673). Recently bioferroelectric properties of biological objects had developed to the biomedical applications. One of this specific features is the nonlinear response on the weak actions (irradiation, external fields, various kind of nutrition etc.) in the vicinity of the critical for human organism (bifurcation) point, characterized biological object on various levels as on molecular, cell as on the whole organism level.

Journal of Applied Physics, 2015

Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid... more Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid (DNA). In the DNA molecule, thymine binds to adenine via two hydrogen bonds, thus stabilizing the nucleic acid structure and is involved in pairing and replication. Here, we show that synthetic thymine microcrystals grown from the solution exhibit local piezoelectricity and apparent ferroelectricity, as evidenced by nanoscale electromechanical measurements via Piezoresponse Force Microscopy. Our experimental results demonstrate significant electromechanical activity and polarization switchability of thymine, thus opening a pathway for piezoelectric and ferroelectric-based applications of thymine and, perhaps, of other DNA nucleobase materials. The results are supported by molecular modeling of polarization switching under an external electric field.

Математическая биология и биоинформатика, 2011

Electronic structure and self-polarization of P(VDF-TrFE) Langmuir-Blodgett nanofilms according t... more Electronic structure and self-polarization of P(VDF-TrFE) Langmuir-Blodgett nanofilms according to their thickness, composition and structural conformation under temperature phase transition were analyzed. Both thermostimulated exoelectron emission (TSEE) spectroscopy and computational simulation, including quantum-chemical calculations from first principles, were provided. PVDF and composite P(VDF-TrFE) (70:30) molecular chains as Trans and Gauche conformers as well as crystal cells were modeled for these agreedupon TSEE analyses. The quantum-chemical calculations and the computational simulation were based on the density functional theory (DFT) as well as semiempirical (PM3) methods. It was demonstrated that the energies of electron states as well as the total energies of the studied PVDF and P(VDFTrFE) molecular clusters during phase transformation influenced electron work function and electron affinity. The performed combined analysis of the TSEE experimental data as well as the computational data of the molecular models showed the effectiveness of that joined approach. TSEE for the first time was in use for contactless measurements of nanofilm polarization and characterizations of the phase transition. The proposed new method can be widely used in nanobiomedicine, particularly in development of new bone bio-implants, including built-in sensors (new smart nanotechnology).