Mikhail Mazo | Semenov Institute of Chemical Physics (ICP RAS) (original) (raw)

Papers by Mikhail Mazo

Research paper thumbnail of The “sugar” coarse-grained DNA model

Journal of Molecular Modeling, 2017

Research paper thumbnail of Molecular dynamics simulation of two-sided chemical modification of carbon nanoribbons on a solid substrate

Doklady Physical Chemistry, 2017

Research paper thumbnail of Molecular Simulation of Plastic Deformation of Oligomer Systems

Advanced Structured Materials, 2018

Molecular dynamic simulation of low-temperature uniaxial compression and tension of a glass from ... more Molecular dynamic simulation of low-temperature uniaxial compression and tension of a glass from 1000 molecules of C13H28 oligomer is carried out. Stress-strain diagrams, an influence of deformation on density of the glass, and connection between local density and atom rearrangements are discussed. The influence of original level of stress on initial rate of stress relaxation are also investigated. The modeling results of mechanical behavior are in good agreement with experimental data for glassy polymers, which allows one to use MD modeling for further in-depth study of glass behavior mechanisms under mechanical actions.

Research paper thumbnail of Structure and free volume of fluorine-containing polyetherimides with pendant di-tert-butyl groups investigated by molecular dynamics simulation

Polymer, 2022

The study is focused on the investigation of structural properties of 5 polyetherimides (PEIs) co... more The study is focused on the investigation of structural properties of 5 polyetherimides (PEIs) containing 1,4-bis-[{2′ -trifluoromethyl 4′ -(4′′ -aminophenyl)phenoxy}]-2,5-di-tert-butylbenzene diamine monomer (FMTBDA) and 5 different dianhydride monomers (PMDA, BTDA, ODPA, 6FDA, and BPADA) using molecular dynamics simulations.
32 independent models were built for each polymer. Densities calculated for the modeled samples were compared with the experimental ones, giving difference of up to 6%. Accessible free volume (AFV) distribution was evaluated for the investigated polymers. It was shown that AFV for all the probe sizes decreased in a row:
PMDA > BTDA~6FDA > ODPA > BPADA, which is in line with the experimental gas transport parameters shown previously. Bimodal AFV distribution was demonstrated. Specific surface area (SSA) was calculated for the models of polymers, and fragments composing the inner surface of the free volume were determined. Analysis of
the elements of the free volume surface has shown that sp3 carbon (Сsp3), carbonyl oxygen (OC=O), and fluorine (F) atoms tend to form free volume elements, while imide nitrogen (Nimide) and ether oxygen (Oether) tend to compose polymer bulk.

Research paper thumbnail of Спектр колебаний орторомбического полиэтилена в терагерцовом диапазоне: теория и численный эксперимент

Используя метод нормальных мод в рамках силового поля AMBER ff99, получен полный набор колебатель... more Используя метод нормальных мод в рамках силового поля AMBER ff99, получен полный набор колебательных мод кристалла орторомбического полиэтилена. В низкочастотной области до 500 см-1 построены все дисперсионные кривые и полный спектр колебаний, проведен анализ нормальных мод. Отдельно рассмотрены колебания, соответствующие плоским волнам вдоль полимерных цепочек. Проведено сравнение результатов с экспериментальными данными по неупругому рассеянию нейтронов и расчетами других авторо

Research paper thumbnail of Formation of a Hollow Core in Dendrimers in Solvents

Macromolecular Chemistry and Physics, 2021

Research paper thumbnail of Effects of generation number, spacer length and temperature on the structure and intramolecular dynamics of siloxane dendrimer melts: molecular dynamics simulations

Soft Matter, 2020

The structure and properties of two homologous series of polysiloxane dendrimer melts are studied... more The structure and properties of two homologous series of polysiloxane dendrimer melts are studied by extensive atomistic molecular dynamics simulations.

Research paper thumbnail of Plastic Deformation in Disordered Solids: The State of the Art and Unresolved Problems

Crystalline materials are deformed plastically through crystallographic mechanisms based on the l... more Crystalline materials are deformed plastically through crystallographic mechanisms based on the lattice’s periodicity. However, plasticity of disordered solids can’t be described in these terms due to an absence of regular lattices. To find the best way of the description of plastic response for disordered solids (DSs) became a serious challenge for material science and solid-state physics. This paper discusses current views on mechanism of plastic deformation in DSs and touches some problems in the field. It is broadly accepted now that one, common mechanism of plasticity operates in all DSs, independent on their chemical nature and interaction potentials. Such mechanism is dictated by the structural disorder of glasses. Many details of the mechanism are not well understood yet. Important features of the mechanism are discussed in this paper, and several problems, which do not permit the field to develop further successfully are considered.

Research paper thumbnail of Computer modelling of structure and dynamics of C-50 n-paraffin crystal, hexagonal phase of C-50 crystal and ethylene/propylene statistical copolymers

Macromolecular Symposia, 1999

Research paper thumbnail of High-temperature quasi-hexagonal phase in the simplest model of a polymer crystal

Doklady Physical Chemistry, 2008

ISSN 0012-5016, Doklady Physical Chemistry, 2008, Vol. 418, Part 2, pp. 15–18. © Pleiades Publish... more ISSN 0012-5016, Doklady Physical Chemistry, 2008, Vol. 418, Part 2, pp. 15–18. © Pleiades Publishing, Ltd., 2008.Original Russian Text © E.A. Zubova, A.I. Musienko, N.K. Balabaev, E.B. Gusarova, M.A. Mazo, L.I. Manevich, Al.Al. Berlin, 2008, published in Doklady Akademii Nauk, 2008,Vol. 418, No. 4, pp. 493–496.

Research paper thumbnail of MD Calculation Mechanical Properties of Fluorographene

We present the results for the elastic properties of a single layered carbon monofluoride or fluo... more We present the results for the elastic properties of a single layered carbon monofluoride or fluorographen (FG). The calculations were performed by molecular dynamics (MD) simulation using a force field with both bonded and non-bonded interatomic contributions, and the periodic boundary conditions in two dimensions, representing an infinite "nanoplate". Simulations were fulfilled both for three basic conformations of FG (1) and for the FG with number counts of structural defects. The elastic modulus was calculated from the curves of force versus displacement obtained at slow rates of deformation. Bending stiffness was estimated independently from the nonlinear deformation under compression. The atomistic results are explained in terms of a continuum model for the thin plates. In the last years the great attention is paid to the investigations of properties of one layered membranes of graphen and similar materials. It is connected with their unique electric and heart- condu...

Research paper thumbnail of The COMPASS force field: Validation for carbon nanoribbons

Physica E: Low-dimensional Systems and Nanostructures

Research paper thumbnail of Structure and Properties of High and Low Free Volume Polymers Studied by Molecular Dynamics Simulation

Computation

Using molecular dynamics, a comparative study was performed of two pairs of glassy polymers, low ... more Using molecular dynamics, a comparative study was performed of two pairs of glassy polymers, low permeability polyetherimides (PEIs) and highly permeable Si-containing polytricyclononenes. All calculations were made with 32 independent models for each polymer. In both cases, the accessible free volume (AFV) increases with decreasing probe size. However, for a zero-size probe, the curves for both types of polymers cross the ordinate in the vicinity of 40%. The size distribution of free volume in PEI and highly permeable polymers differ significantly. In the former case, they are represented by relatively narrow peaks, with the maxima in the range of 0.5–1.0 Å for all the probes from H2 to Xe. In the case of highly permeable Si-containing polymers, much broader peaks are observed to extend up to 7–8 Å for all the gaseous probes. The obtained size distributions of free volume and accessible volume explain the differences in the selectivity of the studied polymers. The surface area of A...

Research paper thumbnail of Adsorption of Silicon-Containing Dendrimers: Effects of Chemical Composition, Structure, and Generation Number

Polymers

We studied the conformational behavior of silicon-containing dendrimers during their adsorption o... more We studied the conformational behavior of silicon-containing dendrimers during their adsorption onto a flat impenetrable surface by molecular dynamics (MD) simulations. Four homologous series of dendrimers from the 4th up to the 7th generations were modeled, namely, two types of carbosilane dendrimers differing by the functionality of the core Si atom and two types of siloxane dendrimers with different lengths of the spacers. Comparative analysis of the fractions of adsorbed atoms belonging to various structural layers within dendrimers as well as density profiles allowed us to elucidate not only some general trends but also the effects determined by dendrimer specificity. In particular, it was found that in contrast to the carbosilane dendrimers interacting with the adsorbing surface mainly by their peripheral layers, the siloxane dendrimers with the longer –O–Si(CH3)2–O spacers expose atoms from their interior to the surface spreading out on it. These findings are important for th...

Research paper thumbnail of A Comparative Study of Intramolecular Mobility of Single Siloxane and Carbosilane Dendrimers via Molecular Dynamics Simulations

Polymers

A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the f... more A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the fourth to the seventh generations belonging to the siloxane and carbosilane families, differing in spacer length, core functionality, and the type of chemical bonds, has been performed via atomic molecular dynamics simulations. The average radial and angular positions of all Si branching atoms of various topological layers within the dendrimer interior, as well as their variations, have been calculated, and the distributions of the relaxation times of their radial and angular motions have been found. It has been shown that the dendrons of all the dendrimers elongate from the center and decrease in a solid angle with an increasing generation number. The characteristic relaxation times of both angular and radial motions of Si atoms are of the order of a few nanoseconds, and they increase with an increasing generation number and decrease with temperature, with the angular relaxation times be...

Research paper thumbnail of 2D Chain Models of Nanoribbon Scrolls

Advanced Structured Materials

Research paper thumbnail of Using spiral chain models for study of nanoscroll structures

Research paper thumbnail of Molecular and Dynamic Simulation of Low-Temperature Deformation of Explicit Atom Model of Glassy Polymethylene

Vestnik Volgogradskogo gosudarstvennogo universiteta. Serija 10. Innovatcionnaia deiatel’nost’, 2015

Research paper thumbnail of Molecular dynamics simulation of carbosilane dendrimer structure

Research paper thumbnail of Molecular Dynamics Simulation of Vitrification and Plastic Deformation of a Two-Dimensional Lennard-Jones Mixture

A computer model of a two-dimensional atomic glass is generated by molecular dynamics. This model... more A computer model of a two-dimensional atomic glass is generated by molecular dynamics. This model consists of 500 Lennard-Jones particles of two different diameters. A volume-temperature diagram is obtained. The bend found on this diagram at T = 0.288 is interpreted as the glass transition. Density fluctuations and changes in the particles coordination numbers at the glass transition are studied by means of Voronoy polygons. The spatial correlation functions for particle displacements in the liquid and glassy states are analyzed. It is found that the glass structure is always a frozen liquid structure. Below the glass transition particle displacements from their equilibrium positions become spatially correlated, and the correlation length is greater than the model's size. Unusual roton-like collective vibrational modes are found in the glass. The simulation of shear deformation shows that these modes may play an important role in the plastic deformation. No correlation is found between the diffusional mobility of particles and their local free volumes. This fact contradicts the main physical concept upon which a free volume approach is based. Ein Computermodell eines zweidimensionalen atomaren Glases wird mit Molekulardynamik generiert. Das Modell besteht aus 500 Lennard-Jones Teilchen mit zwei verschiedenen Durchmessern. Ein Volu-men-Temperaturdiagramm wird erhalten, in. dem die Krummung bei T = 0,28~ als Glasubergang interpretiert wird. Dichteschwankungen und Anderungen der Koordinationszahlen der Teilchen beim Glasubergang werden mit Voronoy-Polygonen studiert. Die raumlichen Korrelationsfunktionen der Teilchenverschiebung im flussigen und glasartigen Zustand werden untersucht. Es wird gefunden, daB die Glasstruktur immer eine eingefrorene Flussigkeitsstruktur ist. Unter dem Glasubergang werden die Verschiebungen der Partikel weg von den Gleichgewichtspositionen raumlich korreliert, und die Korrelationslange ist groBer als die ModellgroBe. Uniibliche rotationsahnliche kollektive Eigenschwin-gungen werden im Glas gefunden. Die Simulation von Scherung zeigt, daB die Eigenschwingungen eine wichtige Rolle in der plastischen Deformierung haben konnten. Es kann keine Korrelation gefunden werden zwischen Diffusionsmobilitat von Teilchen und ihrem freiem Volumen. Dies widerspricht dem grundlegenden physikalischen Modell, das auf dem Konzept des freien Volumens basiert.

Research paper thumbnail of The “sugar” coarse-grained DNA model

Journal of Molecular Modeling, 2017

Research paper thumbnail of Molecular dynamics simulation of two-sided chemical modification of carbon nanoribbons on a solid substrate

Doklady Physical Chemistry, 2017

Research paper thumbnail of Molecular Simulation of Plastic Deformation of Oligomer Systems

Advanced Structured Materials, 2018

Molecular dynamic simulation of low-temperature uniaxial compression and tension of a glass from ... more Molecular dynamic simulation of low-temperature uniaxial compression and tension of a glass from 1000 molecules of C13H28 oligomer is carried out. Stress-strain diagrams, an influence of deformation on density of the glass, and connection between local density and atom rearrangements are discussed. The influence of original level of stress on initial rate of stress relaxation are also investigated. The modeling results of mechanical behavior are in good agreement with experimental data for glassy polymers, which allows one to use MD modeling for further in-depth study of glass behavior mechanisms under mechanical actions.

Research paper thumbnail of Structure and free volume of fluorine-containing polyetherimides with pendant di-tert-butyl groups investigated by molecular dynamics simulation

Polymer, 2022

The study is focused on the investigation of structural properties of 5 polyetherimides (PEIs) co... more The study is focused on the investigation of structural properties of 5 polyetherimides (PEIs) containing 1,4-bis-[{2′ -trifluoromethyl 4′ -(4′′ -aminophenyl)phenoxy}]-2,5-di-tert-butylbenzene diamine monomer (FMTBDA) and 5 different dianhydride monomers (PMDA, BTDA, ODPA, 6FDA, and BPADA) using molecular dynamics simulations.
32 independent models were built for each polymer. Densities calculated for the modeled samples were compared with the experimental ones, giving difference of up to 6%. Accessible free volume (AFV) distribution was evaluated for the investigated polymers. It was shown that AFV for all the probe sizes decreased in a row:
PMDA > BTDA~6FDA > ODPA > BPADA, which is in line with the experimental gas transport parameters shown previously. Bimodal AFV distribution was demonstrated. Specific surface area (SSA) was calculated for the models of polymers, and fragments composing the inner surface of the free volume were determined. Analysis of
the elements of the free volume surface has shown that sp3 carbon (Сsp3), carbonyl oxygen (OC=O), and fluorine (F) atoms tend to form free volume elements, while imide nitrogen (Nimide) and ether oxygen (Oether) tend to compose polymer bulk.

Research paper thumbnail of Спектр колебаний орторомбического полиэтилена в терагерцовом диапазоне: теория и численный эксперимент

Используя метод нормальных мод в рамках силового поля AMBER ff99, получен полный набор колебатель... more Используя метод нормальных мод в рамках силового поля AMBER ff99, получен полный набор колебательных мод кристалла орторомбического полиэтилена. В низкочастотной области до 500 см-1 построены все дисперсионные кривые и полный спектр колебаний, проведен анализ нормальных мод. Отдельно рассмотрены колебания, соответствующие плоским волнам вдоль полимерных цепочек. Проведено сравнение результатов с экспериментальными данными по неупругому рассеянию нейтронов и расчетами других авторо

Research paper thumbnail of Formation of a Hollow Core in Dendrimers in Solvents

Macromolecular Chemistry and Physics, 2021

Research paper thumbnail of Effects of generation number, spacer length and temperature on the structure and intramolecular dynamics of siloxane dendrimer melts: molecular dynamics simulations

Soft Matter, 2020

The structure and properties of two homologous series of polysiloxane dendrimer melts are studied... more The structure and properties of two homologous series of polysiloxane dendrimer melts are studied by extensive atomistic molecular dynamics simulations.

Research paper thumbnail of Plastic Deformation in Disordered Solids: The State of the Art and Unresolved Problems

Crystalline materials are deformed plastically through crystallographic mechanisms based on the l... more Crystalline materials are deformed plastically through crystallographic mechanisms based on the lattice’s periodicity. However, plasticity of disordered solids can’t be described in these terms due to an absence of regular lattices. To find the best way of the description of plastic response for disordered solids (DSs) became a serious challenge for material science and solid-state physics. This paper discusses current views on mechanism of plastic deformation in DSs and touches some problems in the field. It is broadly accepted now that one, common mechanism of plasticity operates in all DSs, independent on their chemical nature and interaction potentials. Such mechanism is dictated by the structural disorder of glasses. Many details of the mechanism are not well understood yet. Important features of the mechanism are discussed in this paper, and several problems, which do not permit the field to develop further successfully are considered.

Research paper thumbnail of Computer modelling of structure and dynamics of C-50 n-paraffin crystal, hexagonal phase of C-50 crystal and ethylene/propylene statistical copolymers

Macromolecular Symposia, 1999

Research paper thumbnail of High-temperature quasi-hexagonal phase in the simplest model of a polymer crystal

Doklady Physical Chemistry, 2008

ISSN 0012-5016, Doklady Physical Chemistry, 2008, Vol. 418, Part 2, pp. 15–18. © Pleiades Publish... more ISSN 0012-5016, Doklady Physical Chemistry, 2008, Vol. 418, Part 2, pp. 15–18. © Pleiades Publishing, Ltd., 2008.Original Russian Text © E.A. Zubova, A.I. Musienko, N.K. Balabaev, E.B. Gusarova, M.A. Mazo, L.I. Manevich, Al.Al. Berlin, 2008, published in Doklady Akademii Nauk, 2008,Vol. 418, No. 4, pp. 493–496.

Research paper thumbnail of MD Calculation Mechanical Properties of Fluorographene

We present the results for the elastic properties of a single layered carbon monofluoride or fluo... more We present the results for the elastic properties of a single layered carbon monofluoride or fluorographen (FG). The calculations were performed by molecular dynamics (MD) simulation using a force field with both bonded and non-bonded interatomic contributions, and the periodic boundary conditions in two dimensions, representing an infinite "nanoplate". Simulations were fulfilled both for three basic conformations of FG (1) and for the FG with number counts of structural defects. The elastic modulus was calculated from the curves of force versus displacement obtained at slow rates of deformation. Bending stiffness was estimated independently from the nonlinear deformation under compression. The atomistic results are explained in terms of a continuum model for the thin plates. In the last years the great attention is paid to the investigations of properties of one layered membranes of graphen and similar materials. It is connected with their unique electric and heart- condu...

Research paper thumbnail of The COMPASS force field: Validation for carbon nanoribbons

Physica E: Low-dimensional Systems and Nanostructures

Research paper thumbnail of Structure and Properties of High and Low Free Volume Polymers Studied by Molecular Dynamics Simulation

Computation

Using molecular dynamics, a comparative study was performed of two pairs of glassy polymers, low ... more Using molecular dynamics, a comparative study was performed of two pairs of glassy polymers, low permeability polyetherimides (PEIs) and highly permeable Si-containing polytricyclononenes. All calculations were made with 32 independent models for each polymer. In both cases, the accessible free volume (AFV) increases with decreasing probe size. However, for a zero-size probe, the curves for both types of polymers cross the ordinate in the vicinity of 40%. The size distribution of free volume in PEI and highly permeable polymers differ significantly. In the former case, they are represented by relatively narrow peaks, with the maxima in the range of 0.5–1.0 Å for all the probes from H2 to Xe. In the case of highly permeable Si-containing polymers, much broader peaks are observed to extend up to 7–8 Å for all the gaseous probes. The obtained size distributions of free volume and accessible volume explain the differences in the selectivity of the studied polymers. The surface area of A...

Research paper thumbnail of Adsorption of Silicon-Containing Dendrimers: Effects of Chemical Composition, Structure, and Generation Number

Polymers

We studied the conformational behavior of silicon-containing dendrimers during their adsorption o... more We studied the conformational behavior of silicon-containing dendrimers during their adsorption onto a flat impenetrable surface by molecular dynamics (MD) simulations. Four homologous series of dendrimers from the 4th up to the 7th generations were modeled, namely, two types of carbosilane dendrimers differing by the functionality of the core Si atom and two types of siloxane dendrimers with different lengths of the spacers. Comparative analysis of the fractions of adsorbed atoms belonging to various structural layers within dendrimers as well as density profiles allowed us to elucidate not only some general trends but also the effects determined by dendrimer specificity. In particular, it was found that in contrast to the carbosilane dendrimers interacting with the adsorbing surface mainly by their peripheral layers, the siloxane dendrimers with the longer –O–Si(CH3)2–O spacers expose atoms from their interior to the surface spreading out on it. These findings are important for th...

Research paper thumbnail of A Comparative Study of Intramolecular Mobility of Single Siloxane and Carbosilane Dendrimers via Molecular Dynamics Simulations

Polymers

A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the f... more A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the fourth to the seventh generations belonging to the siloxane and carbosilane families, differing in spacer length, core functionality, and the type of chemical bonds, has been performed via atomic molecular dynamics simulations. The average radial and angular positions of all Si branching atoms of various topological layers within the dendrimer interior, as well as their variations, have been calculated, and the distributions of the relaxation times of their radial and angular motions have been found. It has been shown that the dendrons of all the dendrimers elongate from the center and decrease in a solid angle with an increasing generation number. The characteristic relaxation times of both angular and radial motions of Si atoms are of the order of a few nanoseconds, and they increase with an increasing generation number and decrease with temperature, with the angular relaxation times be...

Research paper thumbnail of 2D Chain Models of Nanoribbon Scrolls

Advanced Structured Materials

Research paper thumbnail of Using spiral chain models for study of nanoscroll structures

Research paper thumbnail of Molecular and Dynamic Simulation of Low-Temperature Deformation of Explicit Atom Model of Glassy Polymethylene

Vestnik Volgogradskogo gosudarstvennogo universiteta. Serija 10. Innovatcionnaia deiatel’nost’, 2015

Research paper thumbnail of Molecular dynamics simulation of carbosilane dendrimer structure

Research paper thumbnail of Molecular Dynamics Simulation of Vitrification and Plastic Deformation of a Two-Dimensional Lennard-Jones Mixture

A computer model of a two-dimensional atomic glass is generated by molecular dynamics. This model... more A computer model of a two-dimensional atomic glass is generated by molecular dynamics. This model consists of 500 Lennard-Jones particles of two different diameters. A volume-temperature diagram is obtained. The bend found on this diagram at T = 0.288 is interpreted as the glass transition. Density fluctuations and changes in the particles coordination numbers at the glass transition are studied by means of Voronoy polygons. The spatial correlation functions for particle displacements in the liquid and glassy states are analyzed. It is found that the glass structure is always a frozen liquid structure. Below the glass transition particle displacements from their equilibrium positions become spatially correlated, and the correlation length is greater than the model's size. Unusual roton-like collective vibrational modes are found in the glass. The simulation of shear deformation shows that these modes may play an important role in the plastic deformation. No correlation is found between the diffusional mobility of particles and their local free volumes. This fact contradicts the main physical concept upon which a free volume approach is based. Ein Computermodell eines zweidimensionalen atomaren Glases wird mit Molekulardynamik generiert. Das Modell besteht aus 500 Lennard-Jones Teilchen mit zwei verschiedenen Durchmessern. Ein Volu-men-Temperaturdiagramm wird erhalten, in. dem die Krummung bei T = 0,28~ als Glasubergang interpretiert wird. Dichteschwankungen und Anderungen der Koordinationszahlen der Teilchen beim Glasubergang werden mit Voronoy-Polygonen studiert. Die raumlichen Korrelationsfunktionen der Teilchenverschiebung im flussigen und glasartigen Zustand werden untersucht. Es wird gefunden, daB die Glasstruktur immer eine eingefrorene Flussigkeitsstruktur ist. Unter dem Glasubergang werden die Verschiebungen der Partikel weg von den Gleichgewichtspositionen raumlich korreliert, und die Korrelationslange ist groBer als die ModellgroBe. Uniibliche rotationsahnliche kollektive Eigenschwin-gungen werden im Glas gefunden. Die Simulation von Scherung zeigt, daB die Eigenschwingungen eine wichtige Rolle in der plastischen Deformierung haben konnten. Es kann keine Korrelation gefunden werden zwischen Diffusionsmobilitat von Teilchen und ihrem freiem Volumen. Dies widerspricht dem grundlegenden physikalischen Modell, das auf dem Konzept des freien Volumens basiert.