Polymerization-induced self-assembly (PISA) enables the fabrication of polymeric nano-objects with tunable morphology and surface functionality. To obtain diverse nanostructured morphologies with antioxidant gallol pendants, a gallol methacrylate homopolymer (PM12) was synthesized as a steric stabilizer and subsequently chain-extended with N-phenylmethacrylamide (NP) to yield PM12-b-PNPm diblock copolymers via reversible addition-fragmentation chain transfer dispersion polymerization (RAFTDP) in alcoholic media. Depending on the block length of the PNPm segment, an array of morphologies, including micelles, worm-like aggregates, and vesicles, was obtained, as characterized by dynamic light scattering (DLS) and transmission electron microscopy (TEM). The experimentally observed morphology evolution was supported by molecular dynamics (MD) simulations using two complementary approaches: (i) atomistic MD to probe the local conformations of PM12-b-PNPm and its aggregation-driving block, and (ii) coarse-grained MD to investigate aggregate morphologies, thereby providing deeper insight into polymer self-assembly. Furthermore, deprotection of gallol methoxy (-OCH3) groups produced hydroxyl (-OH)-rich shells, endowing the polymers with antioxidant functionality, as confirmed by 1,1-diphenyl-2-picrylhydrazyl (DPPH center dot) and 2,2-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid (ABTS center dot & thorn;) assays.

While previous studies have illuminated the behavior of poly(gallol methacrylate)-block-poly(N-phenylmethacrylamide) copolymers (PM-b-PNP) in polar alcoholic mixtures, their performance in non-polar environments remains an uncharted territory. In this study, full-atomistic molecular dynamics (MD) simulations were first employed to investigate the conformational behavior and aggregation of experimentally relevant homo- and block copolymer architectures in heptane. The theoretical findings were subsequently supported through experimental studies using polymers synthesized via controlled reversible addition fragmentation chain transfer (RAFT) polymerization. Our results highlight the critical role of intramolecular hydrogen bonding in stabilizing specific conformations and helix-like structures of PNP homopolymers and the leading role of attractive van der Waals interactions in the aggregation of block copolymers.

In this study, we investigate how molecular density-governed by dendrimer generation and branching functionality-influences the conformational behavior and hydrogen bonding of OH-terminated carbosilane dendrimers in water, air, toluene, and at water-air and water-toluene interfaces by atomistic molecular dynamics simulations. We focus on the 4-3 series (G2-G4), featuring a tetrafunctional core and trifunctional branching, and compare it with the denser, more rigid 4-4G3 dendrimer of the third generation (tetrafunctional at both core and branching points). In hydrophobic environments, terminal OH groups form linear intramolecular aggregates; the 4-4G3 exhibits markedly reduced toluene uptake (10% vs 40% volume change for 4-3G4) and severely restricted intramolecular dynamics, with some OH groups remaining kinetically trapped near the core-a phenomenon requiring microsecond-scale simulations for proper characterization. In aqueous solution, 4-3 dendrimers expose OH groups at their periphery to form hydrogen bonds with water, whereas 4-4G3 retains a significant fraction of OH groups internally, forming intramolecular H-bonds instead. At interfaces, 4-3 dendrimers adopt flattened "umbrella" conformations to maximize interfacial H-bonding with water, swelling slightly into toluene to form biconvex shapes, while 4-4G3 remains nearly spherical due to steric constraints, forming over four times more intramolecular H-bonds and fewer with water than the more flexible 4-3G4. These findings establish molecular density as a key determinant of solvation, dynamics, and interfacial adaptability, providing a foundation for understanding structure-composition-property relationships in dendrimer monolayers under lateral confinement.

Amphiphilic dendrimers represent a promising class of nanoscale building blocks for functional materials, yet their conformational behavior, solvation, and interfacial activity remain incompletely understood. In this work, we employ atomistic molecular dynamics simulations to investigate G2-G4 carbosilane dendrimers functionalized with ethylene glycol terminal groups of two lengths-R1 (one ethylene glycol unit) and R3 (three units)-in water, toluene, and at fluid interfaces (water-toluene and water-air). Both types of dendrimers adopt compact, nearly spherical conformations in water but swell significantly (~83% in volume for G4) in toluene, a good solvent for the hydrophobic core. At the water-toluene interface, the dendrimers remain fully solvated in the toluene phase and show no surface activity. In contrast, at the water-air interface, they adsorb and adopt a mildly anisotropic, biconvex conformation, with a modest deformation. The total number of hydrogen bonds is reduced by ~50% compared to bulk water. Notably, the R3 dendrimers form more hydrogen bonds overall due to their higher oxygen content, which may contribute to the enhanced stability of their monolayers observed experimentally. These results demonstrate how dendrimer generation as well as terminal group length and hydrophilicity finely tune dendrimer conformation, hydration, and interfacial behavior, which are key factors for applications in nanocarriers, interfacial engineering, and self-assembled materials. The validated simulation protocol provides a robust foundation for future studies of multi-dendrimer systems and monolayer formation.

The drift of multiply protonated poly(ethylene oxide) chains in helium in electrostatic fields of various strengths is simulated using the molecular dynamics method. The simulation results are compared with the predictions of the kinetic theory of ion mobility, which relates the effect of increasing field strength to increasing ion temperature. As would be expected, the internal temperature of the ion Tion increases with increasing random kinetic energy received by the ion from the field. However, it grows more slowly than expected in the two-temperature theory. Ion mobility is calculated as a function of the field strength E at constant gas temperature T (300 K) and as a function of T at low E. The results of these two series of calculations are compared at the same internal ion temperatures. The results coincide at Tion close to T. At high ion temperatures, they diverge somewhat (by about 8

Due to the absence of specific interactions, carbosilane dendrimers are ideal models to study the effect of a hyperbranched regular structure on the molecular response to external influences. In this work, we have studied the conformational behavior of single polybutylcarbosilane dendrimers under confinement between impermeable flat surfaces using atomistic molecular dynamics simulations. Dendrimers of different generations belonging to two homologous series with a tetra-functional core and three- and four-functional branches were simulated. The analysis of the dependence of the internal energy of the dendrimers on the wall distance allowed us to determine the critical degree of compression at which the dendrimers are able to change their shape without energy loss. The effects of generation number and branching functionality on the number of wall contacts, density distribution and shape changes were elucidated. It was found that for high generation dendrimers, the inner layers are not accessible for external interaction. It was shown that the excess stresses occurring at high compressions are concentrated in the structural center of the dendrimer. The nature of the elastic response, which is strongly nonlinear, was analyzed at different compressions depending on the dendrimer architecture and generation. We believe that our results are useful for further studies of dendrimer films under compression and can also serve as a basis for developing model concepts to describe the dynamics of dendrimer melts.

The H 2 O–3-amino-1-propanol (3AP) system at 300 K was studied by molecular dynamics, graph theory, and Delaunay simplex methods. All the molecules were shown to be bound into a three-dimensional network of hydrogen bonds over the entire range of concentrations in the system. The characteristics of the networks and their concentration dependences were determined. The frequency at which the environment of molecules changes is discussed. The results were compared with those for mixed networks in aqueous solutions of 1,3-propanediol and monoethanolamine.

Communicated by Ramaswamy H. Sarma.

Networks of hydrogen bonds in mixtures of ethylene glycol (EG) and ethylenediamine (ED) are studied and described via molecular dynamics, graph theory, and Delaunay simplices. Results are compared to data on EG–H2O and ED–H2O systems.

Molecular dynamics simulations are used to study the drift of singly protonated poly(ethylene oxide) chains in helium in strong electrostatic fields. The behavior of the temperature, mobility and size of these ions is analyzed at various gas pressures and different lengths of the polymer chain. The internal temperature of the ion increases with increasing field strength in accordance with the increase in the random kinetic energy received by the ion from the field. This affects the mobility of the ion directly and through a change in the collision cross section associated with the unfolding of the polymer chain. At low gas pressures (from 384 to 1538 Torr), the reduced mobility is determined by the ratio of the field strength E to the gas density N and does not depend on the gas pressure. At higher gas pressures, it depends on the gas pressure at high E / N . This is due to the fact that under these conditions, the gas flow creates a significant tension in the polymer chain, which increases the size of the chain and the collision cross section. In strong fields, the ion ceases to rotate freely, since the field tends to align the dipole moment of the ion with the field. This reduces the collision cross section and partially compensates for changes in the collision cross section and ion mobility caused by the unfolding of the polymer chain.

The drift of singly protonated poly(ethylene oxide)s in helium under the action of an electrostatic field is simulated by the molecular dynamic method. The polymer chains are long, from 40 to 160 monomer units. The field strength is in the range from ~105 to ~107 V/m, the gas pressure varies from ~0.5 to ~6 atm. The ion mobility is obtained from the simulated drift velocity. The reduced mobility is approximately constant in all but the strongest fields and does not depend on the gas pressure. An increase in the polymer chain length leads to the expected decrease in mobility. The collision cross section is calculated in the simplest approximation using the simulated ion temperature as the effective temperature characterizing the energy of ion-gas collisions. The limits of applicability of this approximation are determined using the cross-sectional area of the ion obtained from the drag coefficient. In contrast to the size of the ion, the collision cross section decreases with increasing ion temperature, which agrees with the experimental results for a number of singly charged oligomers. The reasons for this effect are discussed. The effect of random ion diffusion on the simulated drift velocity and mobility is characterized.

Filamentous actin is one of the main components of the eukaryotic cellular cytoskeleton. In the cell, it performs such functions as cell motility, cell reshaping, cytokinesis, exo- and endocytosis, redistribution of surface receptors, and others. Since filamentous actin is a muscle tissue protein it also plays an important role in muscle contraction together with proteins myosin and titin. Therefore, the study of mechanical properties of filamentous actin is an important and urgent task in the fields of molecular biology and biophysics. In this work, the stretching of two models of filamentous actin was simulated at three constant velocities (0.1, 0.05 and 0.01 Å/ps) using the method of molecular dynamics. The first model was taken from the Protein Data Bank and the second model was built. From the analysis of the trajectories obtained, it follows that the second model of filamentous actin turned out to be more mechanically stable in comparison with the first model.

Hydroxyapatite (HAP) is the main mineral component of bones and teeth. Due to its biocompatibility, HAP is widely used in medicine as a filler that replaces parts of lost bone and as an implant coating that promotes new bone growth. The modeling and calculations of the structure and properties of HAP showed that various structural defects have a significant effect on the properties of the material. By varying these structural heterogeneities, it is possible to increase the biocompatibility of HAP. An important role here is played by OH group vacancies, which are easily formed when these hydroxyl groups leave OH channels of HAP. In this case, the temperature dependence of the concentration of OH ions, which also determines the thermal behavior of HAP, is important. To study the evaporation of OH ions from HAP structures with increasing temperatures, molecular dynamics simulation (MDS) methods were used in this work. As a program for MDS modeling, we used the PUMA-CUDA software package. The initial structure of HAP, consisting of 4 × 4 × 2 = 32 unit cells of the hexagonal HAP phase, surrounded by a 15-Å layer of water was used in the modelling. Multiple and statistically processed MDS, running calculations in the range of 700–1400 K, showed that active evaporation of OH ions begins at the temperature of 1150 K. The analysis of the obtained results in comparison with those available in the literature data shows that these values are very close to the experiments. Thus, this MDS approach demonstrates its effective applicability and shows good results in the study of the thermal behavior of HAP.

1,3-Propanediol aqueous solutions are widely used in cryobiology, due to the strong supercooling of a liquid phase caused by mixed water–diol networks in these solutions. These networks are described by means of molecular dynamics, theory of graphs, and Delaunay simplices. They are then compared to mixed networks in water–ethylene glycol systems.

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 similar to 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 sp(3) carbon (C-sp3), carbonyl oxygen (O-C=O), and fluorine (F) atoms tend to form free volume elements, while imide nitrogen (N-imide) and ether oxygen (O-ether) tend to compose polymer bulk.

Лаборатория молекулярной динамики была образована в 1988 году.Основным направлением ее деятельности была определена разработка методов вычислительного эксперимента для моделирования структуры и динамики биомолекулярных систем.Это научное направление было заложено задолго до создания лаборатории -в период организации института в 1972 году, -и первоначально поддерживалось в Лаборатории вычислительной математики, из которой и произошло выделение группы молекулярной динамики в самостоятельное научное подразделение.Методы молекулярного моделирования в настоящее время являются общепризнанным инструментом изучения свойств вещества на молекулярном уровне.Особенно перспективно их применение при решении фундаментальных и прикладных задач молекулярной биофизики и биоинженерии, при изучении наноструктур и создании наноприборов.Конструирование молекулярных приборов, способных осуществлять хранение и передачу сигналов, требует детального знания тепловой динамики отдельных молекул и их комплексов.В таких приборах необходимо управлять процессами, в которых величина сигнала сравнима с тепловым шумом.На успех можно рассчитывать только в случае, если механизм управления основывается на знании корреляций всех движений в молекулярной системе.Осредненные статистические характеристики поведения молекул могут оказаться недостаточными для этого.Проектирование сборки молекул в определенные конструкции также требует знания их динамического поведения.Наиболее детальную информацию о механизмах функционирования и структурно-динамической организации молекулярных систем в нанометровом диапазоне длин способны дать методы молекулярной динамики и Монте-Карло

Our task was to determine the most stable packing of peptides in β-layers to construct an oligomer structure for fibril growth. The β-layers consisting of eight short peptides with the amino acid sequences IVRGVVVAID, VDSWNVLVAG (VESWNVLVAG), KLVFFAEDVG, and IIGLMVGGVV were built. These sequences correspond to the amyloidogenic regions of ribosomal S1 protein from E. coli, protein glucantransferase Bgl2p from the yeast cell wall, and Aβ peptide. First, the amyloidogenic regions were predicted theoretically, and then were confirmed experimentally. Four β-layers with different orientation of the peptides in the layers and the layers relative to each other were constructed. To determine the most stable packing of β-strands, the molecular dynamic (MD) simulations in explicit water were carried out. Two charge states (pH3 and pH5) for each β-layer were considered. The fraction of the secondary structure was a measure of stability for β-layers. β-Layers, in which β-strands are antiparallel relative to each other, were the most stable. Using this packing for β-strands, we constructed the oligomer structures and also checked their stability by using MD simulations.

Protein tyrosine phosphatases constitute a family of cytosolic and receptor-like signal transducing enzymes that catalyze the hydrolysis of phospho-tyrosine residues of phosphorylated proteins. PTP1B, encoded by PTPN1, is a key negative regulator of insulin and leptin receptor signaling, linking it to two widespread diseases: type 2 diabetes mellitus and obesity. Here, we present crystal structures of the PTP1B apo-enzyme and a complex with a newly identified allosteric inhibitor, 2-(2,5-dimethyl-pyrrol-1-yl)5-hydroxy-benzoic acid, designated as P00058. The inhibitor binding site is located about 18A away from the active center. However, the inhibitor causes significant re-arrangements in the active center of enzyme: residues 45-50 of catalytic Tyr-loop are shifted at their Ca-atom positions by 2.6 to 5.8 A. We have identified an event of allosteric signal transfer from the inhibitor to the catalytic area using molecular dynamic simulation. Analyzing change of complex structure along the fluctuation trajectory we have found the large Ca-atom shifts in external strand, residues 25-40, which occur at the same time with the shifts in adjacent catalytic p-Tyr-loop. Coming of the signal to this loop arises due to dynamic fluctuation of protein structure at about 4.0 nanoseconds after the inhibitor takes up its space.