Molecular Dynamics Simulation Method Research Articles

Disclosing the dependencies of ferroelectric and piezoelectric performances on crystalline states of P(VDF‐TrFE) films by molecular dynamics simulations

AbstractWe present a molecular dynamics simulation method including x‐ray diffractometer pattern calculation, mean square displacement (MSD), and nonbonding energy distribution (NED) to disclose the dependencies of condensed structure on its crystalline process of the poly(vinylidene fluoride‐trifluoroethylene) (P(VDF‐TrFE)) films. For comparison, the P(VDF‐TrFE) solution is casted into the films, and followed that different thermal processes are performed to fabricate the crystalline states of the films. Simulation and experimental results have good consistency, indicating that high temperature annealing can effectively promote all‐trans β phase in the crystal region of P(VDF‐TrFE). As such, P(VDF‐TrFE) 80/20 mol% annealing at 140°C shows a higher MSD (~27.5 Å2) and a faster reducing rate of NED than that of other films, contributing to a large maximum polarization (Ps) of ~15.5 μC cm−2, high a remnant polarization (Pr) of ~11.8 μC cm−2, and an attractive piezoelectric strain coefficient (d33) of −27.1 pC N−1 under 200 MV m−1, respectively, and providing a reference for the applications of P(VDF‐TrFE) in flexible sensors, actuators, transducers, and so forth.

Tunable viscoelasticity of bulk fullerene network via high-temperature annealing

Although the experimental transformation of C60 bulk into various functional carbon materials at a certain temperature and pressure has been extensively explored, the understanding of the structural transformation mechanisms and the energy dissipation mechanisms of the derived topologies at the atomic scale is still poor. By using the molecular dynamics (MD) simulations method, the structural transformation of C60 bulk to various carbon materials is studied. Besides, the mechanisms of energy dissipation of three typical structures are revealed and the effects of loading frequency, temperature, loading amplitude, and pre-strain on the storage, loss modulus, and dumping ratio of three typical structures were investigated by dynamic mechanical analysis (DMA). The results show that due to the difference in structural morphology and mechanical behaviors under cyclic loading, three typical structures show different viscoelastic mechanical properties which could also be tuned by changing related parameters. This work systematically investigates the viscoelastic mechanical properties of bulk fullerene network during different annealing processes and corresponding energy dissipation mechanisms and provides important references for further design and application.

MD investigation on the differences in the dynamic interactions between the specific ligand azamulin and two CYP3A isoforms, 3A4 and 3A5

The unmarked potential drug molecule azamulin has been found to be a specific inhibitor of CYP3A4 and CYP3A5 in recent years, but this molecule also shows different binding ability and affinity to the two CYP3A isoforms. In order to explore the microscopic mechanism, conventional molecular dynamics (MD) simulation methods were performed to study the dynamic interactions between two isoforms and azamulin. The simulation results show that the binding of the ligand leads to different structural properties of two CYP3A proteins. First of all, compared with apo-CYP3A4, the binding of the ligand azamulin can lead to changes in the structural flexibility of CYP3A4, i.e., holo-CYP3A4 is more flexible than apo-CYP3A4. The structural changes of CYP3A5 are just the opposite. The ligand binding increases the rigidity of CYP3A5. Furthermore, the representative structures of the production phase in the MD simulation were in details analyzed to obtain the microscopic interactions between the ligand azamulin and two CYP3A isoforms at the atomic level. It is speculated that the difference of composition and interaction of the active sites is the fundamental cause of the change of structural properties of the two proteins. Communicated by Ramaswamy H. Sarma

Polysaccharides screening for pulmonary mucus penetration by molecular dynamics simulation and in vitro verification

Mucus penetration is one of the physiologic barriers of inhalation and nanocarriers can effectively facilitate the permeation of drugs. The interactions between the nanocarriers and mucin are crucial for penetration across the mucus layer on the respiratory tract. In this study, we proposed a molecular dynamics (MD) simulation method for the screening of polysaccharides that acted as the surface modification materials for inhalable nano-preparations to facilitate mucus penetration. MD revealed all-atom interactions between the monomers of polysaccharides, including dextran (DEX)/hyaluronic acid (HA)/carboxymethyl chitosan (CMCS) and the human mucin protein MUC5AC (hMUC5AC). The obtained data showed that DEX formed stronger non-covalent bonds with hMUC5AC compared to HA and CMCS, which suggested that HA and CMCS had better mucus permeability than DEX. For the in vitro verification, HA/CMCS-coated liposomes and DEX/PEG-inserted liposomes were prepared. The results of mucin interactions and mucus penetration studies confirmed that HA and CMCS possessed the weakest interactions with mucin and facilitated the mucus penetration, which was in consistent with the data from MD simulation. This work may shed light on the MD simulation-based screening of surface modification materials for inhalable nano-preparations to facilitate mucus penetration.

Computational study on the inhibition mechanism of cyclodextran against GTF-SI from Streptococcus mutans focusing on the glucan-binding domain

Glucosyltransferases (GTFs) from Streptococcus mutans (S. mutans) are enzymes that synthesize glucan, a polymer that forms a biofilm causing dental caries. Cyclodextran (CI), which contains a ring structure formed from D-glucose by α-1,6 glycoside linkage, has been reported to strongly inhibit GTFs. In contrast, cyclodextrin, formed by α-1,4 glycoside linkage, has almost no inhibitory activity. In this study, we examined the inhibition mechanism of CI through computational chemistry, focusing on the glucan-binding domain of GTF-SI, which is one of GTFs produced by S. mutans. Analysis using molecular dynamics simulation and fragment molecular orbital method demonstrated a clear difference in the molecular interaction mechanism between α-1,6- and α-1,4-linked oligosaccharides. The calculated affinity of α-1,6-linked oligosaccharides was higher than that of α-1,4-linked oligosaccharides. Additionally, geometry optimization based on density functional theory revealed that three amino acids—Q1282, K1284, and S1302—play an essential role in the binding with α-1,6-linked oligosaccharides. These results successfully explain the inhibition mechanism of CI.

Improved microalgae carbon fixation and microplastic sedimentation in the lake through in silico method

The impact of microplastics in lake water environments on microalgae carbon fixation and microplastic sedimentation has attracted global attention. The molecular dynamic simulation method was used to design microplastic additive proportioning schemes for improving microalgae carbon fixation and microplastic sedimentation. Results showed that the harm of microplastics can be effectively alleviated by adjusting the proportioning scheme of plastic additives. Besides, the decabromodiphenyl oxide (DBDPO) was identified as the main additive that affect the microalgae carbon fixation and microplastic sedimentation. Thus, a molecular modification based on CiteSpace visual analysis was firstly used and 12 DBDPO derivatives were designed. After the screening, DBDPO-2 and DBDPO-5 became the environmentally friendly DBDPO alternatives, with the highest microalgae carbon fixation and microplastic sedimentation ability enhancement of over 25 %. Compared to DBDPO, DBDPO derivatives were found easier to stimulate the adsorption and binding ability of surrounding hotspot amino acids to CO2 and ribulose-5-phosphate, increasing the solvent-accessible surface area of microplastics, thus improving the microalgae carbon fixation and microplastic sedimentation ability. This study provides theoretical support for simultaneously promoting the microalgae carbon fixation and microplastic sedimentation in the lake water environment and provides scientific basis for the protection and sustainable development of lake water ecosystem.

Exploring and Designing Potential Inhibitors of SIRT2 in Natural Products by Artificial Intelligence (AI) and Molecular Dynamics Methods

Background:: The histone deacetylase family of proteins, which includes the sirtuins, participates in a wide range of cellular processes, and is intimately involved in neurodegenerative illnesses. The research on sirtuins has garnered a lot of interest. However, there are currently no effective therapeutic drugs. Methods:: In order to explore the potential inhibitors of SIRTs, we first screened four potential lead compounds of SIRT2 in Traditional Chinese Medicine (TCM) for nervous disease using the Auto- Dock Vina method. Then, with Molecular Dynamics (MD) simulation method, we discovered how these inhibitors from Traditional Chinese herbal medicines affect this protein at the atomic level. Results and Discussion:: We found hydrophobic interactions between inhibitors and SIRT2 to be crucial. The small molecules have been found to have strong effect on the residues in the zincbinding domain, exhibiting relationship with the signaling pathway. Finally, based on the conformational characteristics and the MD properties of the four potential inhibitors in TCM, we have designed the new skeleton molecules according to the parameters of binding energy, fingerprint similarity, 3D similarity, and RO5, with AI method using MolAICal software. Conclusion:: We have proposed the candidate inhibitor of SIRT2. Our research has provided a new approach that can be used to explore potential inhibitors from TCM. This could potentially pave the way for the creation of effective medicines.

Shock Hugoniot Calculations of Newly Designed Thermoplastic Elastomers and Comparison with Classical Binder Estane.

Our purpose is to design excellent binder candidates used in polymer-bonded explosives (PBX) according to the calculated shock of Hugoniot. Here, we mainly examined the thermoplastic elastomer (TPE) binders commonly used in PBX formulations. Equilibrium molecular dynamics (MD) simulation and mixing rule methods were used to calculate the shock Hugoniot values of 180 newly designed TPEs. We focused on the influence of the polymerization degree, contents, and types of soft and hard segments composed of TPEs on the shock Hugoniot and compared them with the classic PBX binder, Estane. The results show that the hard segment has an effect on the Hugoniot curve, which gradually diminishes as the degree of polymerization increases. The underlying physical mechanism can be attributed to the presence of a large number of hydrogen bonds in hard segment domains. The shock Hugoniot of TPEs also depends on the type of soft segments. The volume compression rate of TPEs decreases with increasing content of hard segments under a given shock. By comparing with Estane, a TPE binder commonly used in PBX, we ultimately chose several new TPEs with the potential to serve as PBX binders in terms of shock performance.

Molecular dynamics simulation for damping properties of PDMS composite enhanced by the last generation siloxane dendrimer alcohol with hydroxyl terminal groups

In this study, the damping properties of PDMS composite enhanced by last generation siloxane dendrimer alcohol with hydroxyl terminal groups G3-OH were evaluated by all atomic molecular dynamics simulation (AAMDS) method in terms of damping loss factors (DLFs) tanδ, compositional miscibility (|δi−δ0|), cohesive energy density (CED), binding energy (EB) and maximum free volume fraction (FFVmax). Based on the total atomic charge distribution, further, the potential damping mechanism in composite PDMS/G3-OH(100/47) was explored. The simulation results showed that the |δi−δ0| of composite PDMS/G3-OH(100/47) was 0.0939 (J/cm3)0.5, whose good compatibility between the two components laid a solid foundation for the excellent damping performance. As the argument, the tanδ, CED, EB and FFVmax of composite PDMS/G3-OH(100/47) were 0.8073, 1.668 (J/m3)×108, −19877.607 kcal/mol as well as 39.85 % respectively, which were better than 1.2439, 1.390 (J/m3)×108, −14539.327 kcal/mol and 40.71 % of pure PDMS matrix material PDMS/G3-OH(100/0). Furthermore, the multiple hydrogen bond mechanism can perfectly explain the structure-activity relationship between the internal structure and the excellent damping properties of composite PDMS/G3-OH(100/47). Specifically, a total of 19 α-type hydrogen bonds were formed in the composite PDMS/G3-OH(100/47). All in all, according to the evaluation of AAMDS method, the PDMS composite enhanced by 47-equivalent last generation siloxane dendrimer alcohol with hydroxyl terminal groups G3-OH had outstanding damping properties.

Effect of solid solution and vacancies on the mechanical properties of Cu(Al)/Al2Cu/(Cu)Al layered gradient heterostructures

We used molecular dynamics simulation (MD) methods to investigate the effect of diffused solutes and vacancies on the tensile deformation behavior of nano-polycrystalline Cu(Al)/Al2Cu/(Cu)Al layered heterostructures. Simulation results show that the Cu(Al)/Al2Cu/(Cu)Al layered heterostructure with Al-20% Cu has the highest ultimate strength and fracture strain. On this basis, gradient Cu solute in the matrix Al improves the synergistic tensile deformation behavior among the components of the nano-polycrystalline Cu(Al)/Al2Cu/(Cu)Al layered gradient heterostructure. More importantly, gradient Cu solute contributes to the localized strain transfer between component layers, ultimately increasing the fracture strain and ultimate strength. In addition, deformation behavior between polycrystalline Cu(Al)/Al2Cu/(Cu)Al layered gradient heterostructure fails at low tensile strains because the vacancies cause strain concentration of polycrystalline Cu near the interface and weaken strain delocalization in polycrystalline Al.

Stresses in silicon dioxide films deposited from dielectric targets: results of atomistic modeling

The previously proposed method of molecular dynamics simulation of the deposition of thin films from metal targets is adapted to the case of dielectric targets and applied to silicon dioxide films. The possibility of not only silicon atoms leaving the target, but also clusters with oxygen atoms was taken into account by adding O=Si=O molecules to the flow of deposited atoms. Atomistic film clusters were obtained by high-energy and low-energy deposition at different percentages of molecules in the flow of deposited atoms. The values of the stress tensor components are calculated. With high-energy deposition, compressive stresses are observed, with low-energy deposition, tensile stresses are observed. The absolute values of the diagonal components of the stress tensor increase with increasing proportion of molecules in the flow of deposited atoms.

Research on the hot densification mechanism of biomass wastes based on molecular dynamics simulation and components adjustment method

The hot densification process can be used to prepare the biofuel pellets and diversified densification materials with suitable mechanical strength to overcome the natural defects of low energy density and loose structure of biomass wastes and achieve the high value utilization of the renewable resources. In this study, the two typical biomass wastes, cotton stalk (CS) and Chinese fir wood sawdust (WS) are used for the hot densification investigation (85 °C), and the microscopic evolution behavior of the biomass components during the hot densification process is explored through the combination of the component adjustment method and molecular dynamics simulation. The results show that cellulose is the key component to the mechanical strength of biomass pellet, which plays the crucial role of skeleton support in the densification process, and the strength of pellet is positively correlated with the increasing addition ratio of cellulose. Furthermore, crystalline cellulose exhibits the strongest bonding properties in the hot densification process due to the formation of rich hydrogen bonds and the increasing intermolecular attraction force. Lignin has the poorest capability for hydrogen bond formation, and its addition increases the van der Waals repulsive forces, resulting in the poorest densification performance. Hemicellulose shows the better adhesion capability than lignin due to its glassy transition (83.34 °C) and the suitable addition can greatly improve the mechanical property of the pellet, up to 14.26 MPa. There exists the strongest synergistic effect between cellulose and hemicellulose, which is beneficial to the bonding performance between particles to different extent. Hot densification process can promote the formation of hydrogen bond connections between molecules/atoms and the increase of the van der Waals repulsive force in the further compression. The densification performance of biomass is the combined effect of the physical forces, including electrostatic force and van der Waals force.

Unveiling the importance of surface ionization on desalination and ion-sieving performance of graphene oxide membranes

The experimental results have confirmed the negative surface charge of graphene oxide (GO) membranes. However, little work considered the influences of surface ionization on the performance of GO-based desalination or ion-sieving membranes. In this work, the surface charge of GO was included to explore its effects on the desalination performance adopting molecular dynamics (MD) simulation methods. The MD results indicated the enhanced interactions between GO nanochannel and water as well as ions with the increase in surface charge density. Consequently, the water flux enhanced but the ion rejection rate decreased with the increase in surface charge density. We further explored the influences of intercalated cations on the comprehensive desalination performance of GO membranes. The simulation results turned out that the performance of GO nanochannel was optimized at an appropriate interlayer distance. Among all the investigated cases, GO nanochannel intercalated with Mg2+ possesses the best desalination performance. It was found that surface charge density exerted little effect on optimizing the Li+/Mg2+ separation performance. However, Li+/Mg2+ separation performance could be optimized by narrowing the interlayer distance of GO nanochannel. The revealed mechanisms in this work might provide useful suggestions for designing strategies for nanosheet-based membranes to achieve better desalination and ion-sieving performance.

Effect of Cross Nanowall Surface on the Onset Time of Explosive Boiling: A Molecular Dynamics Study

Explosive boiling is a fast-phase transition from an ultra-thin liquid film to vapor under an extremely high heat flux, which typically has been studied using the molecular dynamics simulation (MDS) method. The present MDS study investigated the explosive boiling of a liquid argon nanofilm over different solid copper surfaces with different nanowall patterns, including parallel and cross nanowalls. For each surface, atomic motion trajectories, the number of liquid and vapor argon atoms, heat flux, and, mainly, the onset time of explosive boiling were investigated. The simulation results indicated that explosive boiling occurs earlier on parallel and cross nanowall surfaces than on an ideally smooth surface, regardless of the topology and configuration of the nanowalls. Moreover, the results revealed that by using the cross nanowall surfaces, the onset time of explosive boiling decreased by 0.7–4% compared to the parallel nanowall surfaces. In addition, it was found that the onset time of explosive boiling strongly depends on the potential energy barrier and the movement space between nanowalls for both parallel and cross nanowall surfaces. Furthermore, the simulation findings showed that even though increasing the height of cross nanowalls increases the heat flux and temperature of the fluid argon domain, it does not necessarily result in a shorter onset time for explosive boiling. These findings demonstrate the capability of cross nanowall surfaces for explosive boiling, thereby being utilized in future surface design for thermal management applications.

Insight into miscibility mechanism of multiple components crude oil in CO2/CH4 by molecular dynamic simulation

As one important crude oil recovery method, gas miscible flooding was widely adopted for EOR. However, the effect of crude oil components, injecting gas types, and pressure on miscible performance were scarcely discussed. In this work, molecular dynamics simulation method was employed to investigate the miscible mechanism of four-components crude oil in injecting gases of CO2 and CH4, respectively. The driving force and hindrance force in oil and gas miscible process was discussed to uncover the underlying miscible mechanism. The driving force mainly comes from the interaction between oil and gas, which induces the interdiffusion between oil and gas. The repulsive force stems from the association of oil components, which inhibits the dissolution of oil out of the crude oil colloidal structure. Furthermore, one evaluation standard of miscibility degree oil in gas was proposed based on solubility capability of oil component in injecting gas. Simulation results indicate the CO2 have better miscibility than that of CH4, and the miscibility of four crude oil components follows order of saturates > aromatics > resins > asphaltenes. The miscibility of all four oil components improves with increasing pressure. It is interesting that the miscibility of asphaltene is insensitive to pressure. Our work provides molecular level insight into the oil gas miscible behavior based on multiple components crude oil, and provide quantitative evaluation on miscibility of each oil component. These simulation results might be helpful to theoretical guidance for gas injection development.

Residual water and interfacial bonding effects on the mechanical performance of CNT/fly ash geopolymer binder

AbstractNowadays, geopolymers are advanced alternatives to cementitious materials, where their excellent chemical and fire resistance are some of its most appealing properties. Fly ash geopolymers enable the use of industrial waste materials while converting them into a novel binding material. Their production is accompanied by a much lower CO2 emission when compared to Portland cement. Reinforcing fly ash geopolymers with carbon nanotubes would significantly strengthen its microstructure and with this enhancing the long‐term mechanical and durability performance. The aim of this work is to use reactive molecular dynamics simulation method to optimize the mechanical properties of fly ash geopolymers with nano‐reinforced carbon nanotubes (CNTs). During this study, the impact of humidity and interfacial bonding strength between carbon nanotube and geopolymer is investigated. Our findings show that structural transformations under hydration process comes from the weakening of AlO bond, leading to the elongation of AlO and NaOH bonds, forming aluminum and sodium hydroxyls. Conversely, silicate is not sensitive to water and exhibits hydrophobic behavior. In addition, our results show that there is an optimal value of water content (7.17 wt.%) that makes the geopolymer nanostructure strengthen. The related elastic modulus rises by 21.56%, 20.60%, and 18.41% for Si/Al ratio of 1, 2, and 3, respectively. Inserting carbon nanofillers to fly ash nanostructure has remarkably shown an interesting strength enhancement. More precisely, when interfacial bonding concentration is around 19.36%, it is observed a positively increasing of the compressive strength, shear, indentation and elastic modulus with 39%, 65.2%, 72.3%, and 144.85%, respectively. Reduced density gradient supports that the interaction between carbon nanotube and fly ash geopolymer is dominated by a van der Waals one.

Molecular dynamics simulations of the local structure and physicochemical properties of CaCl2molten salt

AbstractCaCl2molten salt, as a common electrolyte in the process of molten salt electrolysis, has a high decomposition potential and a strong ability to bind O2−. So the study of the structure and properties of CaCl2is significant for the molten salt electrolysis. In this paper, molecular dynamics simulations (MD) method was used to investigate the variation rule of the local structure and physicochemical properties of CaCl2molten salt with temperature. The results show that the temperature has less effect on the heterozygous ion pairs and more effect on the homozygous ion pair. With the increase of temperature, the interaction between ion pairs is weakened, the coordination number decreases, the local structure changes a little, and the structural configuration tends to be an irregular octahedral structure with vacancies. The calculated self-diffusion coefficients, viscosities, and ionic conductivities are consistent well with the reality, but there is a significant error in densities due to the strong polarization effect of Ca2+compared to the reality. The local structure directly determines the thermodynamic properties of the molten salts. This study promotes the basic theoretical research on alkaline earth metal-containing molten salts and is an important reference for the study of molten salt electrolysis process.

Unraveling Molecular Recognition of Glycan Ligands by Siglec-9 via NMR Spectroscopy and Molecular Dynamics Modeling.

Human sialic-acid-binding immunoglobulin-like lectin-9 (Siglec-9) is a glycoimmune checkpoint receptor expressed on several immune cells. Binding of Siglec-9 to sialic acid containing glycans (sialoglycans) is well documented to modulate its functions as an inhibitory receptor. Here, we first assigned the amino acid backbone of the Siglec-9 V-set domain (Siglec-9d1), using well-established triple resonance three-dimensional nuclear magnetic resonance (NMR) methods. Then, we combined solution NMR and molecular dynamic simulation methods to decipher the molecular details of the interaction of Siglec-9 with the natural ligands α2,3 and α2,6 sialyl lactosamines (SLN), sialyl Lewis X (sLeX), and 6-O sulfated sLeX and with two synthetically modified sialoglycans that bind with high affinity. As expected, Neu5Ac is accommodated between the F and G β-strands at the canonical sialic acid binding site. Addition of a heteroaromatic scaffold 9N-5-(2-methylthiazol-4-yl)thiophene sulfonamide (MTTS) at the C9 position of Neu5Ac generates new interactions with the hydrophobic residues located at the G-G' loop and the N-terminal region of Siglec-9. Similarly, the addition of the aromatic substituent (5-N-(1-benzhydryl-1H-1,2,3-triazol-4-yl)methyl (BTC)) at the C5 position of Neu5Ac stabilizes the conformation of the long and flexible B'-C loop present in Siglec-9. These results expose the underlying mechanism responsible for the enhanced affinity and specificity for Siglec-9 for these two modified sialoglycans and sheds light on the rational design of the next generation of modified sialoglycans targeting Siglec-9.

Comparison of Accuracy and Efficiency of Milestoning Variants: Introducing Buffer Milestoning.

The Milestoning algorithm is a method for long-time molecular dynamics simulations. It enables the sampling of rare events. The precise calculations of observables depend on accurately determining the first hitting point distribution (FHPD) for each milestone. There is no analytical expression for FHPD, which is estimated numerically. Several variants of Milestoning offer approximations to the FHPD. Here, we examine in detail the FHPD of an exact calculation and Milestoning variants. We also introduce a new version of the Milestoning algorithm, buffer Milestoning, with a comparable cost to conventional Milestoning but higher accuracy. We use the mean first passage time and the free energy to assess the simulation quality, and we compare the accuracy and efficiency of buffer Milestoning to exact calculations, conventional Milestoning, local-passage-time-weighted Milestoning, Markovian Milestoning with Voronoi tessellation, and exact Milestoning. Conventional Milestoning requires milestone decorrelation. If this condition is not satisfied, it is the least accurate approach of all the techniques we examined. We conclude that for a small increase in cost compared to conventional Milestoning, buffer Milestoning provides accurate results for a range of problems, including more correlated milestones and is, therefore, versatile compared to other variants. Local-passage-time-weighted Milestoning provides accuracy similar to that of buffer Milestoning but at an increased simulation cost. Markovian Milestoning with Voronoi tessellation is the most accurate compared with other approximations, but it is less stable for high barriers and more expensive.

Selective laser sintering of amorphous nanoparticles: Molecular dynamics simulations

The paper investigates the process of liquid-phase sintering of amorphous iron-based nanoparticles by the method of molecular dynamics simulations. The classical molecular dynamics package LAMMPS was used for modeling. Visual analysis of the atomic configurations of nanoparticles during their rapid cooling revealed the self-purification effect of the particles. Partial pair correlation functions and coordination number distribution functions were used to analyze the atomic structure of nanoparticles after sintering. As a result of the analysis of the main structural parameters, which were obtained using the specified functions, differences in the atomic composition and structure of the volume and surface of nanoparticles were established.