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Inhibiting the aggregation of nanoparticles (NPs) to prepare catalysts with a uniform particle size is crucial to control the chirality of single-walled carbon nanotubes (SWCNTs). It has been proven that the quality of SWCNTs can be effectively improved through the use of FeMo NPs with small fractions of Mo. In this work, the nucleation mechanism of FeMo NPs, in which Mo atoms are gradually deposited on the solid-phase Fe55 seeds, is studied via classical molecular dynamics. The results demonstrate that the difference in cohesive energies between the components acts as a driving force for the transformation of FeMo NPs from the solid to the semiliquid phase. Furthermore, the lifetime of the alloy NPs in the semiliquid phase can be controlled by adjusting the Mo feeding rate. This study not only enables one to gain insight into the nucleation mechanism of FeMo NPs but also provides a strategy for restraining the structural fluctuation of NPs in the preparation of alloys with uniform particle size through adjusting the experimental parameters. [ABSTRACT FROM AUTHOR]

Classical (MD) and ab initio (AIMD) molecular dynamics simulations were conducted to investigate the fundamental properties of solid and liquid MgO. AIMD was performed by DFT using the Strongly Conditioned and Appropriately Normed (SCAN) exchange correlation functional. The obtained pair-correlation functions of liquid MgO were used as reference data for the optimization of parameters of classical MD. For the latter, a Born–Mayer–Huggins (BMH) potential was applied, and parameters were adjusted until a best fit of both structural properties was obtained by AIMD and physical properties by experimental data. Different structural, dynamic and thermodynamic properties of solid and liquid MgO were then calculated by classical MD and compared with the literature data. Good agreement was found for the Mg-O bond length, self-diffusion coefficients, density of liquid MgO and for heat content and density of crystalline MgO. Using a void-melting approach, the melting temperature of MgO was found as 3295 ± 30 K, which is in good agreement with the recent experimental work by Ronchi et al. (3250 ± 20 K). The optimized parameters of BMH potential describe well the structural, dynamic and thermodynamic properties of solid and liquid MgO and may be combined with our previous results of a CaO-Al2O3-TiO2 system to calculate the properties of a quaternary CaO-MgO-Al2O3-TiO2 system.

Classical (MD) and ab initio (AIMD) molecular dynamics simulations were conducted to investigate the fundamental properties of solid and liquid MgO. AIMD was performed by DFT using the Strongly Conditioned and Appropriately Normed (SCAN) exchange correlation functional. The obtained pair-correlation functions of liquid MgO were used as reference data for the optimization of parameters of classical MD. For the latter, a Born–Mayer–Huggins (BMH) potential was applied, and parameters were adjusted until a best fit of both structural properties was obtained by AIMD and physical properties by experimental data. Different structural, dynamic and thermodynamic properties of solid and liquid MgO were then calculated by classical MD and compared with the literature data. Good agreement was found for the Mg-O bond length, self-diffusion coefficients, density of liquid MgO and for heat content and density of crystalline MgO. Using a void-melting approach, the melting temperature of MgO was found as 3295 ± 30 K, which is in good agreement with the recent experimental work by Ronchi et al. (3250 ± 20 K). The optimized parameters of BMH potential describe well the structural, dynamic and thermodynamic properties of solid and liquid MgO and may be combined with our previous results of a CaO-Al2O3-TiO2 system to calculate the properties of a quaternary CaO-MgO-Al2O3-TiO2 system. [ABSTRACT FROM AUTHOR]

Ethylenediaminetetraacetic acid (EDTA), which has two amine and four carboxylate protonation sites, forms stable complexes with lanthanide ions. This work analyzes the coordination structure, in atomic resolution, of the Eu3+ ion complexed with EDTA in all its protonation states in aqueous solution. Eu‐EDTA complexes were modeled using classical molecular dynamics (MD) simulations using force field parameters optimized with ab initio molecular dynamics (AIMD) simulations. Structures from the MD simulations were used to predict extended X‐ray absorption fine structure (EXAFS) spectra and compared with EXAFS measurements of the Eu3+ aqua ion and Eu‐EDTA complexes at pH 3 and 11. This work details how Eu‐EDTA complex coordination structures change with increasing protonation of the EDTA ligand in the complex, from the tightly bound unprotonated complex to the unbinding of the fully protonated EDTA ligand from the Eu3+ ion as both become solvated by water. Agreement between predicted and measured EXAFS spectra supports the findings from simulation. [ABSTRACT FROM AUTHOR]

Diethylenetriaminepentaacetic acid (DTPA) is a chelating agent whose complex with the Gd3+ ion is used in medical imaging. DTPA is also used in lanthanide‐actinide separation processes. As protonation of the DTPA ligand can facilitate dissociation of the Gd3+ ion from the Gd‐DTPA complex, this work investigates the coordination structures of the aqueous Gd3+ ion and its environment when chelated by DTPA in eight different DTPA protonation states. Both classical and ab initio molecular dynamics (MD) simulations are conducted to model the solvated complexes. Extended X‐ray absorption fine structure (EXAFS) measurements of the Gd3+aqua ion, and the Gd‐DTPA complex at pH 1 and 11, are compared to EXAFS spectra predicted from the MD simulations to verify the accuracy of the MD structures. The findings of this work provide atomic‐level details into the fluctuating Gd‐DTPA complex environment as the DTPA ligand gradually detaches from the Gd3+ ion with increased protonation. [ABSTRACT FROM AUTHOR]

After briefly discussing the problem of stability/instability of dispersed systems in colloid chemistry, including ideas and concepts dating back to P.A. Rehbinder, the following classification has been proposed for instabilities of individual (free) nanoparticles: (1) instability with respect to the spontaneous disintegration into individual molecules (atoms) or smaller nanoclusters; (2) instability of shape; (3) instability of the integral structure of nanoparticles; (4) instability of the mesoscopic structure; (5) instability of physicochemical characteristics of nanoparticles; and (6) instability with respect to an external environment, including chemical instability, e.g., instability to oxidation. The problems concerning the stability of isomers of metal nanoclusters and of bimetallic core-shell nanostructures are considered as examples. The theoretical concepts of stability and instability have been illustrated by our molecular dynamics data on isomers of Au nanoclusters and mutually inverse (alternative) bimetallic Co@Au and Au@Co core-shell nanostructures, where the first element (before symbol @) corresponds to the central region (core) of a particle, while the second one refers to its shell. [ABSTRACT FROM AUTHOR]

Atomic force microscopes are used, besides their principal function as surface imaging tools, in the surface manipulation and measurement of interfacial properties. In particular, they can be modified to measure lateral friction forces that occur during the sliding of the tip against the underlying substrate. However, the shape, size, and deformation of the tips profoundly affect the measurements in a manner that is difficult to predict. In this work, we investigate the contribution of these effect to the magnitude of the lateral forces during sliding. The surface substrate is chosen to be a few-layer AB-stacked graphene surface, whereas the tip is initially constructed from face-centered cubic gold. In order to separate the effect of deformation from the shape, the rigid tips of three different shapes were considered first, namely, a cone, a pyramid and a hemisphere. The shape was seen to dictate all aspects of the interface during sliding, from temperature dependence to stick–slip behavior. Deformation was investigated next by comparing a rigid hemispherical tip to one of an identical shape and size but with all but the top three layers of atoms being free to move. The deformation, as also verified by an indentation analysis, occurs by means of the lower layers collapsing on the upper ones, thereby increasing the contact area. This collapse mitigates the friction force and decreases it with respect to the rigid tip for the same vertical distance. Finally, the size effect is studied by means of calculating the friction forces for a much larger hemispherical tip whose atoms are free to move. In this case, the deformation is found to be much smaller, but the stick–slip behavior is much more clearly seen. [ABSTRACT FROM AUTHOR]

Context: Nanoscrolls are tube-shaped structures formed when a sheet or ribbon of material is rolled into a cylinder, creating a hollow tube with a diameter on the nanoscale, similar to the papyrus. Carbon nanoscrolls have unique properties that make them useful in various applications, such as energy storage, catalysis, and drug delivery. In this study, we employed classical molecular dynamics simulations to investigate the formation and stability of nanoscrolls composed of graphene and hexagonal boron nitride (hBN) nanoribbons. Using a carbon nanotube (CNT) as a template to trigger their collapsing, we found that graphene/graphene, graphene/hBN, and hBN/hBN could form CNT-wrapped nanoscrolls at ultrafast speeds. We also confirmed that these nanoscrolls are thermally stable and discussed the other products formed from the interaction of these complexes and their temperature dependence. Gr/Gr and hBN/Gr nanoscrolls exhibit similar interlayer distances, while hBN/hBN nanoscrolls have wider interlayer distances than the other two composite nanoscrolls. These features suggest that hBN/hBN composite nanoscrolls could more efficiently capture small molecules because of their greater interlayer spacing. Methods: We conducted molecular dynamics simulations using the Forcite package in the Biovia Materials Studio software, which employs the Universal and Dreiding force fields. We considered an NVT ensemble with a fixed time step of 1.0 fs for a duration of 500 ps. The velocity Verlet algorithm was adopted to integrate the equations of motion of the entire system. We employed the Nosé-Hoover-Langevin thermostat to control the system temperature. The simulations were carried out without periodic boundary conditions, so there was no pressure coupling. [ABSTRACT FROM AUTHOR]

The surface diffusion and intermixing of Ge ad‐atoms over Si (001) 2 × 1 substrates using classical molecular dynamics (CMD) simulations are characterized here. Several interatomic potentials, parametrizations, and parameter mixing rules are contemplated. A novel simulation scheme is devised to characterize the effective frequency of surface diffusion and intermixing events overcoming the inherent difficulties related to their interdependency in heteroepitaxial systems. The effective energy barriers of these events encompass different atomistic mechanisms weighted by their occurrence probabilities. The overall description of surface diffusion and intermixing based on Stillinger–Weber (SW) potential is in agreement with ab initio calculations and experimental observations, though some atomistic details differ. This study is extended to Si(001) substrates with stressed Ge monolayers grown on top. It is found that Ge ad‐atom dynamics is accelerated with respect to the case of the pure Si substrate and that diffusion across dimer rows is mainly mediated by the atomic exchange of the Ge ad‐atom with a Ge atom on the surface. [ABSTRACT FROM AUTHOR]

Inspired by the urge to determine the underlying mechanism of the induction of toxic effects of state-of-the-art two-dimensional (2D) nanomaterials such as graphene and hexagonal boron nitride (h-BN) toward biomolecules, herein we study the interactions between these nanomaterials with a model protein hen egg white lysozyme (HEWL), employing classical molecular dynamics simulations. It is revealed that the protein gets easily adsorbed on both of the 2D materials, with the interaction energy being much higher in the case of h-BN, suggesting a significantly stronger adsorption affinity. The interactions of aromatic amino acid residues such as tyrosine and tryptophan along with few aliphatic residues such as arginine, lysine, and asparagine with the 2D materials are found to be pronounced, and most of the residues taking part in adsorption are nearly the same for both materials. While the secondary structure of HEWL remains nearly unaltered upon adsorption on graphene, h-BN massively perturbs both the α-helix and β-sheet components through the disruption of intraprotein hydrogen bonds, which are in turn sine quo non for the preservation of the structural integrity. It is demonstrated that the disruption of the secondary structure is due to pronounced thermodynamic preference for the adsorption of the constituent amino acid residues on h-BN compared to their spatial disposition within the proteins. The calculated release times from the adsorbed state are found to be orders of magnitude higher in the case of h-BN compared to graphene, and it is unlikely that the protein would get released in accessible time scales unless dislodged by the application of an external force. The present study contributes to the fundamental understanding of the nanotoxicity of emerging 2D materials toward proteins, thereby aiding experimentalists to design biocompatible 2D materials for nano-biomedical usage and device fabrication. [ABSTRACT FROM AUTHOR]

Whether or not specific ion effects determine the charge storage properties of aqueous graphene and graphite-based supercapacitors remains a highly debated topic. In this work we present a multiscale quantum mechanics – classical molecular dynamics (QMMD) investigation of aqueous mono- and divalent salt electrolytes in contact with fully polarizable charged graphene sheets. By computing both the electrochemical double layer (EDL) and quantum capacitance we observe a constant electrode specific capacitance with cationic radii and charge. Counterintuitively, we determine that a switch in the cation adsorption mechanism from inner to outer Helmholtz layers leads to negligible changes to the EDL capacitance, this appears to be due to the robust electronic structure of the graphene electrodes. However, the ability of ions (such as K+) with a relatively low hydration free energy to penetrate the inner Helmholtz plane and adsorb directly on the electrode surface is found to slow their diffusion parallel to the interface. Ions in the outer Helmholtz layer are found to have higher diffusivity at the surface due to their position in ion channels between water layers. Our results show that surface effects such as the surface polarization and the partial dehydration and local structuring of ions on the surface underpin the behaviour of cations at the interface and add a vital new perspective on trends in ion mobilities seen under confinement. [Display omitted] [ABSTRACT FROM AUTHOR]

Atomic force microscopes are used, besides their principal function as surface imaging tools, in the surface manipulation and measurement of interfacial properties. In particular, they can be modified to measure lateral friction forces that occur during the sliding of the tip against the underlying substrate. However, the shape, size, and deformation of the tips profoundly affect the measurements in a manner that is difficult to predict. In this work, we investigate the contribution of these effect to the magnitude of the lateral forces during sliding. The surface substrate is chosen to be a few-layer AB-stacked graphene surface, whereas the tip is initially constructed from face-centered cubic gold. In order to separate the effect of deformation from the shape, the rigid tips of three different shapes were considered first, namely, a cone, a pyramid and a hemisphere. The shape was seen to dictate all aspects of the interface during sliding, from temperature dependence to stick–slip behavior. Deformation was investigated next by comparing a rigid hemispherical tip to one of an identical shape and size but with all but the top three layers of atoms being free to move. The deformation, as also verified by an indentation analysis, occurs by means of the lower layers collapsing on the upper ones, thereby increasing the contact area. This collapse mitigates the friction force and decreases it with respect to the rigid tip for the same vertical distance. Finally, the size effect is studied by means of calculating the friction forces for a much larger hemispherical tip whose atoms are free to move. In this case, the deformation is found to be much smaller, but the stick–slip behavior is much more clearly seen.

We introduced a novel machine-learned interatomic potential (MLIP) by thoroughly discussing the step–by–step MLIP creation process using precise but limited data. This study explored the mechanical properties of hexagonal boron nitride (hBN) nanosheets and addressed the challenges of accurately predicting their structural properties. We explored the use of ab initio molecular dynamics and classical molecular dynamics (CMD) simulation techniques, emphasizing the necessity for a more effective and efficient solution. We also discussed the machine learning procedure to construct an effective interatomic potential. Furthermore, we address techniques for evaluating the performance and robustness of MLIPs on unseen datasets. Using the newly formed MLIP in a CMD simulation, we investigated the mechanical attributes of hBN nanosheets, exploring the fluctuations in sheet strength across a range of dimensions, temperatures, and varying numbers of layers. We obtained an average Young’s modulus in the range of 980–1000 GPa at 1 K, whereas the average failure stress and strain were approximately 106 GPa and 0.16, respectively. Our results demonstrate significant improvements in the accuracy of hBN nanosheets compared to prior studies, highlighting the effectiveness of MLIP in achieving higher precision with minimal computational cost. This study offers comprehensive analysis and theoretical exploration, delivering valuable insights into MLIP and the mechanical properties of hBN nanosheets, and paves the way for future applications in materials science and engineering.

In recent years, the synthesis of two-dimensional (2D) materials, particularly the crystalline and disordered phases of 2D transition metal chalcogenides (TMCs), has gained considerable attention due to their wider electronic band gaps. This distinctive feature is pivotal in shaping their potential applications in solar cells, sensors, field-effect transistors (FETs), and photocatalysis for water decomposition. In the present study, we report molecular dynamics simulation of 2d disordered configuration of ZnX and CdX (X: S, Se) compounds using the Stillinger–Weber potential. We have explored their structural features by calculating their radial distribution functions and ring statistics. These systems are thermodynamically stable. The disordered network with numerous voids in these compounds play a pivotal role in lowering their melting temperature compared to their 2D crystalline counterparts, which falls within the range of 600 K to 700 K. The phonon density of states for all these systems shows a higher number of lower frequency (acoustic) modes than optical modes, which is understandably due to the presence of open regions and 2-fold sites in such systems. • Molecular dynamics simulations of 2d disordered ZnX and CdX (X: S, Se) via LAMMPS. • Construction of 2d disordered ZnX and CdX (X: S, Se) via melt-quench method using Stillinger–Weber potential. • Structural features (dominantly composed of six-membered rings, with additional four, eight, and larger rings) analyzed via RDFs and ring statistics. • Thermal properties(disordered networks lower melting temperatures to 600–700 K) analyzed via diffusion coefficient and specific heat. • Phonon density shows more acoustic modes due to open regions and 2-fold sites. [ABSTRACT FROM AUTHOR]

This research examines the structural, chemical, electronic, and optical properties of fullerene-based 2D qHP polymer sheets doped with and without boron and nitrogen. Utilizing density functional theory (DFT) with PBE and HSE functionals, alongside van der Waals interactions and classical simulations, we discovered that BN-doped qHP C 60 materials show improved conductivity and adsorption characteristics, exhibiting semiconducting behaviour with increased carrier mobility. qHP C 58 B 1 N 1 shows high conductivity (∼ 1 0 12 Ω − 1 cm − 1 s − 1 at 300 K) compared to qHP C 60 and qHP C 54 B 3 N 3 . These qHP sheets have cohesive energies of −8.75 (C 60), −8.70 ( C 58 B 1 N 1 ), and −8.67 ( C 54 B 3 N 3 ), in the unit of eV, indicating greater stability than graphene and h-BN. Optical analysis suggests qHP C 60 can absorb UV photons up to 1.1 eV, having an optical bandgap estimated to be between 0.95 and 1.65 eV and a refractive index larger than one. They have moderate direct electronic bandgaps and anisotropic mechanical properties, with Young's modulus of 180–200 GPa. These structures transition abruptly from elastic to fracture at a critical strain threshold, with similar thermal stability and melting points around 3900 K. These results highlight the potential of a single dopant pair in qHP fullerene monolayers for next-generation 2D nano-electronic applications. [Display omitted] • BN-doped qHP C 60 monolayers show improved conductivity and adsorption via DFT analysis. • Boron nitride doping in qHP C 60 monolayer boosts carrier mobility and semiconducting behavior. • Cohesive energy shows high stability, increased reactivity in BN-doped qHP C 60 monolayers. • qHP C 60 monolayers absorb UV photons up to 1.1 eV, showing strong mechanical stability. [ABSTRACT FROM AUTHOR]

Small molecule antagonists that bind to the ligand-binding domain (LBD) of estrogen receptor alpha (ERα) are effective in treating ERα-positive breast cancer patients. However, acquired treatment resistance is observed in the presence of somatic mutations in LBD of ERα. Y537S is the most aggressive mutation, causing constitutive activity of ERα in the absence of ligand and reducing the affinity and sensitivity of certain antagonists such as 4-hydroxy tamoxifen (4-OHT). To better understand the mechanism of resistance to 4-OHT, we performed a comparative study of wild-type and Y537S mutant ERα in complex with 4-OHT using classical molecular dynamics and metadynamics. The results of this study indicated that Helix 12 (H12) disruption is a typical allosteric effect of 4-OHT, allowing the receptor to maintain an antagonistic conformation. The Y537S mutation induces the loss of this effect by stabilising H12 through the newly formed H-bond between E380 and S537, thereby strengthening H12 to adopt an agonistic conformation even when 4-OHT is bound. The obtained results and the approaches applied in this study could be used as proof of principle for discovering more potent ERα inhibitors to overcome the endocrine resistance. [ABSTRACT FROM AUTHOR]

[Display omitted] The integration of 2D-graphitic carbon (G) with 1D-carbon nanofiber (CF) allows for the unique properties of 2D graphitic carbon to be combined with the low densities, mechanical performance, and high surface area required for applications across the energy and sustainability landscape. Through a combination of experiments and numerical modeling, we demonstrate the transformation of standard egg-white (EW) proteins into an ultralightweight G-CF aerogel with a multiscale structure. The resulting covalently-bonded hierarchical structure, derived from the complex underlying protein configuration, exhibits a density that is two orders of magnitude lower than existing state-of-the-art materials. We apply this material to the challenges of desalination and water purification, notably demonstrating that the G-CF aerogel significantly improves upon existing materials, capturing 98.2% of ionic impurities and 99.9% of nano/microplastic contamination from seawater. [ABSTRACT FROM AUTHOR]

Single-component organic solar cells (SCOSCs) have attracted extensive attention due to their simplified device manufacturing and excellent stability. However, the relationship between morphology and charge carrier mobility in the active layers of SCOSCs is not well understood. In this work, we present a comprehensive investigation on this issue by studying four dyads (fullerenes as acceptor units) used as materials of active layers in small-molecule single-component organic solar cells (SM-SCOSCs), in which dyad 4 created the record of power conversion efficiency (PCE) of SM-SCOSC until now. Utilizing a multiscale theoretical approach, the results identify that the acceptor-acceptor stacking is dominant in amorphous films, significantly improving electron mobility and lowering hole mobility. We also find the importance of achieving a balance between electron and hole mobility to further improve PCE of SM-SCOSC because dyad 4 exhibits a more balanced electron/hole mobility than the other three molecules. These findings indicate the importance of tuning and enhancing donor-donor and acceptor-acceptor stacking simultaneously, offering insights for the design and optimization of future SM-SCOSC., (© 2024 Wiley-VCH GmbH.)

The properties of an aqueous solution of NaNO2 were studied by classical molecular dynamics based on the newly performed parameterization of the interaction potential of the ion with water molecules. It was shown that the first hydration shell around the ion has a radius of at least 3.8 Å, and the weakest hydrogen bonds formed between the H2O molecules and the nitrogen atom of the ion. Because of weaker hydrogen bonds, the orientational relaxation times of ions in solution are shorter than those of H2O molecules. The self-diffusion coefficient of is greater than that of Na+, which agrees with the experimental data. The vibrational properties of the hydrated ion, studied using the power spectrum of atomic vibrations, showed insignificant deviations from the experimental data. [ABSTRACT FROM AUTHOR]

[Display omitted] Molecular interactions in the quaternary fluid system acetic acid– n -propanol– n -propyl acetate–water were analyzed by classical and ab initio molecular dynamics methods. It was shown that ab initio molecular dynamics simulation can reproduce the molecular mobility tendency and structural features of a multicomponent system without empirical parameters. [ABSTRACT FROM AUTHOR]

Surface functionalization of metal nanoparticles (NPs), e.g., using peptides and proteins, has recently attracted a considerable attention in the field of design of therapeutics and diagnostics. The possibility of diverse functionalization allows them to selectively interact with proteins, while the metal core ensures solubility, making them tunable therapeutic agents against diseases due to mis-folding or aggregation. On the other hand, their action is limited by possible self-aggregation, which could be, however, prevented based on the full understanding of their phase diagram as a function of the environmental variables (temperature, ionic strength of the solution, concentration) and intrinsic characteristics (size, charge, amount, and type of functional groups). A common modeling strategy to study the phase behavior is to represent the NPs as spheres interacting via effective potentials implicitly accounting for the solvation effects. Their size put the NPs into the class of colloids, albeit with particularly complex interactions including both attractive and repulsive features, and a consequently complex phase diagram. In this work, we review the studies exploring the phases of these systems starting from those with only attractive or repulsive interactions, displaying a simpler disperse-clustered-aggregated transitions. The phase diagram is here interpreted focusing on the universal aspects, i.e., those dependent on the general feature of the potentials, and available data are organized in a parametric phase diagram. We then consider the potentials with competing attractive short range well and average-long-range repulsive tail, better representing the NPs. Through the proper combination of the attractive only and repulsive only potentials, we are able to interpret the appearance of novel phases, characterized by aggregates with different structural characteristics. We identify the essential parameters that stabilize the disperse phase potentially useful to optimize NP therapeutic activity and indicate how to tune the phase behavior by changing environmental conditions or the NP chemical–physical properties.

n the last two decades, colloidal semiconductor nanocrystals have emerged as a phenomenal research topic due to their size-dependent optoelectronic properties and to their outstanding versatility in many technological applications. In this review, we provide an historical account of the most relevant computational works that have been carried out to understand atomistically the electronic structure of these materials, including the main requirements needed for the preparation of nanocrystal models that align well with the experiments. We further discuss how the advancement of these computational tools has affected the analysis of these nanomaterials over the years. We focus our review on the three main families of colloidal semiconductor nanocrystals: group II-VI and IV-VI metal chalcogenides, group III-V metal pnictogenides and metal halides, in particular lead-based halide perovskites. We discuss the most recent research frontiers and outline the future outlooks expected in this field from a computational perspective.

[Display omitted] • Physical properties of eutectic mixtures are studied in the presence of water. • The liquid segregates into water and eutectic domains above 40 wt% water. • Water disrupts the hydrogen bonding network which improves eutectic interactions with CO 2. Deep eutectic solvents (DESs) are versatile solvents for various applications including CO 2 separations due to their good solvent strength, low volatilities, high thermal stabilities, and tunable properties. Properties of DESs alter with the presence of water and especially in applications where the solvent is in direct contact with air such as CO 2 removal from the atmosphere. This study employs classical molecular dynamics (MD) simulations to examine the impact of water (0 to 70 wt%) on the liquid structure and physical interactions in a eutectic solvent composed of an ionic liquid (IL) 1-ethyl-3-methylimidazolium 2-cyanopyrrolide, [EMIM][2CNPyr], that functions as a hydrogen bond acceptor (HBA) and with three different hydrogen bond donors (HBDs): ethylene glycol (EG), propylene glycol (PG), and monoethanolamine (MEA). It is found that water preferentially solvates HBDs and weakens the hydrogen-bonding interactions between [2CNpyr] and the HBDs, thus resulting in significant structural changes that lead to enhanced interactions between CO 2 and [EMIM], [2CNpyr], and MEA. Although these systems represent CO 2 -chemisorbing solvents in practice, the physical interactions in the presence of water as examined herein provides guidance on their phase behavior and tuning of physical properties by composition for targeted applications including CO 2 separations. [ABSTRACT FROM AUTHOR]

A detailed understanding of the connections of fabrication and processing to structural and thermal properties of low-dimensional nanostructures is essential to design materials and devices for phononics, nanoscale thermal management, and thermoelectric applications. Silicon provides an ideal platform to study the relations between structure and heat transport since its thermal conductivity can be tuned over 2 orders of magnitude by nanostructuring. Combining realistic atomistic modeling and experiments, we unravel the origin of the thermal conductivity reduction in ultrathin suspended silicon membranes, down to a thickness of 4 nm. Heat transport is mostly controlled by surface scattering: rough layers of native oxide at surfaces limit the mean free path of thermal phonons below 100 nm. Removing the oxide layers by chemical processing allows us to tune the thermal conductivity over 1 order of magnitude. Our results guide materials design for future phononic applications, setting the length scale at which nanostructuring affects thermal phonons most effectively.

Using solid nanoparticles (NPs) as catalysts is the most effective method to achieve catalytic growth of single-walled carbon nanotubes (SWCNTs) with ultrapure chirality. Until now, SWCNTs with a suitable chirality purity have not been prepared in experiments. That is, the evolution of solid NPs during the catalytic growth of SWCNTs is in contradiction with the original concept of a changeless structure. Hence, in this work, the evolution mechanism of solid cobalt NPs during the nucleation process of SWCNTs is analyzed through molecular dynamics. Similar to the experimental observations, the results show that a drastic structural fluctuation of the NPs occurs during the nucleation of SWCNTs. This structural fluctuation is caused by the fact that the elastic strain energy and surface energy of the NPs can be tuned when a carbon gradient exists between the subsurface and interior of the NP. Furthermore, such a carbon gradient can be reduced by changing the carbon feeding rate. This work not only reveals the evolution mechanism of solid catalysts during the nucleation of SWCNTs but also provides prospects for realizing solid catalysts with a changeless structure by tuning the experimental parameters., (© 2024 Wiley‐VCH GmbH.)

Nowadays, boron nitride has attracted a great deal of attention due to its physical (chemical) properties, facile synthesis, and experimental characterization, indicating great potential for industrial application. Based on this, we develop here a theoretical study on boron nitride nanoflakes built-up from hexagonal boron nitride nanosheets exhibiting hexagonal, rectangular, and triangular shapes. In order to investigate geometry effects such as those due to the presence of armchair and zigzag edges and distinct shapes, we analyzed their properties from both classical and quantum viewpoints. Using classical molecular dynamics calculations, we show that the nanosheets preserve their structural stability at high temperatures, while DFT calculations demonstrate HOMO–LUMO energy gap variation within the theoretical energy gaps of h-BN in bulk and 2D crystals. Besides that, we have also found that boron nitride nanoflakes structures have spatially symmetrical spin densities. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to illustrate our contribution to general plasma physics studies obtained since the 90s with multiple versions and adaptations of the classical molecular dynamics (CMD) simulation interactive code called BinGo. After a description of the particulars of the CMD simulation models and the BinGo code suite, some applications are discussed for illustration. These results validate the CMD simulation as a powerful tool of investigation for hot dense plasmas. [ABSTRACT FROM AUTHOR]

Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis, and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of efficiently exploring a vast conformational space in order to seek for the actual transition path for systems whose complexity is already high in the stable states. Here we report a strategy that simplifies this task attacking the complexity on several sides. We first apply a minimalist coarse-grained model to Calmodulin, based on an empirical force field with a partial structural bias, to explore the transition paths between the apo-closed state and the Ca-bound open state of the protein. We then select representative structures along the trajectory based on a structural clustering algorithm and build a cleaned-up trajectory with them. We finally compare this trajectory with that produced by the online tool MinActionPath, by minimizing the action integral using a harmonic network model, and with that obtained by the PROMPT morphing method, based on an optimal mass transportation-type approach including physical constraints. The comparison is performed both on the structural and energetic level, using the coarse-grained and the atomistic force fields upon reconstruction. Our analysis indicates that this method returns trajectories capable of exploring intermediate states with physical meaning, retaining a very low computational cost, which can allow systematic and extensive exploration of the multi-stable proteins transition pathways.

Artemis is an endonuclease responsible for breaking hairpin DNA strands during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance, its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, and the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulations, both classically and at the hybrid quantum mechanics/molecular mechanics level, we evidenced the stable interaction modes of Artemis with a model DNA strand. We also analyzed the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.

The mechanical properties of nanocrystalline materials differ dramatically from those of conventional ones. In particular, the yield strength noticeably grows as grain size decreases. On the other hand, the grain size is not the only factor affecting the yield strength. Extended ingrain defects such as dislocations and stacking faults also contribute to the strength of materials. Modification of the mechanical properties of plutonium and its alloys via grain refinement is of interest because of their use in civil and military nuclear technologies, e.g. , as a component of metallic nuclear fuel. But the experimental study of plutonium is hampered by its high chemical and radiological activity harmful to human health. That is why theoretical and computational techniques proved to be useful for investigation into plutonium properties must be applied first, prior to experimental ones. In the paper the atomistic simulation approach is applied to directly calculate the mechanical properties of nanocrystalline face centered cubic δ -phase Pu-Ga alloys, in particular, the ambient conditions quasi-static yield stress dependence on grain size and extended defect concentration. The range of grain sizes studied is 40 − 200 n m. A deviation from the Hall-Petch relation is demonstrated. The effect of the alloying addition redistribution inside grains as well as between the grains is also evaluated. Image 1 [ABSTRACT FROM AUTHOR]

Quantum dots (QDs) are semiconductor nanocrystals that exhibit exceptional properties not found in their bulk counterparts. They have attracted extensive academic and industrial attentions due to their quantum confinement effects and unique photophysical properties. Computational approaches such as first principles and classical molecular dynamics simulations are indispensable tools in both scientific studies and industrial applications of QDs. In this review, the state‐of‐the‐art progress in computational simulations of optical, electronic and thermal properties of QDs is summarized and discussed. First, the physics of QDs in low dimensional materials are comprehensively reviewed. Then, the theoretical basis and practical applications of two main computational methods are presented. Properties of QDs revealed by computational studies are summarized respectively. Finally, the paper was concluded with comments on future directions in computational modeling of QDs. [ABSTRACT FROM AUTHOR]

Graphical abstract Abstract Boron oxide (B 2 O 3) is investigated by a combination of ab initio (DFT-based) molecular dynamics (MD) simulations and classical MD simulations. From the trajectories of the ab initio MD simulation, we derive a three-body interaction potential which is used in classical MD simulations to study various structural and dynamic properties on larger time and length scales than possible in the ab initio simulations. Differences and similarities to the structure and dynamics of other network glass formers such as SiO 2 and GeO 2 are discussed. Moreover, various properties as obtained from the simulations are compared to those from experiments of B 2 O 3. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • The anisotropic nature of water and ions dynamics is quantified. • The deceleration effects of confinement on electrolyte dynamics are computed. • Ion concentration affects the electrolyte dynamics on an ion specific way. • Collisions of particles on HAP walls are crucial to determine out-of-plane diffusion. Abstract Hydroxyapatite (HAP) is the principal phase of bones, where the presence of ions in the fluids within HAP pores is critical to important phenomena such as bone remodeling, mineralization and fossilization. Classical molecular dynamics simulations of HAP pores ranging from 2 to 120 nm, containing pure water and aqueous solutions of CaCl 2 and of CaF 2 , were conducted to quantify the effect of confinement and solution composition on the dynamic properties of water and ions. Diffusion coefficients were obtained from formulations adapted to diffusion processes parallel and perpendicular to the HAP walls. A change in diffusion mechanism is observed in the direction perpendicular to the HAP walls: after a transition period proportional to the pore size, the mean squared displacement scales with the square-root of the time instead of being linear. The presence of CaCl 2 and CaF 2 decelerates water and ion dynamics, and changes in ion concentration modify the in-plane dynamics more strongly than the out-plane dynamics of ions in HAP pores. [ABSTRACT FROM AUTHOR]

Abstract While the electronic stoppage of charged fission fragments is relatively well understood, the subsequent energy cascade is not. Recent efforts to investigate this cascade and predict the resulting damage have used a two-temperature model (TTM) of the electronic and phononic systems coupled with a classical molecular dynamics (MD) simulation of the crystal lattice. In order to accurately predict the track radius produced by a fission fragment in UO 2 , this model (TTM + MD) requires that UO 2 , an insulator, have metallic properties, e.g., a substantial electron thermal conductivity and heat capacity. However, it has been predicted that UO 2 becomes metallic under large pressures, and we perform ab initio (DFT-HSE) simulations to support this prediction. We show that the average U-U bond length decreases within and near the ion track during TTM + MD simulations, supporting the use of volume contraction to model the pressurized UO 2 cell. Additionally, we evaluate the electron, phonon, and electron-phonon coupling properties of UO 2 for variations in the pressure. In particular, we calculate the electronic heat capacity and thermal conductivity, and the electron-phonon energy coupling for use in subsequent TTM + MD simulations. The ab initio parameterized TTM + MD simulations provide a set of the track radii predictions which bracket and include the experimentally observed radii. The accuracy of the ab initio parameterized TTM + MD simulations depends on the pressure and degree of electron-phonon non-equilibrium assumed during the ab initio calculations. We suggest improvements to the current TTM + MD methodology in light of these results. Still, we show that the pressure-induced transition of UO 2 from insulator to metal and subsequent energy transfer from the electronic to phononic systems can accurately explain radiation damage during swift, heavy ion stoppage in UO 2. We make some additional observations regarding the accumulation and recombination of damage along the ion track and make comparison to the common SRIM model of ion stoppage and damage accumulation. [ABSTRACT FROM AUTHOR]

The adiabatic sound velocity of liquid argon is calculated by means of classical molecular dynamics simulations via the COMPASS force field, at the temperature of 388 K and the pressure range of 0.5–2.0 GPa. The isothermal sound velocity of liquid argon is obtained from the fluctuations of the supercell volume via Fluctuation Formula. Then, the adiabatic sound velocity is calculated from isothermal sound velocity by the Landau–Placzek ratio derived from the dynamic structure factor of the system. The calculated adiabatic sound velocities of liquid argon are in good agreement with the former Brillouin scattering measurements. [ABSTRACT FROM AUTHOR]

Fluidity of lipid membranes is known to play an important role in the functioning of living organisms. The fluorescent probe Laurdan embedded in a lipid membrane is typically used to assess the fluidity state of lipid bilayers by utilizing the sensitivity of Laurdan emission to the properties of its lipid environment. In particular, Laurdan fluorescence is sensitive to gel vs liquid–crystalline phases of lipids, which is demonstrated in different emission of the dye in these two phases. Still, the exact mechanism of the environment effects on Laurdan emission is not understood. Herein, we utilize dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC) lipid bilayers, which at room temperature represent gel and liquid–crystalline phases, respectively. We simulate absorption and emission spectra of Laurdan in both DOPC and DPPC bilayers with quantum chemical and classical molecular dynamics methods. We demonstrate that Laurdan is incorporated in heterogeneous fashion in both DOPC and DPPC bilayers, and that its fluorescence depends on the details of this embedding. [ABSTRACT FROM AUTHOR]

For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification. [ABSTRACT FROM AUTHOR]

Focal adhesion kinase (FAK) is required for signaling in the heart. S910 phosphorylated FAK is known to cause pathological cardiac hypertrophy. The switching of FAK between its inactive (-i), activated (-a) and hyperactive (-h) state is controlled by phosphorylation. FAK consists of three domains, namely: FERM, Kinase, and FAT joined by linkers L1 and L2. The structural basis of FAK phosphorylation and signaling to the downstream pathways is not understood. In this work, we carried out homology modeling and domain assembly of full length human iFAK and aFAK. 100 ns classical molecular dynamic simulations were performed using AMBER14 and effect of S910 phosphorylation on FAK was investigated. The iFAK model superposed on a small angel X-ray scattering (SAXS) derived model with RMSD of 1.18 Å for 590 Cα atoms. aFAK showed S910 phosphorylation site in L2 shielded by FERM. S910 phosphorylation in hFAK led to its exposure accompanied by a large conformational change and exposing the previously buried Grb2 interaction site responsible for causing cardiac hypertrophy. The models of FAK are in agreement with diverse experimental data and observed differences in biological action. Understanding the structure activity relationships of FAK in response to phosphorylation is important for its future therapeutic modulation. [ABSTRACT FROM AUTHOR]

This work investigates the ion transport mechanisms in binary and ternary electrolyte systems based on polymers and ionic liquids for Na-ion batteries. Molecular dynamics (MD) simulations were performed on poly(ethylene oxide) (PEO) and ionic liquids (IL) based electrolytes, bis(trifluoromethanesulfonyl)imide (TFSI)/N-methyl-N-propylpyrrolidinium (Pyr13) and bis(fluorosulfonyl)imide (FSI)/Pyr13, varying the composition at 0, 5, 10 and 20 wt% over a range of temperatures from 313 to 400 K. The simulations could satisfactorily reproduce the experimental densities and trends in diffusivities and conductivity data. It was observed that there exists a stronger interaction between sodium ions and the FSI anions as compared to the TFSI counterparts, correlated to a difference in interaction energy between the ionic species. This controls how well the different ILs act as plasticizers for the Na-PEO system, with TFSI actually displaying lower conductivity for low IL loadings while the conductivity increases continuously for the FSI counterparts. Moreover, the simulations show that the sodium ions interact more strongly with the polymer at lower temperatures, leading to a lower polymer free volume which explains the trends in ionic transport. Thereby, these MD simulations unveil an interplay between the coordination chemistry and the dynamic properties in these ternary polymer-ionic liquid-salt electrolytes, and how the coordination strength controls the conductive properties. [Display omitted] [ABSTRACT FROM AUTHOR]

Various isomers of free clusters of zirconium ZrN (N=4÷15) were studied. The results were obtained using molecular dynamics simulation and many-body Clery and Rosato interaction potential. The average length and the binding energy, the coordination number and the frequency of occurrence of various isomers were calculated.

We report a multi-scale simulation study of the photocycle of the rhodopsins. The quasi-atomistic representation (“united atoms” UA) of retinal is combined with a minimalist coarse grained (CG, one-bead-per amino acid) representation of the protein, in a hybrid UA/CG approach, which is the homolog of QM/MM, but at lower resolution. An accurate multi-stable parameterization of the model allows simulating each state and transition among them, and the combination of different scale representation allows addressing the entire photocycle. We test the model on bacterial rhodopsin, for which more experimental data are available, and then also report results for mammalian rhodopsins. In particular, the analysis of simulations reveals the spontaneous appearance of meta-stable states in quantitative agreement with experimental data.

Background: Free-standing carbon nanomembranes (CNM) with molecular thickness and macroscopic size are fascinating objects both for fundamental reasons and for applications in nanotechnology. Although being made from simple and identical precursors their internal structure is not fully known and hard to simulate due to the large system size that is necessary to draw definite conclusions.Results: We performed large-scale classical molecular dynamics investigations of biphenyl-based carbon nanomembranes. We show that one-dimensional graphene-like stripes constitute a highly symmetric quasi one-dimensional energetically favorable ground state. This state does not cross-link. Instead cross-linked structures are formed from highly excited precursors with a sufficient amount of broken phenyls.Conclusion: The internal structure of the CNM is very likely described by a disordered metastable state which is formed in the energetic initial process of electron irradiation and depends on the process of relaxation into the sheet phase.

Molecular dynamics with the modified embedded atom model (MEAM) for interatomic interaction is applied to direct simulations of dislocation dynamics in fcc δ -phase Pu-Ga alloys. First, parameters of the MEAM potential are fitted to accurately reproduce experimental phonon dispersion curves and phonon density of states at ambient conditions. Then the stress-velocity dependence for edge dislocations as well as Pierls stress are obtained in direct MD modeling of dislocation motion using the shear stress relaxation technique. The simulations are performed for different gallium concentrations and the dependence of static yield stress on Ga concentration derived demonstrates good agreement with experimental data. Finally, the influence of radiation defects (primary radiation defects, nano-pores, and radiogenic helium bubbles) on dislocation dynamics is investigated. It is demonstrated that uniformly distributed vacancies and nano-pores have little effect on dislocation dynamics in comparison with that of helium bubbles. The results of the MD simulations evidence that the accumulation of the radiogenic helium in the form of nanometer-sized bubbles is the main factor affecting strength properties during long-term storage. The calculated dependence of static yield stress on helium bubbles concentration for fcc Pu 1 w t . % Ga is in good agreement with that obtained in experiments on accelerated aging. The developed technique of static yield stress evaluation is applicable to δ -phase Pu-Ga alloys with arbitrary Ga concentrations. [ABSTRACT FROM AUTHOR]

We present results of molecular dynamic simulation of continuous graphene monolayer on Cu(111). In this paper, we investigate the dependencies of the average binding energy and the average binding distance on the temperature. The interaction between carbon and copper atoms was described by Lennard-Jones potential. It is shown that the binding energy practically remains constant in a wide range of temperatures 0-800 K. However, in the same temperature range, the binding distance of graphene on Cu(111) surface has a linear dependence on temperature. The dependence of the linear thermal expansion coefficient of the binding distance on Lennard-Jones parameters has been calculated. We suggest a simple theoretical model to explain this dependence qualitatively. [ABSTRACT FROM AUTHOR]

The statistical properties of rough surfaces at the nanoscale are studied using classical molecular dynamics. Atomistic fcc blocks of gold are generated with different crystal orientations, and with rough surfaces having the same root-mean-square roughness with variable power spectral density (PSD) slopes and roll-off wavenumbers. The process of rough surface generation may result in thermodynamically unstable sharp spatial features. In order to relax the structure, the blocks are equilibrated at 300 K . It is found that all surfaces experience changes in their roughness, regardless of their crystal orientation or temperature, although the changes are only temperature-independent when T ≤ 0.4 T m . Based on the analyzed PSDs of the equilibrated substrates, two methods for generating pseudo-stable rough surfaces are introduced and discussed. [ABSTRACT FROM AUTHOR]

Models of the hydrogenoxalate (bioxalate, charge −1) and oxalate (charge −2) anions were developed for classical molecular dynamics (CMD) simulations and parametrized against ab initio molecular dynamics (AIMD) data from our previous study (Kroutil et al. (2016) J Mol Model 22:210). The interactions of the anions with water were described using charges scaled according to the electronic continuum correction approach with rescaling of nonbonded parameters (ECCR), and those descriptions of anion interactions were found to agree well with relevant AIMD and experimental results. The models with full RESP charges showed excessively strong electrostatic interactions between the solute and water molecules, leading to an overstructured solvation shell around the anions and thus to a diffusion coefficient that was much too low. The effect of charge scaling was more evident for the oxalate dianion than for the hydrogenoxalate anion. Our work provides CMD models for ions of oxalic acid and extends previous studies that showed the importance of ECCR for modeling divalent ions and ions of organic compounds. [ABSTRACT FROM AUTHOR]