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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]

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]

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]

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]

[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]

[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]

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 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]

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]

Predicting the fate of accident-melted nuclear fuel-cladding requires the understanding of the thermophysical properties which are lacking or have large scatter due to high-temperature experimental challenges. Using equilibrium classical molecular dynamics (MD), we predict the properties of melted UO 2 and ZrO 2 and compare them with the available experimental data and the predictive models. The existing interatomic potential models have been developed mainly for the polymorphic solid phases of these oxides, so they cannot be used to predict all the properties accurately. We compare and decipher the distinctions of those MD predictions using the specific property-related autocorrelation decays. The predicted properties are density, specific heat, heat of fusion, compressibility, viscosity, surface tension, and the molecular and electronic thermal conductivities. After the comparisons, we provide readily usable temperature-dependent correlations (including UO 2 -ZrO 2 compounds, i.e. corium melt). [ABSTRACT FROM AUTHOR]

The most representative member of the Ras subfamily is its HRas isoform. Ras proteins being GTPases, possess an intrinsic activity to hydrolyze the GTP molecule to GDP. During the transition phases, between active and inactive states, P-loop and switch regions show maximum variations. Various hot-spot Ras mutants (G12 V, A59G, Q61L etc) have been reported, that limit the protein's conformation in the permanent active state. In the present study, we aim to explore the structural dynamics of one such crucial mutant of Ras namely A59G which belongs to the conserved Switch II region of the protein. Approximately ∼15 μs of Classical Molecular Dynamics (CMD) simulations have been carried out on the mutant and wild-type complexes. Further, a metadynamics simulation of 500 ns was also carried out, which suggests an energy barrier of ∼9.56 kcal/mol between wild-type and mutant conformation. We demonstrate the role of water molecule in maintaining the required interaction networks in the pre-hydrolysis state, its impact on A59G mutation, distinct orientation of the Gln61 residue in two conformations, disruption of crucial Gly60 and γ phosphate and the change in the Switch II region. The outcome of our study captures the pre-hydrolysis state of the HRas protein. It also establishes the fact that this mutation makes the movement of Switch II region and the conserved DXXGQ motif highly constrained, which is known to be an important requirement for hydrolysis. This suggests that the A59G mutation may decrease the rate of intrinsic hydrolysis as well as GAP-mediated hydrolysis. [ABSTRACT FROM AUTHOR]

Flexibility is involved in a wide range of biological processes, such as protein assembly and binding recognition. EPSP synthase is an enzyme that must undergo a large conformational change to accommodate its ligands into its binding cavity. However, although the structure of EPSP synthase has been determined, its plasticity has not been explored in depth. Therefore, in this work, we extensively examined the influence of the flexibility of Mycobacterium tuberculosis EPSP (MtEPSP) synthase on the function of this protein using classical and replica-exchange metadynamics simulations. We were able to identify five well-populated conformational clusters for MtEPSP synthase: two corresponding to open, one to ajar, and two to closed conformations. We also pinpointed three hydrophobic regions that are responsible for guiding transitions among these states. Taken together, the new findings presented here indicate how the hydrophobic regions modulate the flexibility of MtEPSP synthase, and they highlight the importance of considering these dynamic features in drug design projects employing this enzyme as a target. [ABSTRACT FROM AUTHOR]

Recent experiments have shown that electric double-layer capacitors utilizing electrodes consisting of graphene edge plane exhibit higher capacitance than graphene basal plane. However, theoretical understanding of this capacitance enhancement is still limited. Here we applied a self-consistent joint density functional theory calculation on the electrode/electrolyte interface and found that the capacitance of graphene edge plane depends on the edge type: zigzag edge has higher capacitance than armchair edge due to the difference in their electronic structures. We further examined the quantum, dielectric, and electric double-layer (EDL) contributions to the total capacitance of the edge-plane electrodes. Classical molecular dynamics simulation found that the edge planes have higher EDL capacitance than the basal plane due to better adsorption of counter-ions and higher solvent accessible surface area. Our work therefore has elucidated the capacitive energy storage in graphene edge planes that take into account both the electrode's electronic structure and the EDL structure. [ABSTRACT FROM AUTHOR]

Molybdenum (Mo) nanoparticles (NPs) are one of the most effective refractory catalysts for preparing single-walled carbon nanotubes (SWCNTs) with high chirality. In this work, the evolution of Mo NPs at the initial stage of catalytic growth of SWCNT was investigated. It was found that NPs underwent transformation between the solid and semi-liquid phases during gradual deposition of C atoms, even though the deposition temperature was far below the melting point of NPs. Such transformation was caused by the elastic strain in NPs that could be manipulated by carbon (C) atoms. Furthermore, the results indicated that the lifetime of NPs in the semi-liquid state could be controlled by adjusting the feeding rate of C atoms. This work not only provides useful insight into the evolution of Mo NPs during the early stage of the catalytic growth of SWCNTs, but also opens up new prospects for controlling the lifetime of NPs in the semi-liquid phase by changing the experimental parameters. [Display omitted] [ABSTRACT FROM AUTHOR]

Polycrystalline structure plays an important role in the macroscopic properties of a solid material. In this paper we propose a new code to generate a polycrystalline material at the atomic scale. Our polycrystalline systems are based on the random generation from initial germs. From a mechanical point of view, it brings new features as for example ductility of 3D polycrystalline aluminium. By using molecular dynamics simulations, we also show the effect of temperature on a geological material, olivine, one of the most abundant silicate mineral of the Earth upper mantle. The importance of porous media is also considered (e.g. metals). [ABSTRACT FROM AUTHOR]

The paper presents a theoretical investigation into the response of δ -phase Pu–Ga alloys to self-irradiation. Using classical molecular dynamics we investigate the long-term behavior of primary radiation defects (vacancies) in the face-centered cubic lattice of the alloys under ambient conditions. High diffusive migration energy barriers and the corresponding low mobility of vacancies do not allow us to track their dynamics in the lattice by direct molecular dynamics simulations. Instead, we use the Helmholtz free energy to investigate the equilibrium thermodynamics of metastable microconfigurations of Pu–Ga crystals with artificially introduced vacancy clusters in various regular and random configurations. The Helmholtz free energy of the microconfigurations are calculated with the thermodynamic integration method. Based on the free energy evaluation we draw conclusions about the relative thermodynamic stability of various microconfigurations under ambient conditions. The equilibrium parameters of vacancy clusters in the bulk of the lattice and in the presence of edge dislocations are estimated. [ABSTRACT FROM AUTHOR]

The lithium metal battery is one of today's most promising high-energy-density storage devices. Its full-scale implementation depends on solving operational and safety issues intrinsic to the Li metal high reactivity leading to uncontrolled electrolyte decomposition and uneven Li deposition. In this work, we study the spontaneous formation of the solid electrolyte interphase (SEI) upon contact of Li metal with the electrolyte and describe the heterogeneous SEI morphological features. Multiple electrolyte formulations based on lithium bis(fluorosulfonyl)imide (LiFSI), dimethoxyethane (DME), dimethyl carbonate (DMC), 1,2,2-tetrafluoroethyl-2,2,3,3-tetrafluoropropyl ether (TTE) and bis(2,2,2-trifluoroethyl) ether (BTFE) are used. Findings include the description of the SEI evolution from dispersed LiO, LiS, LiN, and LiF clusters to a continuous and compact inorganic phase in which the LiO and LiF content depend on the presence of fluorine diluents. The role of the DME ether solvent helping the growth of a "wet-SEI" is compared to that of the highly unstable carbonate DMC, which decomposes into complex radical oligomers that might contribute to further electrolyte decomposition. The impact of the electrolyte-to-anode ratio on LiFSI decomposition is highlighted. Finally, we suggest the existence of a critical LiFSI concentration and electrolyte-to-anode ratio that could potentially balance the rate of electrolyte depletion and lithium consumption. • SEI composition and structure determined from electrolyte components. • Main SEI tuning variables: salt concentration and electrolyte to anode ratio. • SEI evolution demonstrated during initial formation stages. [ABSTRACT FROM AUTHOR]

• MEA + EAE + sulfolane biphasic absorbent was developed with better performance than MEA. • Tunable phase separation property was achieved by varying the concentration ratios. • Strong hydrogen bonding and interaction promoting phase separation were analyzed. • Liquid-liquid phase separation mechanism was revealed by classical MD simulations. To reduce the regeneration energy consumption for CO 2 capture, an advanced monoethanolamine (MEA) + 2-(ethylamino)ethanol (EAE) + sulfolane biphasic aqueous solution was developed, and the phase separation mechanism was explored. The effects of the concentration ratio on the phase separation behavior, CO 2 absorption performance, CO 2 loading at the phase separation point, and CO 2 desorption performance of MEA + EAE + sulfolane solutions were investigated comprehensively in experiments. The 3 M MEA + 2 M EAE + 5 M sulfolane showed the best properties with a large CO 2 loading of 0.32 mol/mol at the phase separation point and the relative low regeneration energy consumption, which is comparable to 5 M MEA in absorption with an improved desorption performance. The molecular mechanism of phase separation was revealed by molecular dynamics simulations, illustrating that strong hydrogen bonding between amine products and water and enhanced intermolecular interaction among amine products, would promote an aggregation of amine products. This study provides a promising candidate for energy-efficient CO 2 capture with molecular insights into a liquid–liquid phase separation. [ABSTRACT FROM AUTHOR]

• MEA + EAE + sulfolane biphasic absorbent was developed with better performance than MEA. • Tunable phase separation property was achieved by varying the concentration ratios. • Strong hydrogen bonding and interaction promoting phase separation were analyzed. • Liquid-liquid phase separation mechanism was revealed by classical MD simulations. To reduce the regeneration energy consumption for CO 2 capture, an advanced monoethanolamine (MEA) + 2-(ethylamino)ethanol (EAE) + sulfolane biphasic aqueous solution was developed, and the phase separation mechanism was explored. The effects of the concentration ratio on the phase separation behavior, CO 2 absorption performance, CO 2 loading at the phase separation point, and CO 2 desorption performance of MEA + EAE + sulfolane solutions were investigated comprehensively in experiments. The 3 M MEA + 2 M EAE + 5 M sulfolane showed the best properties with a large CO 2 loading of 0.32 mol/mol at the phase separation point and the relative low regeneration energy consumption, which is comparable to 5 M MEA in absorption with an improved desorption performance. The molecular mechanism of phase separation was revealed by molecular dynamics simulations, illustrating that strong hydrogen bonding between amine products and water and enhanced intermolecular interaction among amine products, would promote an aggregation of amine products. This study provides a promising candidate for energy-efficient CO 2 capture with molecular insights into a liquid–liquid phase separation. [ABSTRACT FROM AUTHOR]

The ionization potential of an ion embedded in a plasma, lowered due to the whole of the charged particles (ions and electrons) interacting with this ion, is the so-called plasma effect. A numerical plasma model based on classical molecular dynamics has been developed recently. It is capable to describe a neutral plasma at equilibrium involving ions of various charge states of the same atom together with electrons. This code is used here to investigate the ionization potential depression (IPD). The study of the IPD is illustrated and discussed for aluminum plasmas at mid and solid density and electron temperatures varying from 50eV to 190eV. The method relies on a sampling of the total potential energy of the electron located at an ion being ionized. The potential energy of such electron results from all of the interacting charged particles interacting with it. [ABSTRACT FROM AUTHOR]

We present classical and DFT-based molecular dynamics (MD) simulations of carbon in the warm dense matter regime (ρ= 3.7 g/cc, 0.86 eV < T <8.62 eV [T < 100 eV for classical MD]). Two different classical interatomic potentials are used: 1. LCBOP, designed to simulate condensed (e.g. solid) phases of C, and 2. linearly screened Coulomb (Yukawa) potentials. It is shown that LCBOP over-predicts minima and maxima in the pair correlation functions of liquid-C in this regime when compared to the DFT-MD results. The screened Coulomb model, while under-correlating at low-T, seems to produce the correct qualitative features in the static ionic pair distributions at the highest-T. However, both approaches predict the decay in the ionic contribution of the specific heat as T → ∞ to be much slower than that predicted by a model based on DFT-MD. These differences in the MD-derived equations of state in warm dense regimes could have important consequences when using classical inter-ionic forces such as these in large-scale MD simulations aimed at studying, for instance, processes of relevance to inertial confinement fusion when C is used as an ablator material. [ABSTRACT FROM AUTHOR]

The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The paper presents a theoretical study of the response of δ -phase Pu–Ga alloys to self-irradiation. We investigate the long-term behaviour of He atoms in the face-centred cubic (fcc) lattice under ambient conditions by means of classical molecular dynamics. Because of the relatively low diffusive mobility of He atoms in the lattice their dynamics cannot be tracked directly in molecular dynamics simulations. Instead, we use the Helmholtz free energy function to investigate the equilibrium thermodynamics of metastable microconfigurations of perfect crystals with artificially introduced He atoms in different configurations. The Helmholtz free energy of the microconfigurations are calculated using the thermodynamic integration method. Based on the free energy evaluation, inferences about the relative thermodynamic stability of various microconfigurations under ambient conditions are drawn. Estimates of the equilibrium parameters of He bubbles in the lattice and the distribution of He bubble radii are calculated and compared to those observed experimentally. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The tensile behavior of single crystalline nanotube bundles was studied using classical molecular dynamics. Stillinger-Weber potential was used to describe the atom-atom interactions. The bundles consisted of several individual nanotubes with {100} side planes. The simulation results show that the nanotube bundles show a brittle to ductile transition (BDT) by changing the temperatures. The fracture of nanotube bundles is ruled by a thermal activated process, higher temperature will lead to the decrease of the critical stress. At high temperatures the individual nanotube in the bundles interact with each other, which induces the increase of the critical stress of bundles. [ABSTRACT FROM AUTHOR]

Highlights: [•] We treat theoretically highly charged ions-small argon clusters collisions. [•] Coulomb interaction between argon ions of the cluster plays an important role. [•] The cluster remains intact during the collision time. [•] The average charge per atom decreases with increasing cluster size. [ABSTRACT FROM AUTHOR]

The parameters of thermoelectric performance for thermal conductivity are investigated and need to more and more small value. In this work an analytical simulation model is affected of Bi doped PbTe compound on thermal properties simulated by classical molecular dynamics (MD). The MD simulation has been applied with temperature pressure and volume influence interatomic interaction by Lenard-Jone formula and atoms vacancy. The potential parameter is based on Busing-Ida function contribution thermodynamics equilibrium which ignored phase transition with the cluster atoms site 4 × 4 × 4 on 512 atoms (256 cations and 256 anions). The lattice parameter, compressibility, linear thermal expansion coefficient and heat capacity are calculated. The result for thermal conductivity of PbTe is decreased by doping Bi and strong agreement with experimental data. [ABSTRACT FROM AUTHOR]

Ras is one of the most common oncogenes in human cancers. It belongs to a family of GTPases that functions as binary conformational switches by timely switching of their conformations from GDP to GTP and vice versa. It attains the final active state structure via an intermediate GTP-bound state. The transition between these states is a millisecond-time-scale event. This makes studying this mechanism beyond the scope of classical molecular dynamics. In the present study, we describe the activation pathway of the HRas protein complex along the distance-based reaction coordinate using steered molecular dynamics. Approximately ~720 ns of MD simulations using CMD and SMD was performed. We demonstrated the change in orientation and arrangement of the two switch regions and the role of various hydrogen bonds during the activation process. The weighted histogram analysis method was also performed, and the potential of mean force was calculated between the inactive and active via the intermediate state (state 1) of HRas. The study indicates that water seems to play a crucial role in the activation process and to transfer the HRas protein from its intermediate state to the fully active state. The implications of our study hereby suggest that the HRas activation mechanism is a multistep process. It starts from the inactive state to an intermediate state 1 followed by trapping of water molecules and flipping of the Thr35 residue to form a fully active state (state 2). This state 2 also comprises Gly60, Thr35, GTP, Mg and water-forming stable interactions. [ABSTRACT FROM AUTHOR]

Highlights: [•] We treat theoretically highly charged ions-argon dimer collisions. [•] Tunneling is important for large impact parameters. [•] Coulomb interaction between argon ions of the dimer plays an important role. [•] The dimer remains intact during the collision time. [Copyright &y& Elsevier]

Abstract: This paper reports the results of a classical molecular dynamics (CMD) study of molecular water adsorption on MO2- and SrO-terminated SrMO3 (001) surfaces (M=Ti, Zr) at 300K with ½ML and 1ML coverage. Models of the force fields for the water–crystalline oxide interfaces have been proposed. These force fields describe the oxide–oxide, water–oxide and water–water interactions, as well as interactions within the water molecule itself. The water–water and flexible water intramolecular potentials have been adopted from Toukan and Rahman (Phys. Rev. B 31 (1985) 2643–2648). The results of CMD simulations of the structure of the water layers at the oxide surfaces are discussed in terms of the most probable configurations. The power spectra of the water hydrogen velocity autocorrelation functions have been calculated using the CMD trajectories. The calculated power spectra permit us to consider the vibrational modes of the different structural species formed by the water molecules at the oxide surfaces and to analyse the level of binding of these species, both between themselves and to the surface. [Copyright &y& Elsevier]