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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. [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]

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]

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]

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]

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]

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]

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]

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]

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]

The interaction of interstitial hydrogen (H) with dislocations and point defects in tungsten (W) is studied via numerical simulation within the framework of classical molecular dynamics (MD). Two alternative models are considered to describe the interatomic interactions: the embedded-atom method (EAM) and the bond-saturation model (the bond-order potential (BOP)). The calculated results are compared with data obtained via ab initio quantum-mechanical simulation. The potential developed recently within the framework of the EAM model demonstrated better agreement with the ab initio results than the BOP one. Molecular- statics calculations showed that hydrogen atoms are attracted by the dislocation core in both cases of screw and edge dislocations. The classical MD simulation of hydrogen diffusion in the vicinity of the edge dislocation demonstrated one-dimensional migration along the dislocation line. [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 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]

The classical molecular dynamics method is employed to simulate the interaction of screw and edge dislocations with interstitial perfect dislocation loops (of 2 and 5 nm in diameter) in the austenitic model alloy FeNiCr at temperatures of T = 300-900 K. Perfect loops can be created from Frank loops during the plastic deformation of irradiated austenitic steels applied in nuclear reactors. As a result, the dislocation-defect interaction mechanisms are established and classified. The loop absorption mechanisms, which are related to the formation of free channels capable of enhancing radiation-induced steel embrittlement, are revealed. The effectivenesses of loop absorption observed during their interaction with screw and edge dislocations, as well as unpinning stresses required for a dislocation to overcome the defect acting as an obstacle, are compared versus the material temperature, defect size, and interaction geometry. [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]

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]

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]

We have investigated the high-pressure behavior of low-cristobalite form of AlPO4 (c-AlPO4) using a combination of Raman scattering, synchrotron powder X-ray diffraction, and classical molecular dynamics simulations. Our experiments indicate that under non-hydrostatic conditions c-AlPO4 initially transforms to a monoclinic phase, which then transforms to the Cmcm phase via an intermediate, disordered structure. In contrast, X-ray diffraction measurements made under hydrostatic conditions show that the ambient structure transforms directly to the Cmcm phase. Our classical molecular dynamics simulations, carried out under hydrostatic conditions, also show that c-AlPO4 directly transforms to the Cmcm phase at <13 GPa. [ABSTRACT FROM AUTHOR]

In this study, we investigated the limits of classical molecular simulation on the estimation of thermodynamic properties of cryogenic hydrogen. Three empirical potentials, the Lennard-Jones (LJ) potential, two-centre LJ (2CLJ) potential, and modified Buckingham (exp-6) potential and an ab initio potential model derived by the molecular orbital calculation were applied. Molecular dynamics (MD) simulations were performed across a wide density–temperature range. Using these data, the equation of state (EOS) was obtained by Kataoka's method, and they were compared with National Institute of Standards and Technology (NIST) data using the principle of corresponding states. As a result, it was confirmed that the potential model has a large effect on the estimated thermodynamic properties of cryogenic hydrogen. On the other hand, from the viewpoint of the principle of corresponding states, we obtained the same results from the empirical potential models as from the ab initio potential showing that the potential model has only a small effect on the reduced EOS: the classical MD results could not reproduce the NIST data in the high-density region. This difference is thought to arise from the quantum effect in actual liquid hydrogen. [ABSTRACT FROM PUBLISHER]

Simulations using ab initio quantum mechanical charge field molecular dynamics (QMCF MD) and classical molecular dynamics using two-body and three-body potentials were performed to investigate the hydration of the Ca2+ ion at different temperatures. Results from the simulations demonstrate significant effects of temperature on solution dynamics and the corresponding composition and structure of hydrated Ca2+. Substantial increase in ligand exchange events was observed in going from 273.15 K to 368.15 K, resulting in a redistribution of coordination numbers to lower values. The effect of temperature is also visible in a red-shift of the ion-oxygen stretching frequencies, reflecting weakened ligand binding. Even the moderate increase from ambient to body temperature leads to significant changes in the properties of Ca2+ in aqueous environment. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [ABSTRACT FROM AUTHOR]

In the present work we have modeled the Michaelis complex of the cyclic-Adenosine Monophosphate Dependent (cAMD) Protein Kinase A (PKA) with Mg2ATP and the heptapeptide substrate Kemptide by classical molecular dynamics. The chosen synthetic substrate is relevant for its high efficiency and small size, and it has not been used in previous theoretical studies. The structural analysis of the data generated along the 6 ns simulation indicates that the modeled substrate–enzyme complex mimics the substrate binding pattern known for PKA. The values of the average prereactive distances obtained from the simulation do not exclude any of the two limiting situations proposed as mechanisms in the literature for the phosphorylation reaction (dissociative and associative) because the system oscillates between configurations compatible with each of them. Furthemore, the results obtained for the average interaction distances between active site residues concord in suggesting the plausability of an alternative third reaction mechanism. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) has experienced a significant growth in the recent decades. Simulating systems consisting of hundreds of thousands of atoms is a routine task of computational chemistry researchers nowadays. Thanks to the straightforwardly parallelizable structure of the algorithms, the most promising method to speed‐up MD calculations is exploiting the large‐scale processing power offered by the parallel hardware architecture of graphics processing units or GPUs. Programming GPUs is becoming easier with general‐purpose GPU computing frameworks and higher levels of abstraction. In the recent years, implementing MD simulations on graphics processors has gained a large interest, with multiple popular software packages including some form of GPU‐acceleration support. Different approaches have been developed regarding various aspects of the algorithms, with important differences in the specific solutions. Focusing on published works in the field of classical MD, we describe the chosen implementation methods and algorithmic techniques used for porting to GPU, as well as how recent advances of GPU architectures will provide even more optimization possibilities in the future. This article is characterized under:Software > Simulation MethodsComputer and Information Science > Computer Algorithms and ProgrammingMolecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods [ABSTRACT FROM AUTHOR]