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Elemental tellurium, a prototypical one‐dimensional van der Waals material, has recently been found to crystallize quickly from the liquid on a nanosecond timescale, yet the inherent mechanism is not clear. Here, by combining in situ high‐energy synchrotron radiation X‐ray diffraction with ab initio molecular‐dynamics simulation, it is found that trigonal crystalline Te completely melts into the liquid phase at 450 °C, and recrystallizes into the trigonal phase for temperatures lower than 380 °C without the formation of any other phase. This directly confirms the recent proposal of a crystal‐liquid‐crystal phase transition in this material underlying the observed electrical‐switching process. Atomic‐scale, melt‐quench computer simulations show that liquid Te is capable of crystallizing within a time of 25 ps in the vicinity of templating crystallization interfaces. This ultrafast crystallization ability of Te can be understood as being due to delayed Peierls distortions during a quench and therefore a high atomic mobility over a wide range of temperature. This finding opens the way to develop a crystal‐liquid‐crystal, phase‐transition‐based selector switch with an ultrafast switching speed. [ABSTRACT FROM AUTHOR]

Lithium disilicate glasses and glass–ceramics are good potential candidates for biomedical applications, solid‐state batteries, and serve as models of nucleation and crystal growth. Moreover, these glasses exhibit a phase separation that influences their nucleation and crystallization behavior. The atomistic mechanisms of the phase separation and their pressure dependence are unclear so far. Here, we used molecular dynamics simulations supported by experiments to assess the spatial heterogeneity of lithium disilicate glasses prepared under pressure. We show that the glass heterogeneity decreases with increasing the pressure under which the system was cooled and almost disappears at pressures around 30 GPa. The origin of the heterogeneity is due to the attraction between Li cations to form clustering channels, which decreases with pressure. Through our results, we hope to provide valuable insights and guidance for making glass–ceramics with controlled crystallization. [ABSTRACT FROM AUTHOR]

A polymer model exhibiting heterogeneous Johari–Goldstein (JG) secondary relaxation is studied by extensive molecular-dynamics simulations of states with different temperature and pressure. Time–temperature–pressure superposition of the primary (segmental) relaxation is evidenced. The time scales of the primary and the JG relaxations are found to be highly correlated according to a power law. The finding agrees with key predictions of the Coupling Model (CM) accounting for the decay in a correlation function due to the relaxation and diffusion of interacting systems. Nonetheless, the exponent of the power law, even if it is found in the range predicted by CM ( 0 < ξ < 1 ), deviates from the expected one. It is suggested that the deviation could depend on the particular relaxation process involved in the correlation function and the heterogeneity of the JG process. [ABSTRACT FROM AUTHOR]

Surface tension, vapor density of OPC-water and SPC/HW-heavy-water models have been estimated at low temperatures using the scaled model. The free-energy difference, -ΔF, of n-molecules and (n-1)-molecules plus a free probe has been calculated using the Bennett acceptance ratio with the aid of Monte-Carlo simulations. Our results show that the relation between the free-energy difference divided by kBT and the number of molecules to the power minus one-third is linear for n>6. Consequently, the surface tension can be extracted from the straight line slope, whereas the vapor density can be extracted from the intercept, which is proportional to the logarithmic ratio of liquid density to that of vapor density. By scaling the free-energy differences, for at least three different temperatures, to TCT−1, we estimated the critical temperature and hence the surface tension and the vapor density at a wide range of temperatures. The free-energy differences have been calculated at 240K, 260K, and 280K for OPC-water, and at 260K, 280K, and 300K for the SPC/HW-heavy water model.

• The crack propagation of Nb 3 Sn at the atomic scale is obtained by molecular dynamics simulations. • The electronic structure evolution at the crack tip is determined by first principles calculations. • The spatial distribution characteristics of strain, atom arrangements, electronic band structure distortions, and critical temperature are given. • The degradation of critical temperature of Nb 3 Sn caused by crack propagation is explained by a given trans -scale model. The irreversible degradation of Nb 3 Sn critical performance caused by the crack propagation brings challenges to the reliability of Nb 3 Sn service equipment. In this paper, the crack propagation behavior of Nb 3 Sn single crystal was studied by molecular dynamics method. The results show that amorphous transformation occur in Nb 3 Sn samples with cracks under the applied loading conditions. On the basis of these results, the electronic structures of different regions in the cracked sample are studied by first principles method. The critical temperature response in this process is analyzed in combination with our proposed trans -scale electromechanical coupling model. The physical mechanism behind the critical temperature degradation caused by the transition between the cracked surface and the amorphous zone at the crack tip is discussed. Amorphous states and the crack surface destroy the special kind of bonding in the atom chain direction, inducing the electronic band structure distortions. The density of states curve of Nb 3 Sn no longer exhibits the characteristic peaks near the Fermi surface observed in cubic crystalline Nb 3 Sn. The intrinsic relationship between the crack propagation, the electronic structure evolution driven by the local atomic rearrangements, and the irreversible critical temperature degradation of cracked Nb 3 Sn is revealed by the given model. The results deepen the understanding of the electromechanical coupling behavior of Nb 3 Sn under complex deformation. [ABSTRACT FROM AUTHOR]

Membrane-bound guanylate cyclases (GCs), which synthesize the second messenger guanosine-3′, 5′-cyclic monophosphate, differ in their activation modes to reach the active state. Hormone peptides bind to the extracellular domain in hormone-receptor-type GCs and trigger a conformational change in the intracellular, cytoplasmic part of the enzyme. Sensory GCs that are present in rod and cone photoreceptor cells have intracellular binding sites for regulatory Ca2+-sensor proteins, named guanylate-cyclase-activating proteins. A rotation model of activation involving an α-helix rotation was described as a common activation motif among hormone-receptor GCs. We tested whether the photoreceptor GC-E underwent an α-helix rotation when reaching the active state. We experimentally simulated such a transitory switch by integrating alanine residues close to the transmembrane region, and compared the effects of alanine integration with the point mutation V902L in GC-E. The V902L mutation is found in patients suffering from retinal cone–rod dystrophies, and leads to a constitutively active state of GC-E. We analyzed the enzymatic catalytic parameters of wild-type and mutant GC-E. Our data showed no involvement of an α-helix rotation when reaching the active state, indicating a difference in hormone receptor GCs. To characterize the protein conformations that represent the transition to the active state, we investigated the protein dynamics by using a computational approach based on all-atom molecular dynamics simulations. We detected a swinging movement of the dimerization domain in the V902L mutant as the critical conformational switch in the cyclase going from the low to high activity state. [ABSTRACT FROM AUTHOR]

A polymer model exhibiting heterogeneous Johari–Goldstein (JG) secondary relaxation is studied by extensive molecular-dynamics simulations of states with different temperature and pressure. Time–temperature–pressure superposition of the primary (segmental) relaxation is evidenced. The time scales of the primary and the JG relaxations are found to be highly correlated according to a power law. The finding agrees with key predictions of the Coupling Model (CM) accounting for the decay in a correlation function due to the relaxation and diffusion of interacting systems. Nonetheless, the exponent of the power law, even if it is found in the range predicted by CM (0<ξ<1), deviates from the expected one. It is suggested that the deviation could depend on the particular relaxation process involved in the correlation function and the heterogeneity of the JG process.

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

The molecular-dynamics simulation of impacts of accelerated argon cluster ions with titanium surface is carried out. The dependences of the dimensions of the produced defects and of the number of sputtered titanium atoms on the cluster-ion dimensions, energies, and incidence angles are studied. [ABSTRACT FROM AUTHOR]

The paper studies the disturbance energy absorption and distribution according to the type of system internal energy under cyclic uniaxial tension of a nanosized rod. The external action is described as follows: V X = V 0 ⋅ sin (ωt). For calculations the method of molecular dynamics was applied. The influence of oscillation frequency and amplitude on the external disturbance energy absorption by the system has been determined. Unlabelled Image • Disturbance energy absorption is researched at the cyclic mechanical load. • Increase of both frequency and amplitude result in growth of energy absorption by rod. • Frequency increase has effect on view of energy increment dependence on time. • Amplitude growth almost has no effect on view of energy increment dependence on time. • Failure of nano-rod begins with calculated critical value of atomic plane dispersion. [ABSTRACT FROM AUTHOR]

We investigate the interaction of edge dislocation with θ′ phase in aluminum matrix using atomistic simulations. The thickness of θ′ phase is chosen to be constant of 2.2 nm and the diameter is varied in range from 3 to 10 nm. It is shown that first interactions of dislocation with θ′ phase occur according to the mechanism of Orowan loop formation around the obstacle. In this case, the cross-slip processes, the formation of dislocation jogs in adjacent slip plane and the emission of vacancies upon the return of a segment to the initial slip plane are possible. During these interactions, the material of θ′ phase is subjected to high shear stresses up to 3 GPa in a layer of 2 nm thickness. Such a high stress leads to a θ′ phase cutting on the third or fourth overcoming of the obstacle by dislocation. A study is carried out of the dependence of the average stress in the system on the size of inclusion and the distance between inclusions. It is shown that an increase in the diameter of inclusion causes an increase in the average stresses in the system in proportion close to the square root of the diameter of the inclusion. Increasing the distance between inclusions causes the inversely proportional reduction of the average stress. The conducted investigation of the strain rate sensitivity showed that in the case of high shear rates, the average stresses in the system continuously increase that does not allow applying the time averaging procedure to them. The described effect is also registered in the case of pure aluminum. The existence of two regions on the temperature dependence of the average stresses in the system on the strain rate in the case of θ′ phase, previously described by Yanilkin et al. (2014) for the Guinier-Prestone zones, is confirmed. In the case of high strain rates, heating of the system leads to a decrease in the dislocation velocity, while at low strain rates the dislocation velocity increases with increasing temperature at a fixed shear rate. An interesting result obtained with long-term molecular-dynamics simulations when the tracing time is up to 2 ns, there is a tendency to reduce the average stress in the system through time. This result can be explained by destruction of the structure and form of θ' phase. The law of motion of a dislocation in the approximation of the constancy of θ′ phase properties is proposed to describe the response of the system to shear deformation. The model contains a dislocation mass, phonon friction, and takes into account the effect of the inclusion of θ' phase through an increase in the elastic energy of a dislocation during the formation of the Orowan loop around an obstacle. • Mechanism of overcoming of θ' phase by edge dislocation in aluminum is studied with an atomistic simulation. • First 3-4 interactions occur by Orowan mechanism, while subsequent ones lead to the cutting of the θ' phase. • High rate of shear deformation provokes increase in acting stresses that makes time averaging impossible. • Heating leads to increase in dislocation velocity at low shear rate and decrease in dislocation velocity at high rate. • Continuum model of the dislocation motion is proposed in the approximation of constancy of θ' phase properties. [ABSTRACT FROM AUTHOR]

We study, using molecular-dynamics (MD) simulation, the spreading kinetics and equilibrium shape of liquid Pb droplets on an Al (111) substrate. The Al-Pb solid-liquid interface was found previously [Phys. Rev. Lett, 110 , 096102 (2013)] to exhibit solid-liquid interfacial premelting at temperatures below the Al melting point. Because the Al(111) free surface does not exhibit premelting, the spreading of a Pb droplet is accompanied by a simultaneous surface transition from a faceted to a premelted Al substrate. Here, we examine how the coupling of the droplet spreading to the premelting affects the spreading kinetics and compare the results to two standard limiting mechanisms of droplet spreading: hydrodynamic spreading , in which the spreading energy dissipation is dominated by viscous relaxation, and kinetic spreading , where interfacial friction dominates. These two mechanisms predict different power-law dependency for the droplet radius versus time. For temperatures where premelting is present (between 875 K and the melting point of aluminum), kinetic spreading is observed at intermediate times. Because Pb droplets only partially wet the surface, the droplet radius at long times relaxes exponentially to the equilibrium droplet shape. Spreading simulations of a faceted system at 625 K [below the Al(111) roughening temperature] show that this system is consistent with a hydrodynamic spreading mechanism. However, when we examine a system at 922.38 K in which premelting is artificially suppressed by introducing harmonic constraints to give surface vibrations consistent with the Al(111) free surface, we observe a kinetic spreading mechanism - as in the premelted system. When premelting is suppressed, the equilibrium contact angle is observed to be significantly larger than when premelting is present even at the same temperatures. Thus, we conclude that the presence of the premelting layer has a significant effect on the thermodynamics Al(111)/Pb solid-liquid interface, but little effect on the mechanism of spreading. We also observe that the structure of the droplet contact line in the presence of the premelting layer is described by two contact angles (instead of the usual one) due to the presence of the additional premelting layer, and resembles structures seen in reactive wetting systems. [ABSTRACT FROM AUTHOR]

ABSTRACT The relation between elasticity and yielding is investigated in a model polymer solid by Molecular-Dynamics simulations. By changing the bending stiffness of the chain and the bond length, semicrystalline and disordered glassy polymers - both with bond disorder - as well as nematic glassy polymers with bond ordering are obtained. It is found that in systems with bond disorder the ratio τY/ G between the shear yield strength τY and the shear modulus G is close to the universal value of the atomic metallic glasses. The increase of the local nematic order in glasses leads to the increase of the shear modulus and the decrease of the shear yield strength, as observed in experiments on nematic thermosets. A tentative explanation of the subsequent reduction of the ratio τY/ G in terms of the distributions of the per-monomer stress is offered. © 2017 Wiley Periodicals, Inc. J. Polym. Sci. Part B: Polym. Phys. 2017, 55, 1760-1769 [ABSTRACT FROM AUTHOR]

Martensitic transformation, reverse martensitic transformation, twinning, and detwinning of equiatomic nickel⁻titanium shape-memory alloy (NiTi SMA) under the action of a shock wave are studied using a molecular-dynamics simulation. In the loading process of a shock wave, B2 austenite is transformed into B19′ martensite, whereas in the unloading process of the shock wave, B19′ martensite is transformed into B2 austenite. With repeated loading and unloading of the shock wave, martensitic transformation occurs along with twinning, but reverse martensitic transformation appears along with detwinning. The mechanisms for the twinning and detwinning of NiTi SMA subjected to a shock wave are revealed in order to lay the theoretical foundation to investigate the shape-memory effect and superelasticity.

Gas-expanded liquids have received significant interest as catalytic reaction media. While most GXL studies involve CO 2 as the expansion gas, there is growing interest in non-CO 2 based GXLs, especially when the expansion gas is also a reactant. In this work, we focus on ethylene as an expansion gas, motivated by recent experimental studies on the catalytic epoxidation of ethylene using ethylene-expanded methanol/H 2 O 2 /water mixtures within metal doped silica mesopores. Reported simulation studies on GXLs, even for bulk properties, have been primarily limited to single-component or binary systems. Here we extend the use of simulation to the study of a bulk ternary GXL system - namely, ethylene-expanded mixtures of methanol and water mixtures. We investigate the phase behavior and transport properties in the liquid phase with respect to temperature, pressure and water content. The model force fields are validated by comparing compositions and transport properties to existing experiments. In addition, we study local liquid solvation structure as a function of composition. [ABSTRACT FROM AUTHOR]

The interaction of water with cellulose stages many unresolved questions. Here 2 H MAS NMR and IR spectra recorded under carefully selected conditions in 1 H- 2 H exchanged, and re-exchanged, cellulose samples are presented. It is shown here, by a quantitative and robust approach, that only two of the three available hydroxyl groups on the surface of cellulose fibrils are exchanging their hydrogen with the surrounding water molecules. This finding is additionally verified and explained by MD simulations which demonstrate that the 1 HO(2) and 1 HO(6) hydroxyl groups of the constituting glucose units act as hydrogen-bond donors to water, while the 1 HO(3) groups behave exclusively as hydrogen-bond acceptors from water and donate hydrogen to their intra-chain neighbors O(5). We conclude that such a behavior makes the latter hydroxyl group unreactive to hydrogen exchange with water. [ABSTRACT FROM AUTHOR]

In the paper, the wettability of different phases of TiO 2 thin films (anatase, brookite, and rutile) have been studied using molecular-dynamics simulation. The principle of micro-wetting is discussed. The simulation results show that the contact angle decreases upon increasing the interaction energy between the water and the titanium dioxide interface during the wetting process. The values of contact angles from large to small are: rutile, brookite and anatase. The calculated equilibrium contact angles are 73.9°, 59.2°, and 43.7°, respectively. The reason is that the structural connection and the arrangement of the surface microtopography directly affect the movement of water droplets on the surface of the material, thus affecting the wettability. In addition, the amount of the interaction energy and the radial distribution function between these three interfaces and the droplets are calculated, and the density change of the droplet is analyzed further which indicate the difference in wetting between the three crystal structures. At the same time, by simulating and comparing the wettability of the trench surface and the original surface of anatase, it is inferred that the rough interface increases the contact angle with the droplet and reduces the wettability. [Display omitted] • MD method is performed to identify the dynamic process of various titanium dioxide crystal structures wettability. • Intermolecular forces show the principle of wettability. • Theoretical wettability of titania phases is supported with experimental results with a good agreement between these insights. • The difference in the wettability of three phases is explained by chemical composition and micro-surface structure. [ABSTRACT FROM AUTHOR]

We report a systematic computational analysis of the mechanical behavior of plasma-facing component (PFC) tungsten focusing on the impact of void and helium (He) bubble defects on the mechanical response beyond the elastic regime. Specifically, we explore the effects of porosity and He atomic fraction on the mechanical properties and structural response of PFC tungsten, at varying temperature and bubble size. We find that the Young modulus of defective tungsten undergoes substantial softening that follows an exponential scaling relation as a function of matrix porosity and He atomic content. Beyond the elastic regime, our high strain rate simulations reveal that the presence of nanoscale spherical defects (empty voids and He bubbles) reduces the yield strength of tungsten in a monotonically decreasing fashion, obeying an exponential scaling relation as a function of tungsten matrix porosity and He concentration. Our detailed analysis of the structural response of PFC tungsten near the yield point reveals that yielding is initiated by emission of dislocation loops from bubble/matrix interfaces, mainly 1 / 2 ⟨111⟩ shear loops, followed by gliding and growth of these loops and reactions to form ⟨100⟩ dislocations. Furthermore, dislocation gliding on the ⟨111⟩{211} twin systems nucleates 1 / 6 ⟨111⟩ twin regions in the tungsten matrix. These dynamical processes reduce the stress in the matrix substantially. Subsequent dislocation interactions and depletion of the twin phases via nucleation and propagation of detwinning partials lead the tungsten matrix to a next deformation stage characterized by stress increase during applied straining. Our structural analysis reveals that the depletion of twin boundaries (areal defects) is strongly impacted by the density of He bubbles at higher porosities. After the initial stress relief upon yielding, increase in the dislocation density in conjunction with decrease in the areal defect density facilitates the initiation of dislocation-driven deformation mechanisms in the PFC crystal.

Hard spheres are a central and important model reference system for both homogeneous and inhomogeneous fluid systems. In this paper we present new high-precision molecular-dynamics computer simulations for a hard sphere fluid at a planar hard wall. For this system we present benchmark data for the density profile p(z) at various bulk densities, the wall surface free energy j, the excess adsorption Г, and the excess volume ve x, which is closely related to Г. We compare all benchmark quantities with predictions from state-of-the-art classical density functional theory calculations within the framework of fundamental measure theory. While we find overall good agreement between computer simulations and theory, significant deviations appear at sufficiently high bulk densities. [ABSTRACT FROM AUTHOR]

Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and Aβ peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH ≤ 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR. [ABSTRACT FROM AUTHOR]

• The electromechanical coupling effect in Nb 3 Sn was scale-coupled. • It includes a strain-regulated electronic structure, grain boundary contours at the atomic scale, and strain-modulated superconducting macroscale transition properties. • The linkage between the micro-meso-macro-scales was revealed by the proposed trans-scale model. • Strain-regulated electronic structures control the superconducting transition of single crystals Nb 3 Sn. • Grain boundary deformation amplified this effect, inducing different responses in single- and polycrystal Nb 3 Sn. Based on molecular dynamics (MD) simulations of Nb 3 Sn crystals under high pressure, a physics-based trans-scale model of the superconducting transition of high-pressure Nb 3 Sn is proposed. This model investigates the electromechanical coupling effect of Nb 3 Sn and discusses the effect of grain boundary deformation on electromechanical coupling through simulations. The simulated results demonstrate that the strain-induced electronic structure evolution and accompanying variations in the density of states (DOS) at the Fermi surface control the superconducting transition of single-crystal Nb 3 Sn. This effect is amplified by the stress concentrations at the grain boundary intersections, leading to the obviously different electromechanical responses of high-pressure single-crystal and polycrystal Nb 3 Sn. It was further found that the electromechanical coupling effect in Nb 3 Sn was scale coupled, including a strain-regulated electronic structure, grain boundary contours of strained Nb 3 Sn at the atomic scale, local atom stress distribution, and intrinsic connections between the strain-modulated superconducting and normal-state transport properties (at the macroscale level). The linkage between the micro-meso-macro-scales was qualitatively reproduced by the proposed model, where the three principal strain components and their differences represent the response-controlling parameters. The grain boundary zone was critical to further determine the reversible–irreversible transition of the electromechanical coupling effects in Nb 3 Sn. The proposed analytical and simulation models provided important theoretical guidance for understanding the empirical relation obtained experimentally. Additionally, they presented a method for the parameterization of electromechanical coupling in Nb 3 Sn. [Display omitted] [ABSTRACT FROM AUTHOR]

The inhomogeneous structure of a fluid at a wall can be characterised in several ways. Within a thermodynamic description, the surface free energy γ and the excess adsorption Γ are of central importance. For theoretical studies, closed expression of γ and Γ can be very valuable; however, even for a well-studied model system such as a hard-sphere fluid at a planar hard wall, the accuracy of existing expressions for γ and Γ, compared to precise computer simulation data, can still be improved. Here, we compare several known expressions for γ and Γ to the most precise computer simulation data. While good agreement is generally found at low to intermediate fluid densities, the existing parameterisations show significant deviation at high density. In this work, we propose new parameterisations for γ and Γ that agree with the simulation data within statistical error over the entire fluid density range. [ABSTRACT FROM PUBLISHER]

Molecular-dynamics simulations of a liquid of short linear molecules have been performed to investigate the correlation between the particle dynamics in the cage of the neighbors and the local geometry. The latter is characterized in terms of the size and the asphericity of the Voronoi polyhedra. The correlation is found to be poor. In particular, in spite of the different Voronoi volumes around the end and the inner monomers of a molecule, all the monomers exhibit coinciding displacement distribution when they are caged (as well as at longer times during the structural relaxation). It is concluded that the fast dynamics during the cage trapping is a non-local collective process involving monomers beyond the nearest neighbors. [ABSTRACT FROM AUTHOR]

Hard spheres are a central and important model reference system for both homogeneous and inhomogeneous fluid systems. In this paper we present new high-precision molecular-dynamics computer simulations for a hard sphere fluid at a planar hard wall. For this system we present benchmark data for the density profile ρ(z) at various bulk densities, the wall surface free energy γ, the excess adsorption Γ, and the excess volume v_{ex}, which is closely related to Γ. We compare all benchmark quantities with predictions from state-of-the-art classical density functional theory calculations within the framework of fundamental measure theory. While we find overall good agreement between computer simulations and theory, significant deviations appear at sufficiently high bulk densities.

In the present paper, the results of the molecular-dynamics simulation of Ni, Cu and Au in liquid and supercooled liquid states are displayed. The potentials of interatomic interaction within the framework of the embedded-atom method are used to generate realistic atomic configurations. The structural analysis of the cluster structure has been conducted with the use of the bond orientational order parameter. In contrast with previous findings, we take into the account 5d-metal (Au) and using the same approach for simulation of different liquid metals. It is shown that the local icosahedral order is present, and it enhances at supercooling of the melts of the metals under discussion. The results are insensitive to the model describing interatomic bonds and the size of the system. Such behavior is most general from the topological perspective for d-metals with close-packed premelting structure. [ABSTRACT FROM AUTHOR]

The exopolysaccharide alginate is an important component of biofilms produced by Pseudomonas aeruginosa, a major pathogen that contributes to the demise of cystic fibrosis patients. Alginate exits the cell via the outer membrane porin AlgE. X-ray structures of several AlgE crystal forms are reported here. Whilst all share a common β-barrel constitution, they differ in the degree to which loops L2 and T8 are ordered. L2 and T8 have been identified as an extracellular gate (E-gate) and a periplasmic gate (P-gate), respectively, that reside on either side of an alginate-selectivity pore located midway through AlgE. Passage of alginate across the membrane is proposed to be regulated by the sequential opening and closing of the two gates. In one crystal form, the selectivity pore contains a bound citrate. Because citrate mimics the uronate monomers of alginate, its location is taken to highlight a route through AlgE taken by alginate as it crosses the pore. Docking and molecular-dynamics simulations support and extend the proposed transport mechanism. Specifically, the P-gate and E-gate are flexible and move between open and closed states. Citrate can leave the selectivity pore bidirectionally. Alginate docks stably in a linear conformation through the open pore. To translate across the pore, a force is required that presumably is provided by the alginate-synthesis machinery. Accessing the open pore is facilitated by complex formation between AlgE and the periplasmic protein AlgK. Alginate can thread through a continuous pore in the complex, suggesting that AlgK pre-orients newly synthesized exopolysaccharide for delivery to AlgE. [ABSTRACT FROM AUTHOR]

The atomistic molecular-dynamics simulations of the initial stage of myoglobin adsorption on amorphous polystyrene surfaces with varying hydrophobicity are presented. The polystyrene surfaces as non-oxidized (hydrophobic) and oxidized (hydrophilic) films, both in united-atoms and dummy-hydrogen atoms representations are modeled. The protein is placed initially at different distances and orientations from the polymer. We monitor the interactions between the protein and the polystyrene surface for the same polystyrene surface in contact with the protein in different initial orientations and for one initial orientation of the protein in contact with different polystyrene surfaces. By comparing the stability and the number of myoglobin-polystyrene atomic contacts and the interaction energies, it is found that the initial contact of the protein with the hydrophobic polystyrene surfaces is stronger than with the hydrophilic ones. The orientations of the myoglobin in which the more rigid protein parts face the polymer exhibit stronger initial contact with the polymeric surface. [ABSTRACT FROM AUTHOR]

Abstract: Using molecular-dynamics simulation, we study the sputtering induced by energetic impacts of projectile clusters containing and 1000 atoms. Both a metallic target and a van-der-Waals-bonded material are studied. We focus on self-bombardment at perpendicular incidence. The total emission yield is composed of the sputter yield of the target material and the reflection yield of reflected projectile cluster atoms. The dependence of these yields on the impact energy shows a slow transition from reflection- to sputter-dominated emission. Similarities and differences between the emission yield of metals and of van-der-Waals-bonded materials are discussed. [Copyright &y& Elsevier]