892 resultados para Replica-exchange molecular dynamics
Resumo:
The self-diffusion properties of pure CH4 and its binary mixture with CO2 within MY zeolite have been investigated by combining an experimental quasi-elastic neutron scattering (QENS) technique and classical Molecular dynamics simulations. The QENS measurements carried out at 200 K led to an unexpected self-diffusivity profile for Pure CH4 with the presence of a maximum for a loading of 32 CH4/unit cell, which was never observed before for the diffusion of apolar species in azeolite system With large windows. Molecular dynamics simulations were performed using two distinct microscopic models for representing the CH4/NaY interactions. Depending on the model, we are able to fairly reproduce either the magnitude or the profile of the self-diffusivity.Further analysis allowed LIS to provide some molecular insight into the diffusion mechanism in play. The QENS measurements report only a slight decrease of the self-diffusivity of CH4 in the presence of CO2 when the CO2 loading increases. Molecular dynamics simulations successfully capture this experimental trend and suggest a plausible microscopic diffusion mechanism in the case of this binary mixture.
Resumo:
This thesis concerns the dynamics of nanoparticle impacts on solid surfaces. These impacts occur, for instance, in space, where micro- and nanometeoroids hit surfaces of planets, moons, and spacecraft. On Earth, materials are bombarded with nanoparticles in cluster ion beam devices, in order to clean or smooth their surfaces, or to analyse their elemental composition. In both cases, the result depends on the combined effects of countless single impacts. However, the dynamics of single impacts must be understood before the overall effects of nanoparticle radiation can be modelled. In addition to applications, nanoparticle impacts are also important to basic research in the nanoscience field, because the impacts provide an excellent case to test the applicability of atomic-level interaction models to very dynamic conditions. In this thesis, the stopping of nanoparticles in matter is explored using classical molecular dynamics computer simulations. The materials investigated are gold, silicon, and silica. Impacts on silicon through a native oxide layer and formation of complex craters are also simulated. Nanoparticles up to a diameter of 20 nm (315000 atoms) were used as projectiles. The molecular dynamics method and interatomic potentials for silicon and gold are examined in this thesis. It is shown that the displacement cascade expansionmechanism and crater crown formation are very sensitive to the choice of atomic interaction model. However, the best of the current interatomic models can be utilized in nanoparticle impact simulation, if caution is exercised. The stopping of monatomic ions in matter is understood very well nowadays. However, interactions become very complex when several atoms impact on a surface simultaneously and within a short distance, as happens in a nanoparticle impact. A high energy density is deposited in a relatively small volume, which induces ejection of material and formation of a crater. Very high yields of excavated material are observed experimentally. In addition, the yields scale nonlinearly with the cluster size and impact energy at small cluster sizes, whereas in macroscopic hypervelocity impacts, the scaling 2 is linear. The aim of this thesis is to explore the atomistic mechanisms behind the nonlinear scaling at small cluster sizes. It is shown here that the nonlinear scaling of ejected material yield disappears at large impactor sizes because the stopping mechanism of nanoparticles gradually changes to the same mechanism as in macroscopic hypervelocity impacts. The high yields at small impactor size are due to the early escape of energetic atoms from the hot region. In addition, the sputtering yield is shown to depend very much on the spatial initial energy and momentum distributions that the nanoparticle induces in the material in the first phase of the impact. At the later phases, the ejection of material occurs by several mechanisms. The most important mechanism at high energies or at large cluster sizes is atomic cluster ejection from the transient liquid crown that surrounds the crater. The cluster impact dynamics detected in the simulations are in agreement with several recent experimental results. In addition, it is shown that relatively weak impacts can induce modifications on the surface of an amorphous target over a larger area than was previously expected. This is a probable explanation for the formation of the complex crater shapes observed on these surfaces with atomic force microscopy. Clusters that consist of hundreds of thousands of atoms induce long-range modifications in crystalline gold.
Resumo:
We report the quasielastic neutron scattering (QENS) and molecular dynamics (MD) investigations into diffusion of pentane isomers in zeolite NaY. The molecular cross section perpendicular to the long molecular axis varies for the three isomers while the mass and the isomer-zeolite interaction remains essentially unchanged. Both QENS and MD results show that the branched isomers neopentane and isopentane have higher self-diffusivities as compared with n-pentane at 300 K in NaY zeolite. This result provides direct experimental evidence for the existence of nonmonotonic, anomalous dependence of self-diffusivity on molecular diameter known as the levitation effect. The energetic barrier at the bottleneck derived from MD simulations exists for n-pentane which lies in the linear regime while no such barrier is seen for neopentane which is located clearly in the anomalous regime.Activation energy is in the order E-a(n-pentane)>E-a(isopentane)>E-a(neopentane) consistent with the predictions of the levitation effect. In the liquid phase, it is seen thatD(n pentane)>D(isopentane)>D(neopentane) and E-a(n-pentane)< E-a(isopentane)< E-a(neopentane). Intermediate scattering function for small wavenumbers obtained from MD follows a single exponential decay for neopentane and isopentane. For n-pentane, a single exponential fit provides a poor fit especially at short times. Cage residence time is largest for n-pentane and lowest for neopentane. For neopentane, the width of the self-part of the dynamic structure factor shows a near monotonic decrease with wavenumber. For n-pentane a minimum is seen near k=0.5 A degrees(-1) suggesting a slowing down of motion around the 12-ring window, the bottleneck for diffusion. Finally, the result that the branched isomer has a higher diffusivity as compared with the linear analog is at variation from what is normally seen.
Resumo:
Nucleation is the first step in a phase transition where small nuclei of the new phase start appearing in the metastable old phase, such as the appearance of small liquid clusters in a supersaturated vapor. Nucleation is important in various industrial and natural processes, including atmospheric new particle formation: between 20 % to 80 % of atmospheric particle concentration is due to nucleation. These atmospheric aerosol particles have a significant effect both on climate and human health. Different simulation methods are often applied when studying things that are difficult or even impossible to measure, or when trying to distinguish between the merits of various theoretical approaches. Such simulation methods include, among others, molecular dynamics and Monte Carlo simulations. In this work molecular dynamics simulations of the homogeneous nucleation of Lennard-Jones argon have been performed. Homogeneous means that the nucleation does not occur on a pre-existing surface. The simulations include runs where the starting configuration is a supersaturated vapor and the nucleation event is observed during the simulation (direct simulations), as well as simulations of a cluster in equilibrium with a surrounding vapor (indirect simulations). The latter type are a necessity when the conditions prevent the occurrence of a nucleation event in a reasonable timeframe in the direct simulations. The effect of various temperature control schemes on the nucleation rate (the rate of appearance of clusters that are equally able to grow to macroscopic sizes and to evaporate) was studied and found to be relatively small. The method to extract the nucleation rate was also found to be of minor importance. The cluster sizes from direct and indirect simulations were used in conjunction with the nucleation theorem to calculate formation free energies for the clusters in the indirect simulations. The results agreed with density functional theory, but were higher than values from Monte Carlo simulations. The formation energies were also used to calculate surface tension for the clusters. The sizes of the clusters in the direct and indirect simulations were compared, showing that the direct simulation clusters have more atoms between the liquid-like core of the cluster and the surrounding vapor. Finally, the performance of various nucleation theories in predicting simulated nucleation rates was investigated, and the results among other things highlighted once again the inadequacy of the classical nucleation theory that is commonly employed in nucleation studies.
Resumo:
Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.
Resumo:
ingle tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G(7)) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. There quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Angstrom from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Nai counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. in the absence of any coordinated ion. due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.
Resumo:
The asymmetric stress strain behavior under tension/compression in an initial < 100 > B-2-NiAl nanowire is investigated considering two different surface configurations i.e., < 100 >/(0 1 0) (0 0 1) and < 100 >/(0 1 1) (0 - 1 1). This behavior is attributed to two different deformation mechanisms namely a slip dominated deformation under compression and a known twinning dominated deformation under tension. It is also shown that B2 -> BCT (body-centered-tetragonal) phase transformation under tensile loading is independent of the surface configurations for an initial < 100 > oriented NiAl nanowire. Under tensile loading, the nanowire undergoes a stress-induced martensiticphase transformation from an initial B2 phase to BCT phase via twinning along {110} plane with failure strain of similar to 0.30. On the other hand, a compressive loading causes failure of these nanowires via brittle fracture after compressive yielding, with a maximum failure strain of similar to-0.12. Such brittle fracture under compressive loading occurs via slip along {110} plane without any phase transformations. Softening/hardening behavior is also reported for the first time in these nanowires under tensile/compressive loadings, which cause asymmetry in their yield strength behavior in the stress strain space. Result shows that a sharp increase in energy with increasing strain under compressive loading causes hardening of the nanowire, and hence, gives improved yield strength as compared to tensile loading. (C) 2010 Elsevier Ltd. All rights reserved.
Resumo:
The details of cage-to-cage migration have been obtained from an analysis of the molecular dynamics trajectory of a probe adsorbate. It is observed that particles utilize the region within a radius of 2 angstrom from the window center but with diffusion taking place predominantly at 1.6 angstrom from the window center and a potential energy of nearly -12 kJ/mol. A barrier of about 0.5 kJ/mol is observed for surface-mediated diffusion. Surprisingly, for diffusion without surface mediation for a particle going from one cage center to another, there is an attractive well near the window instead of a barrier. At low adsorbate concentrations and room temperature, the predominant mode for cage-to-cage migration is surface-mediated diffusion. The analysis suggests that particles slide along the surface of the inner walls of the alpha-cages during migration from one cage to another.
Resumo:
The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.
Resumo:
Valinomycin is an important ionophore which exhibits a high conformational flexibility. The study of various conformations adopted by this molecule together with the study of flexibility in a given conformation can throw light on the ion transport by the ionophore across the membrane. Molecular dynamics (MD) studies are ideal to characterize the flexibility in different parts of the molecule and can also give an idea of various conformations adopted by the molecule at a given temperature. Hence MD studies at 100K have been carried out on the minimized crystal structure of the molecule to scan the possible conformations in the neighbourhood of the well known 'bracelet' like structure of uncomplexed Valinomycin, Properties, like the flexibility, average values, r.m.s. fluctuations of the various intramolecular hydrogen bonds are discussed. Energy minimization has been carried out on selected MD simulated points to analyze the characteristics of the unique conformation adopted by this molecule at this temperature.
Resumo:
Molecular dynamics calculations on methane sorbed in NaY (Si/Al = 3.0) employing realistic methane-methane and methane-zeolite intermolecular potential functions at different temperatures (50, 150, 220, and 300 K) and concentrations (2, 4, 6, and 8 molecules/cage) are reported. The thermodynamic results are in agreement with the available experimental data. Guest-guest and guest-host radial distribution functions (rdfs), energy distribution functions, distribution of cage occupancy, center-of-cage-center-of-mass (coc-com) rdfs, velocity autocorrelation functions for com and angular motion and the Fourier transformed power spectra, and diffusion coefficients are presented as a function of temperature and concentration. At 50 K, methane is localized near the adsorption site. Site-site migration and essentially free rotational motion are observed at 150 K. Molecules preferentially occupy the region near the inner surface of the alpha-cage. The vibrational frequencies for the com of methane shift toward higher values with decreasing temperature and increasing adsorbate concentration. The observed frequencies for com motion are 36, 53, and 85 cm-1 and for rotational motion at 50 K, 95 and 150 cm-1 in agreement with neutron scattering data. The diffusion coefficients show a type I behavior as a function of loading in agreement with NMR measurements. Cage-to-cage diffusion is found to be always mediated by the surface.
Resumo:
The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ?70 in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.
Resumo:
Nanosecond scale molecular dynamics simulations have been performed on antiparallel Greek key type d(G(7)) quadruplex structures with different coordinated ions, namely Na+ and K+ ion, water and Na+ counter ions, using the AMBER force field and Particle Mesh Ewald technique for electrostatic interactions. Antiparallel structures are stable during the simulation, with root mean square deviation values of similar to1.5 Angstrom from the initial structures. Hydrogen bonding patterns within the G-tetrads depend on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate different cations. However, alternating syn-anti arrangement of bases along a chain as well as in a quartet is maintained through out the MD simulation. Coordinated Na+ ions, within the quadruplex cavity are quite mobile within the central channel and can even enter or exit from the quadruplex core, whereas coordinated K+ ions are quite immobile. MD studies at 400 K indicate that K+ ion cannot come out from the quadruplex core without breaking the terminal G-tetrads. Smaller grooves in antiparallel structures are better binding sites for hydrated counter ions, while a string of hydrogen bonded water molecules are observed within both the small and large grooves. The hydration free energy for the K+ ion coordinated structure is more favourable than that for the Na+ ion coordinated antiparallel quadruplex structure.
Resumo:
Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures
Resumo:
The structures of a PbO.SiO2 glass and melt have been studied using molecular dynamics simulation employing Born-Mayer-Huggins pair potentials. Various pair distribution functions are presented and discussed. Pb-Pb correlations persist in the melt, in agreement with experimental observations. The calculated and experimental radial distribution functions are compared.