Molecular Dynamics Simulations of Homogeneous Nucleation

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.

Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.

Probing ultrafast carrier dynamics, nonlinear absorption and refraction in core-shell silicon nanowires

We investigate the relaxation dynamics of photogenerated carriers in silicon nanowires consisting of a crystalline core and a surrounding amorphous shell, using femtosecond time-resolved differential reflectivity and transmission spectroscopy at 3.15 eV and 1.57 eV photon energies. The complex behaviour of the differential transmission and reflectivity transients is the mixed contributions from the crystalline core and the amorphous silicon on the nanowire surface and the substrate where competing effects of state-filling and photoinduced absorption govern the carrier dynamics. Faster relaxation rates are observed on increasing the photogenerated carrier density. Independent experimental results on crystalline silicon-on-sapphire (SOS) help us in separating the contributions from the carrier dynamics in crystalline core and the amorphous regions in the nanowire samples. Further, single-beam z-scan nonlinear transmission experiments at 1.57 eV in both open- and close-aperture configurations yield two-photon absorption coefficient beta (similar to 3 cm/GW) and nonlinear refraction coefficient gamma (-2.5 x 10 (-aEuro parts per thousand 4) cm(2)/GW).

CUDA-for-clusters: a system for efficient execution of CUDA kernels on multi-core clusters

Rapid advancements in multi-core processor architectures coupled with low-cost, low-latency, high-bandwidth interconnects have made clusters of multi-core machines a common computing resource. Unfortunately, writing good parallel programs that efficiently utilize all the resources in such a cluster is still a major challenge. Various programming languages have been proposed as a solution to this problem, but are yet to be adopted widely to run performance-critical code mainly due to the relatively immature software framework and the effort involved in re-writing existing code in the new language. In this paper, we motivate and describe our initial study in exploring CUDA as a programming language for a cluster of multi-cores. We develop CUDA-For-Clusters (CFC), a framework that transparently orchestrates execution of CUDA kernels on a cluster of multi-core machines. The well-structured nature of a CUDA kernel, the growing popularity, support and stability of the CUDA software stack collectively make CUDA a good candidate to be considered as a programming language for a cluster. CFC uses a mixture of source-to-source compiler transformations, a work distribution runtime and a light-weight software distributed shared memory to manage parallel executions. Initial results on running several standard CUDA benchmark programs achieve impressive speedups of up to 7.5X on a cluster with 8 nodes, thereby opening up an interesting direction of research for further investigation.

Hydrophobic hydration driven self-assembly of curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of beta-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer. (C) 2014 AIP Publishing LLC.

Where the Lake Meets the Sea: Strong Reproductive Isolation Is Associated with Adaptive Divergence between Lake Resident and Anadromous Three-Spined Sticklebacks

Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback (Gasterosteus aculeatus L.) forms are numerous and common throughout the species distribution, offering an opportunity to examine these contrasting hypotheses in greater detail. This study reports on an interesting new contact zone located in a tidally influenced lake catchment in western Ireland, characterised by high polymorphism for lateral plate phenotypes. Using neutral and QTL-linked microsatellite markers, we tested whether the high diversity observed in this contact zone arose as a result of introgression or reproductive isolation between divergent forms: we found strong support for the latter hypothesis. Three phenotypic and genetic clusters were identified, consistent with two divergent resident forms and a distinct anadromous completely plated population that migrates in and out of the system. Given the strong neutral differentiation detected between all three morphotypes (mean FST = 0.12), we hypothesised that divergent selection between forms maintains reproductive isolation. We found a correlation between neutral genetic and adaptive genetic differentiation that support this. While strong associations between QTL linked markers and phenotypes were also observed in this wild population, our results support the suggestion that such associations may be more complex in some Atlantic populations compared to those in the Pacific. These findings provide an important foundation for future work investigating the dynamics of gene flow and adaptive divergence in this newly discovered stickleback contact zone.

Femtosecond dynamics of molecules and clusters

The real-time dynamics of multiphoton ionization and fragmentation of molecules - Na_2 , Na_3 - and clusters - Na_n, Hg_n - has been studied in molecular beam experiments employing ion and electron spectroscopy together with femtosecond pump-probe techniques. Experiments with Na_2 and Na_3 reveal unexpected features of the dynamics of the absorption of several photons as seen in the one- and three dimensional vibrational wave packet motion in different potential surfaces and in high laser fields. Cluster size dependent studies of physical properties such as absorption resonances, lifetimes and decay channels have been performed using tunable femtosecond light pulses in resonance enhanced multiphoton ionization (REMPI) of the cluster size under investigation. This method failed in ns-laser experiments due to the ultrafast decay of the studied cluster. For Na_n, cluster we find that for cluster sizes n \le 21 molecular excitations and properties prevail over collective excitations of plasmon-like resonances. In the case of Hg_n cluster prompt formation of singly and doubly charged cluster are observed up to n \approx 60. The transient multiphoton ionization spectra show a 'short' time wave packet dynamics, which is identical for singly and doubly charged mercury clusters while the 'long' time fragmentation dynamics is different.

Vegetation and environmental dynamics in the southern Black Sea region since 18 kyr BP derived from the marine core 22-GC3

Sediments from the Black Sea, a region historically dominated by forests and steppe landscapes, are a valuable source of detailed information on the changes in regional terrestrial and aquatic environments at decadal to millennial scales. Here we present multi-proxy environmental records (pollen, dinoflagellate cysts, Ca, Ti and oxygen isotope data) from the uppermost 305 cm of the core 22-GC3 (42°13.53′N, 36°29.55′E) collected from a water depth of 838 m in the southern part of the Black Sea in 2007. The records span the last ~ 18 kyr (all ages are given in cal kyr BP). The pollen data reveal the dominance of the Artemisia-steppe in the region, suggesting rather dry/cold environments ~ 18–14.5 kyr BP. Warming/humidity increase during melt-water pulses (~ 16.1–14.5 kyr BP), indicated by δ18O records from the 22-GC3 core sediment and from the Sofular Cave stalagmite, is expressed in more negative δ13C values from the Sofular Cave, usually interpreted as the spreading of C3 plants. The records representing the interstadial complex (~ 14.5–12.9 kyr BP) show an increase in temperature and moisture, indicated by forest development, increased primary productivity and reduced surface run-off, whereas the switch from primary terrigenous to primary authigenic Ca origin occurs ~ 500 yr later. The Younger Dryas cooling is clearly demonstrated by more negative δ13C values from the Sofular Cave and a reduction of pines. The early Holocene (11.7–8.5 kyr BP) interval reveals relatively dry conditions compared to the mostly moist and warm middle Holocene (8.5–5 kyr BP), which is characterized by the establishment of the species-rich warm mixed and temperate deciduous forests in the low elevation belt, temperate deciduous beech-hornbeam forests in the middle and cool conifer forest in upper mountain belt. The border between the early and middle Holocene in the vegetation records coincides with the opening of the Mediterranean corridor at ~ 8.3 kyr BP, as indicated by a marked change in the dinocyst assemblages and in the sediment lithology. Changes in the pollen assemblages indicate a reduction in forest cover after ~ 5 kyr BP, which was likely caused by increased anthropogenic pressure on the regional vegetation.

Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

Paradigm shift to enhanced water supply planning through augmented grids, scarcity pricing and adaptive factory water : a system dynamics approach

This paper details a system dynamics model developed to simulate proposed changes to water governance through the integration of supply, demand and asset management processes. To effectively accomplish this, interconnected feedback loops in tariff structures, demand levels and financing capacity are included in the model design, representing the first comprehensive life-cycle modelling of potable water systems. A number of scenarios were applied to Australia's populated South-east Queensland region, demonstrating that introducing temporary drought pricing (i.e. progressive water prices set inverse with availability), in conjunction with supply augmentation through rain-independent sources, is capable of efficiently providing water security in the future. Modelling demonstrated that this alternative tariff structure reduced demand in scarcity periods thereby preserving supply, whilst revenues are maintained to build new water supply infrastructure. In addition to exploring alternative tariffs, the potential benefits of using adaptive pressure-retarded osmosis desalination plants for both potable water and power generation was explored. This operation of these plants for power production, when they would otherwise be idle, shows promise in reducing their net energy and carbon footprints. Stakeholders in industry, government and academia were engaged in model development and validation. The constructed model displays how water resource systems can be reorganised to cope with systemic change and uncertainty.

Molecular dynamics modelling of diffusional formation of titanium carbide clusters in iron matrix

Molecular dynamics simulation was employed to study the atomic interactions in titanium carbides and iron matrix containing carbon and titanium, which are significant for understanding the formation of titanium carbide cluster during precipitate process. The atoms trajectory and diffusion coefficients of carbon in titanium carbide were analyzed to provide a vacancy-exchanging mechanism and clarify the carbon concentration dependence of carbon diffusion in titanium carbide. The dependence of the formation of titanium carbide cluster in iron matrix on carbon was determined from the study of atoms diffusivity, cluster formation and formation energy of titanium carbide cluster. The simulation results provided insight into the carbon diffusion process and improved the understanding of the formation of titanium carbide cluster.