Theoretical study of the finite temperature spectroscopy in van der Waals clusters. III Solvated Chromophore as an effective diatomics

The absorption spectroscopy of calcium-doped argon clusters is described in terms of an effective diatomics molecule Ca-(Ar_n), in the framework of semiclassical vertical transitions. We show how, upon choosing a suitable reaction coordinate, the effective finite-temperature equilibrium properties can be obtained for the ground- and excited-surfaces from the potential of mean force (PMF). An extension of the recent multiple range random-walk method is used to calculate the PMF over continuous intervals of distances. The absorption spectra calculated using this single-coordinate description are found to be in good agreement with the spectra obtained from high-statistics Monte Carlo data, in various situations. For CaAr$_{13}$, we compare the performances of two different choices of the reaction coordinate. For CaAr_37, the method is seen to be accurate enough to distinguish between different low-energy structures. Finally, the idea of casting the initial many-body problem into a single degree of freedom problem is tested on the spectroscopy of calcium in bulk solid argon.Comment: 8 pages, 9 figure

Theoretical study of finite temperature spectroscopy in van der Waals clusters. II Time-dependent absorption spectra

Using approximate partition functions and a master equation approach, we investigate the statistical relaxation toward equilibrium in selected CaAr$_n$ clusters. The Gaussian theory of absorption (previous article) is employed to calculate the average photoabsorption intensity associated with the 4s^2-> 4s^14p^1 transition of calcium as a function of time during relaxation. In CaAr_6 and CaAr_10 simple relaxation is observed with a single time scale. CaAr_13 exhibits much slower dynamics and the relaxation occurs over two distinct time scales. CaAr_37 shows much slower relaxation with multiple transients, reminiscent of glassy behavior due to competition between different low-energy structures. We interpret these results in terms of the underlying potential energy surfaces for these clusters.Comment: 10 pages, 9 figure

Stacked clusters of polycyclic aromatic hydrocarbon molecules

Clusters of polycyclic aromatic hydrocarbon (PAH) molecules are modelled using explicit all-atom potentials using a rigid body approximation. The PAH's considered range from pyrene (C10H8) to circumcoronene (C54H18), and clusters containing between 2 and 32 molecules are investigated. In addition to the usual repulsion-dispersion interactions, electrostatic point-charge interactions are incorporated, as obtained from density functional theory calculations. The general electrostatic distribution in neutral or singly charged PAH's is reproduced well using a fluctuating charges analysis, which provides an adequate description of the multipolar distribution. Global optimization is performed using a variety of methods, including basin-hopping and parallel tempering Monte Carlo. We find evidence that stacking the PAH molecules generally yields the most stable motif. A structural transition between one-dimensional stacks and three-dimensional shapes built from mutiple stacks is observed at larger sizes, and the threshold for this transition increases with the size of the monomer. Larger aggregates seem to evolve toward the packing observed for benzene in bulk.Difficulties met in optimizing these clusters are analysed in terms of the strong anisotropy of the molecules. We also discuss segregation in heterogeneous clusters and vibrational properties in the context of astrophysical observations.Comment: 12 pages, 7 figure

Composition-induced structural transitions in mixed rare-gas clusters

The low-energy structures of mixed Ar--Xe and Kr--Xe Lennard-Jones clusters are investigated using a newly developed parallel Monte Carlo minimization algorithm with specific exchange moves between particles or trajectories. Tests on the 13- and 19- atom clusters show a significant improvement over the conventional basin-hopping method, the average search length being reduced by more than one order of magnitude. The method is applied to the more difficult case of the 38-atom cluster, for which the homogeneous clusters have a truncated octahedral shape. It is found that alloys of dissimilar elements (Ar--Xe) favor polytetrahedral geometries over octahedra due to the reduced strain penalty. Conversely, octahedra are even more stable in Kr--Xe alloys than in Kr_38 or Xe_38, and they show a core-surface phase separation behavior. These trends are indeed also observed and further analysed on the 55-atom cluster. Finally, we correlate the relative stability of cubic structures in these clusters to the glassforming character of the bulk mixtures.Comment: 14 pages, 8 figures, 5 tables PRB vol 70, in pres

Phase changes in 38 atom Lennard-Jones clusters. II: A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical

We study the 38-atom Lennard-Jones cluster with parallel tempering Monte Carlo methods in the microcanonical and molecular dynamics ensembles. A new Monte Carlo algorithm is presented that samples rigorously the molecular dynamics ensemble for a system at constant total energy, linear and angular momenta. By combining the parallel tempering technique with molecular dynamics methods, we develop a hybrid method to overcome quasi-ergodicity and to extract both equilibrium and dynamical properties from Monte Carlo and molecular dynamics simulations. Several thermodynamic, structural and dynamical properties are investigated for LJ$_{38}$, including the caloric curve, the diffusion constant and the largest Lyapunov exponent. The importance of insuring ergodicity in molecular dynamics simulations is illustrated by comparing the results of ergodic simulations with earlier molecular dynamics simulations.Comment: Journal of Chemical Physics, accepte

Evaluation of a microbial muramidase supplementation on growth performance, apparent ileal digestibility, and intestinal histology of broiler chickens

The current study evaluated the effects of different inclusion levels of microbial muramidase (Muramidase 007, DSM Nutritional Products) on gastrointestinal functionality by determination of apparent ileal digestibility (AID) of nutrients, investigation of intestinal histomorphology, and quantification of resulting growth performance. Four maize-wheat-soybean experimental diets were produced without (C) and with different dosages of muramidase: low (L, 25,000 LSU(F)/kg), medium (M, 35,000 LSU(F)/kg), and high (H, 45,000 LSU(F)/kg); diets were fed to broilers for 35 d. At the end of the experiment, AID of ether extract (EE), crude protein (CP), Ca, and P were determined and samples of the mid-jejunum and -ileum were collected for histomorphological observations. Data were subjected to ANOVA analysis using the GLM procedure. Orthogonal polynomial contrasts were used to assess linear and quadratic effects of different levels of the muramidase. At the end of the trial, Muramidase 007 supplementation linearly increased body weight gain and decreased feed conversion ratio (FCR) (P ≤ 0.05). Adding the muramidase to broiler diets also linearly increased the European poultry efficiency factor (P ≤ 0.05). Inclusion of the muramidase in broiler diets linearly increased AID of CP, EE, and P (P ≤ 0.05), and the H group had a higher AID of EE and CP compared to C group (P ≤ 0.05). Microbial muramidase supplementation linearly increased ileal villus length to crypt depth ratio and decreased the number of ileal CD45 cells (P ≤ 0.05). Broilers fed M and H diets had fewer number of CD45 cells in the ileum compared to those in C group (P ≤ 0.05). In conclusion, the results of the present study demonstrated that inclusion of the microbial muramidase in broiler diets could increase AID of key nutrients and improve growth performance in broilers. Adding microbial muramidase to broiler diets can therefore be considered as an interesting prospect to improve gastrointestinal functionality. Biological mechanisms causing these improvements need to be studied further

Theoretical study of finite temperature spectroscopy in van der Waals clusters. I. Probing phase changes in CaAr_n

The photoabsorption spectra of calcium-doped argon clusters CaAr_n are investigated at thermal equilibrium using a variety of theoretical and numerical tools. The influence of temperature on the absorption spectra is estimated using the quantum superposition method for a variety of cluster sizes in the range 6<=n<=146. At the harmonic level of approximation, the absorption intensity is calculated through an extension of the Gaussian theory by Wadi and Pollak [J. Chem. Phys. vol 110, 11890 (1999)]. This theory is tested on simple, few-atom systems in both the classical and quantum regimes for which highly accurate Monte Carlo data can be obtained. By incorporating quantum anharmonic corrections to the partition functions and respective weights of the isomers, we show that the superposition method can correctly describe the finite-temperature spectroscopic properties of CaAr_n systems. The use of the absorption spectrum as a possible probe of isomerization or phase changes in the argon cluster is discussed at the light of finite-size effects.Comment: 17 pages, 9 figure

Dual branes in topological sigma models over Lie groups. BF-theory and non-factorizable Lie bialgebras

We complete the study of the Poisson-Sigma model over Poisson-Lie groups. Firstly, we solve the models with targets $G$ and $G^*$ (the dual group of the Poisson-Lie group $G$) corresponding to a triangular $r$-matrix and show that the model over $G^*$ is always equivalent to BF-theory. Then, given an arbitrary $r$-matrix, we address the problem of finding D-branes preserving the duality between the models. We identify a broad class of dual branes which are subgroups of $G$ and $G^*$, but not necessarily Poisson-Lie subgroups. In particular, they are not coisotropic submanifolds in the general case and what is more, we show that by means of duality transformations one can go from coisotropic to non-coisotropic branes. This fact makes clear that non-coisotropic branes are natural boundary conditions for the Poisson-Sigma model.Comment: 24 pages; JHEP style; Final versio