Infinite swapping in curved spaces

2openE. Curotto;Massimo MellaE., Curotto; Mella, Massim

Quantum Monte Carlo simulations of selected ammonia clusters (n=2-5): Isotope effects on the ground state of typical hydrogen bonded systems

Variational Monte Carlo, diffusion Monte Carlo, and stereographic projection path integral simulations are performed on eight selected species from the (NH(3))(n), (ND(3))(n), (NH(2)D)(n), and (NH(3))(n-1)(ND(3)) clusters. Each monomer is treated as a rigid body with the rotation spaces mapped by the stereographic projection coordinates. We compare the energy obtained from path integral simulations at several low temperatures with those obtained by diffusion Monte Carlo, for two dimers, and we find that at 4 K, the fully deuterated dimer energy is in excellent agreement with the ground state energy of the same. The ground state wavefunction for the (NH(3))(2-5) clusters is predominantly localized in the global minimum of the potential energy. In all simulations of mixed isotopic substitutions, we find that the heavier isotope is almost exclusively the participant in the hydrogen bond. (C) 2010 American Institute of Physics. [doi:10.1063/1.3506027

Structure and energetics of ammonia clusters (NH3)n (n=3-20) investigated using a rigid-polarizable model derived from ab initio calculations

An analytical model has been developed to describe the interaction between rigid ammonia molecules including the explicit description of induction. The parameters of the model potential were chosen by fitting high quality ab initio data obtained using second-order Moller-Plesset (MP2) perturbation theory and extended basis sets. The description of polarization effects is introduced by using a noniterative form of the "charge on spring model", the latter accounting for more than 95% of the dipole induction energy and of the increased molecular dipole. Putative global minima for (NH3)(n) (n = 3-20) have been optimized using this new model, the structure and energetics of the clusters with n = 3-5 being found in good agreement with previous ab initio results including electronic correlation. Results for larger species have been compared with previous structural studies where only nonpolarizable models were employed. Our model predicts larger binding energies for any cluster size than previous analytical surfaces, the results often suggesting a reorganization of the relative energy ranking and a different structure for the global minimum

Thermodynamic properties of ammonia clusters (NH(3))(n) n=2-11: Comparing classical and quantum simulation results for hydrogen bonded species

Classical and quantum simulations of ammonia clusters in the dimer through the hendecamer range are performed using the stereographic projection path integral. Employing the most recent polarizable potential to describe intermolecular interactions, energetic and structural data obtained with our simulations provide support for a more fluxional or flexible nature at low temperature of the ammonia dimer, pentamer, and hexamer than in the other investigated species. The octamer and the hendecamer display a relatively strong melting peak in the classical heat capacity and a less intense but significant melting peak in the quantum heat capacity. The latter are shifted to lower temperature (roughly 15 and 40 K lower, respectively) by the quantum effects. The features present in both classical and quantum constant volume heat capacity are interpreted as an indication of melting even in the octamer case, where a large energy gap is present between its global minimum and second most stable species. We develop a first order finite difference algorithm to integrate the geodesic equations in the inertia ellipsoid generated by n rigid nonlinear bodies mapped with stereographic projections. We use the technique to optimize configurations and to explore the potential surface of the hendecamer

Importance sampling for quantum Monte Carlo in manifolds: Addressing the time scale problem in simulations of molecular aggregates

Several importance sampling strategies are developed and tested for stereographic projection diffusion Monte Carlo in manifolds. We test a family of one parameter trial wavefunctions for variational Monte Carlo in stereographically projected manifolds which can be used to produce importance sampling. We use the double well potential in one dimensional Euclidean space to study systematically sampling issues for diffusion Monte Carlo. We find that diffusion Monte Carlo with importance sampling in manifolds is orders of magnitude more efficient compared to unguided diffusion Monte Carlo. Additionally, diffusion Monte Carlo with importance sampling in manifolds can overcome problems with nonconfining potentials and can suppress quasiergodicity effectively. We obtain the ground state energy and the wavefunction for the Stokmayer trimer. (c) 2008 American Institute of Physics

Amine functionalization of cholecyst-derived extracellular matrix with generation 1 PAMAM dendrimer

This document is the unedited author's version of a Submitted Work that was subsequently accepted for publication in Biomacromolecules, copyright © American Chemical Society after peer review. To access the final edited and published work, see http://pubs.acs.org/doi/pdf/10.1021/bm701055k.A method to functionalize cholecyst-derived extracellular matrix (CEM) with free amine groups was established in an attempt to improve its potential for tethering of bioactive molecules. CEM was incorporated with Generation-1 polyamidoamine (G1 PAMAM) dendrimer by using N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide and N-hydroxysuccinimide cross-linking system. The nature of incorporation of PAMAM dendrimer was evaluated using shrink temperature measurements, Fourier transform infrared (FTIR) assessment, ninhydrin assay, and swellability. The effects of PAMAM incorporation on mechanical and degradation properties of CEM were evaluated using a uniaxial mechanical test and collagenase degradation assay, respectively. Ninhydrin assay and FTIR assessment confirmed the presence of increasing free amine groups with increasing quantity of PAMAM in dendrimer-incorporated CEM (DENCEM) scaffolds. The amount of dendrimer used was found to be critical in controlling scaffold degradation, shrink temperature, and free amine content. Cell culture studies showed that fibroblasts seeded on DENCEM maintained their metabolic activity and ability to proliferate in vitro. In addition, fluorescence cell staining and scanning electron microscopy analysis of cell-seeded DENCEM showed preservation of normal fibroblast morphology and phenotype

A j-Walking Algorithm for Microcanonical Simulations: Applications to Lennard-Jones Clusters

The j-walking method, previously developed to solve quasiergodicity problems in canonical simulations, is extended to simulations in the microcanonical ensemble. The implementation of the method in the microcanonical ensemble parallels that in the canonical case. Applications are presented in the microcanonical ensemble to cluster melting phenomena for Lennard-Jones clusters containing 7 and 13 particles. Significant difficulties are encountered in achieving ergodicity when Metropolis Monte Carlo methods are applied to these systems, and the difficulties are removed by the j-walking method

Rigid Quantum Monte Carlo Simulations of Condensed Molecular Matter: Water Clusters in the n=2 ―˃ 8 Range

The numerical advantage of quantum Monte Carlo simulations of rigid bodies relative to the flexible simulations is investigated for some simple systems. The results show that if high frequency modes in molecular condensed matter are predominantly in the ground state, the convergence of path integral simulations becomes nonuniform. Rigid body quantum parallel tempering simulations are necessary to accurately capture thermodynamic phenomena in the temperature range where the dynamics are influenced by intermolecular degrees of freedom; the stereographic projection path integral adapted for quantum simulations of asymmetric tops is a significantly more efficient strategy compared with Cartesian coordinate simulations for molecular condensed matter under these conditions. The reweighted random series approach for stereographic path integral Monte Carlo is refined and implemented for the quantum simulation of water clusters treated as an assembly of rigid asymmetric tops

Asymptotic Convergence Rates of Fourier Path Integral Methods

The asymptotic rates of convergence of thermodynamic properties with respect to the number of Fourier coefficients, kmax, included in Fourier path integral calculations are derived. The convergence rates are developed both with and without partial averaging for operators diagonal in coordinate representation and for the energy. Properties in the primitive Fourier method are shown to converge asymptotically as 1/kmax whereas the asymptotic convergence rate is shown to be 1/kmax 2 when partial averaging is included. Properties are shown to converge at the same rate whether full partial averaging or gradient partial averaging is used. The importance of using the proper operator to optimize convergence rates in partial averaging calculations is emphasized

Tratamiento enzimático en la extracción de aceite y obtención de antioxidantes a partir de semilla de onagra, Oenothera biennis, por prensado en frío

The aim of this work was to improve the yield in evening primrose oil extraction and the antioxidant potential of the residual meal using an enzyme assisted extraction process with cold pressing. Among four commercial enzymes, a mixture of two of them was selected in order to evaluate the effect of enzyme-substrate ratio, temperature, moisture and period of time of the enzymatic pretreatment on the extracted oil. The oil yield increased by 12% when the seeds were pretreated with 2% enzyme-substrate ratio of a mixture of 100G Ultrazym and Cellubrix (1:1) for 15 h at 40oC and 40% moisture. The defatted meal obtained from the enzyme aided process enhanced its phenol content and improved its potential antioxidant activity in comparison to the control from 250 to 276 mg of phenols/g of meal and from 1463 to 1558 mg of trolox/g of meal respectively.Se espera que el tratamiento enzimático, previo al prensado en frío, de la semilla de Oenothera biennis, mejore el rendimiento de extracción de aceite y la cantidad de antioxidantes extraídos de la harina residual. De una serie de cuatro preparados enzimáticos comerciales, se selecciona el más adecuado, el cual es evaluado bajo distintas condiciones de incubación: razones enzima/sustrato, tiempo, humedad y temperatura. El rendimiento aumenta un 12 % cuando se realiza un doble prensado sobre la semilla tratada con una mezcla enzimática formulada con Ultrazym 100G y Cellubrix en razón 1:1, concentración enzima/sustrato del 2 % p/p (base húmeda), durante 15 horas de incubación a 45 °C y 40 % de humedad. La harina residual desgrasada aumenta su contenido de antioxidantes desde 250 a 276 mg de fenoles expresados en catequina y el extracto mejora su actividad antioxidante desde 1463 a 1558 mg de trolox por gr de harina