A novel approach using nonlinear surfaces for dynamic aperture optimization in MBA synchrotron light sources.

MBA cell-based synchrotron light sources have enabled an unprecedented increase in beam coherence and brightness, greatly benefiting the scientific disciplines that rely on X-ray techniques. However, controlling the electron dynamics is a theoretical and technological challenge, due to the large number of parameters to adjust and constraints to satisfy when designing modern synchrotrons. Having versatile tools for the description and manipulation of electron dynamics could favor the design of these accelerators and lead to progress on several fronts in the understanding of matter. In this paper, a formalism based on the use of nonlinear geometric surfaces represented by polynomial quasi-invariants, to analyze and optimize the dynamic aperture of electrons in MBA storage rings, is introduced. The formalism considers on- and off-momentum particle dynamics. Within the optimization scheme, different objective functions defined in terms of the nonlinear surfaces, which are minimized using genetic algorithm methods, are proposed. A remarkable horizontal dynamic aperture exceeding 19 mm is obtained for the design particle of a synchrotron model with 86 pm [Formula: see text] rad emittance along with a dynamic aperture above 5 mm for momentum deviations of ± 3[Formula: see text]. According to the results presented, this formalism could be greatly useful for manipulating the dynamical properties of electrons in synchrotrons light sources close to the diffraction limit.

Increasing beam stability zone in synchrotron light sources using polynomial quasi-invariants.

The objective of this article is to propose a scheme to increase the stability zone of a charged particles beam in synchrotrons using a suitable objective function that, when optimized, inhibits the resonances onset in phase space and the dynamic aperture of electrons in storage rings can be improved. The proposed technique is implemented by constructing a quasi-invariant in a neighborhood of the origin of the phase space, then, by using symbolic computation software, sets of coupled differential equations for functions involved in nonlinear dynamics are obtained and solved numerically with periodic boundary conditions. The objective function is constructed by proposing that the innermost momentum solution branch of the polynomial quasi-invariant approaches to the corresponding ellipse of the linear dynamics. The objective function is optimized using a genetic algorithm, allowing the dynamic aperture to be increased. The quality of results obtained with this scheme are compared with particle tracking simulations performed with available software in the field, showing good agreement. The scheme is applied to a synchrotron light source model that can be classified as third generation due to its emittance.

A molecular dynamics study proposing the existence of statistical structural heterogeneity due to chain orientation in the POPC-cholesterol bilayer.

We performed molecular dynamics simulations of a lipid bilayer consisting of POPC and cholesterol at temperatures from 283 to 308K and cholesterol concentrations from 0 to 50% mol/mol. The purpose of this study was to look for the existence of structural differences in the region delimited by these parameters and, in particular, in a region where coexistence of liquid disordered and liquid ordered phases has been proposed. Our interest in this range of concentration and temperature responds to the fact that polyene ionophore activity varies considerably along it. Two force fields, CHARMM36 and Slipids, were compared in order to determine the most suitable. Both force fields predict non-monotonic behaviors consistent with the existence of phase transitions. We found the presence of lateral structural heterogeneity, statistical in nature, in some of the bilayers occurring in this range of temperatures and sterol concentrations. This heterogeneity was produced by correlated ordering of the POPC tails and not due to cholesterol enrichment, and lasts for tens of nanoseconds. We relate these observations to the action of polyenes in these membranes.

Morphology and dynamics of domains in ergosterol or cholesterol containing membranes.

The effect of cholesterol and ergosterol on supported lipid bilayers composed of 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and egg sphingomyelin (eSM) in a 1/1 M ratio was studied using atomic force microscopy. The addition of ergosterol or cholesterol to these membranes considerably modifies both the structure and the dynamics of the domains present in them. The height of the eSM enriched domains increases with concentration of both sterols, but more markedly with ergosterol. The height of the POPC enriched domains increases with concentration in a similar manner for both sterols. This effect is larger for eSM than for POPC when ergosterol, not cholesterol, is present. Domain coverage increases with both sterols at 5 mol% but decreases at 20 mol% and almost disappears at 40 mol%. The size of the eSM enriched domains decreases with sterol concentration, more markedly with cholesterol. Bilayer rupture forces show that overall stiffness increases with the addition of 5 mol% cholesterol, but only for the eSM enriched domains with ergosterol at the same concentration. At larger sterol concentrations the stiffness of both regions becomes reduced. At 40 mol% sterol concentration, both membranes present the same rupture force value. To gain mechanistic insight into these observations we performed Quantum Mechanical calculations and Molecular Dynamics simulations of the sterol molecules. We found that conformational freedom for the sterol molecules is quite different. This difference might be behind the observed phenomena. Finally, the different action of sterols on membrane properties is related to the sterol-dependent ionophoretic activity of polyene antibiotics.

Hydration of CH3HgOH and CH3HgCl compared to HgCl2, HgClOH, and Hg(OH)2: A DFT microsolvation cluster approach.

We address the aqueous microsolvation of the CH3HgCl and CH3HgOH molecules using a stepwise hydration scheme including up to 33 water molecules and compare our results with the previously studied HgCl2, HgClOH, and Hg(OH)2 complexes. Optimized geometries and Gibbs free energies were obtained at the B3PW91/aug-RECP(Hg)-6-31G(d,p) level. At least 33 water molecules were required to build the first solvation shell around both methylmercury compounds. Optimized geometries were found having favorable interactions of water molecules with Hg, Cl, and the OH moiety. Born-Oppenheimer molecular dynamics simulations were performed on the largest CH3HgX(X = Cl, OH)-(H2O)33 clusters at the same level of theory. Born-Oppenheimer molecular dynamics simulations at T = 300 K (ca. 0.62 kcal/mol) revealed the presence of configurations with hydrogen-bonded networks that include the OH moiety in CH3HgOH and exclude both the Hg and Cl in CH3HgCl, favoring a clathrate-type structure around the methyl moiety. The comparison to the microsolvated HgClOH, Hg(OH)2, and HgCl2 molecules showed that, in all cases, the water molecules easily move away from Cl, thus supporting the idea that HgCl2 behaves as a non-polar solute. The theoretical (LIII edge) X-ray absorption near edge structure spectra are obtained and found in good agreement with experimental data, especially for the CH3HgCl species.

X-ray accelerated photo-oxidation of As(III) in solution.

We performed near edge X-ray absorption spectroscopy (XANES) measurements on the arsenic K-edge of As(III) in solution under acidic and basic conditions, after exposure of the solutions to air. Spectra were recorded for increasing exposure times to the X-rays used to perform absorption spectroscopy measurements. We did not find changes for the solution under acidic conditions, whereas we observed significant changes in the case of solution under alkaline conditions. To interpret these changes, we compared the obtained spectra with XANES spectra of As(III) and As(V) solutions under alkaline conditions, not exposed to air, and used as standards. Principal component fits using these standards indicate an accelerated conversion of As(III) to As(V) due to the exposure to X-rays.

Interpretation of X-ray absorption spectra of As(III) in solution using Monte Carlo simulations.

We performed X-ray absorption spectroscopy measurements on the arsenic K-edge of As(III) in solution under acidic conditions. Extended X-ray absorption fine structure (EXAFS) and X-ray near edge structure (XANES) spectra were compared with theoretical calculations which use local atomic structure configurations, either derived from density functional theory (DFT) energy minimization (EM) calculations or based on classical Monte Carlo (MC) simulations, for a As(OH)3 cluster surrounded by water molecules. The nearest arsenic-oxygen distances obtained from the fit of the XAFS spectra are consistent with the distances present in configurations derived from Monte Carlo simulations but not with those obtained from DFT-EM calculations. Calculations of XANES using either DFT-EM or the average configuration obtained from MC simulations do not reproduce the XANES spectra in the vicinity of the absorption edge. However, specific local atomic structural configurations of the As(OH)3 and water molecules, obtained from MC simulations, which show some ordering of water molecules up to 5 Å from the arsenic, reproduce qualitatively the experimental spectra. These results highlight the capability of XANES to yield information about hydration of ions in solution.

Liquid methanol Monte Carlo simulations with a refined potential which includes polarizability, nonadditivity, and intramolecular relaxation.

Monte Carlo simulations of liquid methanol were performed using a refined ab initio derived potential which includes polarizability, nonadditivity, and intramolecular relaxation. The results present good agreement between the energetic and structural properties predicted by the model and those predicted by ab initio calculations of methanol clusters and experimental values of gas and condensed phases. The molecular level picture of methanol shows the existence of both rings and linear polymers in the methanol liquid phase.

Water liquid-vapor equilibria predicted by refined ab initio derived potentials.

Coexistence properties for water near the critical point using several ab initio models were calculated using grand canonical Monte Carlo simulations with multiple histogram reweighting techniques. These models, that have proved to yield a good reproduction of the water properties at ambient conditions, perform rather well, improving the performance of a previous ab initio model. It is also shown that bulk geometry and dipole values, predicted by the simulation, can be used and a good approximation obtained with a polarizable rigid water model but not when polarization is excluded.

Water models based on a single potential energy surface and different molecular degrees of freedom.

Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernandez-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors--nonadditivity, polarizability, and intramolecular flexibility--are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force field improves by the quality of the molecular calculations, all levels of modeling can be improved.