Monte Carlo free energy calculations using electronic structure methods

The molecular mechanics-based importance sampling function (MMBIF) algorithm [R. Iftimie, D. Salahub, D. Wei, and J. Schofield, J. Chem. Phys. 113, 4852 (2000)] is extended to incorporate semiempirical electronic structure methods in the secondary Markov chain, creating a fully quantum mechanical Monte Carlo sampling method for simulations of reactive chemical systems which, unlike the MMBIF algorithm, does not require the generation of a system-specific force field. The algorithm is applied to calculating the potential of mean force for the isomerization reaction of HCN using thermodynamic integration. Constraints are implemented in the sampling using a modification of the SHAKE algorithm, including that of a fixed, arbitrary reaction coordinate. Simulation results show that sampling efficiency with the semiempirical secondary potential is often comparable in quality to force fields constructed using the methods suggested in the original MMBIF work. The semiempirical based importance sampling method presented here is a useful alternative to MMBIF sampling as it can be applied to systems for which no suitable MM force field can be constructed.     

On permutable meromorphic functions

We study the class \({\mathcal{M}}\) of functions meromorphic outside a countable closed set of essential singularities. We show that if a function in \({\mathcal{M}}\), with at least one essential singularity, permutes with a non-constant rational map g, then g is a Möbius map that is not conjugate to an irrational rotation. For a given function \({f \in\mathcal{M}}\) which is not a Möbius map, we show that the set of functions in \({\mathcal{M}}\) that permute with f is countably infinite. Finally, we show that there exist transcendental meromorphic functions \({f : \mathbb{C} \to \mathbb{C}}\) such that, among functions meromorphic in the plane, f permutes only with itself and with the identity map.     

A dynamic study of earthworm feeding ecology -using stable isotopes

Changes in the specific diet of earthworms with time in relation to landuse changes and two different climates were studied by analysing (13)C and (15)N natural abundance in soils and animals. Soil samples from three depths (0-10, 10-20 and 20-30 cm) and earthworms were collected from two sites: Santiago (Northwest Spain) and North Wyke (Southwest England) both consisting of replicated long-term grasslands and recently converted to maize plots. Earthworms were hand-sorted in the field at the peak of the maize growth and after harvesting at both sites. In the Spanish plots, nine and eight earthworm species, all belonging to the three ecological categories (epigeic, anecic and endogeic), were found under maize and permanent pasture, whereas at the English site five and seven different species were, respectively, identified. At both sites (13)C isotopic values of the earthworm tissues reflected changes in diet from C(3) to C(4) with epigeic and epi/anecic worms in the maize plots showing one delta unit difference in relation to the ones found in the grassland plots. Anecic worms seemed to be less responsive to landuse changes. The higher (13)C values of the Spanish soils were also reflected in the earthworm tissues when compared with the English samples. (15)N values showed no clear relationship with the cropping treatments but were clearly related to the ecological grouping, with endogeic worms reaching the highest values whereas for the epigeic and epi/anecic species the lowest values were obtained. This finding was also previously recorded by other authors1 and suggests that, in the future, stable isotope techniques could also be a useful tool in taxonomic studies. Copyright 1999 John Wiley & Sons, Ltd.     

Secondary ion yields produced by keV atomic and polyatomic ion impacts on a self-assembled monolayer surface

A suite of keV polyatomic or 'cluster' projectiles was used to bombard unoxidized and oxidized self-assembled monolayer surfaces. Negative secondary ion yields, collected at the limit of single ion impacts, were measured and compared for both molecular and fragment ions. In contrast to targets that are orders of magnitude thicker than the penetration range of the primary ions, secondary ion yields from polyatomic projectile impacts on self-assembled monolayers show little to no enhancement when compared with monatomic projectiles at the same velocity. This unusual trend is most likely due to the structural arrangement and bonding characteristics of the monolayer molecules with the Au(111). Copyright 1999 John Wiley & Sons, Ltd.     

Multiple ionization of argon in coincidence with projectile ions in 60–120 MeV Si q+-Ar collisions

A projectile ion-recoil ion coincidence technique has been employed to study the multiple ionization and the charge transfer processes in collisions of 60–120 MeV Si ^q+ (q = 4−14) ions with neutral argon atoms. The relative contribution of different ionization channels, namely; direct ionization, electron capture and electron loss leading to the production of slow moving multiply charged argon recoil ions have been investigated. The data reported on the present collision system result from a direct measurement in the considered impact energy for the first time. The total ionization cross-sections for the recoil ions are shown to scale as q ^1.7/E _p ^0.5 , where E _p is the energy in MeV of the projectile and q its charge state. The recoil fractions for the cases of total- and direct ionizations are found to decrease with increasing recoil charge state j. The total ionization fractions of the recoils are seen to depend on q and to show the presence of a ‘shell-effect’ of the target. Further, the fractions are found to vary as 1/j ² upto j = 8+. The average recoil charge state 〈j〉 increases slowly with q and with the number of lost or captured electrons from or into the projectile respectively. The projectile charge changing cross-sections σ _qq′ are found to decrease with increasing q for loss ionization and to increase with q for direct-and capture ionization processes respectively. The physics behind various scaling rules that are found to follow our data for different ionization processes is reviewed and discussed.     

C. fumago chloroperoxidase is also a dehaloperoxidase: oxidative dehalogenation of halophenols

We have examined the H2O2-dependent oxidative dehalogenation of 2,4,6-trihalophenols and p-halophenols catalyzed by Caldariomyces fumago chloroperoxidase (CCPO). CCPO is significantly more robust than other peroxidases and can function under harsher reaction conditions, and so its ability to dehalogenate halophenols could lead to its use as a bioremediation catalyst for aromatic dehalogenation reactions. Optimal catalysis occurred under acidic conditions (100 mM potassium phosphate solution, pH 3.0). UV-visible absorption spectroscopy, high-performance liquid chromatography, and gas chromatography/mass spectrometry clearly identified the oxidized reaction product for CCPO-catalyzed dehalogenation of 2,4,6-trihalophenols as the corresponding 2,6-dihalo-1,4-benzoquinones. This reaction has previously been reported for two His-ligated heme-containing peroxidases (see Osborne, R. L.; Taylor, L. O.; Han, K. P.; Ely, B.; Dawson, J. H. Biochem. Biophys. Res. Commun. 2004, 324, 1194-1198), but this is the first example of a Cys-ligated heme-containing peroxidase functioning as a dehaloperoxidase. The relative catalytic efficiency (turnover number) of CCPO reported herein is comparable to that of horseradish peroxidase (Ferrari, R. P.; Laurenti, E.; Trotta, F. J. Biol. Inorg. Chem. 1965, 4, 232-237). The mechanism of dehalogenation has been probed using p-halophenols as substrates. Here the major product is a dimer with 1,4-benzoquinone as the minor product. An electron-transfer mechanism is proposed that accounts for the products formed from both the 2,4,6-trihalo- and p-halophenols. Finally, we note that this is the first case of a peroxidase known primarily for its halogenation ability being shown to also dehalogenate substrates.     

Modeling the interface between islet amyloid polypeptide and insulin-based aggregation inhibitors: correlation to aggregation kinetics and membrane damage

Human islet amyloid polypeptide (hIAPP) forms cytotoxic fibrils in type-2 diabetes and insulin is known to inhibit formation of these aggregates. In this study, a series of insulin-based inhibitors were synthesized and assessed for their ability to slow aggregation and impact hIAPP-induced membrane damage. Computational studies were employed to examine the underlying mechanism of inhibition. Overall, all compounds were able to slow aggregation at sufficiently high concentrations (10× molar excess); however, only two peptides showed any inhibitory capability at the 1:1 molar ratio (EALYLV and VEALYLV). The results of density functional calculations suggest this is due to the strength of a salt bridge formed with the Arg11 side chain of hIAPP and the inhibitors' ability to span from the Arg11 to past the Phe15 residue of hIAPP, blocking one of the principal amyloidogenic regions of the molecule. Unexpectedly, slowing fibrillogenesis actually increased damage to lipid membranes, suggesting that the aggregation process itself, rather than the fibrilized peptide, may be the cause of cytotoxicity in vivo.     

Overcoming the boundary effects in surface spline interpolation

Surface spline interpolation when the domain is all of R^d isknown to converge much faster to the data function f than inthe case when the domain is the unit ball. This difference isunderstood to be due to boundary effects which, as will be shown,also affect the size of the surface spline's coefficients. Wepropose a modified form of surface spline interpolation which,to a great extent, overcomes these boundary effects. This modifiedsurface spline interpolant uses only the values of f at thegiven interpolation points.     

WADM and radiation MHD simulations of compact multi-planar and cylindrical wire arrays at 1 MA currents

The radiative performance of Z-pinches created by the imploding wire array loads is defined by the ablation and implosion dynamics of these loads. Both these processes can be effectively modeled by the Wire Ablation Dynamics Model (WADM), which extends the formalism exploited earlier for the cylindrical wire arrays to the loads of arbitrary geometries. The WADM calculates the ablation rates for each array wire and provides the important dynamic parameters, such as the specific mass and velocity of the imploding plasma, which can be used to estimate the shapes of the x-ray pre-pulse and, partially, the main x-ray burst. The applications of the WADM also extend to combined material wire array loads. The ablation and implosion dynamics of novel Prism Planar Wire Array (PPWA) and combined material (Mo/Al/Mo) Triple Planar Wire Array (TPWA) loads are discussed in detail. The combined WADM and radiation MHD simulation is applied to model the radiative performance of the precursor plasma column, created by the imploding stainless steel compact cylindrical wire array. As the radiation effects intensify with the mass accumulation at the array center, the simulation reveals the transformation of quasi-uniform precursor column into a heterogeneous plasma structure with strong density and temperature gradients. We find that radiative performance of the precursor plasma is greatly affected by the load geometry as well as by the wire material.