Analyzing the n→π* Electronic Transition of Formaldehyde in Water. A Sequential Monte Carlo/Time-Dependent Density Functional Theory

The n→π* absorption transition of formaldehyde in water is analyzed using combined and sequential classical Monte Carlo (MC) simulations and quantum mechanics (QM) calculations. MC simulations generate the liquid solute-solvent structures for subsequent QM calculations. Using time-dependent density functional theory in a localized set of gaussian basis functions (TD-DFT/6-311++G(d,p)) calculations are made on statistically relevant configurations to obtain the average solvatochromic shift. All results presented here use the electrostatic embedding of the solvent. The statistically converged average result obtained of 2300 cm-1 is compared to previous theoretical results available. Analysis is made of the effective dipole moment of the hydrogen-bonded shell and how it could be held responsible for the polarization of the solvent molecules in the outer solvation shells.

A century of research: what have we learned about the interaction of Trypanosoma cruzi with host cells?

Since the discovery of Trypanosoma cruzi and the brilliant description of the then-referred to "new tripanosomiasis" by Carlos Chagas 100 years ago, a great deal of scientific effort and curiosity has been devoted to understanding how this parasite invades and colonises mammalian host cells. This is a key step in the survival of the parasite within the vertebrate host, and although much has been learned over this century, differences in strains or isolates used by different laboratories may have led to conclusions that are not as universal as originally interpreted. Molecular genotyping of the CL-Brener clone confirmed a genetic heterogeneity in the parasite that had been detected previously by other techniques, including zymodeme or schizodeme (kDNA) analysis. T. cruzi can be grouped into at least two major phylogenetic lineages: T. cruzi I, mostly associated with the sylvatic cycle and T. cruzi II, linked to human disease; however, a third lineage, T. cruziIII, has also been proposed. Hybrid isolates, such as the CL-Brener clone, which was chosen for sequencing the genome of the parasite (Elias et al. 2005, El Sayed et al. 2005a), have also been identified. The parasite must be able to invade cells in the mammalian host, and many studies have implicated the flagellated trypomastigotes as the main actor in this process. Several surface components of parasites and some of the host cell receptors with which they interact have been described. Herein, we have attempted to identify milestones in the history of understanding T. cruzi- host cell interactions. Different infective forms of T. cruzi have displayed unexpected requirements for the parasite to attach to the host cell, enter it, and translocate between the parasitophorous vacuole to its final cytoplasmic destination. It is noteworthy that some of the mechanisms originally proposed to be broad in function turned out not to be universal, and multiple interactions involving different repertoires of molecules seem to act in concert to give rise to a rather complex interplay of signalling cascades involving both parasite and cellular components.

Status of Early 19th-Century Names Authored in Parallel by Wied and Schinz for South American Reptiles and Amphibians, with Designations of Three Nomina Protecta

Prince Maximilian zu Wied's great exploration of coastal Brazil in 1815-1817 resulted in important collections of reptiles, amphibians, birds, and mammals, many of which were new species later described by Wied himself The bulk of his collection was purchased for the American Museum of Natural History in 1869, although many ""type specimens"" had disappeared earlier. Wied carefully identified his localities but did not designate type specimens or type localities, which are taxonomic concepts that were not yet established. Information and manuscript names on a fraction (17 species) of his Brazilian reptiles and amphibians were transmitted by Wied to Prof. Heinrich Rudolf Schinz at the University of Zurich. Schinz included these species (credited to their discoverer ""Princ. Max."") in the second volume of Das Thierreich ... (1822). Most are junior objective synonyms of names published by Wied. However, six of the 17 names used by Schinz predate Wied's own publications. Three were manuscript names never published by Wied because he determined the species to be previously known. (1) Lacerta vittata Schinz, 1822 (a nomen oblitum) = Lacerta striata sensu Wied (a misidentification, non Linnaeus nec sensu Merrem) = Kentropyx calcarata Spix, 1825, herein qualified as a nomen protectum. (2) Polychrus virescens Schinz, 1822 = Lacerta marmorata Linnaeus, 1758 (now Polychrus marmoratus). (3) Scincus cyanurus Schinz, 1822 (a nomen oblitum) = Gymnophthalmus quadrilineatus sensu Wied (a misidentification, non Linnaeus nec sensu Merrem) = Micrablepharus maximiliani (Reinhardt and Lutken, ""1861"" [1862]), herein qualified as a nomen protectum. Qualifying Scincus cyanurus Schinz, 1822, as a nomen oblitum also removes the problem of homonymy with the later-named Pacific skink Scincus cyanurus Lesson (= Emoia cyanura). The remaining three names used by Schinz are senior objective synonyms that take priority over Wied's names. (4) Bufo cinctus Schinz, 1822, is senior to Bufo cinctus Wied, 1823; both, however, are junior synonyms of Bufo crucifer Wied, 1821 = Chaunus crucifer (Wied). (5) Agama picta Schinz, 1822, is senior to Agama picta Wied, 1823, requiring a change of authorship for this poorly known species, to be known as Enyalius pictus (Schinz). (6) Lacerta cyanomelas Schinz, 1822, predates Teius cyanomelas Wied, 1824 (1822-1831) both nomina oblita. Wied's illustration and description shows cyanomelas as apparently conspecific with the recently described but already well-known Cnemidophorus nativo Rocha et al., 1997, which is the valid name because of its qualification herein as a nomen protectum. The preceding specific name cyanomelas (as corrected in an errata section) is misspelled several ways in different copies of Schinz's original description (""cyanom las,"" ""cyanomlas,"" and cyanom""). Loosening, separation, and final loss of the last three letters of movable type in the printing chase probably accounts for the variant misspellings.

Combining Monte Carlo simulation and density-functional theory to describe the spectral changes of Na(2) in liquid helium

Spectral changes of Na(2) in liquid helium were studied using the sequential Monte Carlo-quantum mechanics method. Configurations composed by Na(2) surrounded by explicit helium atoms sampled from the Monte Carlo simulation were submitted to time-dependent density-functional theory calculations of the electronic absorption spectrum using different functionals. Attention is given to both line shift and line broadening. The Perdew, Burke, and Ernzerhof (PBE1PBE, also known as PBE0) functional, with the PBE1PBE/6-311++G(2d,2p) basis set, gives the spectral shift, compared to gas phase, of 500 cm(-1) for the allowed X (1)Sigma(+)(g) -> B (1)Pi(u) transition, in very good agreement with the experimental value (700 cm(-1)). For comparison, cluster calculations were also performed and the first X (1)Sigma(+)(g) -> A (1)Sigma(+)(u) transition was also considered.

Liquid polymorphism, order-disorder transitions and anomalous behavior: A Monte Carlo study of the Bell-Lavis model for water

The Bell-Lavis model for liquid water is investigated through numerical simulations. The lattice-gas model on a triangular lattice presents orientational states and is known to present a highly bonded low density phase and a loosely bonded high density phase. We show that the model liquid-liquid transition is continuous, in contradiction with mean-field results on the Husimi cactus and from the cluster variational method. We define an order parameter which allows interpretation of the transition as an order-disorder transition of the bond network. Our results indicate that the order-disorder transition is in the Ising universality class. Previous proposal of an Ehrenfest second order transition is discarded. A detailed investigation of anomalous properties has also been undertaken. The line of density maxima in the HDL phase is stabilized by fluctuations, absent in the mean-field solution. (C) 2009 American Institute of Physics. [doi:10.1063/1.3253297]

Combined Monte Carlo and quantum mechanics study of the solvatochromism of phenol in water. The origin of the blue shift of the lowest pi-pi* transition

A combined and sequential use of Monte Carlo simulations and quantum mechanical calculations is made to analyze the spectral shift of the lowest pi-pi* transition of phenol in water. The solute polarization is included using electrostatic embedded calculations at the MP2/aug-cc-pVDZ level giving a dipole moment of 2.25 D, corresponding to an increase of 76% compared to the calculated gas-phase value. Using statistically uncorrelated configurations sampled from the MC simulation,first-principle size-extensive calculations are performed to obtain the solvatochromic shift. Analysis is then made of the origin of the blue shift. Results both at the optimized geometry and in room-temperature liquid water show that hydrogen bonds of water with phenol promote a red shift when phenol is the proton-donor and a blue shift when phenol is the proton-acceptor. In the case of the optimized clusters the calculated shifts are in very good agreement with results obtained from mass-selected free jet expansion experiments. In the liquid case the contribution of the solute-solvent hydrogen bonds partially cancels and the total shift obtained is dominated by the contribution of the outer solvent water molecules. Our best result, including both inner and outer water molecules, is 570 +/- 35 cm(-1), in very good agreement with the small experimental shift of 460 cm(-1) for the absorption maximum.

The isotropic nuclear magnetic shielding constants of acetone in supercritical water: A sequential Monte Carlo/quantum mechanics study including solute polarization

The nuclear isotropic shielding constants sigma((17)O) and sigma((13)C) of the carbonyl bond of acetone in water at supercritical (P=340.2 atm and T=673 K) and normal water conditions have been studied theoretically using Monte Carlo simulation and quantum mechanics calculations based on the B3LYP/6-311++G(2d,2p) method. Statistically uncorrelated configurations have been obtained from Monte Carlo simulations with unpolarized and in-solution polarized solute. The results show that solvent effects on the shielding constants have a significant contribution of the electrostatic interactions and that quantitative estimates for solvent shifts of shielding constants can be obtained modeling the water molecules by point charges (electrostatic embedding). In supercritical water, there is a decrease in the magnitude of sigma((13)C) but a sizable increase in the magnitude of sigma((17)O) when compared with the results obtained in normal water. It is found that the influence of the solute polarization is mild in the supercritical regime but it is particularly important for sigma((17)O) in normal water and its shielding effect reflects the increase in the average number of hydrogen bonds between acetone and water. Changing the solvent environment from normal to supercritical water condition, the B3LYP/6-311++G(2d,2p) calculations on the statistically uncorrelated configurations sampled from the Monte Carlo simulation give a (13)C chemical shift of 11.7 +/- 0.6 ppm for polarized acetone in good agreement with the experimentally inferred result of 9-11 ppm. (C) 2008 American Institute of Physics.

Monte Carlo investigation of the critical behavior of Stavskaya's probabilistic cellular automaton

Stavskaya's model is a one-dimensional probabilistic cellular automaton (PCA) introduced in the end of the 1960s as an example of a model displaying a nonequilibrium phase transition. Although its absorbing state phase transition is well understood nowadays, the model never received a full numerical treatment to investigate its critical behavior. In this Brief Report we characterize the critical behavior of Stavskaya's PCA by means of Monte Carlo simulations and finite-size scaling analysis. The critical exponents of the model are calculated and indicate that its phase transition belongs to the directed percolation universality class of critical behavior, as would be expected on the basis of the directed percolation conjecture. We also explicitly establish the relationship of the model with the Domany-Kinzel PCA on its directed site percolation line, a connection that seems to have gone unnoticed in the literature so far.

Simulation of Soil Carbon Dynamics under Sugarcane with the CENTURY Model

Currently there is a trend for the expansion of the area cropped with sugarcane (Saccharum officinarum L.), driven by an increase in the world demand for biofuels, due to economical, environmental, and geopolitical issues. Although sugarcane is traditionally harvested by burning dried leaves and tops, the unburned, mechanized harvest has been progressively adopted. The use of process based models is useful in understanding the effects of plant litter in soil C dynamics. The objective of this work was to use the CENTURY model in evaluating the effect of sugarcane residue management in the temporal dynamics of soil C. The approach taken in this work was to parameterize the CENTURY model for the sugarcane crop, to simulate the temporal dynamics of soil C, validating the model through field experiment data, and finally to make predictions in the long term regarding soil C. The main focus of this work was the comparison of soil C stocks between the burned and unburned litter management systems, but the effect of mineral fertilizer and organic residue applications were also evaluated. The simulations were performed with data from experiments with different durations, from 1 to 60 yr, in Goiana and Timbauba, Pernambuco, and Pradopolis, Sao Paulo, all in Brazil; and Mount Edgecombe, Kwazulu-Natal, South Africa. It was possible to simulate the temporal dynamics of soil C (R(2) = 0.89). The predictions made with the model revealed that there is, in the long term, a trend for higher soil C stocks with the unburned management. This increase is conditioned by factors such as climate, soil texture, time of adoption of the unburned system, and N fertilizer management.

Modeling soil organic carbon dynamics in Oxisols of Ibiruba (Brazil) with the Century Model

introduction of conservation practices in degraded agricultural land will generally recuperate soil quality, especially by increasing soil organic matter. This aspect of soil organic C (SOC) dynamics under distinct cropping and management systems can be conveniently analyzed with ecosystem models such as the Century Model. In this study, Century was used to simulate SOC stocks in farm fields of the Ibiruba region of north central Rio Grande do Sul state in Southern Brazil. The region, where soils are predominantly Oxisols, was originally covered with subtropical woodlands and grasslands. SOC dynamics was simulated with a general scenario developed with historical data on soil management and cropping systems beginning with the onset of agriculture in 1900. From 1993 to 2050, two contrasting scenarios based on no-tillage soil management were established: the status quo scenario, with crops and agricultural inputs as currently practiced in the region and the high biomass scenario with increased frequency of corn in the cropping system, resulting in about 80% higher biomass addition to soils. Century simulations were in close agreement with SOC stocks measured in 2005 in the Oxisols with finer texture surface horizon originally under woodlands. However, simulations in the Oxisols with loamy surface horizon under woodlands and in the grassland soils were not as accurate. SOC stock decreased from 44% to 50% in fields originally under woodland and from 20% to 27% in fields under grasslands with the introduction of intensive annual grain crops with intensive tillage and harrowing operations. The adoption of conservation practices in the 1980s led to a stabilization of SOC stocks followed by a partial recovery of native stocks. Simulations to 2050 indicate that maintaining status quo would allow SOC stocks to recover from 81% to 86% of the native stocks under woodland and from 80% to 91 % of the native stocks under grasslands. Adoption of a high biomass scenario would result in stocks from 75% to 95% of the original stocks under woodlands and from 89% to 102% in the grasslands by 2050. These simulations outcomes underline the importance of cropping system yielding higher biomass to further increase SOC content in these Oxisols. This application of the Century Model could reproduce general trends of SOC loss and recovery in the Oxisols of the Ibiruba region. Additional calibration and validation should be conducted before extensive usage of Century as a support tool for soil carbon sequestration projects in this and other regions can be recommended. (C) 2009 Elsevier B.V. All rights reserved.

Fragmentation of a Neotropical migratory fish population by a century-old dam

Loss of connectivity in impounded rivers is among the impacts imposed by dams, and mitigation measures such as fish passages might not accomplish their purpose of reestablishing an efficient bi-directional gene flow in the fish populations affected. As a consequence, fish populations remain fragmented, and a new interpopulational structure may develop, with increased risk of reduced genetic diversity and stochastic extinction. In order to evaluate the effects of the Gavio Peixoto Dam, which was constructed almost a century ago on the Jacar,-Gua double dagger u River in the Upper Parana River basin, Brazil, a comparative morphometric study was undertaken on the populations of the Neotropical migratory characid fish Salminus hilarii living up- and downstream of this dam. Population dynamics, spatial segregation, and habitat use by different age classes were monitored for 2 years. We found that segregation caused by the dam and long periods with no efficient connection by fish passages have led to fragmentation and interpopulational structuring of S. hilarii, as revealed by canonical variable analysis of morphometric features. The fish populations occupying the up- and downstream sections have succeeded in performing short-distance reproductive migrations in the main river and tributaries, have found suitable habitats for completing their life cycle, and have been able to maintain distinct small-sized populations so far.