Molecular simulations of metal adsorption to bacterial surfaces

The atomic-scale interactions that occur between cations and the metal-binding cell wall components common to many gram-positive bacteria were investigated using molecular simulations techniques. We examined the adsorption of Cd and Pb onto peptidoglycan and teichoic acid components of the bacterial cell wall using classical energy force field methods. Within the framework of molecular mechanics and the Cerius² modeling software, we used energy minimization, conformational analysis, and molecular dynamics to examine the different components of the cell wall and to determine relative binding energies and structural configurations of the cell wall components, both with and without the metals present. Electronic structure calculations of representative metal-organic complexes validate the more practical classical methods required in simulating the large number of atoms associated with the cell wall components. The classical force field simulations were conducted in both gas phase and solvated periodic cells. Force field-based simulation techniques can adequately describe the interactions of Cd with the cell wall, defining both metal ion coordinations and binding distances. However, the classical force field approach is inconsistent in describing the observed Pb-cell wall interactions due to possible limitations in the force field parameters, the propensity for Pb to form hydroxides at circumneutral pH, or the dominance of other adsorption mechanisms.     

A bivariate meta-Gaussian density for use in hydrology

Convenient bivariate densities found in the literature are often unsuitable for modeling hydrologic variates. They either constrain the range of association between variates, or fix the form of the marginal distributions. The bivariate meta-Gaussian density is constructed by embedding the normal quantile transform of each variate into the Gaussian law. The density can represent a full range of association between variates and admits arbitrarily specified marginal distributions. Modeling and estimation can be decomposed into i) independent analyses of the marginal distributions, and ii) investigation of the dependence structure. Both statistical and judgmental estimation procedures are possible. Some comparisons to recent applications of bivariate densities in the hydrologic literature motivate and illustrate the model.     

Use of Rhodamine water tracer in the marshland upwelling system

Rhodamine water tracer (RWT) was used to characterize the migration of waste water within the saline subsurface of a marshland upwelling system (MUS), which is an alternative on-site waste water treatment system for coastal areas. Field tracer studies were performed to investigate the fresh waste water plume movement within the saline ground water. Pore velocities were calculated using first detection times and ranged from 0.68 to 10.7 x 10(-4) cm/sec for the loamy sandy soil matrix present at the site. Use of RWT in the field also allowed determination of main and preferential flowpaths. One- and two-dimensional laboratory experiments were performed using silica sand to investigate the interactions of the organically rich waste water with RWT within the zone surrounding the point of injection (one-dimensional) and the impact of background salinity on plume movement (two-dimensional). The results from these studies were used to help explain the field data. One-dimensional breakthrough curves revealed retardation factors for the RWT in the waste water mixture of 1.73 to 1.90. These results were similar to other researchers, indicating little interaction between the waste water and RWT. Variations in pore water salinity (5, 15, 25, and 35 ppt) were found to have a significant effect on pore water velocities of the fresh water plume (two-dimensional), indicating the need to incorporate background salinities into the design process for MUS.     

Climate change and coastal flooding in Metro Boston: impacts and adaptation strategies

Sea level rise (SLR) due to climate change will increase storm surge height along the 825 km long coastline of Metro Boston, USA. Land at risk consists of urban waterfront with piers and armoring, residential areas with and without seawalls and revetments, and undeveloped land with either rock coasts or gently sloping beachfront and low-lying coastal marshes. Risk-based analysis shows that the cumulative 100 year economic impacts on developed areas from increased storm surge flooding depend heavily upon the adaptation response, location, and estimated sea level rise. Generally it is found that it is advantageous to use expensive structural protection in areas that are highly developed and less structural approaches such as floodproofing and limiting or removing development in less developed or environmentally sensitive areas.     

Fiscal geographies: “Placing” taxation in urban geography

As the state’s primary means of both redistributing wealth and incentivizing private investment, tax plays an outsized role in a range of critical urban processes, including (re)development, gentrification, financialization, and local and regional governance. We argue, through reference to existing literature in urban and economic geography, as well as our own research on taxation and the state, that urban scholarship could benefit by close and careful engagement with taxation and the tax system. We term this new vein of research “fiscal geographies” and see it as offering potential for more nuanced study of urban political economy, politics, and processes.     

Late Pleistocene and Early Holocene lake‐level fluctuations in the Lahontan Basin,Nevada: Implications for the distribution of archaeological sites

The Great Basin of the western U.S. contains a rich record of Late Pleistocene and Holocene lake‐level fluctuations as well as an extensive record of human occupation during the same time frame. We compare spatial‐temporal relationships between these records in the Lahontan basin to consider whether lake‐level fluctuations across the Pleistocene‐Holocene transition controlled distribution of archaeological sites. We use the reasonably well‐dated archaeological record from caves and rockshelters as well as results from new pedestrian surveys to investigate this problem. Although lake levels probably reached maximum elevations of about 1230–1235 m in the different subbasins of Lahontan during the Younger Dryas (YD) period, the duration that the lakes occupied the highest levels was brief. Paleoindian and Early Archaic archaeological sites are concentrated on somewhat lower and slightly younger shorelines (_1220–1225 m) that also date from the Younger Dryas period. This study suggests that Paleoindians often concentrated their activities adjacent to large lakes and wetland resources soon after they first entered the Great Basin. © 2008 Wiley Periodicals, Inc.     

Mineralized and unmineralized calderas in Spain; Part II, evolution of the Rodalquilar caldera complex and associated gold-alunite deposits

The Rodalquilar caldera complex is located in the western part of the Cabo de Gata volcanic field in southeastern Spain and is the first documented example of epithermal gold-alunite mineralization within a caldera in Europe. The Rodalquilar caldera is an oval collapse structure having a maximum diameter of 8 km and formed at 11 Ma from eruption of the Cinto ash-flow tuff. The oval Lomilla caldera, with a diameter of 2 km, is nested within the central resurgent dome of the older Rodalquilar caldera. The Lomilla caldera resulted from the eruption of the Lazaras ash-flow tuff which was ponded within the moat of the Rodalquilar caldera. The last phase of volcanic activity in the caldera complex was the emplacement of hornblende andesite flows and intrusions. This magmatic event resulted in structural doming of the caldera, opening of fractures and faults, and provided the heat source for the large hydrothermal systems which deposited quartz-alunite type gold deposits and base metal vein systems. The gold-alunite deposits are enclosed in areas of intense acid sulfate alteration and localized in ring and radial faults and fractures present in the east wall of the Lomilla caldera. Like other acid-sulfate type deposits, the Rodalquilar gold-alunite deposits are closely related in time and space to porphyritic, intermediate composition magma emplaced along caldera structures but unrelated to the caldera forming magmatic system.     

Understanding groundwater processes by representing aquifer heterogeneity in the Maules Creek Catchment, Namoi Valley (New South Wales, Australia)

A FEFLOW three-dimensional (3D) groundwater model is developed to enhance the understanding of groundwater processes in the complex alluvial stratigraphy of Maules Creek Catchment (New South Wales, Australia). The aquifer vertical heterogeneity is replicated by indexing 204 lithological logs into units of high or low hydraulic conductivity, and by developing a 3D geological conceptual model with a vertical resolution based on the average lithological unit thickness for the region. The model mesh is populated with the indexed geology using nearest neighbour gridding. The calibrated model is successful in simulating the observed flow dynamics and in quantifying the important water-budget components. This indicates that the lateral groundwater flow from the mountainous region is the main inflow component of the system. Under natural conditions, the Namoi River acts as a sink of water, but groundwater abstraction increasingly removes a large amount of water each year causing dewatering of the system. The pumping condition affects the river–aquifer interaction by reversing the flow, from gaining to losing river conditions during the simulation period. The procedure is relevant for the development of groundwater models of heterogeneous systems in order to improve the understanding of the interplay between aquifer architecture and groundwater processes.     

A note on first-order normalizations of perturbed Keplerian systems

Techniques are developed to facilitate the transformation of a perturbed Keplerian system into Deláunay normal form at first order. The implicit dependence of the Hamiltonian on 1, the mean anomaly, through the explicit variable f, the true anomaly, or E, the eccentric anomaly, is removed through first order for terms of the form:

Recharge and Groundwater Flow Within an Intracratonic Basin,Midwestern United States

The conservative nature of chloride (Cl^?) in groundwater and the abundance of geochemical data from various sources (both published and unpublished) provided a means of developing, for the first time, a representation of the hydrogeology of the Illinois Basin on a basin‐wide scale. The creation of Cl^? isocons superimposed on plan view maps of selected formations and on cross sections across the Illinois Basin yielded a conceptual model on a basin‐wide scale of recharge into, groundwater flow within and through the Illinois Basin. The maps and cross sections reveal the infiltration and movement of freshwater into the basin and dilution of brines within various geologic strata occurring at basin margins and along geologic structures. Cross‐formational movement of brines is also seen in the northern part of the basin. The maps and cross sections also show barriers to groundwater movement created by aquitards resulting in areas of apparent isolation/stagnation of concentrated brines within the basin. The distribution of Cl^? within the Illinois Basin suggests that the current chemical composition of groundwater and distribution of brines within the basin is dependent on five parameters: (1) presence of bedrock exposures along basin margins; (2) permeability of geologic strata and their distribution relative to one another; (3) presence or absence of major geologic structures; (4) intersection of major waterways with geologic structures, basin margins, and permeable bedrock exposures; and (5) isolation of brines within the basin due to aquitards, inhomogeneous permeability, and, in the case of the deepest part of the basin, brine density effects.