39 research outputs found
Interpretasi Lingkungan Pengendapan Formasi Talang Akar Berdasarkan Data Cutting dan Wireline Log pada Lapangan X Cekungan Sumatera Selatan
A sedimentary environment is a part of earth\u27s surface which is physically, chemically and biologically distinct from adjacent terrains (Selley, 1988). The study of the depositional environment is one goal of many studiesconducted for academic purpose and economically purpose in oil and gas exploration. The study of the depositionalenvironment requires a fairly comprehensive analysis as to sequencestratigraphy facies analysis to obtain detailedinterpretations or conclusions. The purpose of this study is to analyze cutting and wireline logs to determinelithology, facies and sedimentation history of theTalang Akar formation field X in South Sumatra basin. The method used to analyze the formation of depositional environment of Talang Akar field X in SouthSumatra basin is the cutting description in order to know the composition of the constituent formations. While theanalysis conducted is cutting analysis to get lithofacies interpretation, second is well log analysis method to getsubsurface data such as physical rock properties then electrofacies analysis based on gamma ray log pattern andthird is stratigraphy sequence analysis method so sea level changed can be known. Stratigraphy sequenceinterpretation did base on facies and gamma ray log pattern changed. Pratama-1 well lithology consists of shale, siltstone, very fine sandstone until medium sandstone andlimestones. While the well lithology Pratama-2 is composed of shale, very fine until medium sandstone and siltstone.Facies found in wells Pratama-1 consists of distributary channel fill, prodelta, distal bar, distributary mouth bar,and marsh. Facies in wells Pratama-2 is a mud flat and mixed flat. In Pratama-1 wells are 2 sets sequence that bounded by 2 sequence boundary, with a stratigraphic unit LST, TST and HST with progradation andretrogradation stacking patterns. While the Pratama-2 wells contained one stratigraphic unit sequence that is onlyTST in progradation and agradation stacking patterns. Based on this analysis the Talang Akar formation field X inSouth Sumatra basin has a transitional depositional environment
Attachment of Pathogenic Prion Protein to Model Oxide Surfaces
Prions are the infectious agents
in the class of fatal neurodegenerative
diseases known as transmissible spongiform encephalopathies, which
affect humans, deer, sheep, and cattle. Prion diseases of deer and
sheep can be transmitted via environmental routes, and soil is has
been implicated in the transmission of these diseases. Interaction
with soil particles is expected to govern the transport, bioavailability
and persistence of prions in soil environments. A mechanistic understanding
of prion interaction with soil components is critical for understanding
the behavior of these proteins in the environment. Here, we report
results of a study to investigate the interactions of prions with
model oxide surfaces (Al<sub>2</sub>O<sub>3</sub>, SiO<sub>2</sub>) using quartz crystal microbalance with dissipation monitoring and
optical waveguide light mode spectroscopy. The efficiency of prion
attachment to Al<sub>2</sub>O<sub>3</sub> and SiO<sub>2</sub> depended
strongly on pH and ionic strength in a manner consistent with electrostatic
forces dominating interaction with these oxides. The presence of the N-terminal portion
of the protein appeared to promote attachment to Al<sub>2</sub>O<sub>3</sub> under globally electrostatically repulsive conditions.
We evaluated the utility of recombinant prion protein as a surrogate
for prions in attachment experiments and found that its behavior differed
markedly from that of the infectious agent. Our findings suggest that
prions would tend to associate with positively charged mineral surfaces
in soils (e.g., iron and aluminum oxides)
Clarithromycin and Tetracycline Binding to Soil Humic Acid in the Absence and Presence of Calcium
Numerous
ionizable organic micropollutants contain positively charged
moieties at pH values typical of environmental systems. Describing
organic cation and zwitterion interaction with dissolved natural organic
matter requires explicit consideration of the pH-dependent speciation
of both sorbate and sorbent. We studied the pH-, ionic strength-,
and concentration-dependent binding of relatively large, organic cations
and zwitterions (viz., the antibiotics clarithromycin and tetracycline)
to dissolved humic acid in the absence and presence of Ca<sup>2+</sup> and evaluated the ability of the NICA-Donnan model to describe the
data. Clarithromycin interaction with dissolved humic acid was well
described by the model including the competitive effect of Ca<sup>2+</sup> on clarithromycin binding over a wide range of solution
conditions by considering only the binding of the cationic species
to low proton-affinity sites in humic acid. Tetracycline possesses
multiple ionizable moieties and forms complexes with Ca<sup>2+</sup>. An excellent fit to experimental data was achieved by considering
tetracycline cation interaction with both low and high proton-affinity
sites of humic acid and zwitterion interaction with high proton-affinity
sites. In contrast to clarithromycin, tetracycline binding to humic
acid increased in the presence of Ca<sup>2+</sup>, especially under
alkaline conditions. Model calculations indicate that this increase
is due to electrostatic interaction of positively charged tetracycline-Ca
complexes with humic acid rather than due to the formation of ternary
complexes, except at very low TC concentrations
A Hybrid Molecular Dynamics/Multiconformer Continuum Electrostatics (MD/MCCE) Approach for the Determination of Surface Charge of Nanomaterials
The
surface charge of nanomaterials determines their stability
in solution and interaction with other molecules and surfaces, yet
experimental determination of surface charge of complex nanomaterials
is not straightforward. We propose a hybrid approach that iteratively
integrates explicit solvent molecular dynamics simulations and a multiconformer
continuum electrostatic model (MCCE) to efficiently sample the configurational
and titration spaces of surface ligands of nanomaterials. Test calculations
of model systems indicate that the iterative approach converges rapidly
even for systems that contain hundreds of titratable sites, making
the approach complementary to more elaborate methods such as explicit
solvent-based constant-pH molecular dynamics. The hybrid method is
applied to analyze the p<i>K</i><sub>a</sub> distribution
of alkylamines attached to a carbon-based nanoparticle as a function
of ligand density, nanoparticle surface curvature, and ligand heterogeneity.
The results indicate that functionalization strategies can modulate
the p<i>K</i><sub>a</sub> of surface ligands and therefore
charge properties of nanomaterials (e.g., surface charge, charge capacitance).
The hybrid computational approach makes a major step toward guiding
the design of nanomaterials with desired charge properties
Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling
Motivated
by specific applications and the recent work of Gao and
co-workers on integrated tempering sampling (ITS), we have developed
a novel sampling approach referred to as integrated Hamiltonian sampling
(IHS). IHS is straightforward to implement and complementary to existing
methods for free energy simulation and enhanced configurational sampling.
The method carries out sampling using an effective Hamiltonian constructed
by integrating the Boltzmann distributions of a series of Hamiltonians.
By judiciously selecting the weights of the different Hamiltonians,
one achieves rapid transitions among the energy landscapes that underlie
different Hamiltonians and therefore an efficient sampling of important
regions of the conformational space. Along this line, IHS shares similar
motivations as the enveloping distribution sampling (EDS) approach
of van Gunsteren and co-workers, although the ways that distributions
of different Hamiltonians are integrated are rather different in IHS
and EDS. Specifically, we report efficient ways for determining the
weights using a combination of histogram flattening and weighted histogram
analysis approaches, which make it straightforward to include many
end-state and intermediate Hamiltonians in IHS so as to enhance its
flexibility. Using several relatively simple condensed phase examples,
we illustrate the implementation and application of IHS as well as
potential developments for the near future. The relation of IHS to
several related sampling methods such as Hamiltonian replica exchange
molecular dynamics and λ-dynamics is also briefly discussed
Dynamics and Morphology of Nanoparticle-Linked Polymers Elucidated by Nuclear Magnetic Resonance
Nanoparticles
are frequently modified with polymer layers to control
their physical and chemical properties, but little is understood about
the morphology and dynamics of these polymer layers. We report here
an NMR-based investigation of a model polymer-modified nanoparticle,
using multiple NMR techniques including <sup>1</sup>H NMR, diffusion-ordered
spectroscopy (DOSY), total correlation spectroscopy (TOCSY), and <i>T</i><sub>2</sub> relaxometry to characterize the dynamics of
the nanoparticle–polymer interface. Using 5 nm detonation nanodiamond
covalently linked to poly(allylamine) hydrochloride as a model system,
we demonstrate the use of NMR to distinguish between free and bound
polymer and to characterize the degree to which the segments of the
nanoparticle-wrapping polymer are mobile (loops and tails) versus
immobile (trains). Our results show that the polymer-wrapped nanoparticle
contains a large fraction of highly mobile polymer segments, implying
that the polymer extends well into solution away from the nanoparticle
surface. Flexible, distal polymer segments are likely to be more accessible
to extended objects such as cell membranes, compared with polymer
segments that are in close proximity to the nanoparticle surface.
Thus, these flexible segments may be particularly important in controlling
subsequent interactions of the nanoparticles. While reported here
for a model system, the methodology used demonstrates how NMR methods
can provide important insights into the structure and dynamics at
nanoparticle–polymer interfaces, leading to new perspectives
on the behavior and interactions of polymer-functionalized nanoparticles
in aqueous systems
Root Uptake of Pharmaceuticals and Personal Care Product Ingredients
Crops irrigated with reclaimed wastewater or grown in biosolids-amended
soils may take up pharmaceuticals and personal care product ingredients
(PPCPs) through their roots. The uptake pathways followed by PPCPs
and the propensity for these compounds to bioaccumulate in food crops
are still not well understood. In this critical review, we discuss
processes expected to influence root uptake of PPCPs, evaluate current
literature on uptake of PPCPs, assess models for predicting plant
uptake of these compounds, and provide recommendations for future
research, highlighting processes warranting study that hold promise
for improving mechanistic understanding of plant uptake of PPCPs.
We find that many processes that are expected to influence PPCP uptake
and accumulation have received little study, particularly rhizosphere
interactions, in planta transformations, and physicochemical properties
beyond lipophilicity (as measured by <i>K</i><sub>ow</sub>). Data gaps and discrepancies in methodology and reporting have
so far hindered development of models that accurately predict plant
uptake of PPCPs. Topics warranting investigation in future research
include the influence of rhizosphere processes on uptake, determining
mechanisms of uptake and accumulation, in planta transformations,
the effects of PPCPs on plants, and the development of predictive
models
Plant-Induced Changes to Rhizosphere pH Impact Leaf Accumulation of Lamotrigine but Not Carbamazepine
Many
ionizable organic contaminants (IOCs) are present in treated
wastewater used to irrigate edible crops and accumulate in plants
under field conditions. Phytoavailability of IOCs with p<i>K</i><sub>a</sub> values between 4 and 9 may be affected by the pH of
the rhizosphere (the water and soil within 2–3 mm of the root
surface). Plants can alter rhizosphere pH by 2–3 units in either
direction in response to nutrient availability. The effects of plant
modulation of rhizosphere pH on IOC accumulation have not been previously
reported. Here we provide direct evidence that plant-driven changes
in rhizosphere pH impact accumulation of an IOC in plant leaves. Using
a modified hydroponic system, we found that rhizosphere pH was higher
by 1.5–2.4 units when plants received only nitrate rather than
a combination of nitrate and ammonium. Plant-driven changes to rhizosphere
pH altered accumulation of lamotrigine (p<i>K</i><sub>a</sub> = 5.7) but not carbamazepine, a non-ionizable contaminant. Lamotrigine
accumulation in leaves correlated strongly with the concentration
of the neutral species available in porewater. We expect plant-driven
changes in rhizosphere pH to be important across a wide range of plant
species and IOCs. Consideration of plant modulation of rhizosphere
pH may be necessary to accurately predict IOC bioaccumulation
Mineral licks as environmental reservoirs of chronic wasting disease prions
<div><p>Chronic wasting disease (CWD) is a fatal neurodegenerative disease of deer, elk, moose, and reindeer (cervids) caused by misfolded prion proteins. The disease has been reported across North America and recently discovered in northern Europe. Transmission of CWD in wild cervid populations can occur through environmental routes, but limited ability to detect prions in environmental samples has prevented the identification of potential transmission “hot spots”. We establish widespread CWD prion contamination of mineral licks used by free-ranging cervids in an enzootic area in Wisconsin, USA. We show mineral licks can serve as reservoirs of CWD prions and thus facilitate disease transmission. Furthermore, mineral licks attract livestock and other wildlife that also obtain mineral nutrients via soil and water consumption. Exposure to CWD prions at mineral licks provides potential for cross-species transmission to wildlife, domestic animals, and humans. Managing deer use of mineral licks warrants further consideration to help control outbreaks of CWD.</p></div
Adsorption of Insecticidal Cry1Ab Protein to Humic Substances. 2. Influence of Humic and Fulvic Acid Charge and Polarity Characteristics
Assessing the fate and potential risks of transgenic
Cry proteins
in soils requires understanding of Cry protein adsorption to soil particles.
The companion paper provided evidence that patch-controlled electrostatic
attraction (PCEA) and the hydrophobic effect contributed to Cry1Ab
protein adsorption to an apolar humic acid (HA). Here, we further
assess the relative importance of these contributions by comparing
Cry1Ab adsorption to seven humic substances varying in polarity and
charge, at different solution pH and ionic strength, <i>I</i>. Cry1Ab adsorption to relatively apolar HAs at <i>I</i> = 50 mM exhibited rapid initial rates, was extensive, and was only
partially reversible at pH 5–8, whereas adsorption to more
polar fulvic acids was weak and reversible or absent at pH >6.
The
decrease in adsorption with increasing HS polarity at all tested pH
strongly supports a large contribution from the hydrophobic effect
to adsorption, particularly at <i>I</i> = 50 mM when PCEA
was effectively screened. Using insect bioassays, we further show
that Cry1Ab adsorbed to a selected HA retained full insecticidal activity.
Our results highlight the need to consider adsorption to soil organic
matter in models that assess the fate of Cry proteins in soils