Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections

For (H2O)n where n = 1–10, we used a scheme combining molecular dynamics sampling with high level ab initio calculations to locate the global and many low lying local minima for each cluster. For each isomer, we extrapolated the RI-MP2 energies to their complete basis set limit, included a CCSD(T) correction using a smaller basis set and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled and unscaled harmonic vibrational frequencies. The vibrational scaling factors were determined specifically for water clusters by comparing harmonic frequencies with VPT2 fundamental frequencies. We find the CCSD(T) correction to the RI-MP2 binding energy to be small (

Computational Study of the Hydration of Sulfuric Acid Dimers: Implications for Acid Dissociation and Aerosol Formation

We have investigated the thermodynamics of sulfuric acid dimer hydration using ab initio quantum mechanical methods. For (H2SO4)2(H2O)n where n = 0−6, we employed high-level ab initio calculations to locate the most stable minima for each cluster size. The results presented herein yield a detailed understanding of the first deprotonation of sulfuric acid as a function of temperature for a system consisting of two sulfuric acid molecules and up to six waters. At 0 K, a cluster of two sulfuric acid molecules and one water remains undissociated. Addition of a second water begins the deprotonation of the first sulfuric acid leading to the di-ionic species (the bisulfate anion HSO4−, the hydronium cation H3O+, an undissociated sulfuric acid molecule, and a water). Upon the addition of a third water molecule, the second sulfuric acid molecule begins to dissociate. For the (H2SO4)2(H2O)3 cluster, the di-ionic cluster is a few kcal mol−1 more stable than the neutral cluster, which is just slightly more stable than the tetra-ionic cluster (two bisulfate anions, two hydronium cations, and one water). With four water molecules, the tetra-ionic cluster, (HSO4−)2(H3O+)2(H2O)2, becomes as favorable as the di-ionic cluster H2SO4(HSO4−)(H3O+)(H2O)3 at 0 K. Increasing the temperature favors the undissociated clusters, and at room temperature we predict that the di-ionic species is slightly more favorable than the neutral cluster once three waters have been added to the cluster. The tetra-ionic species competes with the di-ionic species once five waters have been added to the cluster. The thermodynamics of stepwise hydration of sulfuric acid dimer is similar to that of the monomer; it is favorable up to n = 4−5 at 298 K. A much more thermodynamically favorable pathway forming sulfuric acid dimer hydrates is through the combination of sulfuric acid monomer hydrates, but the low concentration of sulfuric acid relative to water vapor at ambient conditions limits that process.

Lipopolysaccharide and lipoteichoic acid induce different immune responses in the bovine mammary gland

Different pathogens, such as Escherichia coli and Staphylococcus aureus, can be responsible for different outcomes of mastitis; that is, acute and severe or chronic and subclinical. These differences in the disease could be related to different mammary responses to the pathogens. The objective of this study was to determine if intramammary challenge with the endotoxins lipopolysaccharide (LPS), from E. coli, and lipoteichoic acid (LTA), from Staph. aureus, induce different immune responses in vivo in milk cells and mammary tissue. To provide a reference level for comparing the challenge and to show the different stimulation of the mammary immune system on a quantitatively similar level, dosages of LPS and LTA were chosen that induced an increase of somatic cells in milk to similar maxima. One udder quarter in each of 21 lactating dairy cows was challenged with 0.2 mug of LPS or 20 mug of LTA. From these quarters and from respective control quarters, milk cells or tissue biopsies were obtained at 0, 6, and 12h relative to the challenge to measure mRNA expression of tumor necrosis factor-alpha (TNFalpha), IL-1beta, IL-8, lactoferrin, and RANTES (regulated upon activation, normal T-cell expressed and secreted). Furthermore, if no biopsies were performed, hourly milk samples were taken for measurement of somatic cell count, lactate dehydrogenase (LDH), and TNFalpha. Somatic cell count increased in all treatments to similar maxima with LPS and LTA treatments. Concentrations of TNFalpha in milk increased with LPS but not with LTA. The activity of LDH in milk increased in both treatments and was more pronounced with LPS than with LTA. The mRNA expression of TNFalpha, IL-1beta, IL-8, and RANTES showed increases in milk cells, and LPS was a stronger inducer than LTA. Lactoferrin mRNA expression decreased in milk cells with LPS and LTA treatments. The measured factors did not change in either treatment in mammary tissue. Challenge of udder quarters with dosages of LPS and LTA that induce similar increases in SCC stimulate the appearance of different immune factor patterns. This dissimilar response to LPS and LTA may partly explain the different course and intensity of mastitis after infection with E. coli and Staph. aureus, respectively.

Immediate and delayed transplantation of mesenchymal stem cells improve muscle force after skeletal muscle injury in rats

Mesenchymal stem cell (MSC) therapy is a promising approach for regaining muscle function after trauma. Prior to clinical application, the ideal time of transplantation has to be determined. We investigated the effects of immediate and delayed transplantation. Sprague-Dawley rats received a crush trauma to the left soleus muscle. Treatment groups were transplanted locally with 2 × 10(6) autologous MSCs, either immediately or 7 days after trauma. Saline was used as sham therapy. Contraction force tests and histological analyses were performed 4 weeks after injury. GFP-labelled MSCs were followed after transplantation. The traumatized soleus muscles of the sham group displayed a reduction of twitch forces to 36 ± 17% and of tetanic forces to 29 ± 11% of the non-injured right control side, respectively. Delayed MSC transplantation resulted in a significant improvement of contraction maxima in both stimulation modes (twitch, p = 0.011; tetany, p = 0.014). Immediate transplantation showed a significant increase in twitch forces to 59 ± 17% (p = 0.043). There was no significant difference in contraction forces between muscles treated by immediate and delayed cell transplantation. We were able to identify MSCs in the interstitium of the injured muscles up to 4 weeks after transplantation. Despite the fundamental differences of the local environment, which MSCs encounter after transplantation, similar results could be obtained with respect to functional muscle regeneration. We believe that transplanted MSCs residing in the interstitial compartment evolve their regenerative capabilities through paracrine pathways. Our data suggest a large time window of the therapeutical measures.

Cascading climate effects and related ecological consequences during past centuries

The interface between climate and ecosystem structure and function is incompletely understood, partly because few ecological records start before the recent warming phase. Here, we analyse an exceptional 100-yr long record of the great tit (Parus major) population in Switzerland in relation to climate and habitat phenology. Using structural equation analysis, we demonstrate an uninterrupted cascade of significant influences of the large-scale atmospheric circulation (North-Atlantic Oscillation, NAO, and North-sea – Caspian Pattern, NCP) on habitat and breeding phenology, and further on fitness-relevant life history traits within great tit populations. We then apply the relationships of this analysis to reconstruct the circulation-driven component of fluctuations in great tit breeding phenology and productivity on the basis of new seasonal NAO and NCP indices back to 1500 AD. According to the structural equation model, the multi-decadal oscillation of the atmospheric circulation likely led to substantial variation in habitat phenology, productivity and consequently, tit population fluctuations with minima during the "Maunder Minimum" (∼ 1650–1720) and the Little Ice Age Type Event I (1810–1850). The warming since 1975 was not only related with a quick shift towards earlier breeding, but also with the highest productivity since 1500, and thus, the impact of the NAO and NCP has contributed to an unprecedented increase of the population. A verification of the structural equation model against two independent data series (1970–2000 and 1750–1900) corroborates that the retrospective model reliably depicts the major long-term NAO/NCP impact on ecosystem parameters. The results suggest a complex cascade of climate effects beginning at a global scale and ending at the level of individual life histories. This sheds light on how large-scale climate conditions substantially affect major life history parameters within a population, and thus influence key ecosystem parameters at the scale of centuries.

The long-term mechanical integrity of non-reinforced PEEK-OPTIMA polymer for demanding spinal applications: experimental and finite-element analysis

Polyetheretherketone (PEEK) is a novel polymer with potential advantages for its use in demanding orthopaedic applications (e.g. intervertebral cages). However, the influence of a physiological environment on the mechanical stability of PEEK has not been reported. Furthermore, the suitability of the polymer for use in highly stressed spinal implants such as intervertebral cages has not been investigated. Therefore, a combined experimental and analytical study was performed to address these open questions. A quasi-static mechanical compression test was performed to compare the initial mechanical properties of PEEK-OPTIMA polymer in a dry, room-temperature and in an aqueous, 37 degrees C environment (n=10 per group). The creep behaviour of cylindrical PEEK polymer specimens (n=6) was measured in a simulated physiological environment at an applied stress level of 10 MPa for a loading duration of 2000 hours (12 weeks). To compare the biomechanical performance of different intervertebral cage types made from PEEK and titanium under complex loading conditions, a three-dimensional finite element model of a functional spinal unit was created. The elastic modulus of PEEK polymer specimens in a physiological environment was 1.8% lower than that of specimens tested at dry, room temperature conditions (P<0.001). The results from the creep test showed an average creep strain of less than 0.1% after 2000 hours of loading. The finite element analysis demonstrated high strain and stress concentrations at the bone/implant interface, emphasizing the importance of cage geometry for load distribution. The stress and strain maxima in the implants were well below the material strength limits of PEEK. In summary, the experimental results verified the mechanical stability of the PEEK-OPTIMA polymer in a simulated physiological environment, and over extended loading periods. Finite element analysis supported the use of PEEK-OPTIMA for load-bearing intervertebral implants.

Exposure dating of Late Glacial and pre-LGM moraines in the Cordon de Doña Rosa, Northern/Central Chile (~ 31°S)

Despite the important role of the Central Andes (15–30° S) for climate reconstruction, knowledge about the Quaternary glaciation is very limited due to the scarcity of organic material for radiocarbon dating. We applied 10Be surface exposure dating (SED) on 22 boulders from moraines in the Cordon de Doña Rosa, Northern/Central Chile (~31° S). The results show that several glacial advances in the southern Central Andes occurred during the Late Glacial between ~14.7±1.5 and 11.6±1.2 ka. A much more extensive glaciation is dated to ~32±3 ka, predating the temperature minimum of the global LGM (Last Glacial Maximum: ~20 ka). Reviewing these results in the paleoclimatic context, we conclude that the Late Glacial advances were most likely caused by an intensification of the tropical circulation and a corresponding increase in summer precipitation. High-latitude temperatures minima, e.g. the Younger Dryas (YD) and the Antarctic Cold Reversal (ACR) may have triggered individual advances, but current systematic exposure age uncertainties limit precise correlations. The absence of LGM moraines indicates that moisture advection was too limited to allow significant glacial advances at ~20 ka. The tropical circulation was less intensive despite the maximum in austral summer insolation. Winter precipitation was apparently also insufficient, although pollen and marine studies indicate a northward shift of the westerlies at that time. The dominant pre-LGM glacial advances in Northern/Central Chile at ~32 ka required lower temperatures and increased precipitation than today. We conclude that the westerlies were more intense and/or shifted equatorward, possibly due to increased snow and ice cover at higher southern latitudes coinciding with a minimum of insolation.

Molecular interaction between perthiolated [beta]-cyclodextrin (CD) and the guests molecules adamantaneacetic acid (AD) and ferroceneacetic acid (FC); and the effect of the interaction on the electron transition of CD anchored particles

The molecular interactions between the host molecule, perthiolated beta-cyclodextrin (CD), and the guest molecules, adamantaneacetic acid (AD) and ferroceneacetic acid (FC), have been inestigated theoretically in both the gas and aqueous phases. The major computations have been carried out at the theoretical levels, RHF/6-31G and B3LYP/6- 31G. MP2 electronic energies were also computed based at the geometries optimized by both the RHF and B3LYP methods in the gas phase to establish a better estimate of the correlation effect. The solvent phase computations were completed at the RHF/6-31G and B3LYP/6-31G levels using the PCM model. The most stable structures optimized in gas phase by both the RHF and B3LYP methods were used for the computations in solution. A method to systematically manipulate the relative position and orientation between the interacting molecules is proposed. In the gas phase, six trials with different host-guest relative positions and orientations were completed successfully with the B3LYP method for both the CD-AD and CD-FC complexes. Only four trials were completed with RHF method. In the gas phase, the best results from the RHF method gives for the association Gibbs free energy (ΔG°) values equal to -32.21kj/mol for CD-AD and -25.73kj/mol for CD-FC. And the best results from the B3LYP method have ΔG° equal to -47.57kj/mol for CD-AD and -41.09kj/mol for CD-FC. The MP2 correction significantly lowers ΔG° based on the geometries from both methods. For the RHF structure, the MP2 computations lowered ΔG° to -60.64kj/mol for CD-AD and -54.10 for CD-FC. For the structure from the B3LYP method, it was reduced to -59.87 kj/mol for CD-AD and -54.84 kj/mol for CDFC. The RHF solvent phase calculations yielded following results: ΔG°(aq) equals 107.2kj/mol for CD-AD and 111.4kj/mol for CD-FC. Compared with the results from the RHF method, the B3LYP method provided clearly better solvent phase results with ΔG° (aq) equal to 38.64kj/mol for CD-AD and 39.61kj/mol for CD-FC. These results qualitatively explain the experimental observations. However quantitatively they are in poor agreement with the experimental values available in the literature and those recently published by Liu et al. And the reason is believed to be omission of hydrophobic contribution to the association. Determining the global geometrical minima for these very large systems was very difficult and computationally time consuming, but after a very thorough search, these were identified. A relevant result of this search is that when the complexes, CD-AD and CD-FC, are formed, the AD and FC molecules are only partially embedded inside the CD cavity. The totally embedded complexes were found to have significantly higher energies. The semiempirical method, ZINDO, was employed to investigate the effect of complexation on the first electronic excitation of CD anchored to a metal nano-particle. The computational results revealed that after complexation to FC, the transition intensity declines to about 25% of the original value, and after complexation with AD, the intensity drops almost 50%. The tighter binding and transition intensity of CD-AD qualitatively agrees with the experimental result that the addition of AD to a solution of CD and FC restores the fluorescence of CD that was quenched by the addition of FC. A method to evaluate the “hydrophobic force” effect is proposed for future work.

Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

Erupted magma volume estimates at Santiaguito and Pacaya Volcanoes, Guatemala using digital elevation models

High resolution digital elevation models (DEMs) of Santiaguito and Pacaya volcanoes, Guatemala, were used to estimate volume changes and eruption rates between 1954 and 2001. The DEMs were generated from contour maps and aerial photography, which were analyzed in ArcGIS 9.0®. Because both volcanoes were growing substantially over the five decade period, they provide a good data set for exploring effective methodology for estimating volume changes. The analysis shows that the Santiaguito dome complex grew by 0.78 ± 0.07 km3 (0.52 ± 0.05 m3 s-1) over the 1954-2001 period with nearly all the growth occurring on the El Brujo (1958-75) and Caliente domes (1971-2001). Adding information from field data prior to 1954, the total volume extruded from Santiaguito since 1922 is estimated at 1.48 ± 0.19 km3. Santiaguito’s growth rate is lower than most other volcanic domes, but it has been sustained over a much longer period and has undergone a change toward more exogenous and progressively slower extrusion with time. At Santiaguito some of the material being added at the dome is subsequently transported downstream by block and ash flows, mudflows and floods, creating channel shifting and areas of aggradation and erosion. At Pacaya volcano a total volume of 0.21 ± 0.05 km3 was erupted between 1961 and 2001 for an average extrusion rate of 0.17 ± 0.04 m3 s-1. Both the Santiaguito and Pacaya eruption rate estimates reported here are minima, because they do not include estimates of materials which are transported downslope after eruption and data on ashfall which may result in significant volumes of material spread over broad areas. Regular analysis of high resolution DEMs using the methods outlined here, would help quantify the effects of fluvial changes to downstream populated areas, as well as assist in tracking hazards related to dome collapse and eruption.

Wavelet-denoising of electroencephalogram and the absolute slope method: a new tool to improve electroencephalographic localization and lateralization

OBJECTIVE: In ictal scalp electroencephalogram (EEG) the presence of artefacts and the wide ranging patterns of discharges are hurdles to good diagnostic accuracy. Quantitative EEG aids the lateralization and/or localization process of epileptiform activity. METHODS: Twelve patients achieving Engel Class I/IIa outcome following temporal lobe surgery (1 year) were selected with approximately 1-3 ictal EEGs analyzed/patient. The EEG signals were denoised with discrete wavelet transform (DWT), followed by computing the normalized absolute slopes and spatial interpolation of scalp topography associated to detection of local maxima. For localization, the region with the highest normalized absolute slopes at the time when epileptiform activities were registered (>2.5 times standard deviation) was designated as the region of onset. For lateralization, the cerebral hemisphere registering the first appearance of normalized absolute slopes >2.5 times the standard deviation was designated as the side of onset. As comparison, all the EEG episodes were reviewed by two neurologists blinded to clinical information to determine the localization and lateralization of seizure onset by visual analysis. RESULTS: 16/25 seizures (64%) were correctly localized by the visual method and 21/25 seizures (84%) by the quantitative EEG method. 12/25 seizures (48%) were correctly lateralized by the visual method and 23/25 seizures (92%) by the quantitative EEG method. The McNemar test showed p=0.15 for localization and p=0.0026 for lateralization when comparing the two methods. CONCLUSIONS: The quantitative EEG method yielded significantly more seizure episodes that were correctly lateralized and there was a trend towards more correctly localized seizures. SIGNIFICANCE: Coupling DWT with the absolute slope method helps clinicians achieve a better EEG diagnostic accuracy.

Paleoglaciations in Anatolia: A Schematic Review and First Results

Anatolia is situated in the Eastern Mediterranean region between 36 – 42N and 26 – 45E. The geological records of paleoglaciations in the high terrains of Anatolia are key archives to quantify paleoclimate change in the Eastern Mediterranean area. The climate of the Eastern Mediterranean region is influenced by three main atmospheric systems: the main middle to high latitude westerlies, the mid-latitude subtropical high-pressure systems, and the monsoon climate. Glacial geological studies in Turkey have started in the late 19th century. Glacial deposits are found mainly in the eastern, northeastern and southern part of the Anatolian Peninsula. Anatolia is the fundamental element to understand the interactions between paleoenvironment, climatic variations, and development of the human societies. As the Taurus and Black Sea Mountains are sensitively situated for the paleoclimatic reconstructions, a chronostratigraphic framework on the paleoglaciation should be elaborated. The timing of the Last Glacial Maximum (LGM) in Anatolia is still unknown. Our first results from Kavron Valley (Kaçkar Mountains, NE Turkey) are encouraging for the reconstruction of paleoglaciations in Turkey and related paleoclimatological interpretations although it is presently difficult to pinpoint the classical Last Glacial Maximum – Younger Dryas – Little Ice Age moraine sequences in the field.

Evidence for distinct modes of solar activity

The Sun shows strong variability in its magnetic activity, from Grand minima to Grand maxima, but the nature of the variability is not fully understood, mostly because of the insufficient length of the directly observed solar activity records and of uncertainties related to long-term reconstructions. Here we present a new adjustment-free reconstruction of solar activity over three millennia and study its different modes. Methods. We present a new adjustment-free, physical reconstruction of solar activity over the past three millennia, using the latest verified carbon cycle, 14C production, and archeomagnetic field models. This great improvement allowed us to study different modes of solar activity at an unprecedented level of details. Results. The distribution of solar activity is clearly bi-modal, implying the existence of distinct modes of activity. The main regular activity mode corresponds to moderate activity that varies in a relatively narrow band between sunspot numbers 20 and 67. The existence of a separate Grand minimum mode with reduced solar activity, which cannot be explained by random fluctuations of the regular mode, is confirmed at a high confidence level. The possible existence of a separate Grand maximum mode is also suggested, but the statistics is too low to reach a confident conclusion. Conclusions. The Sun is shown to operate in distinct modes – a main general mode, a Grand minimum mode corresponding to an inactive Sun, and a possible Grand maximum mode corresponding to an unusually active Sun. These results provide important constraints for both dynamo models of Sun-like stars and investigations of possible solar influence on Earth’s climate.

Direct linking of Greenland and Antarctic ice cores at the Toba eruption (74 ka BP)

The Toba eruption that occurred some 74 ka ago in Sumatra, Indonesia, is among the largest volcanic events on Earth over the last 2 million years. Tephra from this eruption has been spread over vast areas in Asia, where it constitutes a major time marker close to the Marine Isotope Stage 4/5 boundary. As yet, no tephra associated with Toba has been identified in Greenland or Antarctic ice cores. Based on new accurate dating of Toba tephra and on accurately dated European stalagmites, the Toba event is known to occur between the onsets of Greenland interstadials (GI) 19 and 20. Furthermore, the existing linking of Greenland and Antarctic ice cores by gas records and by the bipolar seesaw hypothesis suggests that the Antarctic counterpart is situated between Antarctic Isotope Maxima (AIM) 19 and 20. In this work we suggest a direct synchronization of Greenland (NGRIP) and Antarctic (EDML) ice cores at the Toba eruption based on matching of a pattern of bipolar volcanic spikes. Annual layer counting between volcanic spikes in both cores allows for a unique match. We first demonstrate this bipolar matching technique at the already synchronized Laschamp geomagnetic excursion (41 ka BP) before we apply it to the suggested Toba interval. The Toba synchronization pattern covers some 2000 yr in GI-20 and AIM-19/20 and includes nine acidity peaks that are recognized in both ice cores. The suggested bipolar Toba synchronization has decadal precision. It thus allows a determination of the exact phasing of inter-hemispheric climate in a time interval of poorly constrained ice core records, and it allows for a discussion of the climatic impact of the Toba eruption in a global perspective. The bipolar linking gives no support for a long-term global cooling caused by the Toba eruption as Antarctica experiences a major warming shortly after the event. Furthermore, our bipolar match provides a way to place palaeo-environmental records other than ice cores into a precise climatic context.