Initiation mechanisms and kinetics of pyrolysis and combustion of JP-10 hydrocarbon jet fuel

In order to investigate the initiation mechanisms and kinetics associated with the pyrolysis of JP-10 (exo-tricyclo[5.2.1.0^2,6]decane), a single-component hydrocarbon jet fuel, we carried out molecular dynamics (MD) simulations employing the ReaxFF reactive force field. We found that the primary decomposition reactions involve either (1) dissociation of ethylene from JP-10, resulting in the formation of a C8 hydrocarbon intermediate, or (2) the production of two C5 hydrocarbons. ReaxFF MD leads to good agreement with experiment for the product distribution as a function of temperature. On the basis of the rate of consumption of JP-10, we calculate an activation energy of 58.4 kcal/mol for the thermal decomposition of this material, which is consistent with a strain-facilitated C−C bond cleavage mechanism in JP-10. This compares well with the experimental value of 62.4 kcal/mol. In addition, we carried out ReaxFF MD studies of the reactive events responsible for oxidation of JP-10. Here we found overall agreement between the thermodynamic energies obtained from ReaxFF and quantum-mechanical calculations, illustrating the usefulness of ReaxFF for studying oxidation of hydrocarbons. The agreement of these results with available experimental observations demonstrates that ReaxFF can provide useful insights into the complicated thermal decomposition and oxidation processes of important hydrocarbon fuels

The ReaxFF Monte Carlo Reactive Dynamics Method for Predicting Atomistic Structures of Disordered Ceramics: Application to the Mo_3VO_x Catalyst

The ReaxFF computational approach is used to resolve partial or mixed occupation of crystallographic sites of the Mo_3VO_x multimetal oxide (MMO) catalyst. It provides insight into the oxidation state and coordination environment of the metal sites, identifies donor-acceptor networks in the catalyst, and predicts selectivity for molecular diffusion into channels of the framework

ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation

To investigate the initial chemical events associated with high-temperature gas-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include additional transition states and chemical reactivity of systems relevant to these reactions and optimized the force field parameters against a quantum mechanics (QM)-based training set. To validate the ReaxFF potential obtained after parameter optimization, we performed a range of NVT−MD simulations on various hydrocarbon/O_2 systems. From simulations on methane/O_2, o-xylene/O_2, propene/O_2, and benzene/O_2 mixtures, we found that ReaxFF obtains the correct reactivity trend (propene > o-xylene > methane > benzene), following the trend in the C−H bond strength in these hydrocarbons. We also tracked in detail the reactions during a complete oxidation of isolated methane, propene, and o-xylene to a CO/CO_2/H_2O mixture and found that the pathways predicted by ReaxFF are in agreement with chemical intuition and our QM results. We observed that the predominant initiation reaction for oxidation of methane, propene, and o-xylene under fuel lean conditions involved hydrogen abstraction of the methyl hydrogen by molecular oxygen forming hydroperoxyl and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, we observed different chemistry compared with the oxidation of isolated hydrocarbons including a change in the type of initiation reactions, which involved both decomposition of the hydrocarbon or attack by other radicals in the system. Since ReaxFF is capable of simulating complicated reaction pathways without any preconditioning, we believe that atomistic modeling with ReaxFF provides a useful method for determining the initial events of oxidation of hydrocarbons under extreme conditions and can enhance existing combustion models

I2B is a Small Cytosolic Protein that Participates in Vacuole Fusion

Saccharomyces cerevisiae vacuole inheritance requires two low molecular weight activities, LMA1 and LMA2. LMA1 is a heterodimer of thioredoxin and protease B inhibitor 2 (IB2). Here we show that the second low molecular weight activity (LMA2) is monomeric IB2. Though LMA2 / IB2 was initially identified as a protease B inhibitor, this protease inhibitor activity is not related to its ability to promote vacuole fusion: ( i ) Low M r protease B inhibitors cannot substitute for LMA1 or LMA2, ( ii ) LMA1 and LMA2 promote the fusionof vacuoles from a strain that has no protease B, ( iii ) low concentrations of LMA2 that fully inhibit protease B do not promote vacuole fusion, and ( iv ) LMA1, in which is complexed with thioredoxin,is far more active than LMA2 / IB2 in promoting vacuole fusion and far less active in inhibiting protease B. These studies establish a new function for IB2

PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI

Remarkable progress has been made by data-driven machine-learning methods in the analysis of MRI scans. However, most existing MRI analysis approaches are crafted for specific MR pulse sequences (MR contrasts) and usually require nearly isotropic acquisitions. This limits their applicability to diverse real-world clinical data, where scans commonly exhibit variations in appearances due to being obtained with varying sequence parameters, resolutions, and orientations -- especially in the presence of pathology. In this paper, we propose PEPSI, the first pathology-enhanced, and pulse-sequence-invariant feature representation learning model for brain MRI. PEPSI is trained entirely on synthetic images with a novel pathology encoding strategy, and enables co-training across datasets with diverse pathologies and missing modalities. Despite variations in pathology appearances across different MR pulse sequences or the quality of acquired images (e.g., resolution, orientation, artifacts, etc), PEPSI produces a high-resolution image of reference contrast (MP-RAGE) that captures anatomy, along with an image specifically highlighting the pathology. Our experiments demonstrate PEPSI's remarkable capability for image synthesis compared with the state-of-the-art, contrast-agnostic synthesis models, as it accurately reconstructs anatomical structures while differentiating between pathology and normal tissue. We further illustrate the efficiency and effectiveness of PEPSI features for downstream pathology segmentations on five public datasets covering white matter hyperintensities and stroke lesions. Code is available at https://github.com/peirong26/PEPSI.Comment: 12 pages, 6 figure

Seasonal and spatial dynamics of the primary vector of plasmodium knowlesi within a major transmission focus in Sabah, Malaysia

Background The simian malaria parasite Plasmodium knowlesi is emerging as a public health problem in Southeast Asia, particularly in Malaysian Borneo where it now accounts for the greatest burden of malaria cases and deaths. Control is hindered by limited understanding of the ecology of potential vector species. Methodology/Principal Findings We conducted a one year longitudinal study of P. knowlesi vectors in three sites within an endemic area of Sabah, Malaysia. All mosquitoes were captured using human landing catch. Anopheles mosquitoes were dissected to determine, oocyst, sporozoites and parous rate. Anopheles balabacensis is confirmed as the primary vector of. P. knowlesi (using nested PCR) in Sabah for the first time. Vector densities were significantly higher and more seasonally variable in the village than forest or small scale farming site. However An. balabacensis survival and P. knowlesi infection rates were highest in forest and small scale farm sites. Anopheles balabacensis mostly bites humans outdoors in the early evening between 1800 to 2000hrs. Conclusions/Significance This study indicates transmission is unlikely to be prevented by bednets. This combined with its high vectorial capacity poses a threat to malaria elimination programmes within the region. Author Summary The first natural infection of Plasmodium knowlesi was reported 40 years ago. At that time it was perceived that the infection would not affect humans. However, now P. knowlesi is the predominant malaria species (38% of the cases) infecting people in Malaysia and is a notable obstacle to malaria elimination in the country. Plasmodium knowlesi has also been reported from all countries in Southeast Asia with the exception of Lao PDR and Timor Leste. In Sabah, Malaysian Borneo cases of human P. knowlesi are increasing. Thus, a comprehensive understanding of the bionomics of the vectors is required so as to enable proper control strategies. Here, we conducted a longitudinal study in Kudat district, Sabah, to determine and characterize the vectors of P. knowlesi within this transmission foci. Anopheles balabacensis was the predominant mosquito in all study sites and is confirmed as vector for P. knowlesi and other simian malaria parasites. The peak biting time was in the early part of the evening between1800 to 2000. Thus, breaking the chain of transmission is an extremely challenging task for the malaria elimination programme

Simulations on the Thermal Decomposition of a Poly(dimethylsiloxane) Polymer Using the ReaxFF Reactive Force Field

To investigate the failure of the poly(dimethylsiloxane) polymer (PDMS) at high temperatures and pressures and in the presence of various additives, we have expanded the ReaxFF reactive force field to describe carbon−silicon systems. From molecular dynamics (MD) simulations using ReaxFF we find initial thermal decomposition products of PDMS to be CH_3 radical and the associated polymer radical, indicating that decomposition and subsequent cross-linking of the polymer is initiated by Si−C bond cleavage, in agreement with experimental observations. Secondary reactions involving these CH_3 radicals lead primarily to formation of methane. We studied temperature and pressure dependence of PDMS decomposition by following the rate of production of methane in the ReaxFF MD simulations. We tracked the temperature dependency of the methane production to extract Arrhenius parameters for the failure modes of PDMS. Furthermore, we found that at increased pressures the rate of PDMS decomposition drops considerably, leading to the formation of fewer CH_3 radicals and methane molecules. Finally, we studied the influence of various additives on PDMS stability. We found that the addition of water or a SiO_2 slab has no direct effect on the short-term stability of PDMS, but addition of reactive species such as ozone leads to significantly lower PDMS decomposition temperature. The addition of nitrogen monoxide does not significantly alter the degradation temperature but does retard the initial production of methane and C_2 hydrocarbons until the nitrogen monoxide is depleted. These results, and their good agreement with available experimental data, demonstrate that ReaxFF provides a useful computational tool for studying the chemical stability of polymers

Development and Application of a ReaxFF Reactive Force Field for Oxidative Dehydrogenation on Vanadium Oxide Catalysts

We have developed a new ReaxFF reactive force field to describe accurately reactions of hydrocarbons with vanadium oxide catalysts. The ReaxFF force field parameters have been fit to a large quantum mechanics (QM) training set containing over 700 structures and energetics related to bond dissociations, angle and dihedral distortions, and reactions between hydrocarbons and vanadium oxide clusters. In addition, the training set contains charge distributions for small vanadium oxide clusters and the stabilities of condensed-phase systems. We find that ReaxFF reproduces accurately the QM training set for structures and energetics of small clusters. Most important is that ReaxFF describes accurately the energetics for various oxidation states of the condensed phases, including V_2O_5, VO_2, and V_2O_3 in addition to metallic V(V^0). To demonstrate the capability of the ReaxFF force field for describing catalytic processes involving vanadium oxides, we performed molecular dynamics (MD) simulation for reactions of a gas of methanol exposed to the (001) surface of V_2O_5. We find that formaldehyde is the major product, in agreement with experiment. These studies find that water desorption from surface VIII sites is facilitated by interlayer bonding