166 research outputs found
A review of wildland fire spread modelling, 1990-present, 1: Physical and quasi-physical models
In recent years, advances in computational power and spatial data analysis
(GIS, remote sensing, etc) have led to an increase in attempts to model the
spread and behaviour of wildland fires across the landscape. This series of
review papers endeavours to critically and comprehensively review all types of
surface fire spread models developed since 1990. This paper reviews models of a
physical or quasi-physical nature. These models are based on the fundamental
chemistry and/or physics of combustion and fire spread. Other papers in the
series review models of an empirical or quasi-empirical nature, and
mathematical analogues and simulation models. Many models are extensions or
refinements of models developed before 1990. Where this is the case, these
models are also discussed but much less comprehensively.Comment: 31 pages + 8 pages references + 2 figures + 5 tables. Submitted to
International Journal of Wildland Fir
A wildland fire model with data assimilation
A wildfire model is formulated based on balance equations for energy and
fuel, where the fuel loss due to combustion corresponds to the fuel reaction
rate. The resulting coupled partial differential equations have coefficients
that can be approximated from prior measurements of wildfires. An ensemble
Kalman filter technique with regularization is then used to assimilate
temperatures measured at selected points into running wildfire simulations. The
assimilation technique is able to modify the simulations to track the
measurements correctly even if the simulations were started with an erroneous
ignition location that is quite far away from the correct one.Comment: 35 pages, 12 figures; minor revision January 2008. Original version
available from http://www-math.cudenver.edu/ccm/report
The kinetic fragility of liquids as manifestation of the elastic softening
We show that the fragility , the steepness of the viscosity and relaxation
time close to the vitrification, increases with the degree of elastic
softening, i.e. the decrease of the elastic modulus with increasing
temperature, in universal way. This provides a novel connection between the
thermodynamics, via the modulus, and the kinetics. The finding is evidenced by
numerical simulations and comparison with the experimental data of glassformers
with widely different fragilities (), leading to a
fragility-independent elastic master curve extending over eighteen decades in
viscosity and relaxation time. The master curve is accounted for by a cavity
model pointing out the roles of both the available free volume and the cage
softness. A major implication of our findings is that ultraslow relaxations,
hardly characterised experimentally, become predictable by linear elasticity.
As an example, the viscosity of supercooled silica is derived over about
fifteen decades with no adjustable parameters.Comment: 7 pages, 6 figures; Added new results, improved the theoretical
sectio
β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides
Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109–122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109–122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109–122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106–126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new atomic-level model for the formation of oligomers and fibrils of the prion protein and suggest that stabilization of β-hairpin structure may enhance cellular toxicity by altering the balance between oligomeric and fibrillar protein assemblies
Factors That Drive Peptide Assembly and Fibril Formation: Experimental and Theoretical Analysis of Sup35 NNQQNY Mutants
Residue mutations have substantial effects on aggregation kinetics and propensities of amyloid peptides and their aggregate morphologies. Such effects are attributed to conformational transitions accessed by various types of oligomers such as steric zipper or single β-sheet. We have studied the aggregation propensities of six NNQQNY mutants: NVVVVY, NNVVNV, NNVVNY, VIQVVY, NVVQIY, and NVQVVY in water using a combination of ion-mobility mass spectrometry, transmission electron microscopy, atomic force microscopy, and all-atom molecular dynamics simulations. Our data show a strong correlation between the tendency to form early β-sheet oligomers and the subsequent aggregation propensity. Our molecular dynamics simulations indicate that the stability of a steric zipper structure can enhance the propensity for fibril formation. Such stability can be attained by either hydrophobic interactions in the mutant peptide or polar side-chain interdigitations in the wild-type peptide. The overall results display only modest agreement with the aggregation propensity prediction methods such as PASTA, Zyggregator, and RosettaProfile, suggesting the need for better parametrization and model peptides for these algorithms
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