243 research outputs found
Heterogeneity in susceptibility dictates the order of epidemiological models
The fundamental models of epidemiology describe the progression of an
infectious disease through a population using compartmentalized differential
equations, but do not incorporate population-level heterogeneity in infection
susceptibility. We show that variation strongly influences the rate of
infection, while the infection process simultaneously sculpts the
susceptibility distribution. These joint dynamics influence the force of
infection and are, in turn, influenced by the shape of the initial variability.
Intriguingly, we find that certain susceptibility distributions (the
exponential and the gamma) are unchanged through the course of the outbreak,
and lead naturally to power-law behavior in the force of infection; other
distributions often tend towards these "eigen-distributions" through the
process of contagion. The power-law behavior fundamentally alters predictions
of the long-term infection rate, and suggests that first-order epidemic models
that are parameterized in the exponential-like phase may systematically and
significantly over-estimate the final severity of the outbreak
The role of vascular endothelial growth factor (VEGF) in repair and recovery from acute respiratory distress syndrome (ARDS)
Acute Respiratory Distress Syndrome (ARDS) is the most extreme form of acute
lung injury and continues to have a significant morbidity and mortality.
Unfortunately, the mechanisms involved in the recovery and repair of the lung
following ARDS remain poorly understood. An understanding of these is pivotal to
improving outcome from acute lung injury. Several observational studies have
suggested a potential relationship between Vascular Endothelial Growth Factor
(VEGF) in the lung and the development/outcome of ARDS. In this thesis, three potential mechanisms underlying these observations have been explored:
1. What is the anatomical distribution of VEGF receptor and isoform expression in
normal and ARDS lung? How does this change at early and later time points
following acute lung injury?
2. Are human type 2 alveolar epithelial (ATII) cells a source of and target for
VEGF? How does exposure to a pro-inflammatory milieu modify their
expression of VEGF isoforms and receptors?
3. Is there a relationship between a functional VEGF polymorphism and
susceptibility to developing and severity of ARDS?
I have demonstrated VEGF receptor expression on both sides of the alveolarcapillary
membrane with upregulation in later ARDS. All three principal isoforms
(VEGF121, VEGF165 and VEGF189) are expressed in normal human lung with uniform
downregulation of all three in early ARDS, which normalises with increasing time
following injury. I have not found any evidence of VEGF isoform switching.
I have also demonstrated human ATII cells are both a significant cellular source of
and a target for VEGF (via VEGF receptor expression) confirming autocrine VEGF
activity in the lung. VEGF is an ATII cell survival factor. ATII cells differentially
respond to pro-inflammatory stimuli by increasing VEGF isoform but not receptor
expression, which may serve as a regulatory control mechanism.
Finally, I have demonstrated the VEGF 936 T allele increases susceptibility to and
the severity of lung injury. The T allele is associated with an increase in plasma
VEGF level in ARDS patients but intra-alveolar levels are unaffected
The phase stability of large-size nanoparticle alloy catalysts at ab initio quality using a nearsighted force-training approach
CoPt nanoparticle catalysts are integral to commercial fuel cells. Such
systems are prohibitive to fully characterize with electronic structure
calculations. Machine-learned potentials offer a scalable solution; however,
such potentials are only reliable if representative training data can be
employed, which typically requires large electronic structure calculations.
Here, we use the nearsighted-force training approach to make high-fidelity
machine-learned predictions on large nanoparticles with 5,000 atoms using
only systematically generated small structures ranging from 38-168 atoms. The
resulting ensemble model shows good accuracy and transferability in describing
relative energetics for CoPt nanoparticles with various shapes, sizes and Co
compositions. It is found that the fcc(100) surface is more likely to form a
L1 ordered structure than the fcc(111) surface. The energy convex hull of
the icosahedron shows the most stable particles have Pt-rich skins and Co-rich
underlayers. Although the truncated octahedron is the most stable shape across
all sizes of Pt nanoparticles, a crossover to icosahedron exists due to a large
downshift of surface energy for CoPt nanoparticle alloys. The downshift can be
attributed to strain release on the icosahedron surface due to Co alloying. We
introduced a simple empirical model to describe the role of Co alloying in the
crossover for CoPt nanoparticles. With Monte-Carlo simulations we additionally
searched for the most stable atomic arrangement for a truncated octahedron with
equal Pt and Co compositions, and also we studied its order-disorder phase
transition. We validated the most stable configurations with a new highly
scalable density functional theory code called SPARC. Lastly, the
order-disorder phase transition for a CoPt nanoparticle exhibits a lower
transition temperature and a smoother transition, compared to the bulk CoPt
alloy.Comment: 26 pages, 8 figure
Ab-initio investigation of finite size effects in rutile titania nanoparticles with semilocal and nonlocal density functionals
In this work, we employ hybrid and generalized gradient approximation (GGA)
level density functional theory (DFT) calculations to investigate the
convergence of surface properties and band structure of rutile titania
(TiO) nanoparticles with particle size. The surface energies and band
structures are calculated for cuboidal particles with minimum dimension ranging
from 3.7 \r{A} (24 atoms) to 10.3 \r{A} (384 atoms) using a highly-parallel
real-space DFT code to enable hybrid level DFT calculations of larger
nanoparticles than are typically practical. We deconvolute the geometric and
electronic finite size effects in surface energy, and evaluate the influence of
defects on band structure and density of states (DOS). The electronic finite
size effects in surface energy vanish when the minimum length scale of the
nanoparticles becomes greater than 10 \r{A}. We show that this length scale is
consistent with a computationally efficient numerical analysis of the
characteristic length scale of electronic interactions. The surface energy of
nanoparticles having minimum dimension beyond this characteristic length can be
approximated using slab calculations that account for the geometric defects. In
contrast, the finite size effects on the band structure is highly dependent on
the shape and size of these particles. The DOS for cuboidal particles and more
realistic particles constructed using the Wulff algorithm reveal that defect
states within the bandgap play a key role in determining the band structure of
nanoparticles and the bandgap does not converge to the bulk limit for the
particle sizes investigated
ElectroLens: Understanding Atomistic Simulations Through Spatially-resolved Visualization of High-dimensional Features
In recent years, machine learning (ML) has gained significant popularity in
the field of chemical informatics and electronic structure theory. These
techniques often require researchers to engineer abstract "features" that
encode chemical concepts into a mathematical form compatible with the input to
machine-learning models. However, there is no existing tool to connect these
abstract features back to the actual chemical system, making it difficult to
diagnose failures and to build intuition about the meaning of the features. We
present ElectroLens, a new visualization tool for high-dimensional
spatially-resolved features to tackle this problem. The tool visualizes
high-dimensional data sets for atomistic and electron environment features by a
series of linked 3D views and 2D plots. The tool is able to connect different
derived features and their corresponding regions in 3D via interactive
selection. It is built to be scalable, and integrate with existing
infrastructure.Comment: accepted to IEEE visualization 2019 conferenc
Soft and transferable pseudopotentials from multi-objective optimization
Ab initio pseudopotentials are a linchpin of modern molecular and condensed
matter electronic structure calculations. In this work, we employ
multi-objective optimization to maximize pseudopotential softness while
maintaining high accuracy and transferability. To accomplish this, we develop a
formulation in which softness and accuracy are simultaneously maximized, with
accuracy determined by the ability to reproduce all-electron energy differences
between Bravais lattice structures, whereupon the resulting Pareto frontier is
scanned for the softest pseudopotential that provides the desired accuracy in
established transferability tests. We employ an evolutionary algorithm to solve
the multi-objective optimization problem and apply it to generate a
comprehensive table of optimized norm-conserving Vanderbilt (ONCV)
pseudopotentials (https://github.com/SPARC-X/SPMS-psps). We show that the
resulting table is softer than existing tables of comparable accuracy, while
more accurate than tables of comparable softness. The potentials thus afford
the possibility to speed up calculations in a broad range of applications areas
while maintaining high accuracy.Comment: 13 pages, 4 figure
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