53,828 research outputs found
Power spectra methods for a stochastic description of diffusion on deterministically growing domains
A central challenge in developmental biology is understanding the creation of robust spatiotemporal heterogeneity. Generally, the mathematical treatments of biological systems have used continuum, mean-field hypotheses for their constituent parts, which ignores any sources of intrinsic stochastic effects. In this paper we consider a stochastic space-jump process as a description of diffusion, i.e., particles are able to undergo a random walk on a discretized domain. By developing analytical Fourier methods we are able to probe this probabilistic framework, which gives us insight into the patterning potential of diffusive systems. Further, an alternative description of domain growth is introduced, with which we are able to rigorously link the mean-field and stochastic descriptions. Finally, through combining these ideas, it is shown that such stochastic descriptions of diffusion on a deterministically growing domain are able to support the nucleation of states that are far removed from the deterministic mean-field steady state
Physics-related epistemic uncertainties in proton depth dose simulation
A set of physics models and parameters pertaining to the simulation of proton
energy deposition in matter are evaluated in the energy range up to
approximately 65 MeV, based on their implementations in the Geant4 toolkit. The
analysis assesses several features of the models and the impact of their
associated epistemic uncertainties, i.e. uncertainties due to lack of
knowledge, on the simulation results. Possible systematic effects deriving from
uncertainties of this kind are highlighted; their relevance in relation to the
application environment and different experimental requirements are discussed,
with emphasis on the simulation of radiotherapy set-ups. By documenting
quantitatively the features of a wide set of simulation models and the related
intrinsic uncertainties affecting the simulation results, this analysis
provides guidance regarding the use of the concerned simulation tools in
experimental applications; it also provides indications for further
experimental measurements addressing the sources of such uncertainties.Comment: To be published in IEEE Trans. Nucl. Sc
BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments
Advances in sequencing techniques have led to exponential growth in
biological data, demanding the development of large-scale bioinformatics
experiments. Because these experiments are computation- and data-intensive,
they require high-performance computing (HPC) techniques and can benefit from
specialized technologies such as Scientific Workflow Management Systems (SWfMS)
and databases. In this work, we present BioWorkbench, a framework for managing
and analyzing bioinformatics experiments. This framework automatically collects
provenance data, including both performance data from workflow execution and
data from the scientific domain of the workflow application. Provenance data
can be analyzed through a web application that abstracts a set of queries to
the provenance database, simplifying access to provenance information. We
evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree
assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a
RASopathy analysis workflow. We analyze each workflow from both computational
and scientific domain perspectives, by using queries to a provenance and
annotation database. Some of these queries are available as a pre-built feature
of the BioWorkbench web application. Through the provenance data, we show that
the framework is scalable and achieves high-performance, reducing up to 98% of
the case studies execution time. We also show how the application of machine
learning techniques can enrich the analysis process
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