3,995 research outputs found
ELM regime classification by conformal prediction on an information manifold
Characterization and control of plasma instabilities known as edge-localized modes (ELMs) is crucial for the operation of fusion reactors. Recently, machine learning methods have demonstrated good potential in making useful inferences from stochastic fusion data sets. However, traditional classification methods do not offer an inherent estimate of the goodness of their prediction. In this paper, a distance-based conformal predictor classifier integrated with a geometric-probabilistic framework is presented. The first benefit of the approach lies in its comprehensive treatment of highly stochastic fusion data sets, by modeling the measurements with probability distributions in a metric space. This enables calculation of a natural distance measure between probability distributions: the Rao geodesic distance. Second, the predictions are accompanied by estimates of their accuracy and reliability. The method is applied to the classification of regimes characterized by different types of ELMs based on the measurements of global parameters and their error bars. This yields promising success rates and outperforms state-of-the-art automatic techniques for recognizing ELM signatures. The estimates of goodness of the predictions increase the confidence of classification by ELM experts, while allowing more reliable decisions regarding plasma control and at the same time increasing the robustness of the control system
A Lagrangian model of copepod dynamics: Clustering by escape jumps in turbulence
Planktonic copepods are small crustaceans that have the ability to swim by
quick powerful jumps. Such an aptness is used to escape from high shear
regions, which may be caused either by flow per- turbations, produced by a
large predator (i.e., fish larvae), or by the inherent highly turbulent
dynamics of the ocean. Through a combined experimental and numerical study, we
investigate the impact of jumping behaviour on the small-scale patchiness of
copepods in a turbulent environment. Recorded velocity tracks of copepods
displaying escape response jumps in still water are here used to define and
tune a Lagrangian Copepod (LC) model. The model is further employed to simulate
the behaviour of thousands of copepods in a fully developed hydrodynamic
turbulent flow obtained by direct numerical simulation of the Navier-Stokes
equations. First, we show that the LC velocity statistics is in qualitative
agreement with available experimental observations of copepods in tur- bulence.
Second, we quantify the clustering of LC, via the fractal dimension . We
show that can be as low as ~ 2.3 and that it critically depends on the
shear-rate sensitivity of the proposed LC model, in particular it exhibits a
minimum in a narrow range of shear-rate values. We further investigate the
effect of jump intensity, jump orientation and geometrical aspect ratio of the
copepods on the small-scale spatial distribution. At last, possible ecological
implications of the observed clustering on encounter rates and mating success
are discussedComment: 13 pages, 9 figure
Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins
abstract: In a typical living cell, millions to billions of proteins—nanomachines that fluctuate and cycle among many conformational states—convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible.
Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.Dissertation/ThesisDoctoral Dissertation Physics 201
Extension of information geometry for modelling non-statistical systems
In this dissertation, an abstract formalism extending information geometry is
introduced. This framework encompasses a broad range of modelling problems,
including possible applications in machine learning and in the information
theoretical foundations of quantum theory. Its purely geometrical foundations
make no use of probability theory and very little assumptions about the data or
the models are made. Starting only from a divergence function, a Riemannian
geometrical structure consisting of a metric tensor and an affine connection is
constructed and its properties are investigated. Also the relation to
information geometry and in particular the geometry of exponential families of
probability distributions is elucidated. It turns out this geometrical
framework offers a straightforward way to determine whether or not a
parametrised family of distributions can be written in exponential form. Apart
from the main theoretical chapter, the dissertation also contains a chapter of
examples illustrating the application of the formalism and its geometric
properties, a brief introduction to differential geometry and a historical
overview of the development of information geometry.Comment: PhD thesis, University of Antwerp, Advisors: Prof. dr. Jan Naudts and
Prof. dr. Jacques Tempere, December 2014, 108 page
- …