Debates—Stochastic subsurface hydrology from theory to practice: why stochastic modeling has not yet permeated into practitioners?

This is the peer reviewed version of the following article: [Sanchez-Vila, X., and D. Fernàndez-Garcia (2016), Debates—Stochastic subsurface hydrology from theory to practice: Why stochastic modeling has not yet permeated into practitioners?, Water Resour. Res., 52, 9246–9258, doi:10.1002/2016WR019302], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/2016WR019302/abstract. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-ArchivingWe address modern topics of stochastic hydrogeology from their potential relevance to real modeling efforts at the field scale. While the topics of stochastic hydrogeology and numerical modeling have become routine in hydrogeological studies, nondeterministic models have not yet permeated into practitioners. We point out a number of limitations of stochastic modeling when applied to real applications and comment on the reasons why stochastic models fail to become an attractive alternative for practitioners. We specifically separate issues corresponding to flow, conservative transport, and reactive transport. The different topics addressed are emphasis on process modeling, need for upscaling parameters and governing equations, relevance of properly accounting for detailed geological architecture in hydrogeological modeling, and specific challenges of reactive transport. We end up by concluding that the main responsible for nondeterministic models having not yet permeated in industry can be fully attributed to researchers in stochastic hydrogeology.Peer ReviewedPostprint (author's final draft

Modeling and analysis of single-molecule experiments

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005.Vita.Includes bibliographical references (p. 281-311).Single molecule experiments offer a unique window into the molecular world. This window allows us to distinguish the behaviors of individual molecules from the behavior of bulk by observing rare events and heterogeneity in the dynamics. This thesis discusses both models for single molecule experiments, including the stretching of DNA in hydrodynamic flows and the diffusion of tracer particles in heterogeneous environments, and methods to analyze single molecule data to allow determination of properties and models for single molecule experiments. These methods of analysis are based on combining information theory and Bayesian methods with physical insight and are applied to several experimental situations.by James B. Witkoskie.Ph.D

Field theoretic formulation and empirical tracking of spatial processes

Spatial processes are attacked on two fronts. On the one hand, tools from theoretical and statistical physics can be used to understand behaviour in complex, spatially-extended multi-body systems. On the other hand, computer vision and statistical analysis can be used to study 4D microscopy data to observe and understand real spatial processes in vivo. On the rst of these fronts, analytical models are developed for abstract processes, which can be simulated on graphs and lattices before considering real-world applications in elds such as biology, epidemiology or ecology. In the eld theoretic formulation of spatial processes, techniques originating in quantum eld theory such as canonical quantisation and the renormalization group are applied to reaction-di usion processes by analogy. These techniques are combined in the study of critical phenomena or critical dynamics. At this level, one is often interested in the scaling behaviour; how the correlation functions scale for di erent dimensions in geometric space. This can lead to a better understanding of how macroscopic patterns relate to microscopic interactions. In this vein, the trace of a branching random walk on various graphs is studied. In the thesis, a distinctly abstract approach is emphasised in order to support an algorithmic approach to parts of the formalism. A model of self-organised criticality, the Abelian sandpile model, is also considered. By exploiting a bijection between recurrent con gurations and spanning trees, an e cient Monte Carlo algorithm is developed to simulate sandpile processes on large lattices. On the second front, two case studies are considered; migratory patterns of leukaemia cells and mitotic events in Arabidopsis roots. In the rst case, tools from statistical physics are used to study the spatial dynamics of di erent leukaemia cell lineages before and after a treatment. One key result is that we can discriminate between migratory patterns in response to treatment, classifying cell motility in terms of sup/super/di usive regimes. For the second case study, a novel algorithm is developed to processes a 4D light-sheet microscopy dataset. The combination of transient uorescent markers and a poorly localised specimen in the eld of view leads to a challenging tracking problem. A fuzzy registration-tracking algorithm is developed to track mitotic events so as to understand their spatiotemporal dynamics under normal conditions and after tissue damage.Open Acces

The structure and reactivity of heterogenous surfaces and study of the geometry of surface complexes

Issued as Progress report, and Statement of costs report, Project no. G-41-674 (continued by G-41-687 and continues G-41-664

Mathematical Studies of Photochemical Air Pollution

In Part I a new, comprehensive model for a chemically reacting plume, is presented, that accounts for the effects of incomplete turbulent macro- and micro- mixing on chemical reactions between plume and ambient constituents. This "Turbulent Reacting Plume Model" (TRPM) is modular in nature, allowing for the use of different levels of approximation of the phenomena involved. The core of the model consists of the evolution equations for reaction progress variables appropriate for evolving, spatially varying systems ("local phenomenal extent of reaction"). These equations estimate the interaction of mixing and chemical reaction and require input parameters characterizing internal plume behavior, such as relative dispersion and fine scale plume segregation. The model addresses deficiencies in previous reactive plume models. Calculations performed with the TRPM are compared with the experimental data of P.J.H. Builtjes for the reaction between NO in a point source plume and ambient O3, taking place in a wind tunnel simulating a neutral atmospheric boundary layer. The comparison shows the TRPM capable of quantitatively predicting the retardation imposed on the evolution of nonlinear plume chemistry by incomplete mixing. Part IA (Chapters 1 to 3) contains a detailed description of the TRPM structure and comparisons of calculations with measurements, as well as a literature survey of reactive plume models. Part IB (Chapters 4 to 7) contains studies on the turbulent dispersion and reaction phenomena and plume dynamics, thus exposing in detail the underlying concepts and methods relevant to turbulent reactive plume modeling. New formulations for describing in-plume phenomena, such as the "Localized Production of Fluctuations Model" for the calculation of the plume concentration variance are included here. Part II (Chapter 8) presents a collection of distribution-based statistical methods that are appropriate for characterizing extreme events in air pollution studies. Applications to the evaluation of air quality standards, formulation of rollback calculations, and to the use of plume models are included here.</p

DYNAMICAL SENSITIVITY ANALYSES OF KINETIC MODELS IN BIOLOGY

Ph.DDOCTOR OF PHILOSOPH

A multiscale study of atomic interactions in the electrochemical double layer applied to electrocatalysis

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 171-182).This work is an integrated study of chemical and electrostatic interactions in the electrochemical double layer, and their significance for accurate prediction of reaction kinetics in electrocatalysis. First, a kinetic model of the oxygen reduction reaction (ORR) on platinum, in connexion with first-principles techniques, is developed to illustrate that a self-consistent description of kinetics and reactant coverages on the surface can help to propose new mechanisms when energy prediction and experimental uncertainties still prevail. ORR kinetic limitation is often rationalized in terms of surface poisoning by parallel reactions, namely water oxidation, and/or as a result of the demanding requirements of Sabatier's principle. The sensitivity analysis presented here suggests that additional mechanisms may have to be considered, in particular self-poisoning by transient 02 dissociation in certain regimes. A common assumption of kinetic studies is that the only effect of electrode bias is to modify the electron chemical potential. To refine our understanding of bias effects in the double layer, a correction code applied to plane-wave DFT techniques is used to realistically simulate an electrochemical setup under potential control as an electrode with variable explicit charge screened by ions in solution. The scheme is first used to shed light on the nature of the stretching frequency shift of CO on Pt(1 11) as a function of electrode potential. It is concluded that the Stark effect interpretation is correct, and more generally, that electrochemistry on metal surfaces may often be correctly described in terms of perturbation theory. Then, hydrogen under-potential deposition on platinum is computed as a function of pH. It is shown that modification of the surface dipole by hydrogen electrosorption couples with the surface charge to make the adsorbant chemical potential pH-dependent. This observation is related to the concept of electrosorption valency. The octahedric-to-cubic nanoparticle shape transition resulting from hydrogen adsorption upon cathodic sweep is then predicted to be more pronounced in alkaline media. Inclusion of surface dipole effects is therefore relevant for surface stability and shape-dependent electroactivity. Third, the correction scheme is applied to develop a model of water dielectric saturation in the strong fields of the double layer. The water molecule dipole is computed in real space and Monte-Carlo simulation techniques are performed for the statistics of proton arrangement. DFT is seen to overestimate the permittivity of ice, confirming the difficulty of water simulation at the first-principles level. However, saturation effects are believed to be qualitatively captured and their influence on reaction kinetics in the double layer from the Frumkin effect is assessed. The impact is rather moderate with at most a factor of 3 in exchange current predictions. Finally, DFT occasional errors in chemisorption energies remain an important drawback for heterogeneous catalysis studies. Here, the vdW-DF functional for inclusion of long-range, dispersion interactions is tested on the prediction of CO adsorption on transition metals. Observed improvement on binding energies and adsorption site ordering comes at the expense of the correct description of metal energetics, suggesting the need for alternative schemes in this case. In conclusion, the purpose of this work is to help the design of electrocatalysts by providing a framework to assess chemical and electrostatic contributions to the kinetics, informed by the complexity and uncertainties attached to the surface and double layer structure.by Nicéphore Bonnet.Ph.D