Pedro da Silva Peixoto

Pedro da Silva Peixoto
University of São Paulo | USP · Departamento de Matemática Aplicada (IME) (São Paulo)

PhD

About

53
Publications
10,693
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3,207
Citations
Citations since 2016
46 Research Items
3155 Citations
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Introduction
I am an Associate Professor at the Applied Mathematics Department of the Institute of Mathematics and Statistics (IME) of the University of São Paulo (USP), Brazil. My main interests are related to numerical analysis of fluid dynamics, geophysical flows, dynamical core development and also numerical methods for seismic imaging. Do not hesitate to contact me in case you wish to establish any research collaboration or would like to discuss any of my projects or papers.
Additional affiliations
March 2014 - present
University of Sao Paulo
Position
  • Professor (Associate)

Publications

Publications (53)
Article
The increasing number of cores in modern supercomputers motivated the search for methods with good scalability to model global problems in geophysical fluid dynamics, including the representation of the atmospheric dynamics in global weather forecasting and climate simulations. Grid-point schemes with quasi-uniform spherical grids, along with expli...
Preprint
Full-text available
Exponential time integrators have been applied successfully in several physics-related differential equations. However, their application in hyperbolic systems with absorbing boundaries, like the ones arising in seismic imaging, still lacks theoretical and experimental investigations. The present work conducts an in-depth study of exponential integ...
Article
Introdução O sequenciamento de genoma viral, projeções e visualizações por meio de modelos matemáticos, estatísticos e computacionais permitem acompanhar a disseminação de doenças infecciosas como a causada pela infecção pelo vírus SARS-CoV-2, a COVID-19. O monitoramento ativo e contínuo da evolução epidemiológica depende diretamente da vigilância...
Preprint
Full-text available
Zoonotic viruses that originate in wildlife harm global human health and economic prosperity. Understanding virus transmission at the human-animal-environment interface is a key component of pandemic risk-reduction. Zoonotic disease emergence is highest in biodiverse, tropical forests undergoing intensive land-use change. Phylodynamic analyses of v...
Article
Full-text available
Full-waveform inversion (FWI) is a high-resolution numerical technique for seismic waves used to estimate the physical characteristics of a subsurface region. The continuous problem involves solving an inverse problem on an infinite domain, which is impractical from a computational perspective. In limited area models, absorbing boundary conditions...
Article
Full-text available
The dynamics of the Earth's atmosphere is characterized by a wide spectrum of oscillations, ranging from hourly to interdecadal and beyond. The low frequency component of the atmospheric variability cannot be understood solely in terms of linear atmospheric waves that have shorter timescales. A newly proposed mechanism, the precession resonance mec...
Article
Full-text available
Peixoto et al. (2020) apresentaram uma metodologia que utiliza dados oriundos da mobilidade de pessoas para classificar municípios de um estado em três zonas de risco (baixo, médio e alto) em relação a uma doença contagiosa transmissível pelo ar. Os autores aplicaram o modelo para avaliar a exposição dos municípios dos estados de São Paulo e Rio de...
Preprint
Full-text available
In this paper, we give pointwise estimates of a Vorono\"i-based finite volume approximation of the Laplace-Beltrami operator on Vorono\"i-Delaunay decompositions of the sphere. These estimates are the basis for a local error analysis, in the maximum norm, of the approximate solution of the Poisson equation and its gradient. Here, we consider the Vo...
Preprint
Full-Waveform Inversion (FWI) is a high-resolution numerical technique for seismic waves used to estimate the physical characteristics of a subsurface region. The continuous problem involves solving an inverse problem on an infinite domain, which is impractical from a computational perspective. In limited area models, absorbing boundaries condition...
Preprint
The increasing number of cores in modern supercomputers motivated the search for methodswith better scalability to model the atmospheric dynamics in global weather forecasting andclimate simulations. This objective renewed the interest in grid-point schemes with quasi-uniform spherical grids, with each alternative providing some good properties and...
Preprint
The COVID-19 pandemic has shed light on how the spread of infectious diseases worldwide are importantly shaped by both human mobility networks and socio-economic factors. Few studies, however, have examined the interaction of mobility networks with socio-spatial inequalities to understand the spread of infection. We introduce a novel methodology, c...
Article
Robot Dance is a computational optimization platform developed in response to the COVID-19 outbreak, to support the decision-making on public policies at a regional level. The tool is suitable for understanding and suggesting levels of intervention needed to contain the spread of infectious diseases when the mobility of inhabitants through a region...
Article
Full-text available
Locally refined grids for global atmospheric models are attractive since they are expected to provide an alternative to solve local phenomena without the requirement of a global high-resolution uniform grid, whose computational cost may be prohibitive. Spherical centroidal Voronoi tessellation (SCVT), as used in the atmospheric Model for Prediction...
Preprint
Full-text available
The dynamics of the Earth's atmosphere is characterized by a wide spectrum of oscillations, ranging from hourly to interdecadal and beyond. The low frequency component of the atmospheric variability cannot be understood solely in terms of linear atmospheric waves that have shorter timescales. A newly proposed mechanism, the precession resonance mec...
Article
Full-text available
During the coronavirus disease 2019 (COVID-19) pandemic, governments used mobility data to assess the effectiveness of social distancing policies, but is it really possible to measure the effectiveness of epidemic control measures using mobility data? In this work, we found that the relationship between mobility data and epidemic metrics is far fro...
Preprint
Full-text available
Mathematical models can provide insights into the control of pandemic COVID-19, which remains a global priority. The dynamics of directly-transmitted infectious diseases, such as COVID-19, are usually described by compartmental models where individuals are classified as susceptible, infected and removed. These SIR models typically assume homogenous...
Article
Full-text available
Although international airports served as main entry points for SARS-CoV-2, the factors driving the uneven geographic spread of COVID-19 cases and deaths in Brazil remain mostly unknown. Here we show that three major factors influenced the early macro-geographical dynamics of COVID-19 in Brazil. Mathematical modeling revealed that the “super-spread...
Preprint
Full-text available
In response to the COVID-19 pandemic, most governments around the world implemented some kind of social distancing policy in an attempt to block the spreading of the virus within a territory. In Brazil, this mitigation strategy was first implemented in March 2020 and mainly monitored by social isolation indicators built from mobile geolocation data...
Preprint
Full-text available
Locally refined grids for global atmospheric models are attractive since they are expected to provide an alternative to solve local phenomena without the requirement of a global high-resolution uniform grid, whose computational cost may be prohibitive. The Spherical Centroidal Voronoi Tesselations (SCVT), as used in the atmospheric Model for Predic...
Article
Full-text available
Unmitigated spread in Brazil Despite an extensive network of primary care availability, Brazil has suffered profoundly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Using daily data from state health offices, Castro et al. analyzed the pattern of spread of COVID-19 cases and deaths in the country from February to...
Article
Full-text available
Introduction Little evidence exists on the differential health effects of COVID-19 on disadvantaged population groups. Here we characterise the differential risk of hospitalisation and death in São Paulo state, Brazil, and show how vulnerability to COVID-19 is shaped by socioeconomic inequalities. Methods We conducted a cross-sectional study using...
Preprint
Full-text available
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, includi...
Article
Full-text available
Attack rate in Manaus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) incidence peaked in Manaus, Brazil, in May 2020 with a devastating toll on the city's inhabitants, leaving its health services shattered and cemeteries overwhelmed. Buss et al. collected data from blood donors from Manaus and São Paulo, noted when transmission began...
Preprint
Full-text available
Background Little evidence exists on the differential health effects of COVID-19 on disadvantaged population groups. Here we characterise the differential risk of hospitalisation and death in São Paulo state, Brazil and show how vulnerability to COVID-19 is shaped by socioeconomic inequalities. Methods We conducted a cross-sectional study using ho...
Preprint
Robot Dance is a computational platform developed in response to the coronavirus outbreak, to support the decision making on public policies at a regional level. The tool is suitable for understanding and suggesting levels of intervention needed to contain the spread of diseases when the mobility of inhabitants through a regional network is a conce...
Preprint
Full-text available
Although its international airports served as the country's main entry points for SARS-CoV-2, the factors driving the uneven geographic spread of COVID-19 cases and deaths in Brazil remain largely unknown. Here we show that four major factors likely accounted for the entire dynamics of COVID-19 in Brazil. Mathematical modeling revealed that, initia...
Article
Full-text available
Decrease of seismic noise level, after reduction of traffic due to the COVID-19 pandemic, has been observed worldwide. The possibility of using seismic noise as another proxy to estimate social isolation was tested with a station within Rio de Janeiro city. We used the isolation index measured from smartphone movement to calibrate the seismic noise...
Article
Full-text available
The spread of SARS-CoV-2 in Brazil Brazil has been hard-hit by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Candido et al. combined genomic and epidemiological analyses to investigate the impact of nonpharmaceutical interventions (NPIs) in the country. By setting up a network of genomic laboratories using harmonized pr...
Article
Asingle software framework is introduced to evaluate numerical accuracy of theA-grid (NICAM) versus C-grid (MPAS) shallow-water model solvers on icosahedral grids. The C-grid staggering scheme excels in numerical noise control and total energy conservation, which results in exceptional long-time integration stability. Its weakness lies in the lack...
Article
Full-text available
Mobile geolocation data is a valuable asset in the assessment of movement patterns of a population. Once a highly contagious disease takes place in a location the movement patterns aid in predicting the potential spatial spreading of the disease, hence mobile data becomes a crucial tool to epidemic models. In this work, based on millions of anonymi...
Preprint
Full-text available
Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus transmission and epidemic spread remain challenging. We investigate the impact of NPIs in Brazil using epidemiological, mobility and genomic data. Mobility-dr...
Article
Full-text available
Snake venoms are complex mixtures of proteins with toxic activities, with many distinct iso-forms, affecting different physiological targets, comprised in a few protein families. It is currently accepted that this diversity in venom composition is an adaptive advantage for venom efficacy on a wide range of prey. However, on the other side, variabil...
Preprint
Full-text available
Mobile geolocation data is a valuable asset in the assessment of movement patterns of a population. Once a highly contagious disease takes place in a location the movement patterns aid in predicting the potential spatial spreading of the disease, hence mobile data becomes a crucial tool to epidemic models. In this work, based on millions of anonymi...
Preprint
In this paper we propose a novel way to integrate time-evolving partial differential equations that contain nonlinear advection and stiff linear operators, combining exponential integration techniques and semi-Lagrangian methods. The general formulation is built from the solution of an integration factor problem with respect to the problem written...
Presentation
Full-text available
The current trend in high-performance computing of a stagnating or even decreasing processor speed poses new challenges to solve PDEs within a particular time frame. Here, disruptive mathematical reformulations which exploit additional degrees of parallelism also in the time dimension gained increasing interest over the last two decades. One of su...
Article
Full-text available
This work focuses on the Parareal parallel-in-time method and its application to the viscous Burgers equation. A crucial component of Parareal is the coarse time stepping scheme, which strongly impacts the convergence of the parallel-in-time method. Three choices of coarse time stepping schemes are investigated in this work: explicit Runge–Kutta, i...
Article
Shallow water models are often adopted as an intermediate step in the development of atmosphere and ocean models, though they are usually tested only with fluid depths relevant to barotropic fluids. Here we investigate numerical instabilities emerging in shallow water models considering small fluid depths, which are relevant for baroclinic fluids....
Article
This paper presents, discusses and analyses a massively parallel-in-time solver for linear oscillatory partial differential equations, which is a key numerical component for evolving weather, ocean, climate and seismic models. The time parallelization in this solver allows us to significantly exceed the computing resources used by parallelization-i...
Article
The linear stability of two well known energy and enstrophy conserving schemes for the vector invariant hydrostatic primitive equations is examined. The problem is analysed for a stably stratified Boussinesq fluid on an f-plane, with a constant velocity field, in height and isopycnal coordinates, by separation of variables into vertical normal mode...
Article
Many newly developed climate, weather and ocean global models are based on quasi uniform spherical polygonal grids, aiming for high resolution and better scalability. Thuburn et al. (2009) and Ringler et al. (2010) developed a C staggered finite volume/difference method for arbitrary polygonal spherical grids suitable for these next generation dyna...
Article
We analyse several vector reconstruction methods, based on the knowledge of only specific pointwise vector components, and extend their use to non-structured polygonal C-grids on the sphere. The emphasis is on the reconstruction of the vector field at arbitrary locations on the sphere, as required by semi-Lagrangian transport schemes. This is done...
Article
To compare integration of bladder acellular matrix (BAM) with the bladder when seeded with mesenchymal stem cells (MSC) and when MSC are injected intravenously (IV). MSCs were isolated from bone marrow of EPM-1 Wistar male rats. Female rats were distributed into: Group A-BAM augmentation; Group B-BAM augmentation and MSCs IV administered; Group C-B...
Article
Full-text available
In Latin America, Bothrops snakes account for most snake bites in humans, and the recommended treatment is administration of multispecific Bothrops antivenom (SAB - soro antibotrópico). However, Bothrops snakes are very diverse with regard to their venom composition, which raises the issue of which venoms should be used as immunizing antigens for t...
Article
Numerical grid imprinting errors have often been observed in global atmospheric models on icosahedral grids. In this paper we analyse the sources of grid imprinting error related to the usual finite volume discretization of the divergence operator. We introduce the concept of alignment of computational cells, and establish that convergence of secon...
Article
This article is dedicated to harmonic wavelet Galerkin methods for the solution of partial differential equations. Several variants of the method are proposed and analyzed, using the Burgers equation as a test model. The computational complexity can be reduced when the localization properties of the wavelets and restricted interactions between diff...
Article
Full-text available
The methods currently used to determine the immunoglobulin avidity index (AI) require the choice of a reference point in the ELISA titration curve. Since both curves, with and without denaturating reagents, seldom run in parallel, the AI value becomes highly dependent on this reference. The new method for AI calculation presented here takes into ac...

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