EPIC 2

08h00-08h50: Tutorial 1 (Python Basics)

Tutor: Lupe Villegas, Instituto de Óptica (IO-CSIC), España

• • Read and write data tables

  • Work with data tables:

    • • Basic statistics

    • Plots with matplotlib

    • Regressions and curve fitting

  • Examples

  • Basic image I/O

08h55-09h45: Artificial Intelligence Talk

"Artificial Intelligence in physics and computing"

Speaker: Albert Sietze This, Univeristy of Groningen, The Netherlands

The field of Artifical Intelligence is expanding and becoming an important part of all scientific disciplines in physical science. Especially Machine Learning is playing a big role in improving simulations in physics, chemistry and biology, In this talk we give a short introduction to the theory behind machine learning and showcase practice examples. We aim to give a basic understanding of what possibilities our out there and help in choosing the right machine learning application. We conclude with a list of useful tools for students to continue learning.

09h45-10h35: Materials Science Talk

"Modelling enantiomeric catalysts: enantioselective hydrogenation of methyl acetoacetate over Ni surfaces"

Tutor: Jorge Ontaneda, Queen Mary University of London, UK

Most of the current knowledge in enantioselective heterogeneous catalysis refers to the hydrogenation of β-ketoester over Ni-based catalysts and the hydrogenation of α-ketoester on Pd-based systems. These reactions require a crucial step in the catalyst preparation: the adsorption of chiral modifiers onto the metal nanoparticles of the catalyst. In the case of the simplest β-ketoester, methyl acetoacetate (MAA), the hydrogenation results in a racemic mixture R- and S-methyl-3-hydroxybutyrate (MHB) when performed over an unmodified Raney Ni catalyst. The reaction, however, can be directed to a high enantiomeric excess if the Ni surface is modified with chiral α-amino acids or α-hydroxy acids. Even though the process is well-characterized in terms of macroscopic quantities, information at molecular scale regarding the influence of chiral modifiers have on adsorption complex of MAA is missing. The understanding of this mechanism would help to achieve and optimize enantioselective behavior of Ni-based catalysts. By combining X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) with Density Functional Theory (DFT) modelling, we have been studying the adsorption complex of reactant MAA and typical chiral modifiers (e.g., alanine, aspartic acid, and tartaric acid) over Ni{111} and Ni{100} surfaces. We have found MAA adsorbs on flat surfaces forming deprotonated enolate species with bidentate coordination, and the molecular plane of the adsorbate leans towards one side. These findings suggest that the role of modifiers in the enantioselective hydrogenation of MAA is to stabilize only one of two possible tilt directions, which would lead to the chiral product formation.

10:40-11:30: Medical Physics Talk

Speaker: Mayra Pallaroso, SOLCA Quito, Ecuador

En dosimetría clínica para radioterapia se abordará brevemente la forma de calcular y cuantificar las dosis que reciben los pacientes oncológicos como parte de su tratamiento, ya sea utilizando haces externos de electrones o fotones o radioisótopos como iridio 192. Para esto se utiliza herramientas informáticas de alto nivel, que tienen algoritmos de cálculo que han sido validados mediante medidas y simulaciones Monte Carlo, y que permiten evaluar con gran precisión y exactitud la distribución de dosis a entregarse en el volumen tumoral y en los órganos de riesgo circundantes. Se presentará las distribuciones de dosis calculadas para las diferentes técnicas de tratamiento como: tridimensional (3D), radioterapia de intensidad modulada (IMRT) y radioterapia modulada al volumen (VMAT) para tratamientos de pelvis, mama y cuello.

11h40-12h30: Materials Science Talk

"A rare event search in neutrino physics"

Tutor: Cloé Girard-Carillo, Johannes Gutenberg University, Mainz, Germany

The neutrino particle remains one of the most mysterious elementary particle. The scientific community is involved in many experiments and model development that could allow to better understand some of its fundamental properties.

11h40-12h30: Cosmology Talk

"Fundamental physics from cosmology"

Speaker: Sylvain Vanneste, Laboratoire de l'Accélérateur Linéaire, France

Cosmology physics is a powerful way to probe various areas of fundamental physics.

Test general relativity, measure the fundamental properties of particles, discover new forms of matter and energy....

By observing the Universe, we can better understand what it is made of.

However, this requires huge experimental setup and ingenious analysis tools.

14h20-16h00: Tutorial ( Coding basics 2)

Tutor: Wladimir Banda-Barragán, Yachay Tech University, Ecuador

• • Python classes

  • Fourier analysis

08h00-08h50: Materials Science Talk

Speaker: Maximilian Menger, University of Groningen, The Netherlands

• • TBD

08h55-10h35/11h40-13h20: Materials Science tutorials 1 and 2

Tutor: Edison Salazar, University of Groningen, The Netherlands

Photoinduced processes play a crucial role in different fields of science, for example, the photoisomerization of the retinal chromophore or the synthesis of vitamin D3. Additionally, they are crucial in the development of new technologies such as molecular electronic devices which can be controlled by light. These processes are governed mainly by nonadiabatic transitions which are radiationless electronic transitions between different non-Born-Oppenheimer states along the dynamic of a chemical reaction. In these two lessons, we are going to implement the Tully algorithm in Python to study a simple avoid crossing model as the first approach to a non-adiabatic transition.

08h55-10h35/11h40-13h20: Particle Physics tutorials 1 and 2

Tutor: Luis Manzanillas, SOLEIL Synchrotron, France

• Brief introduction to Julia

• Basics of detectors for particle physics

• Basics of HPGe detectors

• Reading h5 files containing raw data from a HPGe detector

  • Plotting and understanding the data

  • Finding events in raw data

  • Filters and calibration

  • Energy reconstruction and selection of events

  • Histograms and interpretation of results

10h40-11h30: Particle Physics Talk

Speaker: Cristina Mantilla, Fermilab, USA

• • TBD

08h00-08h50: Biophysics Talk

"Temperature robustness of vertebrate morphogen gradients"

Speaker: Daniel Čapek, University of Konstanz, Germany

During early development the vertebrate body plan is set up by gradients of signaling molecules, termed morphogens, that lead to different transcriptional responses in target tissues. In the wild, embryos of poikilotherm species - i.e. animals whose body temperature changes with the environment - encounter a wide range of temperature regimes, such as the cold of the arctic or the heat of tropical eco systems. Also, day and night temperatures can vary considerably. Since the temperature is typically kept constant in laboratory environments, little is known about how morphogen gradients are affected by these shifts in temperature and how embryos cope with this stress. The Einstein-Stokes equation states that free diffusion scales linearly with the temperature in degrees Kelvin and therefore changes very little at physiological temperatures. Enzymatic reactions, on the contrary, increase their speed by a factor of 2-3 for every 10°C within biologically relevant ranges, described by the van’t Hoff relation. We are analyzing the effect of temperature fluctuations on Nodal-mediated germ layer patterning in eurytherm medaka (Oryzias latipes) embryos. Medaka embryos have a wide temperature tolerance and can even resume development after temperature-induced arrest. We apply live imaging of signaling molecules and measurements of their biophysical properties to mathematically model and experimentally test the effect of temperature fluctuations on morphogen gradient formation and interpretation. This will help us to understand mechanisms of robustness buffering ecological factors during embryogenesis and evolution.

08h55-10h35/11h40-13h20: Tutorials 1 and 2 (Biophysics)

"Intro to Bio-Image Analysis" and "Intro to Reaction-Diffusion simulations"

Tutor: Andrés Morales Navarrete, Friedrich Miescher Laboratory of the Max Planck Society, Germany

• • Explanation about bioimages (i.e. fluorescence microscopy)

  • Bioimage analysis example: quantifying cell morphology from 2D fluorescence micrographs

  • Importing images and plotting images

  • Logical operators (pixel-wise operations)

  • Intensity Transformation

  • Filters and Fourier transformations

  • Segmentation

  • Extracting data from segmented images (e.g. cell area, elongation)

09h45-10h35: Tutorial ( Astrophysics 1)

"Analysing 3D astronomical data cubes"

Tutor: Helga Dénes, ASTRON, The Netherlands

• • Brief explanation on astrophysics behind galaxies and their neutral hydrogen (HI content).

  • Reading in fits data cubes (3D spectral line data - HI data of a galaxy)

  • Plotting slices of the 3D data cube and making moment maps

  • Downloading astronomical images from a database (for the same galaxy as the HI data)

  • Making an overlay of the HI data onto an optical image

  • Calculating some basic statistics for the spectra

  • Averaging the spectra for the galaxy

    • Calculating the HI mass of a galaxy

  • Fitting a Gaussian to spectra

10h40-11h30: Astrophysics talk

"Density of Lyman Alpha Emitter Galaxies at z = 6"

Speaker: Luz Ángela García, Universidad ECCI, Colombia

In this work, we study the number density of Lyman Alpha Emitter (LAE) galaxies, their physical properties, and synthetic spectra at redshift ~ 6 using high-resolution hydrodynamical simulations with radiative transfer from the Thesan project. By recreating the scenario described in Becker et al. 2018, we test the hypothesis that observations to date are missing the vast majority of the high-redshift galaxies' signal since they are extremely faint and, thus, are out of the observational limits of our current telescopes. We also follow the evolution of the neutral Hydrogen fraction, the chemical enrichment of the circum- and intergalactic medium, and specific star formation rate of galaxies in the simulation at the end of Reionization, and evaluate why the detections from HST and the Silverrush project significantly underestimate the number of faint galaxies. Our study indicates an observational bias to massive galaxies in the field. Thus, we forecast the properties of the dwarf galaxies responsible for completing the budget of ionizing photons that concluded the Epoch of Reionization.

10h40-11h30: Tutorial ( Astrophysics 2)

"Analysis of 3D simulations of astrophysical gases"

Tutor: Wladimir Banda-Barragán, Yachay Tech University, Ecuador

• • Simulation data in the HDF5 format.

  • Reading and handling data from numerical simulations

  • Array manipulation, and use of conditionals and loops

  • Application to the analysis of 3D simulations of gas dynamics:

    • Computation of integrated quantities

    • Comparisons of simulations to observations

08h00-08h50: Climate change talk

"Projections of extreme events on South America"

Tutor: Óscar Chimborazo, Yachay Tech University

In this talk, I will show some results about the projections of extreme events on South America using Python and R packages.

08h55-09h45: Materials Science Talk

"OOMMF micromagnetic simulations: An important tool to understand domain wall behavior obtained by Lorentz Transmission Electron Microscopy"

Speaker: María José Benítez, Escuela Politécnica Nacional

The controlled manipulation of magnetic domain walls in laterally constrained ferromagnets is of huge interest for applications in logic devices, spin oscillators, and data storage. Lorentz transmission electron microscopy (LTEM) is a powerful technique to observe magnetic domain walls and to quantify the magnetization state of a sample. However, there are complex magnetic domain walls that cannot be fully understood using LTEM. Therefore, the information provided by micromagnetic simulations is very important. In this talk, I will present several examples of OOMMF micromagnetic simulations that help to understand the results obtained by LTEM.

09h45-10h35: TBD

Tutor: Genevieve Shattow, ThroughPut.ai, United States

TBD

10h40-11h30: Georeferenced count data

Tutor: Diego Morales, Yachay Tech University

Modelling spatial data is a challenging task in statistics. In many applications, the observed data can be modelled using Gaussian, skew-Gaussian or even restricted random field models. However, in several fields, such as population genetics, epidemiology and aquaculture, the data of interest are often count data, and therefore the mentioned models are not suitable for their analysis. Consequently, there is a need for spatial models that are able to properly describe data coming from counting processes.

11h40-13h20: Materials Science Talk

"Momento dipolar eléctrico, topología y cuantización en el modelo tight binding de Su-Schrieffer-Heeger (SSH)"

Tutor: Leonardo Basile, Escuela Politécnica Nacional, Ecuador

En la Materia Condensada, la estrecha interrelación entre electromagnetismo y mecánica cuántica se expresa en forma notable en el Efecto Hall Cuántico, donde la resistividad transversal de un gas electrónico bidimensional, en presencia de un campo magnético perpendicular al gas, es un múltiplo de e2/h o en las exóticas propiedades de los llamados “aislantes topológicos”, donde la interacción spin-órbita crea un gap de energía que lleva a la cuantización de la polarizabilidad magnetoeléctrica del material. El tipo de universalidad que presentan estos fenómenos requiere de nuevos paradigmas de clasificación de estas fases topológicas, que no pueden ser abordadas como resultado de una rotura de simetría. En esta charla se presentará una introducción a las fases topológicas y cuantización a través de estudio del momento dipolar eléctrico en un aislante cristalino. En efecto, no es obvio que la polarización macroscópica de un dieléctrico, es decir el momento dipolar por unidad de volumen, sea el resultado de entidades “independientes polarizables”, como se la presenta en los libros de texto, debido a la naturaleza cuántica de la nube electrónica y la periodicidad del cristal. Con este fin, mediante el modelo SSH y la definición un operador de posición (R. Resta) para calcular el momento dipolar eléctrico compatible con las condiciones de frontera, discutiremos la cuantización de la polarización eléctrica en un aislante cristalino unidimensional.