PROBRAL

Mesoscopic Molecular Dynamics Simulations
Development of Models and Computational Strategies for Complex Structural Bioinformatics Problems
January 2019 to December 2022
Researchers Students Study Missions Work Missions Publications

There is a wide range of unanswered scientific questions which cannot be answered neither by experiments nor by classical modeling and simulation approaches. One question is how to consider microscopic and macroscopic effects in one model. On the one hand, available microscopic approaches (Molecular Dynamics (MD) type) are precise but computational too complex for large or multi-scale problems. On the other hand, several macroscopic methods (Computational Fluid Dynamics (CFD) type) cannot show crucial microscopic effects. Therefore, a mesoscopic scale model is required that closes this gap. For such a Mesoscopic Molecular Dynamics (MMD) model, we propose to take advantage of the Lattice Boltzmann Method (LBM), a modern CFD method, and state-of-the-art MD methods in order to combine both. This MMD model resolves certain microscopic effects important for the considered macroscopic application. In this project, two complementary academic expert groups from Brazil and Germany join together in order to provide an interdisciplinary research and academic education in the fields of mathematics, computer science, biology, chemistry and engineering to PhD students as well as to researchers.

Researchers

Dr. Márcio Dorn - Coordinator
PPGC/INF/UFRGS - Brazil

Dr. Mathias J. Krause - Coordinator
LBRG/IANM/KIT - Germany

Dr. Hugo Verli
CBiot/UFRGS - Brazil

Dr. Ana Lúcia Cetertich Bazzan
PPGC/INF/UFRGS - Brazil

Dr. Rodrigo Ligabue Braun
DF/UFCSPA - Brazil

Dr. Bruno César Feltes
PPGC/INF/UFRGS - Brazil

Dr. Luciana S. Buriol
PPGC/INF/UFRGS - Brazil

Dr. Gudrun Thäter
IANM/KIT - Germany

Dr. Hermann Nirschl
IANM/KIT - Germany

Graduate Students/Collaborators

Pedro Henrique Narloch
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil

Leonardo de Lima Corrêa
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil

Marcelo Depolo Poleto
Ph.D. Candidate
PPGBCM/CBIOT/UFRGS - Brazil

Bruno Iochins Grisci
Ph.D. Candidate
PPGC/INF/UFRGS - Brazil

Marie-Luise Maier
Ph.D. Candidate
LBRG/KIT - Germany

Stefanie Carolin Schutera
Ph.D. Candidate
LBRG/KIT - Germany

Robin Trunk
Ph.D. Candidate
LBRG/KIT - Germany

Stephan Simonis
Ph.D. Candidate
LBRG/KIT - Germany

Study Missions

brazil  ✈  german
INF/UFRGS/Brazil to IANM/KIT/Germany

Ph.D. Candidate - Bruno Iochins Grisci
September, 2019 to August, 2020

Ph.D. Candidate - Pedro Henrique Narloch
September, 2019 to August, 2020


brazil  ✈  german
IANM/KIT/Germany to INF/UFRGS/Brazil

Ph.D Candidate - Stephan Simonis
November, 2019 to December, 2019

Ph.D. Candidate - Robin Trunk
November, 2019 to December, 2019

M.Sc. Candidate - Jonathan Jeppener
November, 2019 to December, 2019

M.Sc. Candidate - Adrian Kummerländer
November, 2019 to December, 2019

Work Missions

brazil  ✈  german
INF/UFRGS/Brazil to IANM/KIT/Germany

Prof. Dr. Márcio Dorn
August, 2019

brazil  ✈  german
INF/UFRGS/Brazil to IANM/KIT/Germany

Prof. Dr. Hugo Verli
August, 2019


brazil  ✈  german
IANM/KIT/Germany to INF/UFRGS/Brazil

Dr. Mathias J. Krause
December, 2019

PROBRAL Workshops

2019 - Workshop Lattice Boltzmann Methods with OpenLB Software Lab
Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil

On December 10 and 11, 2019, we held the workshop "Lattice Boltzmann Methods with OpenLB Software Lab" at the Instituto de Informática from the UFRGS. The workshop was organized by the Structural Bioinformatics and Computational Biology Lab (SBCBLAB/INF/UFRGS - Brazil) and the Lattice Boltzmann Research Group (LBRG/IANM//KIT - Germany). We were happy to host 35 participants, including five speakers from LBRG (KIT, Karlsruhe, Germany).

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PROBRAL Meetings / Presentations

2019 - First Meeting




1st Presentation of Brazilian research to the LBRG

In this meeting of the Lattice Boltzmann Research Group from KIT, the Ph.D. Candidate Bruno Iochins Grisci presented his current work to the German researchers.


2nd Presentation of Brazilian research to the LBRG

In this meeting of the Lattice Boltzmann Research Group from KIT, the Ph.D. Candidate Pedro Henrique Narloch presented his current work to the German researchers.


2019 - Second meeting


2019 - Third meeting

Participation in Events

International workshop on data-driven modeling and optimization in fluid mechanics

This workshop showcased the application of machine learning, evolutionary algorithms, and adjoint-based optimization to fluid dynamics-related problems with special focus on turbulent flows and flow control


7th Heidelberg Laureate Forum

The Ph.D. Candidate Bruno Iochins Grisci was among the 200 young math and Computer Science researchers worldwide invited to attend the Heidelberg Laureate Forum. The event brings together the young researchers with winners of the Abel Award and Field Medalist (math), ACM AM Turing Award and ACM Computing (Computer Science) Award and Nevanlinna Award (Information Science) in Heidelberg, Germany. The focus of the forum is to promote and advance research in these areas, but also to enable contact and exchange of experiences between researchers. For example, the event can balance technical lectures, workshops, and visits to research institutions and local businesses with social activities, dinners, and discussions geared toward interaction among participants. Bruno Grisci was also invited to present his current research, titled "Ranking Relevances from Neural Networks for the Selection of Biological Features

Photos Presentation Video


International Days "Karlsruhe and the World

Organized by the International Affairs Business Unit (INTL), the International Days offered an extensive program of presentations and workshops, cultural contributions, and an exhibition. The program also covered presentations on international scientific and international activities and relations of KIT, as well as the Humboldt-Lightning-Talks, in which Humboldt fellows presented their current research.


The 19th IEEE International Conference on Bioinformatics and BioEngineering

Pedro had a paper published in the 19th annual IEEE International Conference on Bioinformatics and Bioengineering (BIBE). BIBE aims at building synergy between Bioinformatics and Bioengineering/Biomedical, two complementary disciplines that hold great promise for the advancement of research and development in complex medical and biological systems, agriculture, environment, public health, drug design.


X-Meeting 2019 - Dissertation Award

The Ph.D. Candidate Bruno Iochins Grisci was invited to remotely present his Master Dissertation in the category “Dissertation Award” on the X-Meeting 2019. The work, titled "N3O: A NEAT expansion for improving classification and feature selection applied to microarray data", was featured in the top 3 best dissertation in Bioinformatics by the Associação Brasileira de Bioinformática e Biologia Computacional (AB3C).


21st EMBL PhD Symposium: Facing the Future: Challenges and Perspectives in Life Sciences in the 21st Century

The Ph.D, Candidate Bruno Iochins Grisci was among the participants of the PhD Symposium, organized by the European Molecular Biology Laboratory. The event discusses environmental and global health issues, highlight interdisciplinary approaches as physics and informatics in biology, present innovations in life sciences and raise awareness of the challenges within the scientific community including big data, open access and gender equality. Bruno Grisci was also invited to present his current research, titled "Selection of Biological Features by Ranking the Relevances of Neural Networks Inputs".


MathSEE course on Machine Learning

The Ph.D, Candidate Bruno Iochins Grisci was among the participants of the MathSEE course of Machine Learning.

Publications

Gallery