Seminars at the Faculty of Informatics

A Hybrid Computational Framework for Predicting Virus Transmission

The Faculty of Informatics is pleased to announce a seminar given by Artur Yakimovich

DATE: Tuesday, June 25th 2013
PLACE: USI Lugano Campus, room SI-008, Informatics building (Via G. Buffi 13)
TIME: 14.30

Viruses spread between cells, tissues and organisms by cell-free and cell-cell transmission mechanisms. Both mechanisms enhance disease caused by different viruses, but it is difficult to distinguish between them. We have previously characterized the transmission mode of human adenovirus in monolayers of epithelial cells using experimental data from live-cell fluorescence microcopy. Employing these data as experimental parameters we have developed an in silico model using multi-scale hybrid dynamics, cellular automata and particle strength exchange (CA-PSE). Here we present a generalized open source simulation framework based on the model we have developed. Based on the inherent flexibility of the CA-PSE model this framework aims at enabling predictions of spatial spread of from different families, taking into account their different modes of spreading, in particular cell-to-cell and cell-free spreading. The framework promises to be useful for better understanding of various parameters which modulate the viral spreading dynamics. By this, we hope to provide mechanistic insights into commonly used endpoint measurements in virology, such as plaque assays or fluorescent focus forming assays.

(Joint work with Y. Yakimovick, M. Schmid, L. Pelkmans, I.F. Sbalzarini, and U.F. Greber)

Artur Yakimovich received his diploma at the Belarusian State University, Faculty of Chemistry, major: Chemistry of drugs, in 2008.  Since Feb. 2009 he is a PhD student at the Institute of Molecular Life Science, University of Zurich, under the supervision of Prof. Dr. Urs Greber.  In 2012 he became a member of the interdisciplinary PhD program (

HOSTS: Prof. Rolf Krause, Dr. Roberto Croce