PROFILE
The main objective of the Computational Biology Laboratory (DLab) is to produce multi-scale computational models to get insights on the fundamental structure and dynamics underlying complex biological phenomena. To do so, we use and produce computer-based simulation tools by combining advanced mathematical modeling, thermodynamics, physics and chemistry, together with high performance computing (HPC) techniques. Whilst our main goal is to produce a tool for multi-scale simulation of biological systems, we also study biological processes at single scales. At the micro-scale (atomic level), we use tools from molecular modeling and molecular simulations to understand the physicochemical properties that govern intercellular communication mediated by gap-junction channels, the structure and function of water at the nanoscale, and molecular recognition and signal transduction processes mediated by proteins. At the meso-scale (cell level) we use network topology and machine leaning techniques to infer and characterize cell signaling networks, gene regulation and neural coordination. At the macro-scale (population level) we use stochastic rule-based modeling to study the behavioral adaptation of artificial populations (agents) due to the spread of infectious diseases and information.
LAB MEMBERS
Research Head: Tomás Pérez-Acle
Associated Researcher: José Antonio Gárate
Postdoctoral Fellows: Alberto J. Martin • Felipe Villanelo
Graduate Students: Alejandro Bernardin • Sebastián Gutierrez • Sebastián Contreras • Claudia Pareja • Yerko Escalona • Rodrigo Santibañez
Undergraduate Students: Ignacio Fuenzalida • Álvaro Bustos
Research Assistants: David Inostroza • Carlos Yañez
COLLABORATIONS
National Collaborations:
• Juan Carlos Sáez (Departamento de Fisiología, Universidad Católica de Chile)
• Agustín Martínez (Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso)
• Kathleen Withlock (Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso)
• Patricio Orio (Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso)
• Adrian Palacios (Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso)
• Carlos González (Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso)
• Danilo Gonzalez-Nilo (Centro de Bioinformática y Biología Integrativa, UNAB)
International Collaborations:
• Dr. Ruhong Zhou (Head of the Soft Matter Science Group, Computational Biology Center, J.T. Watson IBM Research Center, Yorktown Heights, NY, USA)
• Dr. Martha Skerrett (State University of New York College at Buffalo, NY, USA)
• Dr. Viviana Berthoud (The University of Chicago, IL, USA)
• Dr. Niall English (School of Bioprocess Engineering of the University College Dublin)
• Dr. Chris Oostenbrink (Molecular Modeling and Simulation Group, University of Natural Resources and Life Sciences, Vienna, Austria)