Computational Biology


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.


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


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)


  • Brennan MJ, Karcz J, Vaughn NR, Woolwine-Cunningham Y, DePriest AD, Escalona Y, Perez-Acle T, Skerrett IM. Tryptophan Scanning Reveals Dense Packing of Connexin Transmembrane Domains in Gap Junction Channels Composed of Connexin32. J Biol Chem. 2015 May 12. pii: jbc.M115.650747 | | ABSTRACT
  • Retamal MJ, Cisternas MA, Gutierrez-Maldonado SE, Perez-Acle T, Seifert B, Busch M, Huber P, Volkmann UG. Towards bio-silicon interfaces: formation of an ultra-thin self-hydrated artificial membrane composed of dipalmitoylphosphatidylcholine (DPPC) and chitosan deposited in high vacuum from the gas-phase. J Chem Phys. 2014 Sep 14;141(10):104201. doi: 10.1063/1.4894224. | | ABSTRACT
  • Araya-Secchi R, Perez-Acle T, Kang SG, Huynh T, Bernardin A, Escalona Y, Garate JA, Martínez AD, García IE, Sáez JC, Zhou R. Characterization of a novel water pocket inside the human Cx26 hemichannel structure. Biophys J. 2014 Aug 5;107(3):599-612. doi: 10.1016/j.bpj.2014.05.037. | | ABSTRACT
  • Garate J.A., Perez-Acle T., Oostenbrink C. On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations. Phys Chem Chem Phys. 16(11):5119-5128. (2014) | PDF | ABSTRACT
  • Jara O., Acuña R., García I. E., Maripillán J., Figueroa V., Sáez J. C., Araya-Secchi R., Lagos C. F., Perez-Acle T., Berthoud V. M., Beyer E. C. and Martínez A. D. Critical role of the first transmembrane domain of Cx26 in regulating oligomerization and function. Mol. Biol. Cell. 23, 3299-3311 (2012) | PDF | ABSTRACT
  • Nuñez F., Ravello C., Urbina H. and Perez-Acle T. A rule-based model of a hypothetical zombie outbreak: Insights on the role of emotional factors during behavioral adaptation of an artificial population. (16,05,49): 01-20 (2012) | PDF | ABSTRACT
  • González A., Perez-Acle T., Pardo L. and Deupi X. Molecular basis of ligand dissociation in β-adrenergic receptors. Plos ONE 6 (9): 01-09 (2011) | PDF | ABSTRACT
  • Muñoz F., Mejía-López J., Pérez-Acle T. and Romero A. H. Uniaxial magnetic anisotropy energy of fe wires embedded in carbon nanotubes. ACS Nano. 4 (5): 2883-2891 (2010) | PDF | ABSTRACT
  • Lizama C., Lagos C. F., Lagos-Cabré R., Cantuarias L., Rivera F., Huenchuñir P., Pérez-Acle T., Carrión F. and Moreno R. D. Calpain inhibitors prevent p38 MAPK activation and germ cell apoptosis after heat stress in pubertal rat testes. J. Cell. Physiol. 221 (2): 296-305 (2009) | PDF | ABSTRACT
  • Gonzalez A., Duran Sepulveda L., Araya-Secchi R., Garate J. A., Pessoa-Mahana C. D., Lagos C. F. and Perez-Acle T. Computational modeling study of functional microdomains in cannabinoid receptor type 1. Bioorg. Med. Chem. 16 (8): 4378-4389 (2008) | PDF | ABSTRACT
  • Strobel P., Allard C., Perez-Acle T., Calderon R., Aldunate R. and Leighton F. Myricetin quercetin and catechin-gallate inhibit glucose uptake in isolated rat adipocytes. Biochem. J.  386, 471-478 (2005) | PDF | ABSTRACT
  • Tischler N. D., Gonzalez A., Perez-Acle T., Rosemblatt M. and Valenzuela P. D. T. Hantavirus Gc glycoprotein: evidence for a class II fusion protein. J. Gen. Virol. 86, 2937-2947 (2005) | PDF | ABSTRACT
  • Araya-Secchi R., Garate J. A., Holmes D. S. and Perez-Acle T. Molecular dynamics study of the archaeal aquaporin AqpM. BMC Genomics  11-13 (2001) | PDF | ABSTRACT