John Justine Villar, PhD

I am an Assistant Professor of the UP Department of Computer Science and a regular member of the UP Scientific Computing Laboratory. 

Concurrently, I am a affiliate research fellow at the Drug Discovery Research Center and Institute of Chemistry, University of Miskolc, Hungary, and one of the primary research supervisors of the Science Abroad Program (Hungary) of the University of Toronto.

I can be reached through email at


Mathematical Aspects of Peptide Conformational Analysis Through Quantum Chemical Calculations
Computational Network Biology (Protein Complex Detection in PPI Networks, Chemical Reaction Network Theory in Biological Systems)
Stochastic Modelling, Numerical Optimization and Graph Theoretic Applications in Bioinformatics
Algebraic Systems Biology (Process Algebra and Natural Computing)
Reaction Kinetics Modeling (Biochemical Systems Theory)


I am actively involved in the following ongoing research projects:

1. Construction of Potential Energy Hypersurfaces for Protein Structure Prediction through Quantum Chemical Calculations
Research project with Adrian Roy Valdez, Ph.D., David Setiadi, Ph.D. (University of Toronto, Canada) and Imre Csizmadia, Ph.D. (University of Miskolc, Hungary and University of Toronto, Canada)
This study aims to construct precise potential energy surfaces (PES) of different amino acids through ab initio calculations to provide insights on the potential energy hypersurface given an amino acid sequence. We intend to compare our findings to results from well-known force fields, among others. Furthermore, the relationship between polypeptide PES and amino acid PES are also explored.

2. Modeling Dopamine D1 Receptor Availability and Intracellular Trafficking in Renal Proximal Tubule Cells 
Research project with Carlene P. C. Pilar-Arceo, Ph.D. (Institute of Mathematics, UPD) and Eduardo Mendoza, Ph.D. (The Max Planck Institute of Biochemistry, Germany),  in collaboration with  Pedro Jose, M.D., Ph.D. and Ines Armando, M.D., Ph.D. (University of Maryland School of Medicine, USA)
This attempts to model the dynamics of dopamine D1 receptor trafficking inside human renal proximal tubule cells, as well as its availability at the cell surface. It is known that dopamine synthesis and D1 receptor function affects sodium excretion in genetically hypertensive individuals. Kinetic modeling and mathematical analyses using Chemical Reaction Network Theory help us provide insights about the existence and multiplicity of steady states, as well as their stability if it exists.

3. Cyberphysical Transportation Systems (Phase 1)
PCIEERD-DOST funded project with Dr. Adrian Roy Valdez, Ph.D. as the Project Leader, in collaboration with UP National Center for Transportation Studies and UP Electrical and Electronics Engineering Institute
This project tries to design a intelligent land vehicle control system with advanced computing and sensing capabilities to improve safety and throughput to meet increasing transportaton demands I am currently involved in the Software Research and Development components of the project, where my team work with calibrating models of traffic demand and traffic intersection optimization.