Curriculum Vitae

EDUCATION
Ph.D., Chemical Engineering (Magna Cum Laude), 2009
Cornell University, Ithaca, NY

M.S.E, Chemical Engineering (Summa Cum Laude), 2002
University of Puerto Rico, Mayagüez, PR

B.S.E., Chemical Engineering (Summa Cum Laude), 2000
University of Puerto Rico, Mayagüez, PR


PROFESSIONAL EXPERIENCE
2009-present Postdoc Research Assistant, Department of Physics
Universität Wien, Vienna, Austria
Colaborator: Dr. Christoph Dellago
Title: “Simulating the kinetic of rare events on complex system.”

2004-2009 Graduate Research Assistant, Department of Chemical Engineering
Cornell University, Ithaca, N.Y.
Sloan Foundation Fellow
Department of Education (GAAN) Fellow
Advisor: Dr. Fernando Escobedo
Thesis title: “Thermodynamic and Kinetics Studies of Rare Events in Complex Systems”
1. Extended the use of coarse-grained models to enable thermodynamic and kinetic studies of (i) protein folding, (ii) adsorption phenomena of protein and DNA interactions with surfaces and (iii) split-protein fragmentation and reassembly.
2. Development of novel statistical mechanics models and solving them via molecular dynamic and Monte Carlo methods.
3. Optimization of simulation techniques to kinetic studies of complex processes including: (i) crystal melting of monomer and dimer particles, (ii) protein-protein interactions, and (ii) proteins aggregation.


2003-2004 Research Assistant, Department of Chemical Engineering
University of Puerto Rico, Mayagüez, PR
Advisor: Dr. Julio Briano
Title: “Numerical Simulation of the Chemical-Transport from a Mine Field.”
1. Development of physical and numerical models for chemical signatures compounds from landmines and explosives materials (UXO) transport and detection in soil and atmospheric interface.

2002-2003 Research Assistant, Department of Chemical Engineering
University of Puerto Rico, Mayagüez, PR
Advisor: Dr. José A. Colucci
Title: “Auto-thermal Partial Oxidation Reformer.”
1. Establish the feasibility of using a new catalyst to convert various hydrocarbons, including methanol and isooctane, to a hydrogen-rich product gas to be used in fuel cell for automobile applications.

2000-2002 Graduate Research Assistant, Department of Chemical Engineering
University of Puerto Rico, Mayagüez, PR
Advisor: Dr. José A. Colucci
Thesis title: “Biodiesel from Transesterification of Recycle Vegetable Oil by Ultrasound.” 1.Feedstock quality analysis and development of laboratory expertise for the conceptual design of a Biodiesel manufacturing facility in Puerto Rico.
2.Establish the feasibility of using ultrasound mixing to obtain the displacement of the equilibrium Biodiesel reaction to the products.

2000 Undergraduate Research Assistant, Department of Chemical Engineering
(Spring) University of Puerto Rico, Mayagüez, PR
Advisor: Dr. José A. Colucci
Senior thesis title: “Biomass Fractionation.”
1. Biomass fractionation using steam explosion technique for the separation of lignin, hemicellulose and cellulose from coffee waste processing products and identification of products by gas chromatography coupled with mass spectrophotometer (GC-MS).

HONORS AND AWARDS
- Honor student of the Chemical Engineering Department at University of P. R., 1994-2002.
- Member of dean honor lists at University of Puerto Rico, Mayagüez, 1997-2002.
- University of Puerto Rico President Award, 2002.
- Graduated Summa Cum Laude (B.S.E.), University of Puerto Rico, 2002
- Member student chapter, Golden Key National Honor Society.
- Member student chapter, American Academy of Distinguished Students.
- Member student chapter, National Collegiate Minority Leadership (NCMLA).
- IIQPR Award.
- 1st Place Poster Presentation, IIQPR Assembly of Puerto Rico, 2001.
- 1st Place Poster Presentation, VI AIDIS Assembly of Puerto Rico, 2001.
- 1st Place Poster Presentation, VI Merck local symposium of Puerto Rico, 2002.
- 1st Prize AIDIS Research Projects Competition (Biodiesel Commercialization @ PR), 2002.
- Graduated Summa Cum Laude (M.S.E.), University of Puerto Rico, 2002.


TEACHING EXPERIENCE
1. Fall 2006, Fall 2007 Teaching Assistant, Advance Thermodynamic, Cornell U. Ithaca, N.Y.
2. Spring 2000, Spring 2001 Instructor of Chemical Engineer Laboratory , University of P.R., Mayagüez, P.R.


RESEARCH INTERESTS
- Biotechnology
- Computational biology
- Development of coarse-grained models
- Development and application of theoretical and molecular computer simulation techniques
- Thermodynamic and kinetic modeling of rare events (e.g., biological and polymer science)
- Renewable Energy (Computer simulation and experimental data link)
- Biomedical Engineering


S K I L L S

Computational/Theoretical skills. My main field of expertise is the computational study of molecular systems (biological and soft matter) via Monte Carlo and Molecular Dynamics simulations. Experience in performing abinitio/DFT calculations and force matching simulations for the generation of force field potentials to be used in classical simulations. Expertise in molecular modeling and simulation software: VASP, potfit, IMD, LAMMPS, NAMD, CHARMM and GROMACS. Development, optimization and application of advances path sampling techniques (Forward Flux Sampling, Transition Path Sampling, Transition Interface Sampling, etc.) for the study of dynamical properties (rate constants and mechanistic details) of complex systems. Expertise in free energy methods: Umbrella Sampling, Thermodynamic Integration, Wang-Landau, Metadynamic, etc. Programming: C/C++, fortran 77/90, python, parallel computations with MPI. Mathematica, Matlab, Viualization software (VMD, Pymol).



Experimental techniques. High performance liquid chromatography (HPLC), Gas chromatography (GC) , and GC-mass spectrometry (GC-MS).

PEER-REVIEWED PUBLICATIONS
1. Borrero, E.E., Briano, J.G., Castro, M.E., and Hernandez-Rivera, S.P. (2004) Numerical simulation of the chemical-signature-compounds transport from a mine field. Proceedings of the SPIE, 5415: 533-544.
2. Borrero, E.E., and Colucci J.A. (2005) Biodiesel from an alkaline transesterification reaction of soybean oil using ultrasonic mixing. JAOCS, 82:525-530.
3. Borrero, E.E., and Escobedo, F. (2006) Folding kinetics of a lattice protein via a forward flux sampling approach .J. Chem. Phys. 125:164904-14.
4. Borrero, E.E., and Escobedo, F. (2007) Reaction coordinates and transition pathways of rare events via forward flux sampling. J. Chem. Phys. 127:164101-17.
5. Contreras Martinez, L., Borrero, E.E., Escobedo, F. and DeLisa, M.P. (2007) In silico protein fragmentation reveals the importance of critical nuclei in domain reassembly. BioPhys J., 94:1575-1588.
6. Borrero, E.E., and Escobedo, F. (2008) Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes. J. Chem. Phys. 129:024115 -16.
7. Borrero, E.E., and Escobedo, F. (2009) Simulating the kinetics and thermodynamics of transitions via forward flux/umbrella sampling. J. Phys. Chem. B 113:64634.
8. Velez-Vega C., Borrero, E.E., and Escobedo, F. (2009) Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol. J. Chem. Phys 130:225101.
9. Escobedo, F. Borrero, E.E., and Araque J.C.(2009) Recent Advances of Transition Path Sampling Methods and Applications to Biological Systems. J. Phys.: Condens. Matter 21:333101.
10. Borrero, E.E., Contreras Martinez, L., Escobedo, F. and DeLisa, M.P. (2010) Kinetics and reaction coordinates of the reassembly of protein fragments via forward flux sampling. BioPhys J., 98:1911-1920
11. Velez-Vega C., Borrero, E.E. and Escobedo, F. (2010) Kinetics and mechanism of the unfolding N-L transition of Trp-cage in explicit solvent, via optimized Forward Flux Sampling simulation. J. Chem. Phys. 133:105103.
12. Borrero, E.E. and Dellago, C. (2010) Overcoming barriers in trajectory space: mechanism and kinetics of rare events via Wang-Landau enhanced transition path sampling. J. Chem. Phys. 1133:134112.
13. Borrero, E.E., Weinwurm, M. and Dellago, C. (2010) Optimizing transition interface sampling for simulations of rare events: I. Sampling and staging in the configurational space. (in preparation).
14. Borrero, E.E., and Dellago, C. (2010) Optimizing transition interface sampling for simulations of rare events: II. Kinetic and reaction coordinates. (in preparation).
15. Borrero, E.E., and Dellago, C. (2010) Ergodic sampling of the trajectory space: metadynamics enhanced transition path sampling. (in preparation).