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GUILHERME DUARTE RAMOS MATOS

Ph.D. in Computational Chemistry, UC Irvine (2018)

 
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ABOUT ME

A skilled, creative and communicative researcher with experience in developing and using free energy-based methods to solve chemical and pharmacological problems. 
Research experience in applying rigorous physical reasoning to problems in Chemistry and Pharmacology.
Experience in teaching, counseling, managing team members, delegating activities and achieving group goals.
Comfortable communicating complex data to lay and technical audiences.

 

OVERVIEW

Background & Expertise

 

POSTDOCTORATE ASSOCIATE, STONY BROOK UNIVERSITY

Excited to have joined the Rizzo Lab in SBU to work with the development of the DOCK software and with its applications to different problems in molecular modeling and drug design.

RESEARCH ASSISTANT, UC IRVINE

Worked with free energy calculations in systems of pharmacological interest – solvation free energies of small organic molecules and solubility prediction from absolute chemical potentials of molecular solids and their solution phases. Innovated by using infinite dilution activity coefficients as alternatives to hydration free energies as method validation tools. Curated and updated FreeSolv, the hydration free energy database, with the addition of hydration enthalpies and entropies. Published two first author articles and one article as a collaborator in peer reviewed journals. Currently submitting one last first author paper. Was responsible for coordinating the research group’s meetings and outside activities. Mentored two undergraduate students, Daisy Y. Kyu (2015-2016), Nam Thi (2016).

TEACHING EXPERIENCE

Honors & Majors General Chemistry Lab (UCI, 2013-2014)

Experiments introducing important research techniques and phenomena to Honors and Chemistry Majors at UC Irvine.​

Molecular Pharmacology (UCI, 2015) 

Pharmacology and Biochemistry of Parkinson, Alzheimer and psychiatric diseases.

Computational Organic Chemistry (UCI, 2016)

Study of chemical properties and organic reaction mechanisms using Spartan and Gaussian.

General Chemistry Lab (UCI, 2018)

Experiments introducing research techniques and phenomena to undergraduate students at UC Irvine.

Molecular Spectroscopy (UnB, 2011)

Planned lectures, wrote and graded exams in 1H- and 13C-NMR, COSY and dqf-COSY experiments.

PEER-REVIEWED ARTICLES

  • G. D. R. Matos, D. Y. Kyu, H. H. Loeffler, J. D. Chodera, M. R. Shirts and D. L. Mobley, “Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database,” Journal of Chemical and Engineering Data 62(5):1559-1569 (2017).

  • F. A. R. Silva, M. J. A. Sales, M. Ghoul, L. Chebil, G. D. R. Matos, E. R. Maia, “Molecular dynamics simulations of montmorillonite reinforcing amylose plasticized by Brazilian Cerrado oils: polymer-clay nanocomposite,” MRS Communications, March (2018)

  • G. D. R. Matos and D. L. Mobley, “Challenges of the use of atomistic simulations to predict solubilities of drug-like molecules,” F1000Research, 7:686 (2018)

  • H. H. Loeffler, S. Bosisio, G. D. R. Matos, D. Suh, B. Roux, D. L. Mobley, J. Michel, Julien, “Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software,” Journal of Chemical Theory and Computation, 14: 1559-1569 (2018) 

  • G. D. R. Matos, G. Calabrò, D. L. Mobley, "Infinite Dilution Activity Coefficients as Constraints for Force Field Parameterization and Method Development," Journal of Chemical Theory and Computation, 15: 3066-3074 (2019)

LEADERSHIP

Graduate Student Council Member of the Institute of Chemistry, Universidade de Brasília (2012).
Undergraduate Student Council Member of the Institute of Chemistry, Universidade de Brasília (2010).

HONORS & AWARDS

  • Science without Borders / Ciências sem Fronteiras Scholarship (2013-17)

  • CNPq M.Sc. Scholarship (2011-13)

  • Fellow of the Programa de Educação Tutorial (PET) of the Brazilian Ministry of Education (2008-11)

  • Gold Medal in the 6th Regional Chemistry Olympiad in Brasília, Brazil (2007)

  • Gold Medal in the 5th Regional Chemistry Olympiad in Brasília, Brazil, 2006

EDUCATION

 

PH.D. IN CHEMISTRY, SCHOOL OF PHYSICAL SCIENCES, UC IRVINE

September 2013 - December 2018

Thesis Topics: hydration and solvation free energies of small organic molecules of pharmacological interest; prediction of solubility of molecular solids from absolute free energy calculations; reproducibility of relative hydration calculations across different software; use of infinite dilution activity coefficients as alternative parameters for force field and method development.

Adviser: David L. Mobley

M.SC. IN CHEMISTRY, INSTITUTO DE QUÍMICA, UNIVERSIDADE DE BRASÍLIA

April 2011 - March 2013

Dissertation Topic: use of conceptual DFT and molecular fingerprints obtained from ab initio calculations to predict reaction paths.

Advisers: Fernando C. Rangel and Kleber C. Mundim

B.S. IN CHEMISTRY, INSTITUTO DE QUÍMICA, UNIVERSIDADE DE BRASÍLIA

September 2007 - February 2011

Focus in Physical Chemistry, Organic Chemistry and Mathematical Physics.

SKILLS & INTERESTS

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FREE ENERGY CALCULATIONS AND MOLECULAR SIMULATIONS

Absolute and relative free energy calculations, molecular dynamics and Monte Carlo simulations, machine learning methods in Chemistry and Biochemistry, protein-ligand docking, virtual screening and de novo design of ligands, statistical mechanics, data science.

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RESEARCH INTERESTS

Artificial intelligence in Chemistry, study of protein reaction mechanisms and free energy transformations, solvation, protein-ligand docking, drug design, biochemical signaling.

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TECHNICAL SKILLS

Hard: Python 3.X and 2.7, Fortran, Bash, Mathematica, GROMACS, OpenMM, Yank, OpenEye Toolkits, DOCK6, Gaussian, Psi4, Spartan, Materials Studio, Mercury (CCDC), C++. Microsoft Office, LaTeX.

Soft: Science communication, Improv for teaching

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PERSONAL INTERESTS

World History and politics writing, Science writing, classical art, language learning, gastronomy, clarinet playing.

 

"The spirit is the true self. The spirit, the will to win, and the will to excel are the things that endure"

Marcus Tullius Cicero

 

LET’S CONNECT

I’d love to hear from you.