Numerical modeling of molecular electrostatics and solvation in USM

People

Principal investigator

Christopher D. Cooper

GitHub LinkedIn Twitter
BS, PEng (USM), MS, PhD (Boston University) Mechanical Engineering. CV.

PhD students

Sergio Urzúa

GitHub LinkedIn
BS, PEng, MS, Mechanical Engineering (USM).
Topic: protein-surface interaction

Mauricio Guerrero

GitHub LinkedIn
BS, PEng, MS, Mechanical Engineering (USM).
Topic: FEM-BEM coupling

MS students

Eduardo Hasbún

GitHub LinkedIn
BS, Mechanical Engineering (USM).
Topic: convolutional neural networks for the PB equation

Felipe Vicencio

GitHub LinkedIn
BS, PEng, Mechanical Engineering (USM) Topic: polarizable force fields

Undergraduate students

Gonzalo Rojas

GitHub LinkedIn
Topic: ML for adaptive mesh refinement

Nehemías Sandoval

GitHub LinkedIn
Topic: ML for error estimation

Past members

  • Willy Menacho (MS). Topic: electrostatics in viruses
  • Martín Achondo (MS). Topic: physics informed neural networks
  • Byron Vega (BS, PEng). Topic: linear/nonlinear PB
  • Camila Pérez (BS, PEng). Topic: linear/nonlinear PB
  • Manuel Ruiz (visiting PhD student). Topic: hydrogenase-surface interaction
  • Ian Addison-Smith (BS, PEng). Topic: electrostatic force
  • Ignacio Muñoz (BS, PEng). Topic: nonpolar solvation free energy
  • Elmo Begazo (BS, PEng). Topic: adaptive mesh refinement
  • Stefan Search (BS, Peng). Topic: PBJ software development, boundary integral formulations
  • Kenneth Styles (BS, PEng). Topic: SLIC, PBJ software development.
  • Miguel Godoy (BS, PEng). Topic: uncertainty quantification, PBJ development.
  • Matías Martínez (MS). Topic: virus-scale simulations, parallel computing
  • Javier Gómez (MS). Topic: Stokes flow in biological systems
  • Rodrigo Huencho (BS). Topic: dielectric constant parameterization
  • Valentina Oyarzún (BS, PEng). Topic: nonpolar solvation
  • Joaquín Echaíz (BS, PEng). Topic: nonpolar solvation
  • Vicente Ramm (BS, PEng). Topic: error estimation, adaptive mesh refinement
  • Nicolás Espinoza (BS, PEng). Topic: membrane proteins

Collaborators

  • Lorena A. Barba (GWU, US)
  • Jaydeep P. Bardhan (PNNL, US)
  • Timo Betcke (UCL, UK)
  • Michal Bosy (Kingston, UK)
  • Jehanzeb H. Chaudhry (UNM, US)
  • Marcia Fenley (FSU, US)
  • Carlos D. García (Clemson, US)
  • Horacio V. Guzmán (UAM, Spain and JZI, Slovenia)
  • Jaime Pizarro (USACH, Chile)
  • Elwin van’t Wout (PUC, Chile)