[Alumnos-ii-cs] Coloquio Departamental, Martes 31 de Marzo 12:00, F-106, CC y LPA, CSJ

[Claudio Torres L.]

Estimad at s,

Este *Martes 31 de Marzo a las _*12:00*_* tendremos nuestro coloquio 
departamental en el Auditorio Claudio Matamoros, F-106, (La charla se 
transmitirá por videoconferencia al Laboratorio de Programación 
Avanzado, LPA, San Joaquín.). En esta ocasión *Christopher Cooper, 
Ph.D.* nos presentará su trabajo titulado: "Biomolecular electrostatics 
with continuum models: a boundary integral implementation and 
applications to biosensors".

*Resumen:* The implicit-solvent model uses continuum electrostatic 
theory to represent the potential around biomolecules dissolved in a 
salt solution. This leads to a system of PDEs where the 
Poisson-Boltzmann and Poisson equations are coupled on the molecular 
surface. To solve the resulting system of PDEs efficiently, we wrote a 
fast boundary-element method (with a multipole-based treecode) in Python 
and CUDA (for exploiting GPUs). We call our code PyGBe --- a 
Python-based GPU code for boundary elements. We will show results that 
verify and validate our implementation of PyGBe in the context of 
solvation and binding of biomolecules, comparing it with experimental 
observations, analytical solutions, and other numerical tools.
Our main application of interest looks at the preferred orientation of 
proteins adsorbed on a charged surface, a situation relevant in 
biosensing. Biosensors are designed to detect a target molecule when it 
binds to a ligand molecule, itself attached to the sensor through a 
self-assembled monolayer (SAM). It is key that the binding sites of the 
ligand molecule be adequately exposed to the flow that carries the 
targets, and hence the importance of orientation. In our model, surfaces 
with SAMs are represented by prescribing a charge distribution.
We will present results for three test cases of adsorption. The first 
case is used to verify the code; it compares the numerical result with 
an analytical solution derived by us, valid for a spherical surface 
interacting with a spherical protein with a centered charge. In the 
second case, we used PyGBe to compute the preferred orientation for 
protein G B1 adsorbed on a charged surface and compared the result with 
published molecular dynamics (MD) simulations and experimental 
observations, matching the preferred orientation. In the third and final 
case, we used a full antibody, a common ligand molecule in biosensors 
that is much larger than protein G B1 and would be difficult to simulate 
with MD. This test shows the capability of our code to compute realistic 
systems for bionsensing applications.

*Mini Bio:* Christopher Cooper es instructor académico del Departamento 
de Ingeniería Mecánica de la Universidad Técnica Federico Santa María 
desde marzo del año 2015. Él es ingeniero mecánico de la misma casa de 
estudios (2009), y obtuvo un MS (2012) y un PhD (2015) en ingeniería 
mecánica de Boston University. Su área de investigación es la simluación 
numérica de fenómenos físicos, con aplicaciones en electrostática 
molecular y mecánica de fluidos.

*¡Quedan todos cordialmente invitados! **
***
Cordiales Saludos,

Comité de Coloquio

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