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Estimad@s,<br>
<br>
Solo un recordatorio amigable que hoy habrá una nueva sesión del
nuestro coloquio departamental a las 12:00 hrs en la F-106 en Casa
Central y en el LPA en Campus San Joaquín.<br>
<br>
Cordiales Saludos, <br class="">
<br class="">
Comité de Coloquio<br>
<br>
<br>
On 26/03/15 08:26, Claudio Torres L. wrote:<br>
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Estimad@s,
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class=""> <br class="">
Este *Martes 31 de Marzo a las <u class=""><b class="">12:00</b></u>*
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". <br class="">
<br class="">
*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. <br>
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. <br>
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.<br>
<br class="">
*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.<br>
<br class="">
<b class="">¡Quedan todos cordialmente invitados! </b><b
class=""><br class="">
</b><b class=""> </b><br class="">
Cordiales Saludos, <br class="">
<br class="">
Comité de Coloquio<br>
<br>
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