<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8">
</head>
<body bgcolor="#FFFFFF" text="#000000">
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>
</div>
</div>
</body>
</html>