[Alumnos-ii-cs] Coloquio Departamental, Martes 31 de Marzo 12:00, F-106, CC y LPA, CSJ
Claudio Torres L.
ctorres at inf.utfsm.cl
Tue Mar 31 09:40:24 CLST 2015
Estimad at s,
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.
Cordiales Saludos,
Comité de Coloquio
On 26/03/15 08:26, Claudio Torres L. wrote:
> 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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