[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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