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**Harvard**

Lacroix, L. (2018) *Fast GPU simulations of the FRAP experiment *. Göteborg : Chalmers University of Technology

** BibTeX **

@mastersthesis{

Lacroix2018,

author={Lacroix, Leander},

title={Fast GPU simulations of the FRAP experiment },

abstract={In this thesis we study several models of the Fluorescence Recovery After Photobleaching (FRAP) experiment. FRAP is a technique used to estimate the diﬀusion coefficient of ﬂuids based on Confocal Laser Scanning Microscopy (CLSM). A ﬂuorescent sample is ﬁrst photobleached on a user deﬁned region. Then, by studying the recovery of ﬂuorescence in the bleaching region, one can retrieve important parameters of the ﬂuid such as the diffusion coefficient and binding constants by ﬁtting a model to the data. We implemented and compared three models of the FRAP experiment. The ﬁrst model assumes bleaching and image acquisition is an instantaneous process. The second model, based on the ﬁrst one, introduces multiple bleach frames. The ﬁnal model takes into account the scanning movement of the CLSM and is computationally much more complex. For the instantaneous models, two schemes are introduced and compared against each other to ensure correct implementation of the algorithms. The ﬁrst scheme uses the spectral method to solve the diﬀusion-reaction equations and the second uses a stochastic formulation of the problem. The last model, due to its complexity, has only been implemented stochasticaly. All three models have been implemented on Graphical Processing Units (GPUs) using the OpenCL API in C++. The GPU has a massively parallel architecture that can be exploited for scientiﬁc computing. These schemes are ”embarrassingly parallel” and thus suitable for a GPU implementation. By comparing the diﬀerent models, we see that a good compromise between precision and computing resource is given by the instantaneous bleaching with multiple bleach frames model. Because of the scanning nature of the CLSM, we would expect the last model to reveal some asymmetry in the results. These were only found for extreme and unrealistic parameters and it is thus not necessary to simulate the FRAP experiment with such complexity. },

publisher={Institutionen för matematiska vetenskaper, Chalmers tekniska högskola},

place={Göteborg},

year={2018},

keywords={Index terms — FRAP, Spectral method, GPGPU, OpenCL},

note={36},

}

** RefWorks **

RT Generic

SR Electronic

ID 255839

A1 Lacroix, Leander

T1 Fast GPU simulations of the FRAP experiment

YR 2018

AB In this thesis we study several models of the Fluorescence Recovery After Photobleaching (FRAP) experiment. FRAP is a technique used to estimate the diﬀusion coefficient of ﬂuids based on Confocal Laser Scanning Microscopy (CLSM). A ﬂuorescent sample is ﬁrst photobleached on a user deﬁned region. Then, by studying the recovery of ﬂuorescence in the bleaching region, one can retrieve important parameters of the ﬂuid such as the diffusion coefficient and binding constants by ﬁtting a model to the data. We implemented and compared three models of the FRAP experiment. The ﬁrst model assumes bleaching and image acquisition is an instantaneous process. The second model, based on the ﬁrst one, introduces multiple bleach frames. The ﬁnal model takes into account the scanning movement of the CLSM and is computationally much more complex. For the instantaneous models, two schemes are introduced and compared against each other to ensure correct implementation of the algorithms. The ﬁrst scheme uses the spectral method to solve the diﬀusion-reaction equations and the second uses a stochastic formulation of the problem. The last model, due to its complexity, has only been implemented stochasticaly. All three models have been implemented on Graphical Processing Units (GPUs) using the OpenCL API in C++. The GPU has a massively parallel architecture that can be exploited for scientiﬁc computing. These schemes are ”embarrassingly parallel” and thus suitable for a GPU implementation. By comparing the diﬀerent models, we see that a good compromise between precision and computing resource is given by the instantaneous bleaching with multiple bleach frames model. Because of the scanning nature of the CLSM, we would expect the last model to reveal some asymmetry in the results. These were only found for extreme and unrealistic parameters and it is thus not necessary to simulate the FRAP experiment with such complexity.

PB Institutionen för matematiska vetenskaper, Chalmers tekniska högskola,

LA eng

LK http://publications.lib.chalmers.se/records/fulltext/255839/255839.pdf

OL 30