Cardiovascular Research Symposium /03 May 2011

Cardiovascular Research Conference 2011

- 03 May 2011

Eindhoven- Netherland

For more details click here.

Computer-Aided Patient-Specific Coronary Artery Graft Design Improvements Using CFD Coupled Shape Optimizer

Onur Dur, Sinan Tolga Coskun, Kasim Oguz Coskun, David Frakes, Levent Burak Kara and Kerem Pekkan

This study aims to (i) demonstrate the efficacy of a new surgical planning framework for complex cardiovascular reconstructions, (ii) develop a computational fluid dynamics (CFD) coupled multi-dimensional shape optimization method to aid patient-specific coronary artery by-pass graft (CABG) design and, (iii) compare the hemodynamic efficiency of the sequential CABG, i.e., raising a daughter parallel branch from the parent CABG in patient-specific 3D settings. Hemodynamic efficiency of patient-specific complete revascularization scenarios for right coronary artery (RCA), left anterior descending artery (LAD), and left circumflex artery (LCX) bypasses were investigated in comparison to the stenosis condition. Multivariate 2D constraint optimization was applied on the left internal mammary artery (LIMA) graft, which was parameterized based on actual surgical settings extracted from 2D CT slices. The objective function was set to minimize the local variation of wall shear stress (WSS) and other hemodynamic indices (energy dissipation, flow deviation angle, average WSS, and vorticity) that correlate with performance of the graft and risk of re-stenosis at the anastomosis zone. Once the optimized 2D graft shape was obtained, it was translated to 3D using an in-house ?sketch-based? interactive anatomical editing tool. The final graft design was evaluated using an experimentally validated second-order non-Newtonian CFD solver incorporating resistance based outlet boundary conditions. 3D patient-specific simulations for the healthy coronary anatomy produced realistic coronary flows. All revascularization techniques restored coronary perfusions to the healthy baseline. Multi-scale evaluation of the optimized LIMA graft enabled significant wall shear stress gradient (WSSG) relief (~34%). In comparison to original LIMA graft, sequential graft also lowered the WSSG by 15% proximal to LAD and diagonal bifurcation. The proposed sketch-based surgical planning paradigm evaluated the selected coronary bypass surgery procedures based on acute hemodynamic readjustments of aorta-CA flow. This methodology may provide a rational to aid surgical decision making in time-critical, patient-specific CA bypass operations before in vivo execution.

For more details, click here.

Inverse Problems in Science and Engineering

A meshless CFD approach for evolutionary shape optimization of bypass grafts anastomoses

Improving the blood flow or hemodynamics in the synthetic bypass graft end-to-side distal anastomosis (ETSDA) is an important element for the long-term success of bypass surgeries. An ETSDA is the interconnection between the graft and the operated-on artery. The control of hemodynamic conditions through the ETSDA is mostly dictated by the shape of the ETSDA. Thus, a formal ETSDA shape optimization would serve the goal of improving the ETSDA flowfield. Computational fluid dynamics (CFD) is a convenient tool to quantify hemodynamic parameters; also, the genetic algorithm (GA) is an effective tool to identify the ETSDA optimal shape that modify those hemodynamic quantities such that the optimization objective is met. The present article introduces a unique approach where a meshless CFD solver is coupled to a GA for the purpose of optimizing the ETSDA shape. Three anastomotic models are optimized herein: the conventional ETSDA, the Miller cuff ETSDA and the hood ETSDA. Results demonstrate the effectiveness of the proposed integrated optimization approach in obtaining anastomoses optimal shapes.

For more details click here.

Z. El Zahaba; E. Divob; A. Kassaba

Department of Mechanical, Materials and Aerospace Engineering, University of Central Florida, Orlando, FL, USA
Department of Engineering Technology, University of Central Florida, Orlando, FL, USA

Workshop (15-21 of August 2011)

Medical Informatics Workshop at IKU

Workshop: Advances in Immunology and Cancer Biology

Advances in Immunology and Cancer Biology

15-17 April 2011

Boğaziçi University, Demir Demirgil Hall / Özger Arnas Hall

Registration for the workshop is now open !!!

Take me to the REGISTRATION page.

Download the Workshop Program
Download the Poster

Seminars 13th April_2

The Ethics of Science and Engineering

ITU Electirics and Electronics Faculty 13 April 2011

Seminars 13th April_1

Bogazici University Physics Department, Feza Gursey Seminar Room

13 April 2011 Wednesday 15:30

Deniz Sezer, Sabancı University

Towards understanding of protein conformational changes through simulations of biomolecular and spin dynamics.

One of the most ambitious aims in molecular biophysics?pursued both experimentally and theoretically?is to understand in atomistic detail the functionally relevant conformational transitions of biological molecules. More specifically, the goal is to identify the relevant conformations on the basis of their free energies and to characterize the sequence and time scales of the transitions between these conformations. In principle, this could be achieved computationally through moleculardynamics (MD) simulations. In practice, MD simulations, like any other model, rely on approximations and have their own inherent limitations. Therefore, direct comparison of the MD simulations with experimental data is essential. Among the experimental methods that probe the structure and dynamics of biomolecules electron spin resonance (ESR) spectroscopy provides rich information [1-3]. For example, ESR spectroscopy revealed the open conformations of a potassium channel [4] and a mechanosensitive channel [5] for which only the closed conformations were available from X-ray crystallography. In spite of the utility of ESR spectra, however, their interpretation in terms of the underlying molecular properties is not always unambiguous.

In this talk I will argue that the atomistic picture required for the conclusive interpretation of ESR data can be effectively obtained from MD simulations. In return, the experimental spectra can provide a stringent validation of the MD simulations, thus addressing concerns regarding their limitations. An unambiguous, quantitative comparison of these two techniques can be achieved by calculating the measured ESR spectra directly from the MD simulations. Naturally, such prediction of ESR spectra from ?first principles? poses many challenges. The systematic approach followed in addressing these challenges will be presented. The developed methodology will be illustrated in the context of a spin-labeled protein [6] and a DNA fragment labeled simultaneously with two spin labels [7].
[1] P. P. Borbat, A. J. Costa-Filho, K. A. Earle, J. K. Moscicki, and J. H. Freed. Electron spin resonance in studies of membranes and proteins. Science, 291:266-269, 2001.
[2] Linda Columbus and Wayne L. Hubbell. A new spin on protein dynamics. TIBS, 27:288-295, 2002.
[3] Gail E. Fanucci and David S. Cafiso. Recent advances and applications of site-directed spin labeling. Curr. Opin. Struct. Biol., 16:644-653, 2006.
[4] E. Perozo, D. M. Cortes, and L. G. Cuello. Structural Rearrangements Underlying K+-Channel Activation Gating. Science, 285:73?78, 1999.
[5] E. Perozo, D. M. Cortes, P. Sompornpisut, A. Kloda, and B. Martinac. Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Nature, 418:942?948, 2002.
[6] Deniz Sezer, Jack H. Freed, and Beno?ıt Roux. Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. J. Am. Chem. Soc., 131(7): 2597-2605, 2009.
[7] Deniz Sezer and Snorri Th. Sigurdsson. Simulating electron spin resonance spectra of macromolecules labeled with two dipolar-coupled nitroxide spin labels from trajectories (submitted).

Biographical sketch
Deniz Sezer studied Electrical Engineering and Physics at Bo?gazi¸ci University, graduating in 1998. He obtained his Master?s degree in Physics from the same university in 2000. Between 2000 and 2008 he was a graduate student in the Physics department at Cornell University. During this period he worked successively at the following departments (institutions): Physics (Cornell University), Physiology and Biophysics (Graduate School of Medical Sciences of Cornell University), and Biochemistry and Molecular Biology (The University of Chicago). His PhD research was conducted in the group of Prof. Beno?ıt Roux, who is mostly known for his computational work on potassium channels. From early 2008 until the end of 2009 Deniz was a postdoctoral researcher in the Institute of Physical and Theoretical Chemistry at the University of Frankfurt. There he worked in the group of Prof. Thomas Prisner, who is pushing the limits of electron spin resonance (ESR) spectroscopy by developing new methodologies for the characterization of biomolecular systems. Since February 2010 Deniz is a faculty member in the Faculty of Engineering and Natural Sciences at Sabancı University, where he teaches courses in Structural Biology, Biophysics, and Mathematical Methods for Scientists and Engineers. During both his doctoral and postdoctoral research Deniz worked on the development of computational tools that make possible the interpretation of ESR experiments of biomolecules in terms of their atomic structure and dynamics. He continues working in this direction at Sabancı University.


The posts will be about current news and researches about cardiovascular mechanics and biofluid dynamics in Turkey.