sangria-bib.bib
zhaoJan2010
@ARTICLE{raval2010,
abstract = {{Background? The mechanical fragility index (MFI) is an in vitro measurement of the extent of RBC sublethal injury. Sublethal injury might constitute a component of the RBC storage lesion, thus the MFI was determined serially during routine RBC storage.
Methods? Leucoreduced AS-5- and SAGM-preserved RBCs were stored under routine blood bank conditions. The mechanical fragility (MF) of each unit was serially measured during storage.
Results? For both AS-5 and SAGM units, male and female RBCs demonstrated statistically significant increases in the MFI during storage. The MFI was significantly lower in AS-5 units compared to SAGM units throughout storage. Female RBCs had significantly lower MFI vs. male RBCs in both AS-5 and SAGM units at all times. No significant differences in MFI were observed between ABO groups for both genders for AS-5 RBCs.
Conclusions? The MF of RBCs increases during storage. Both gender and preservation solution influenced the MFI; however, the male:female MFI ratios were similar at all time-points and remained stable, suggesting that gender-based biological differences exist independent of storage solution. The MF could be a useful test for evaluating the effect of novel interventions intended to mitigate the susceptibility of RBCs to sublethal injury during storage.}},
author = {Raval JS, Waters JH, Seltsam A, Scharberg EA, Richter E, Daly AR, Kameneva MV, Yazer MH.},
journal = {Vox Sanguinis},
month = {November},
title = {{The use of the mechanical fragility test in evaluating sublethal RBC injury during storage}},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1423-0410.2010.01365.x/abstract},
year = {2010}
}
zhaoJan2010
@ARTICLE{zhaoJan2010,
abstract = {{The accumulation of platelets near the blood vessel wall or artificial surface is an important factor in the cascade of events responsible for coagulation and/or thrombosis. In small blood vessels and flow channels this phenomenon has been attributed to the blood phase separation that creates a red blood cell (RBC)-poor layer near the wall. We hypothesized that blood soluble drag-reducing polymers (DRP), which were previously shown to lessen the near-wall RBC depletion layer in small channels, may consequently reduce the near-wall platelet excess. This study investigated the effects of DRP on the lateral distribution of platelet-sized fluorescent particles (diam. = 2 ?m, 2.5 × 10?/ml) in a glass square microchannel (width and depth = 100 ?m). RBC suspensions in PBS were mixed with particles and driven through the microchannel at flow rates of 6-18 ml/h with and without added DRP (10 ppm of PEO, MW = 4500 kDa). Microscopic flow visualization revealed an elevated concentration of particles in the near-wall region for the control samples at all tested flow rates (between 2.4 ± 0.8 times at 6 ml/h and 3.3 ± 0.3 times at 18 ml/h). The addition of a minute concentration of DRP virtually eliminated the near-wall particle excess, effectively resulting in their even distribution across the channel, suggesting a potentially significant role of DRP in managing and mitigating thrombosis.}},
author = {Zhao R., Marhefka J.N., Antaki J.F., and Kameneva M.V.},
citeulike-article-id = {21084744},
journal = {Biorheology},
month = {January},
title = {{Drag-reducing polymers reduce near-wall concentration of platelets in microchannel blood flow}},
url = {http://iospress.metapress.com/content/c612403jn2874k77/},
year = {2010}
}
@ARTICLE{sjhIntJEngSci,
abstract = {{Computational prediction of blood damage has become a crucial tool for evaluating blood-wetted medical devices and pathological hemodynamics. A difficulty arises in predicting blood damage under turbulent flow conditions because the total stress is indeterminate. Common practice uses the Reynolds stress as an estimation of the total stress causing damage to the blood cells. This study investigates the error introduced by making this substitution, and further shows that energy dissipation is a more appropriate metric of blood trauma.}},
author = {Hund, Samuel J. and Antaki, James F. and Massoudi, Mehrdad},
citeulike-article-id = {7985260},
citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ijengsci.2010.09.003},
citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0020722510001874},
day = {08},
doi = {10.1016/j.ijengsci.2010.09.003},
issn = {00207225},
journal = {International Journal of Engineering Science},
month = {October},
posted-at = {2010-10-10 23:37:39},
title = {{On the representation of turbulent stresses for computing blood damage}},
url = {http://dx.doi.org/10.1016/j.ijengsci.2010.09.003},
year = {2010}
}
@ARTICLE{sjhThesis,
AUTHOR = {Hund, S.J.},
TITLE = {{\bf A Computational Model of Platelet Mediated Thrombosis for the Evaluation oand Design of Medical Devices}},
JOURNAL = {Carnegie Mellon University, Biomedical Engineering},
ORGANIZATION = {},
MONTH = {September},
YEAR = 2010,
VOLUME = ,
NUMBER = ,
PAGES = {440},
PDF = {},
ABSTRACT = {Platelet mediated thrombosis is a significant source of complications during the use of blood-wetted medical devices. Despite over a hundred years of research, there are no complete mathematical models of this complex spatio-temporal phenomenon. The research of Sorensen et al. has lead to an elegant representation of this process; however it implemented simplified reaction kinetics, lacked shear induces platelet activation (SIPA), and was insufficient to predict platelet activation in disturbed flow. This thesis examines the activation kinetics with the goal of predicting activation that better represent experimentally observed events. Furthermore, it included models for for SIPA by direct activation of the platelets and indirect activation of platelest through hemolysis. Finally an extended convection-diffusion model for platelet transport is presented that predicts the inhomogenous transport of platelets in flowing blood. The performance of the model is demonstrated in three test design problems: 1) ventricular cannulation, 2) cracks, steps, and crevices, and 3) a bearing strut support system.
}
}
@ARTICLE{sjhThesis,
AUTHOR = {Hund, S.J.},
TITLE = {{\bf A Computational Model of Platelet Mediated Thrombosis for the Evaluation oand Design of Medical Devices}},
JOURNAL = {Carnegie Mellon University, Biomedical Engineering},
ORGANIZATION = {},
MONTH = {September},
YEAR = 2010,
VOLUME = ,
NUMBER = ,
PAGES = {440},
PDF = {},
ABSTRACT = {Platelet mediated thrombosis is a significant source of complications during the use of blood-wetted medical devices. Despite over a hundred years of research, there are no complete mathematical models of this complex spatio-temporal phenomenon. The research of Sorensen et al. has lead to an elegant representation of this process; however it implemented simplified reaction kinetics, lacked shear induces platelet activation (SIPA), and was insufficient to predict platelet activation in disturbed flow. This thesis examines the activation kinetics with the goal of predicting activation that better represent experimentally observed events. Furthermore, it included models for for SIPA by direct activation of the platelets and indirect activation of platelest through hemolysis. Finally an extended convection-diffusion model for platelet transport is presented that predicts the inhomogenous transport of platelets in flowing blood. The performance of the model is demonstrated in three test design problems: 1) ventricular cannulation, 2) cracks, steps, and crevices, and 3) a bearing strut support system.
}
}
@ARTICLE{jkimFDA10b,
AUTHOR = {Kim J., Gandini A., and Antaki J.F.},
TITLE = {{\bf Numerical study of magnetic field separator to remove malaria-infected red blood cells from the whole blood}},
JOURNAL = {FDA Workshop on Computer Methods for Cardiovascular Devices},
ORGANIZATION = {},
MONTH = {June},
YEAR = 2010,
VOLUME = ,
NUMBER = ,
PAGES = {},
PDF = {},
ABSTRACT = {
}
}
@ARTICLE{shundFDA10a,
AUTHOR = {Hund S.J., Massoudi M., Antaki J.F.},
TITLE = {{\bf Representation of Turbulent Stress for Computing Blood Damage}},
JOURNAL = {FDA Workshop on Computer Methods for Cardiovascular Devices},
ORGANIZATION = {},
MONTH = {June},
YEAR = 2010,
VOLUME = ,
NUMBER = ,
PAGES = {},
PDF = {./publications/HundSamuel_FDA_ReynoldsStress.pdf},
ABSTRACT = {Computational prediction of blood damage has become a crucial tool for evaluating
blood-wetted medical devices and pathological hemodynamics. A difficulty arises in predicting
blood damage under turbulent flow conditions because the total stress is indeterminate. Common
practice uses the Reynolds stress as an estimation of the total stress. This study investigates
the error introduced by making this substitution, and further shows that energy dissipation is
a more appropriate metric of blood trauma.
}
}
@ARTICLE{massoudi08,
AUTHOR = {Massoudi M. and Antaki J.F.},
TITLE = {{\bf An Anisotropic Constitutive Equation for the Stress Tensor of Blood Based on Mixture Theory}},
JOURNAL = {Mathematical Problems in Engineering},
ORGANIZATION = {},
MONTH = {},
YEAR = 2008,
VOLUME = ,
NUMBER = ,
PAGES = {1-31},
PDF = {},
ABSTRACT = {
}
}
@ARTICLE{zhao08,
AUTHOR = {Zhao R., Marhefka J.N., Shu F., Hund S.J., Kameneva M.V., and Antaki J.F.},
TITLE = {{\bf Micro-flow visualization of red blood cell-enhanced platelet concentration at sudden expansion}},
JOURNAL = {Annals of Biomedical Engineering},
ORGANIZATION = {},
MONTH = {},
YEAR = 2008,
VOLUME = 36,
NUMBER = 7,
PAGES = {1130-41},
PDF = {},
ABSTRACT = {
Microscopic steps and crevices are inevitable features within prosthetic blood-contacting
devices. This study aimed to elucidate the thrombogenicity of the associated microscopic flow
features by studying the transport of fluorescent platelet-sized particles in a suspension of
red blood cells (RBCs) flowing through a 100 microm:200 microm sudden expansion. Micro-flow
visualization revealed a strong influence of hematocrit upon the path of RBCs and spatial
concentration of particles. At all flow rates studied (Re = 8.3-41.7) and hematocrit 20% and
lower, RBC streamlines were found to detach from the microchannel wall creating an RBC-depleted
zone inside the step that was much larger than the cells themselves. However, the observed
distribution of particles was relatively homogeneous. By contrast, the RBC streamlines of
samples with hematocrit equal to or greater than 30% more closely followed the contour of the
microchannel, yet exhibited enhanced concentration of particles within the corner. The
corresponding size of the cell depletion layer was comparable with the size of the cells. This
study implies that local platelet concentration in blood within the physiological range of
hematocrit can be elevated within the flow separation region of a sudden expansion and
implicates the role of RBCs in causing this effect.
}
}
@ARTICLE{zhao07,
AUTHOR = {Zhao R., Kameneva M.V., and Antaki J.F.},
TITLE = {{\bf Investigation of platelet margination phenomena at elevated shear stress}},
JOURNAL = {Biorheology},
ORGANIZATION = {},
MONTH = {},
YEAR = 2007,
VOLUME = 44,
NUMBER = 3,
PAGES = {161-77},
PDF = {},
ABSTRACT = {
}
}
@ARTICLE{zhao06,
AUTHOR = {Zhao R., Antaki J.F., Naik T., Bachman T.N., Kameneva M.V., and Wu Z.J.},
TITLE = {{\bf Microscopic investigation of erythrocyte deformation dynamics}},
JOURNAL = {Biorheology},
ORGANIZATION = {},
MONTH = {},
YEAR = 2006,
VOLUME = 43,
NUMBER = 6,
PAGES = {747-65},
PDF = {},
ABSTRACT = {
The understanding of erythrocyte deformation under conditions of high shear stress and short
exposure time is central to the study of hemorheology and hemolysis within prosthetic blood
contacting devices. A combined computational and experimental microscopic study was conducted
to investigate the erythrocyte deformation and its relation to transient stress fields. A
microfluidic channel system with small channels fabricated using polydimethylsiloxane on the
order of 100 mum was designed to generate transient stress fields through which the
erythrocytes were forced to flow. The shear stress fields were analyzed by three-dimensional
computational fluid dynamics. Microscopic images of deforming erythrocytes were experimentally
recorded to obtain the changes in cell morphology over a wide range of fluid dynamic stresses.
The erythrocyte elongation index (EI) increased from 0 to 0.54 with increasing shear stress up
to 123 Pa. In this shear stress range, erythrocytes behaved like fluid droplets, and deformed
and flowed following the surrounding fluid. Cells exposed to shear stress beyond 123 Pa (up to
5170 Pa) did not exhibit additional elongation beyond EI=0.54. Two-stage deformation of
erythrocytes in response to shear stress was observed: an initial linear elongation with
increasing shear stress and a plateau beyond a critical shear stress.}
}
@ARTICLE{shund09,
AUTHOR = {Hund, S.J. and Antaki J.F.},
TITLE = {{\bf An extended convection diffusion model for red blood cell-enhanced transport of thrombocytes and leukocytes.}},
JOURNAL = {Phys. Med. Biol.},
ORGANIZATION = {},
MONTH = {October},
YEAR = 2009,
VOLUME = 54,
NUMBER = 20,
PAGES = {6415-35},
PDF = {},
ABSTRACT = {
Transport phenomena of platelets and white blood cells (WBCs) are fundamental to the processes of vascular
disease and thrombosis. Unfortunately, the dilute volume occupied by these cells is not amenable to fluid-continuum
modeling, and yet the cell count is large enough that modeling each individual cell is impractical for most
applications. The most feasible option is to treat them as dilute species governed by convection and diffusion;
however, this is further complicated by the role of the red blood cell (RBC) phase on the transport of these cells.
We therefore propose an extended convection-diffusion (ECD) model based on the diffusive balance of a fictitious
field potential, Psi, that accounts for the gradients of both the dilute phase and the local hematocrit. The ECD
model was applied to the flow of blood in a tube and between parallel plates in which a profile for the RBC
concentration field was imposed and the resulting platelet concentration field predicted. Compared to prevailing
enhanced-diffusion models that dispersed the platelet concentration field, the ECD model was able to simulate a
near-wall platelet excess, as observed experimentally. The extension of the ECD model depends only on the ability
to prescribe the hematocrit distribution, and therefore may be applied to a wide variety of geometries to
investigate platelet-mediated vascular disease and device-related thrombosis.}
}
@ARTICLE{kimnj09,
AUTHOR = {Marhefka J.N., Zhao R., Wu Z.J., Velankar S.S., Antaki J.F., and Kameneva M.V.},
TITLE = {{\bf Parametric study of blade tip clearance, flow rate, and impeller speed on blood damage in rotary blood pump.}},
JOURNAL = {Artificial Organs},
ORGANIZATION = {},
MONTH = {June},
YEAR = 2009,
VOLUME = 33,
NUMBER = 6,
PAGES = {468-74},
PDF = {},
ABSTRACT = {
Phenomenological studies on mechanical hemolysis in rotary blood pumps have provided empirical
relationships that predict hemoglobin release as an exponential function of shear rate and time. However, these
relations are not universally valid in all flow circumstances, particularly in small gap clearances. The
experiments in this study were conducted at multiple operating points based on flow rate, impeller speed, and tip
gap clearance. Fresh bovine red blood cells were resuspended in phosphate-buffered saline at about 30% hematocrit,
and circulated for 30 min in a centrifugal blood pump with a variable tip gap, designed specifically for these
studies. Blood damage indices were found to increase with increased impeller speed or decreased flow rate. The
hemolysis index for 50-microm tip gap was found to be less than 200-microm gap, despite increased shear rate. This
is explained by a cell screening effect that prevents cells from entering the smaller gap. It is suggested that
these parameters should be reflected in the hemolysis model not only for the design, but for the practical use of
rotary blood pumps, and that further investigation is needed to explore other possible factors contributing to
hemolysis.}
}
@ARTICLE{marhefkaB09,
AUTHOR = {Kim N.J., Diao C., Ahn K.H., Lee S.J., Kameneva M.V., and Antaki J.F.},
TITLE = {{\bf Drag reducing polymers improve tissue perfusion via modification of the RBC traffic in microvessels}},
JOURNAL = {Bhiorheology},
ORGANIZATION = {},
MONTH = {},
YEAR = 2009,
VOLUME = 46,
NUMBER = 4,
PAGES = {281-92},
PDF = {},
ABSTRACT = {
This paper reports a novel, physiologically significant, microfluidic phenomenon generated by nanomolar
concentrations of drag-reducing polymers (DRP) dissolved in flowing blood, which may explain previously
demonstrated beneficial effects of DRP on tissue perfusion. In microfluidic systems used in this study, DRP
additives were found to significantly modify traffic of red blood cells (RBC) into microchannel branches as well as
reduce the near-wall cell-free layer, which normally is found in microvessels with a diameter smaller than 0.3 mm.
The reduction in plasma layer size led to attenuation of the so-called "plasma skimming" effect at microchannel
bifurcations, increasing the number of RBC entering branches. In vivo, these changes in RBC traffic may facilitate
gas transport by increasing the near vessel wall concentration of RBC and capillary hematocrit. In addition, an
increase in near-wall viscosity due to the redirection of RBC in this region may potentially decrease vascular
resistance as a result of increased wall shear stress, which promotes endothelium mediated vasodilation. These
microcirculatory phenomena can explain the previously reported beneficial effects of DRP on hemodynamics in vivo
observed in many animal studies. We also report here our finding that DRP additives reduce flow separations at
microchannel expansions, deflecting RBC closer to the wall and eliminating the plasma recirculation zone. Although
the exact mechanism of the DRP effects on RBC traffic in microchannels is yet to be elucidated, these findings may
further DRP progress toward clinical use.}
}
@ARTICLE{AnandRajagopal2004,
AUTHOR = {Anand, M. and Rajagopal, K.R.},
TITLE = {{\bf A shear-thinning viscoelastic fluid model for describing the
flow of blood}},
JOURNAL = {International Journal of Cardiovascular Medicine and Science},
ORGANIZATION = {Medical and Engineering Publishers, Inc.},
MONTH = {},
YEAR = 2004,
VOLUME = 4,
NUMBER = 2,
PAGES = {59-68},
PDF = {publications/MAKRR2004.pdf},
ABSTRACT = {
A model is developed for the flow of blood, within a thermodynamic
framework that takes cognizance of the fact that viscoelastic fluids
can remain stress free in several configurations, i.e., such bodies
have multiple natural configurations (see Rajagopal 1995, Rajagopal and
Srinivasa 2000). This thermodynamic framework leads to blood being
characterised by four independent parameters that reflect the
elasticity, the viscosity of the plasma, the formation of rouleaus and
their effect on the viscosity of blood, and the shear thinning that
takes place during the flow. The model emerges in a hierarchy of
increasingly complex nonsimple viscoelastic fluid models, and in this
study two other models in the same class (proposed by Rajagopal and
Srinivasa 2000) are also considered. The efficacy of these models in
describing the response of blood is investigated. Among the models
studied, the proposed model is not only best able to describe the
response of blood but is the first to have rigorous thermodynamic
moorings. The predictions of the model agree exceptionally well with
the data that is available for steady flow and oscillatory flow
experiments, while the two other models are inadequate to describe
oscillatory flows (a serious shortcoming as oscillatory flows are the
most natural flows that blood undergoes).
The procedure for determining (assigning) the material parameters that
characterize blood will be outlined in detail and the results of
numerical simulations are compared with the data. This method is also
used to fix the relaxation times in the model proposed by Yeleswarapu
1996, and the importance of the relaxation times for simulating
pulsatile flow is highlighted.}
}
@ARTICLE{MAKRKRR2003,
AUTHOR = {Anand, M. and Rajagopal, K. and Rajagopal, K.R.},
TITLE = {{\bf A model incorporating some of the mechanical and biochemical
factors underlying clot formation and dissolution in flowing blood}},
JOURNAL = {Journal of Theoretical Medicine},
ORGANIZATION = {Taylor and Francis},
MONTH = {},
YEAR = 2003,
VOLUME = 5,
NUMBER = {3--4},
PAGES = {183-218},
PDF = {publications/JTM2003.pdf},
ABSTRACT = {
Multiple interacting mechanisms control the formation and dissolution
of clots to maintain blood in a state of delicate balance. In addition to a
myriad of biochemical reactions, rheological factors also play a crucial role
in modulating the response of blood to external stimuli. To date, a
comprehensive model for clot formation and dissolution, that takes into
account the biochemical, medical and rheological factors, has not been
put into place, the existing models emphasizing either one or the other of the
factors. In this paper, after discussing the various biochemical, physiologic
and rheological factors at some length, we develop a model for clot formation
and dissolution that incorporates many of the relevant crucial factors that
have a bearing on the problem. The model, though just a first step towards
understanding a complex phenomenon goes further than previous models in
integrating the biochemical, physiologic and rheological factors that come
into play.}
}
@INPROCEEDINGS{cardoze04,
AUTHOR = {Cardoze D. and Cunha A. and Miller G. and Phillips T. and Walkington N.},
TITLE = {{\bf A {B}ezier-based Approach to Unstructured Moving Meshes}},
BOOKTITLE = {Proceedings of the 20th Symposium on Computational Geometry},
YEAR = {2004},
MONTH = {June},
PUBLISHER = {ACM}
}
@MISC{seth-2003,
AUTHOR = {Seth Green and George Turkiyyah and Duane Storti},
TITLE = {{\bf Methods for the large scale simulation of blood cell
membranes}},
HOWPUBLISHED = {Second International Congress on Cardiovascular Mechanics},
YEAR = {2003},
ADDRESS = {Bethesda, Maryland, USA},
NOTE = {Poster session presentation}
}
@ARTICLE{akcelik-2001,
AUTHOR = {V. Akcelik and B. Jaramaz and O. Ghattas},
TITLE = {{\bf Nearly Orthogonal Two-Dimensional Grid Generation with
Aspect Ratio Control}},
JOURNAL = {Journal of Computational Physics},
YEAR = {2001},
VOLUME = {171}
}
@INPROCEEDINGS{NBH01,
AUTHOR = {Aleksandar Nanevski and Guy Blelloch and Robert Harper},
PDF = {publications/icfp01.pdf},
TITLE = {{\bf Automatic Generation of Staged Geometric Predicates}},
BOOKTITLE = {ACM International Conference on Functional Programming (ICFP)},
MONTH = {September},
YEAR = 2001
}
@ARTICLE{wu:2001,
AUTHOR = {Wu ZJ and RK Gottlieb and GW Burgreen and JA Holmes and DC Borzelleca and MV Kameneva and BP Griffith and JF Antaki},
TITLE = {{\bf Investigation of fluid dynamics within a miniature
mixed flow blood pump}},
JOURNAL = {Experiments in Fluids},
YEAR = {2001},
VOLUME = {31}
}
@ARTICLE{antaki:ao,
AUTHOR = {Burgreen GW and Antaki JF and Wu ZJ and Holmes AJ},
TITLE = {{\bf Computational fluid dynamics as a development tool for rotary
blood pumps}},
JOURNAL = {Artificial Organs},
YEAR = {2001},
VOLUME = {25}
}
@INPROCEEDINGS{ABH02,
AUTHOR = {Umut Acar and Guy Blelloch and Robert Harper},
PDF = {publications/popl02.pdf},
TITLE = {{\bf Adaptive Functional Programming}},
BOOKTITLE = {ACM Symposium on Principles of Programming Languages (POPL)},
MONTH = {January},
YEAR = 2002,
ABSTRACT = {
An adaptive computation maintains the relationship between its input
and output as the input changes. Although various techniques for
adaptive computing have been proposed, they remain limited in their
scope of applicability. We propose a general mechanism for adaptive
computing that enables one to make any purely-functional program adaptive.
We show that the mechanism is practical by giving an efficient
implementation as a small ML library. The library consists of three
operations for making a program adaptive, plus two operations for
making changes to the input and adapting the output to these changes.
We give a general bound on the time it takes to adapt the output, and
based on this, show that an adaptive Quicksort adapts its output in
logarithmic time when its input is extended by one key.
To show the safety and correctness of the mechanism we give a formal
definition of AFL, a call-by-value functional language extended
with adaptivity primitives. The modal type system of AFL enforces
correct usage of the adaptivity mechanism, which can only be checked at
run time in the ML library. Based on the AFL dynamic semantics,
we formalize the change-propagation algorithm and prove its correctness.
}
}
@ARTICLE{BCG03,
AUTHOR = {Guy E. Blelloch and Perry Cheng and Phillip B. Gibbons},
TITLE = {{\bf Scalable Room Synchronizations}},
JOURNAL = {Theory of Computing Systems (TOCS)},
YEAR = 2003,
VOLUME = 36,
NUMBER = 5,
ABSTRACT = {
This paper presents a scalable solution to the group mutual exclusion
problem, with applications to linearizable stacks and queues, and
related problems. Our solution allows entry and exit from the
mutually exclusive regions in $O(t_r + \tau)$ time, where $t_r$ is the
maximum time spent in a critical region by a user, and $\tau$ is the
maximum time taken by any instruction, including a fetch-and-add
instruction. This bound holds regardless of the number of users. We
describe how stacks and queues can be implemented using two regions,
one for pushing (enqueueing) and one for popping (dequeueing). These
implementations are particularly simple, are linearizable, and support
access in time proportional to a fetch-and-add operation. In
addition, we present experimental results comparing room
synchronizations with the Keane-Moir algorithm for group mutual
exclusion.}
}
@ARTICLE{BBCHMW01,
AUTHOR = {Guy Blelloch and Hal Burch and Karl Crary and Robert Harper and Gary Miller and Noel Walkington},
PDF = {publications/jfp.pdf},
TITLE = {{\bf Persistent Triangulations}},
JOURNAL = {Journal of Functional Programming (JFP)},
MONTH = {September},
YEAR = 2001,
VOLUME = 11,
NUMBER = 51,
ABSTRACT = {
Triangulations of a surface are of fundamental importance in computational
geometry, computer graphics, and engineering and scientific simulations.
Triangulations are ordinarily represented as mutable graph structures for
which both adding and traversing edges take constant time per operation.
These representations of triangulations make it difficult to support
\emph{persistence}, including ``multiple futures'', the ability to use a
data structure in several unrelated ways in a given computation; ``time
travel'', the ability to move freely among versions of a data structure; or
parallel computation, the ability to operate concurrently on a data
structure without interference.
We present a purely functional interface and representation of triangulated
surfaces, and more generally of simplicial complexes in higher dimensions.
In addition to being persistent in the strongest sense, the interface more
closely matches the mathematical definition of triangulations (simplicial
complexes) than do interfaces based on mutable representations. The
representation, however, comes at the cost of requiring $O(\lg n)$ time for
traversing or adding triangles (simplices), where $n$ is the number of
triangles in the surface. We show both analytically and experimentally that
for certain important cases, this extra cost does not seriously affect
end-to-end running time. Analytically, we present a new randomized
algorithm for 3-dimensional Convex Hull based on our representations for
which the running time matches the $\Omega(n \log n)$ lower-bound for the
problem. This is achieved by using only $O(n)$ traversals of the surface.
Experimentally, we present results for both an implementation of the
3-dimensional Convex Hull and for a terrain modeling algorithm, which
demonstrate that, although there is some cost to persistence, it seems to be
a small constant factor.}
}
@INPROCEEDINGS{miller:imr:2002,
AUTHOR = {Miller G. L. and Pav S. and Wakington N. J.},
TITLE = {{\bf Fully Incremental 3D Delaunay Refinement Mesh
Generation}},
BOOKTITLE = {11th International Meshing Roundtable},
YEAR = {2002}
}
@ARTICLE{kameneva:asaio:2002,
AUTHOR = {Kameneva, MV and Marad, PF and Brugger, JM and Repko, BM and
Wang, JH and Moran, J and Borovetz HS},
TITLE = {{\bf In vitro evaluation of hemolysis and sublethal blood
trauma in a novel subcutaneous vascular access system for
hemodialysis}},
JOURNAL = {ASAIO Journal},
YEAR = {2002},
VOLUME = {48}
}
@ARTICLE{kihara:2003,
AUTHOR = {Kihara, S and Litwak, KN and Nichols, L and Litwak, P and
Kamenevam, MV and Wu, J and Kormos, RL and Griffith, BP},
TITLE = {{\bf Smooth muscle cell hypertrophy of renal cortex
arteries with chronic continuous flow left ventricular assist}},
JOURNAL = {Ann. Thorac. Surg.},
YEAR = {2003},
VOLUME = {75}
}
@ARTICLE{kameneva:2002,
AUTHOR = {Kameneva, MV},
TITLE = {{\bf Hemorheological aspects of flow induced blood trauma}},
JOURNAL = {Biorheology},
YEAR = {2002},
VOLUME = {39}
}
@ARTICLE{kameneva:asaio:2003,
AUTHOR = {Kameneva MV and Repko BM and Krasik EF and Perricelli BC and
Borovetz HS},
TITLE = {{\bf Reduction of hemolysis by polyethylene glycol additives
in red blood cell suspension exposed to mechanical stress}},
JOURNAL = {ASAIO Journal},
YEAR = {2003}
}
@ARTICLE{kihara:organs:2003,
AUTHOR = {Kihara S and Yamazaki K and Litwak KN and Litwak P and
Kameneva MV and Ushiyama H and Tokuno T and Borzelleca DC and Umezu M and
Tomioka J and Tagusari O and Akimoto T and Koyanagi H and Kurosawa H and
Kormos RL and Griffith BP},
TITLE = {{\bf In Vivo Evaluation of
a MPC Polymer Coated Continuous Flow Left Ventricular Assist System}},
JOURNAL = {Artificial Organs},
YEAR = {2003},
VOLUME = {27}
}
@ARTICLE{litwak:asaio:2003,
AUTHOR = {Litwak, KN and Kihara S and Kameneva MV and Litwak P and Uryash A and Wu J and Griffith BP},
TITLE = {{\bf Effects of continuous flow left ventricular assist
device support on skin tissue microcirculation and aortic
hemodynamics}},
JOURNAL = {ASAIO Journal},
YEAR = {2003},
VOLUME = {49}
}
@ARTICLE{liu-noel-2002,
AUTHOR = {Liu, C. and Walkington, N. J.},
TITLE = {{\bf Mixed Methods for the Approximation of Liquid Crystal
Flows}},
JOURNAL = {M2AN},
YEAR = {2002},
VOLUME = {36}
}
@INPROCEEDINGS{BBCK03,
AUTHOR = {Daniel K. Blandford and Guy E. Blelloch and David E. Cardoze and
Clemens Kadow},
PS = {publications/BBCK03.ps},
TITLE = {{\bf Compact Representations of Simplicial Meshes in Two and Three
Dimensions}},
BOOKTITLE = {12th International Meshing Roundtable},
MONTH = SEP,
YEAR = 2003,
ABSTRACT = {We describe data structures for representing simplicial meshes
compactly while supporting online queries and updates efficiently.
Our representation requires about a factor of five less memory
than the most efficient standard representations of triangular or
tetrahedral meshes, while efficiently supporting traversal among
simplices, storing data on simplices, and insertion and deletion of
simplices.
Our implementation of the data structures uses about 5 bytes/triangle
in two dimensions (2D) and 7.5 bytes/tetrahedron in three dimensions
(3D). We use the representations to implement 2D and 3D incremental
algorithms for generating a Delaunay mesh. The 3D algorithm can
generate 100 Million tetrahedrons with 1 Gbyte of memory, including
the space for the coordinates and all data used by the algorithm. The
runtime of the algorithm is as fast as Shewchuk's Pyramid code, the
most efficient we know of, and uses a factor of 3.5 less memory
overall.
}
}
@ARTICLE{liu:siam02,
AUTHOR = {Liu, C. and Walkington, N. J.},
TITLE = {{\bf Convergence of Numerical Approximations of the
Incompressible {Navier Stokes} Equations with Variable Density and Viscosity}},
JOURNAL = {SIAM Journal on Numerical Analysis},
YEAR = {2002}
}
@INPROCEEDINGS{malcevic-2003,
AUTHOR = {Ivan Malcevic},
TITLE = {{\bf Dynamic Finite Element Meshes for 3D Lagrangian CFD}},
BOOKTITLE = {Proceedings of AIAA Computational Fluid Dynamics Conference},
YEAR = {2003}
}
@INPROCEEDINGS{green:acm02,
AUTHOR = {S. Green and G. Turkiyyah and D. Storti},
TITLE = {{\bf Subdivision-Based Multilevel Methods for the Large Scale
Simulation of Thin Shells}},
BOOKTITLE = {Seventh ACM Proceedings on Solid Modeling and Applications},
YEAR = 2002,
ORGANIZATION = {ACM},
PDF = {publications/sm02-107-green.pdf},
URL = {http://students.washington.edu/sgreen/research.html},
ABSTRACT = {
Subdivision surfaces have become a widely used geometric representation
for general curved three dimensional boundary models and thin shells as
they provide a compact and robust framework for modeling 3D geometry.
More recently, the shape functions used in the subdivision surfaces
framework have been proposed as candidates for use as finite element
basis functions in the analysis and simulation of the mechanical
deformation of thin shell structures. The subdivision shape functions
automatically provide the necessary continuity required for representing
the solution of the governing equations, which can be difficult to
provide with other descriptions.
When coupled with standard solvers, however, such simulations do not
scale well. Given the fourth order nature of the governing equations, the
condition number of the underlying stiffness matrices scale poorly as the
number of elements is increased. Run time costs associated with
high-resolution simulations ($10^5$ degrees of freedom or more) become
prohibitive.
In this paper, we describe an algorithm that exploits the hierarchical,
multilevel structure of subdivision surfaces to accelerate the
convergence of solution strategies. The main contribution of the paper
is to show that the subdivision framework can be used not only for
representing the geometry of the solid and the mechanics of the
simulation, but also for accelerating the numerical solution.
Specifically the subdivision matrix and its transpose are used as the
prolongation and restriction operations in a multilevel preconditioner.
Our method allows us to construct practical simulations that are
effective on a broad range of problems. Our examples show that the run
time of the algorithm presented scales nearly linearly in time with
problem size.}
}
@UNPUBLISHED{green:ijnme03,
AUTHOR = {S. Green and G. Turkiyyah and D. Storti},
TITLE = {{\bf 2nd Order Accurate Constraints for Subdivision Elements}},
NOTE = {In submission to International Journal for Numerical
Methods in Engineering},
ABSTRACT = {
We present a new method for enforcing boundary conditions within
subdivision surface finite element simulations of thin shells. The
proposed framework is shown to be second order accurate for displacements
with respect to increasing refinement for simply-supported and clamped
boundary conditions. Second order accuracy on the boundary is consistent
with the accuracy of subdivision based approaches for the interior of a
body. Our proposed framework is applicable to both triangular and
quadrilateral refinement schemes, and does not impose any topological
requirements upon the underlying subdivision control mesh. Several
examples from the Belytschko obstacle course of
benchmark problems are used to demonstrate the convergence of the
scheme.}
}
@ARTICLE{AnandRaj2002,
AUTHOR = {Anand, M. and Rajagopal, K.R.},
TITLE = {{\bf A mathematical model to describe the change in the
constitutive character of blood due to platelet activation}},
JOURNAL = {Comptes Rendus M{\'e}canique},
ORGANIZATION = {Academie des Sciences, Editions scientifiques et
medicales Elsevier SAS},
MONTH = {},
YEAR = 2002,
VOLUME = 330,
NUMBER = 8,
PAGES = {557-562},
PDF = {publications/MAKRR2002.pdf},
ABSTRACT = {
Though a minor component by volume, platelets can have a profound
influence on the flow characteristics of blood and thereby have serious
consequences with regard to cardiovascular functions. Platelets are
extremely sensitive to chemical agents as well as mechanical inputs and
platelet activation is a necessary precursor to many life threatening
medical conditions such as acute myocardial infarction, most strokes,
acute arterial occlusion, venous thrombosis and pulmonary embolism. In
cardiovascular devices such as ventricular assist devices and
prosthetic heart valves, high shear stresses can trigger platelet
activation. Moreover, such devices have artificial surfaces that are
thrombogenic, the thrombotic deposition contributing to the failure of
the device. Thus, there is a need to develop a mathematical model for
the flow of blood that takes into account platelet activation, no such
model being available at the moment.While there has been considerable
amount of work in blood rheology, the role of platelets in the flow
characteristics of blood has been largely ignored. This study addresses
this lacuna.}
}
@UNPUBLISHED{proposal,
AUTHOR = {Guy E. Blelloch and Omar Ghattas and Gary L. Miller and
Noel J. Walkington and James F. Antaki and
Bartley P. Griffith and Marina V. Kameneva Robert L. Kormos and
William R. Wagner and ZhongJun Wu and George M. Turkiyyah},
TITLE = {{\bf {ITR/ACS}: Simulation of flows with Dynamic Interfaces on Multi-Teraflop Computers}},
NOTE = {Sangria Project Proposal},
PS = {publications/proposal.ps.gz},
PDF = {publications/proposal.pdf},
URL = {proposal.html},
ABSTRACT = {
We propose to develop advanced parallel geometric and numerical
algorithms and software for simulating complex flows with dynamic
interfaces. The development of scalable, parallel high-accuracy
algorithms for simulating such flows poses enormous challenges,
particularly on systems with thousands of processors. We will use the
resulting tools to simulate blood flowin artificial heart devices. This
application provides an excellent testbed for the methods we develop:
simulation-based artificial organ design is extremely computationally
challenging and of critical societal importance.
Flows with dynamic interfaces arise in many fluid-solid and fluid-fluid
interaction problems, and are among the most difficult computational
problems in continuum mechanics. Examples abound in the aerospace,
automotive, biomedical, chemical, marine, materials, and wind
engineering sciences. These include large-amplitude vibrations of such
flexible aerodynamic components as high aspect ratio wings and blades;
flows of mixtures and slurries; wind-induced deformation of towers,
antennas, and lightweight bridges; hydrodynamic flows around offshore
structures; interaction of biofluids with elastic vessels; and
materials phase transition problems. We are particularly interested in
modeling the flow of blood, which is a mixture of interacting solid
cells and fluid plasma. Current blood flow models are macroscopic,
treating the mixture as a homogeneous continuum. Microstructural models
resolve individual cell deformations and interactions with the
surrounding fluid plasma. Because of the computational difficulties of
resolving tens of thousands of deforming cellular interfaces, no one to
date has simulated realistic blood flows at the microstructural
level. Yet such simulations are necessary in order to gain a better
understanding of blood damage which is central to improved artificial
organ design and for the development of more rational macroscopic blood
models.
Parallel flow solvers on fixed domains are reasonably well
understood. In contrast, simulating flows with dynamic interfaces is
much more difficult. The central challenges are to develop numerical
algorithms that stably and accurately couple the moving fluid and solid
domains and resolve the deforming interfaces, and geometric algorithms
for evolving and managing the resulting dynamic particle/mesh
systems. The associated dynamic data structures are particularly
troublesome on highly parallel computers, which are made necessary by
the complexity of many applications. Most current methods approach the
difficulties of dynamic interfaces by computing the flow on a fixed,
regular grid. The effect of the dynamic interfaces is then incorporated
either through some type of constraint or force representing the
interface, or through an auxiliary field variable that signifies the
presence of fluid or solid material at a spatial point. Parallelizing
these methods is relatively straightforward, since the flow is computed
on a fixed grid. However, the resulting fixed resolution is a serious
disadvantage if one wants to vary resolution sharply within the
grid. This is the case for example when local interfacial dynamics are
critical, as in blood flow or phase change problems.
Our approach is radically different. We will treat the fluid and solid
domains as collections of particles, with associated meshes, that
evolve over time, and devise numerical algorithms that couple the fluid
and solid together seamlessly. We will attack the difficulty of
generating and managing a constantly evolving mesh/particle system by
creating fundamentally new highly parallel and scalable algorithms for
the convex hull, Delaunay triangulation, meshing, partitioning, and
N-body components. Our preliminary 2D work demonstrates that the
resulting geometric computations can be made very cheap compared to
numerical computations. Despite the conventional wisdom on parallel
dynamic mesh methods, we believe that with careful attention to
fundamental algorithmic issues flow simulations on constantly evolving
domains can be made to scale to the thousands of processors that
characterize multi-teraflop systems.
While microstructural blood flow modeling will serve as our first
application, the computational algorithms and software we create will
be more widely applicable to a variety of fluid solid inter-action
problems. More generally, the core parallel computational geometry
kernels convex hull, Delaunay triangulation, coarsening/refinement,
partitioning, N-body provide generic support for the geometric
computations underlying many dynamic irregular problems. We will create
and publically distribute a portable library of efficient
implementations of these algorithms. Much as the PETSc library has
greatly simplified the task of programming parallel PDE solvers by
providing many of the necessary numerical kernels, we envision a
library of parallel geometric kernels being of great benefit across a
wide range of scientific computing problems that involve dynamic
meshes.
We have assembled a multidisciplinary team that combines Carnegie
Mellon s leadership in computer and computational science with the
University of Pittsburgh Medical Center s world-class program in
artificial organs. This project will support 11 graduate students and a
group of un-dergraduates. These students will be part of a new program
at CMU in Computational Science and Engineering that we are in the
process of establishing. The proposed project will also be part of that
program, and we believe will serve as an archetype of how applications,
computational, computer, and mathematical scientists can work together
to tackle societal problems that cannot be addressed solely from the
vantage of any one discipline. Moreover, we intend to communicate our
work to the broader public (as we have done in the past), in the
process demonstrating how high end computing can contribute to
improving the health of our society. }
}
@ARTICLE{LiWa01,
AUTHOR = {Liu, Chun and Walkington, Noel J.},
TITLE = {{\bf An {E}ulerian description of fluids containing visco-elastic
particles}},
JOURNAL = {Archive for Rational Mechanics and Analysis},
VOLUME = {159},
YEAR = {2001},
NUMBER = {3},
PAGES = {229--252},
ISSN = {0003-9527},
PS = {publications/LiWa01.ps.gz},
PDF = {publications/LiWa01.pdf},
ABSTRACT = {
Equations governing the flow of fluid containing visco-hyperelastic
particles are developed in an Eulerian framework. The novel feature
introduced here is to write an evolution equation for the
strain. It is envisioned that this will simplify numerical codes
which typically compute the strain on Lagrangian meshes moving
through Eulerian meshes. Existence results for the flow of linear
visco-hyperelastic particles in a Newtonian fluid are established
using a Galerkin scheme. }
}
@INPROCEEDINGS{ghattas-malcevic-2000,
AUTHOR = {Omar Ghattas and Ivan Malcevic},
TITLE = {{\bf Parallel dynamic unstructured mesh methods with application
to Lagrangian simulation of flows with deformable boundaries}},
BOOKTITLE = {Proceedings of the 7th International Conference on Numerical
Grid Generation in Computational Field Simulations},
ADDRESS = {Whistler BC, Canada},
MONTH = {September 25--28},
YEAR = {2000}
}
@INPROCEEDINGS{noel-2002,
AUTHOR = {Noel J. Walkington},
TITLE = {{\bf Mathematical Models of Fluids with Structure}},
BOOKTITLE = {Interphase 2002 Conference on Numerical Methods for Free
Boundary Problems},
YEAR = {2002}
}
@ARTICLE{ghattas-malcevic-2002,
AUTHOR = {Omar Ghattas and Ivan Malcevic},
TITLE = {{\bf Dynamic-Mesh Finite Element Method for
Lagrangian Computational Fluid Dynamics}},
JOURNAL = {Finite Elements in Analysis and Design},
YEAR = {2002},
VOLUME = {38}
}
@INPROCEEDINGS{antaki-et-all-sc2000,
AUTHOR = {James F. Antaki and Guy E. Blelloch and Omar Ghattas and Ivan
Malcevic and Gary L. Miller and and Noel J. Walkington},
TITLE = {{\bf A Parallel Dynamic--Mesh Lagrangian Method for Simulation of
Flows with Dynamic Interfaces}},
BOOKTITLE = {Proceedings of Seupercomputing 2000},
YEAR = {2000},
ADDRESS = {Dallas, Texas, USA},
MONTH = {November 4-10},
PS = {publications/sc2000.ps.gz},
PDF = {publications/sc2000.pdf},
ABSTRACT = {
Many important phenomena in science and engineering, including our
motivating problem of microstructural blood flow, can be modeled as
flows with dynamic interfaces. The major challenge faced in simulating
such flows is resolving the interfacial motion. Lagrangian methods are
ideally suited for such problems, since interfaces are naturally
represented and propagated. However, the material description of motion
results in dynamic meshes, which become hopelessly distorted unless
they are regularly regenerated. Lagrangian methods are particularly
challenging on parallel computers, because scalable dynamic mesh
methods remain elusive. Here, we present a parallel dynamic mesh
Lagrangian method for flows with dynamic interfaces. We take an
aggressive approach to dynamic meshing by triangulating the propagating
grid points at every timestep using a scalable parallel Delaunay
algorithm. Contrary to conventional wisdom, we show that the costs of
the geometric components (triangulation, coarsening, refinement, and
partitioning) can be made small relative to the flow solver. For
example, in a simulation of 10 interacting viscous cells with 500,000
unknowns on 64 processors of a Cray T3E, dynamic meshing consumes less
than 5% of a time step. Moreover, our experiments on up to 64
processors show that the computational geometry scales about as well as
the flow solver. Therefore we anticipate that overall scalability on
larger problems will be as good as the flow solver's.}
}