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## Mathematics Faculty: Publications since January 2013

List all publications in the database.    :chronological  alphabetical  combined listing:
%% Addington, Nicolas
@article{fds223834,
Title = {On two rationality conjectures for cubic
fourfolds},
Year = {2014},
Month = {May},
url = {http://arxiv.org/abs/1405.4902},
Key = {fds223834}
}

@article{fds223671,
Author = {N. Addington and M. Lehn},
Title = {On the symplectic eightfold associated to a Pfaffian cubic
fourfold},
Year = {2014},
Month = {April},
url = {http://arxiv.org/abs/1404.5657},
Key = {fds223671}
}

@article{fds223672,
Author = {N. Addington and W. Donovan and E. Segal},
Title = {The Pfaffian-Grassmannian equivalence revisited},
Year = {2014},
Month = {January},
url = {http://arxiv.org/abs/1401.3661},
Key = {fds223672}
}

@article{fds224079,
Author = {N. Addington and R. P. Thomas},
Title = {Hodge theory and derived categories of cubic
fourfolds},
Journal = {Duke Math. J.},
Volume = {163},
Number = {10},
Pages = {1885-1927},
Year = {2014},
url = {http://arxiv.org/abs/1211.3758},
Key = {fds224079}
}

@article{fds223991,
Author = {N. Addington and E. Segal and E. Sharpe},
Title = {D-brane probes, branched double covers, and noncommutative
resolutions},
Journal = {Adv. Theor. Math. Phys.},
Volume = {18},
Number = {6},
Year = {2014},
url = {http://arxiv.org/abs/1211.2446},
Key = {fds223991}
}

@article{fds223494,
Title = {The Brauer group is not a derived invariant},
Year = {2013},
Month = {June},
url = {http://arxiv.org/abs/1306.6538},
Key = {fds223494}
}

@article{fds219852,
Author = {N. Addington and P. Aspinwall},
Title = {Categories of massless D-branes and del Pezzo
surfaces},
Journal = {J. High Energy Phys.},
Volume = {2013},
Number = {7},
Pages = {front matter + 39pp.},
Year = {2013},
url = {http://arxiv.org/abs/1305.5767},
Key = {fds219852}
}

%% Aristotelous, Andreas
@article{fds224099,
Author = {Aristotelous, A. C. and Durrett, R.},
Title = {Fingering in Stochastic Growth Models.},
Journal = {Experimental Mathematics},
Year = {2014},
Month = {July},
Key = {fds224099}
}

@article{fds223440,
Author = {Andreas C. Aristotelous and Ohannes A. Karakashian and Steven
M.Wise},
Title = {Adaptive, Second-Order in Time, Primitive-Variable
Discontinuous Galerkin Schemes for a Cahn-Hilliard Equation
with a Mass Source},
Journal = {IMA Journal of Numerical Analysis},
Year = {2014},
Month = {March},
Key = {fds223440}
}

@article{fds223439,
Author = {A. C. Aristotelous and M. A. Haider},
Title = {Evaluation of Diffusive Transport and Cellular Uptake of
Nutrients in Tissue Engineered Constructs using a Hybrid
Discrete Model},
Journal = {Processes},
Year = {2014},
Month = {March},
Key = {fds223439}
}

@article{fds223438,
Author = {Andreas C. Aristotelous and Richard Durrett},
Title = {Chemical Evolutionary Games},
Journal = {Theoretical Population Biology},
Year = {2014},
Month = {February},
Key = {fds223438}
}

@article{fds223441,
Author = {Andreas C. Aristotelous and Mansoor A. Haider},
Title = {Use of Hybrid Discrete Cellular Models for Identification of
Macroscopic Nutrient Loss in Reaction-Diffusion Models of
Tissues.},
Journal = {Int. J. Numer. Meth. Biomed. Engng.},
Year = {2014},
Month = {February},
Key = {fds223441}
}

@article{fds219212,
Author = {Andreas C. Aristotelous and Ohannes A. Karakashian and Steven
M.Wise},
Title = {A Mixed Discontinuous Galerkin, Convex Splitting Scheme for
a Modified Cahn-Hilliard Equation and an Efficient Nonlinear
Multigrid Solver.},
Journal = {DCDS-B},
Volume = {18},
Number = {9},
Pages = {2211–2238},
Year = {2013},
Month = {November},
Key = {fds219212}
}

%% Aspinwall, Paul S
@article{fds221207,
Author = {N. Addington and P.S. Aspinwall},
Title = {Categories of Massless D-Branes and del Pezzo
Surfaces},
Journal = {JHEP},
Volume = {2013},
Number = {176},
Year = {2013},
Key = {fds221207}
}

@article{fds221208,
Author = {P.S. Aspinwall},
Title = {Some Applications of Commutative Algebra to String
Theory},
Booktitle = {Commutative Algebra, Expository Papers Dedicated to David
Eisenbud on the Occasion of His 65th Birthday},
Year = {2013},
Abstract = {The topological B-model, which is a simplified model of
string theory, is essentially algebraic in nature. We
describe how some calculations in this model may be
performed using methods of commutative algebra. In
particular, we consider the B-model associated with a
Calabi– Yau threefold in the form of a complete
intersection in a toric variety. There is a category of
D-branes associated to matrix factorizations, and we show
how to compute certain products and some Hochschild
cohomology associated to this category. Mirror symmetry and
the notion of stability lead to a notion of monodromy on
this D-brane category. In general this monodromy can be
awkward to compute, but we show how much of the
combinatorial data associated to the monodromy can be
accessed using commutative algebra.},
Key = {fds221208}
}

%% Bar-On, Rann
@misc{fds205138,
Author = {Rann Bar-On and Jack Bookman and Benjamin Cooke and Donna Hall and Sarah
Schott},
Title = {(Re)discovering SoTL Through a Fundamental Challenge:
Helping Students Transition to College Calculus},
Year = {2014},
Keywords = {SoTL calculus undergraduate education},
Abstract = {Teaching and learning occur both inside and outside of the
classroom, but undergraduates' transition to college
mathematics are affected by many factors outside of the
classroom. A collaboration at Duke between mathematics
faculty and the Academic Resource Center (ARC) originally
tool to help less well-prepared students transition to the
calculus curriculum. The collaboration to monitor student
progress and the adaptation of research tools grew initial
voluntary algebra review sessions into an algebra review and
study group program that supports students through the two
course sequence of Laboratory Calculus with Functions I and
II. The collaborators have applied for an NSF grant proposal
to transition the program into the structure of the course
labs to build a formative feedback loop between the
students, undergraduate TAs, and mathematics and ARC
instructors. The grant proposal builds on a collaboration
between the ARC and Chemistry faculty to help pre-med
students navigate a four-course Chemistry sequence through
Organic Chemistry, which trains TAs to monitor not only
content understanding, but self-regulation and metacognitive
development.},
Key = {fds205138}
}

%% Beale, J. Thomas
@article{fds219617,
Author = {S. Tlupova and J. T. Beale},
Title = {Nearly singular integrals in 3D Stokes flow},
Journal = {Commun. Comput. Phys.},
Volume = {14},
Pages = {1207-27},
Year = {2013},
url = {http://www.math.duke.edu/faculty/beale/papers/stokes3d2.pdf},
Key = {fds219617}
}

@article{fds219618,
Author = {W. Ying and J. T. Beale},
Title = {A fast accurate boundary integral method for potentials on
closely packed cells},
Journal = {Commun. Comput. Phys.},
Volume = {14},
Pages = {1073-93},
Year = {2013},
url = {http://www.math.duke.edu/faculty/beale/papers/cpcells2.pdf},
Key = {fds219618}
}

%% Bendich, Paul L.
@article{fds220713,
Author = {Paul Bendich and Herbert Edelsbrunner and Dmitriy Morozov and Amit Patel},
Title = {Homology and Robustness of Level and Interlevel
Sets},
Journal = {Homology, Homotopy, and Applications},
Volume = {15},
Number = {1},
Pages = {51-72},
Editor = {Gunnar Carlsson},
Year = {2013},
Month = {March},
Abstract = {Given a continuous function f : X → R on a topological
space, we consider the preimages of intervals and their
homol- ogy groups and show how to read the ranks of these
groups from the extended persistence diagram of f. In
addition, we quan- tify the robustness of the homology
classes under perturbations of f using well groups, and we
show how to read the ranks of these groups from the same
extended persistence diagram. The special case X = R^3 has
ramifications in the fields of medical imaging and
scientific visualization.},
Key = {fds220713}
}

@article{fds220715,
Author = {Liz Munch and Paul Bendich and Kate Turner and Sayan Mukherjee and Jonathan Mattingly and John Harer},
Title = {Probabalistic Frechet Means and Statistics on
Vineyards},
Year = {2013},
url = {http://arxiv.org/abs/1307.6530},
Abstract = {In order to use persistence diagrams as a true statistical
tool, it would be very useful to have a good notion of mean
and variance for a set of diagrams. In [21], Mileyko and his
collaborators made the rst study of the properties of the
Frechet mean in (Dp;Wp), the space of persistence diagrams
equipped with the p-th Wasserstein metric. In particular,
they showed that the Frechet mean of a nite set of diagrams
always exists, but is not necessarily unique. As an
unfortunate consequence, one sees that the means of a
continuously-varying set of diagrams do not themselves vary
continuously, which presents obvious problems when trying to
extend the Frechet mean de nition to the realm of
vineyards. We x this problem by altering the original de
nition of Frechet mean so that it now becomes a probability
measure on the set of persistence diagrams; in a nutshell,
the mean of a set of diagrams will be a weighted sum of
atomic measures, where each atom is itself the (Frechet
mean) persistence diagram of a perturbation of the input
diagrams. We show that this new de nition de nes a (Holder)
continuous map, for each k, from (Dp)k ! P(Dp), and we
present several examples to show how it may become a useful
statistic on vineyards.},
Key = {fds220715}
}

%% Bertozzi, Andrea L
@booklet{Greer04a,
Author = {J. B. Greer and A. L. Bertozzi},
Title = {H-1 solutions of a class of fourth order nonlinear equations
for image processing},
Journal = {Discrete And Continuous Dynamical Systems},
Volume = {10},
Number = {1-2},
Pages = {349 -- 366},
Year = {2004},
Key = {Greer04a}
}

%% Blake, Lewis D
@book{fds220485,
Author = {Lewis Blake and Michael Reed},
Title = {Laboratory Calculus (2013-2014)},
Year = {2013},
Month = {August},
Key = {fds220485}
}

%% Bobrowski, Omer
@article{fds221191,
Author = {O. Bobrowski and S. Mukherjee},
Title = {The Topology of Probability Distributions on
Manifolds},
Journal = {arXiv: 1307.1123},
Year = {2013},
Key = {fds221191}
}

@article{fds221192,
Author = {R. J. Adler and O. Bobrowski and S. Weinberger},
Title = {Crackle: The Persistent Homology of Noise},
Journal = {arXiv:1301.1466},
Year = {2013},
Key = {fds221192}
}

%% Bookman, Jack
@article{fds218390,
Author = {Emily Lardner and Jack Bookman},
Title = {Lessons Learned in Interdisciplinary Professional
Development Designed to Promote the Teaching of Quantitative
Literacy},
Journal = {Journal of Faculty Development},
Volume = {27},
Number = {2},
Year = {2013},
Month = {May},
Key = {fds218390}
}

@article{fds219344,
Author = {Narayan, Aditee Pradhan and Whicker, Shari A and Staples, Betty and Bookman, Jack and Bartlett, Kathleen and McGann, Kathleen
A},
Title = {The Clinical Skills Fair - An Innovative Curriculum
Evaluation Tool},
Journal = {Journal of Graduate Medical Education},
Year = {2013},
Month = {April},
Key = {fds219344}
}

@article{fds219345,
Author = {Rann Bar-On and Jack Bookman and Benjamin Cooke and Donna Hall and Sarah Schott},
Title = {(Re)discovering SoTL Through a Fundamental Challenge:
Helping Students Transition to College Calculus},
Journal = {MAA Notes},
Year = {2013},
Key = {fds219345}
}

%% Bray, Hubert L.
@article{fds223450,
Author = {H.L. Bray and J. L. Jauregui},
Title = {Time Flat Surfaces and the Monotonicity of the Spacetime
Hawking Mass},
Journal = {Communications in Mathematical Physics},
Year = {2014},
Month = {April},
url = {http://arxiv.org/abs/1310.8638},
Key = {fds223450}
}

@article{fds223121,
Author = {H.L. Bray and J. L. Jauregui and M. Mars},
Title = {Time Flat Surfaces and the Monotonicity of the Spacetime
Hawking Mass II},
Year = {2014},
Month = {February},
url = {http://arxiv.org/abs/1402.3287},
Abstract = {In this sequel paper we give a shorter, second proof of the
monotonicity of the Hawking mass for time flat surfaces
under spacelike uniformly area expanding flows in spacetimes
that satisfy the dominant energy condition. We also include
a third proof which builds on a known formula and describe a
class of sufficient conditions of divergence type for the
monotonicity of the Hawking mass. These flows of surfaces
may have connections to the problem in general relativity of
bounding the total mass of a spacetime from below by the
quasi-local mass of spacelike 2-surfaces in the
spacetime.},
Key = {fds223121}
}

@article{fds220311,
Author = {H.L. Bray and J. L. Jauregui},
Title = {On Curves with Nonnegative Torsion},
Year = {2013},
Month = {December},
url = {http://arxiv.org/abs/1312.5171},
Key = {fds220311}
}

@article{fds220312,
Author = {H.L. Bray and J.L. Jauregui},
Title = {A Geometric Theory of Zero Area Singularities in General
Relativity},
Journal = {Asian Journal of Mathematics},
Volume = {17},
Number = {3},
Pages = {525-560},
Year = {2013},
Month = {September},
url = {http://arxiv.org/abs/0909.0522v1},
Key = {fds220312}
}

@article{fds214520,
Author = {H.L. Bray and A. R. Parry},
Title = {Modeling Wave Dark Matter in Dwarf Elliptical
Galaxies},
Year = {2013},
Month = {January},
url = {http://www.math.duke.edu/~bray/darkmatter/darkmatter.html},
Key = {fds214520}
}

@article{fds220313,
Author = {H.L. Bray},
Title = {On Dark Matter, Spiral Galaxies, and the Axioms of General
Relativity},
Journal = {AMS Contemporary Mathematics Volume, "Geometric Analysis,
Mathematical Relativity, and Nonlinear Partial Differential
Equations"},
Volume = {599},
Publisher = {American Mathematical Society},
Year = {2013},
url = {http://www.math.duke.edu/~bray/darkmatter/darkmatter.html},
Key = {fds220313}
}

%% Bryant, Robert L
@article{fds223639,
Author = {R.L. Bryant},
Title = {Notes on Exterior Differential Systems},
Year = {2014},
Month = {May},
url = {http://arxiv.org/abs/1405.3116},
Keywords = {exterior differential systems Lie theory differential
geometry},
Abstract = {These are notes for a very rapid introduction to the basics
of exterior differential systems and their connection with
what is now known as Lie theory, together with some typical
and not-so-typical applications to illustrate their
use.},
Key = {fds223639}
}

@article{fds223640,
Author = {R.L. Bryant},
Title = {S.-s. Chern's study of almost-complex structures on the
six-sphere},
Year = {2014},
Month = {May},
url = {http://arxiv.org/abs/1405.3405},
Keywords = {6-sphere complex structure exceptional geometry},
Abstract = {In 2003, S.-s. Chern began a study of almost-complex
structures on the 6-sphere, with the idea of exploiting the
special properties of its well-known almost-complex
structure invariant under the exceptional group G2. While he
did not solve the (currently still open) problem of
determining whether there exists an integrable
almost-complex structure on the 6-sphere, he did prove a
significant identity that resolves the question for an
interesting class of almost-complex structures on the
6-sphere.},
Key = {fds223640}
}

%% Cahill, Jason
@article{fds221006,
Author = {J. Cahill and P.G. Casazza and M. Ehler and S. Li},
Title = {Tight and random nonorthogonal fusion frames},
Year = {2013},
url = {http://http://arxiv.org/abs/1309.0532},
Abstract = {First we show that tight nonorthogonal fusion frames are
relatively easy to com by. In order to do this we need to
establish a classification of how to to wire a self adjoint
operator as a product of (nonorthogonal) projection
operators. We also discuss the link between nonorthogonal
fusion frames and positive operator valued measures, we
define and study a nonorthogonal fusion frame potential, and
we introduce the idea of random nonorthogonal fusion
frames.},
Key = {fds221006}
}

@article{fds221008,
Author = {J. Cahill and D.G. Mixon and N. Strawn},
Title = {Connectivity and Irreducibility of Algebraic Varieties of
Finite Unit Norm Tight Frames},
Year = {2013},
url = {http://arxiv.org/abs/1311.4748},
Abstract = {In this paper, we settle a long-standing problem on the
connectivity of spaces of finite unit norm tight frames
(FUNTFs), essentially affirming a conjecture first appearing
in Dykema and Strawn (2003). Our central technique involves
continuous liftings of paths from the polytope of eigensteps
(see Cahill et al. (2012)) to spaces of FUNTFs. After
demonstrating this connectivity result, we refine our
analysis to show that the set of nonsingular points on these
spaces is also connected, and we use this result to show
that spaces of FUNTFs are irreducible in the
algebro-geometric sense, and that generic FUNTFs are full
spark.},
Key = {fds221008}
}

%% Cornwell, Christopher R
@article{fds220821,
Author = {C.R. Cornwell},
Title = {Knot contact homology and representations of knot
groups},
Year = {2013},
url = {http://arxiv.org/abs/1303.4943},
Abstract = {We study certain linear representations of the knot group
that induce augmentations of knot contact homology. This
perspective on augmentations enhances our understanding of
the relationship between the augmentation polynomial and the
A-polynomial of the knot. For example, we show that for
2-bridge knots the polynomials agree and that this is never
the case for (non-2-bridge) torus knots, nor for a family of
3-bridge pretzel knots. In addition, we obtain a lower bound
on the meridional rank of the knot. As a consequence, our
results give another proof that torus knots and a family of
pretzel knots have meridional rank equal to their bridge
number.},
Key = {fds220821}
}

@article{fds220823,
Author = {C.R. Cornwell},
Title = {KCH representations, augmentations, and A-polynomials},
Year = {2013},
url = {http://arxiv.org/abs/1310.7526},
Abstract = {Knot contact homology is an invariant of knots in $\mathbb R^3$, defined via the geometry of the cotangent bundle.
Augmentations of knot contact homology are quite useful for
relating it to other knot invariants. We describe a
correspondence between augmentations and certain
representations of the knot group. The correspondence
implies the 2-variable augmentation polynomial equals a
generalization of the classical A-polynomial. It also
associates to each augmentation a rank, which is bounded by
the bridge number. Like the bridge number, augmentation rank
minus 1 is additive under connect sums. We also describe
properties of augmentations with rank equal to the braid
index.},
Key = {fds220823}
}

%% Daubechies, Ingrid
@article{fds215103,
Author = {B. Cornelis and T.Ruzic, E.Gezels and A.Dooms, A.Pizurica and L.Platisa, J.Cornelis and M. Martens and M.DeMey, I.Daubechies},
Title = {Crack detection and inpainting for virtual restoration of
paintings: The case of the Ghent Altarpiece},
Journal = {Signal Processing},
Volume = {93},
Pages = {605-619},
Publisher = {Elsevier},
Year = {2013},
url = {http://www.sciencedirect.com/science/article/pii/S0165168412002526},
Abstract = {Digital image processing is proving to be of great help in
the analysis and documenta- tion of our vast cultural
heritage. In this paper, we present a new method for the
virtual restoration of digitized paintings with
specialattention for the Ghent Altarpiece (1432), a large
polyptych panel painting of which very few digital
reproductions exist. We achieve our objective by detecting
and digitally removing cracks. The detection of cracks is
particularly difficult because of the varying content
features in different parts of the polyptych. Three new
detection methods are proposed and combined in order to
detect cracks of different sizes as well as varying
brightness. Semi-supervised clustering based post-processing
is used to remove objects falsely labelled as cracks. For
the subsequent inpainting stage, a patch-based technique is
applied to handle the noisy nature of the images and to
increase the performance for crack removal. We demonstrate
the usefulness of our method by means of a case study where
the goal is to improve readability of the depiction of text
in a book, present in one of the panels, in order to assist
paleographers in its deciphering.},
Key = {fds215103}
}

%% Di Cerbo, Luca F.
@article{fds224000,
Author = {G. Di Cerbo and L.F. Di Cerbo},
Title = {A sharp cusp count for complex hyperbolic surfaces and
related results},
Journal = {Arch. Math. (Basel)},
Year = {2014},
Month = {July},
url = {http://arxiv.org/abs/1312.5368},
Key = {fds224000}
}

@article{fds223554,
Author = {L.F. Di Cerbo},
Title = {Generic Properties of Homogeneous Ricci Solitons},
Volume = {14},
Number = {2},
Pages = {225-237},
Year = {2014},
url = {http://arxiv.org/abs/0711.0465},
Key = {fds223554}
}

@article{fds219797,
Author = {L.F. Di Cerbo},
Title = {Classification of Toroidal Compactifications with
3\bar{c}_{2}=\bar{c}^{2}_{1} and \bar{c}_{2}=1},
Year = {2013},
Month = {September},
url = {http://arxiv.org/abs/1309.5516},
Key = {fds219797}
}

@article{fds215945,
Author = {G. Di Cerbo and L.F. Di Cerbo},
Title = {Positivity questions in K\"ahler-Einstein
theory},
Year = {2013},
Month = {February},
url = {http://arxiv.org/abs/1210.0218},
Key = {fds215945}
}

@article{fds215526,
Author = {G. Di Cerbo and L.F. Di Cerbo},
Title = {Effective results for complex hyperbolic
manifolds},
Year = {2013},
Month = {February},
url = {http://arxiv.org/abs/1212.0501v5},
Key = {fds215526}
}

@article{fds222369,
Author = {L.F. Di Cerbo},
Title = {Seiberg-Witten equations on surfaces of logarithmic general
type},
Journal = {Internat. J. Math.},
Volume = {24},
Number = {9},
Pages = {23},
Year = {2013},
url = {http://arxiv.org/abs/1112.0694},
Key = {fds222369}
}

%% Durrett, Rick
@article{fds220505,
Author = {C. Varghese and R. Durrett},
Title = {Phase transition in the quadratic contact process on complex
networks},
Journal = {Physical Review E},
Volume = {87},
Pages = {paper 062819},
Year = {2013},
Key = {fds220505}
}

@article{fds220506,
Author = {Feng Shi and Peter Mucha and R. Durrett},
Title = {Multi-opinion coevolving voter model with infinitely many
phase transitions},
Journal = {Physical Review E},
Year = {2013},
Key = {fds220506}
}

@article{fds220504,
Author = {S. Magura and V. Pong and D. Sivakoff and R. Durrett},
Title = {Two evolving social network models},
Year = {2013},
Key = {fds220504}
}

@article{fds220507,
Author = {R. Durrett and T. Liggett and Y. Zhang},
Title = {The contact process with fast voting},
Journal = {Electronic Journal of Probability},
Year = {2013},
Key = {fds220507}
}

@article{fds220508,
Author = {Andreas Aristotelos and R. Durrett},
Title = {Chemical evolutionary games},
Journal = {Theoretical Population Biology},
Year = {2013},
Key = {fds220508}
}

@article{fds220499,
Author = {R. Durrett and S. Chatterjee},
Title = {A first order phase transition in the threshold theta
contact process on random r-regular graphs and
trees},
Journal = {Stoch. Proc. Appl.},
Volume = {123},
Pages = {561-578},
Year = {2013},
Key = {fds220499}
}

@article{fds220500,
Author = {K. Danesh and R. Durrett and L. Havrilesky and E.
Myers},
Title = {A branching process model of ovarian cancer},
Journal = {J. Theor. Biol.},
Volume = {314},
Pages = {10-15},
Year = {2013},
Key = {fds220500}
}

@article{fds220501,
Author = {J.T. Cox and R. Durrett and E. Perkins},
Title = {Voter model perturbations and reaction diffusion
equations},
Journal = {Asterique},
Volume = {349},
Pages = {1-113},
Year = {2013},
url = {http://arxiv.org/abs/math/1103.1676},
Key = {fds220501}
}

@article{fds220503,
Author = {R. Durrett and S. Moseley},
Title = {Spatial Moran Models. I. Tunneling in the Neutral
Case},
Journal = {Annals Applied Probability},
Year = {2013},
Key = {fds220503}
}

%% Fry, Brendan
@article{fds218670,
Author = {BC Fry and TK Roy and TW Secomb},
Title = {Capillary recruitment in a theoretical model for blood flow
regulation in heterogeneous microvessel networks},
Journal = {Physiological Reports},
Volume = {1},
Number = {3},
Pages = {e00050},
Year = {2013},
Key = {fds218670}
}

%% Gasparovic, Ellen
@article{fds223290,
Author = {G. Bal and J. Bergbauer and E. W. Chambers and E. Gasparovic and R. Hu and K. Leonard and M. Shaker and C. Wenk},
Title = {Skeleton-based recognition of shapes in images via longest
path matching},
Year = {2014},
Key = {fds223290}
}

@article{fds223582,
Author = {James Damon and Ellen Gasparovic},
Title = {Modeling Multi-Object Configurations Via Medial/Skeletal
Year = {2014},
Key = {fds223582}
}

@article{fds220590,
Author = {James Damon and Ellen Gasparovic},
Title = {Medial/Skeletal Linking Structures for Multi-Region
Configurations},
Year = {2013},
url = {http://arxiv.org/abs/1402.5517},
Key = {fds220590}
}

%% Getz, Jayce R.
@article{fds223281,
Author = {J.R. Getz and H. Hahn},
Title = {Algebraic cycles and Tate classes on Hilbert modular
varieties},
Journal = {Int. J. Number Theory},
Volume = {10},
Number = {1},
Pages = {161-176},
Year = {2014},
Abstract = {Let E be a totally real number field that is Galois, and
consider a cuspidal, nondihedral automorphic representation
of GL(2) over E that is in the lowest weight discrete series
at every real place of E. The representation cuts out a
motive'' M from the l-adic middle degree intersection
cohomology of an appropriate Hilbert modular variety. If l
is sufficiently large in a sense that depends on the
representation we compute the dimension of the space of Tate
classes in M. Moreover if the space of Tate classes on this
motive over all finite abelian extensions k/E is at most of
rank one as a Hecke module, we prove that the space of Tate
classes in M is spanned by algebraic cycles.},
Key = {fds223281}
}

@article{fds223471,
Author = {J.R. Getz and H. Hahn},
Title = {A general simple relative trace formula and a relative Weyl
law},
Year = {2014},
Key = {fds223471}
}

@article{fds220702,
Author = {J.R. Getz and P. E. Herman},
Title = {A nonabelian trace formula},
Year = {2013},
Abstract = {Let E/F be an extension of number fi elds with Gal(E/F)
simple and nonabelian. In a recent paper the fi rst named
author suggested an approach to nonsolvable base change and
descent of automorphic representations of GL(2) along such
an extension. Motivated by this we prove a trace formula
whose spectral side is a weighted sum over cuspidal
automorphic representations of GL(2) over E that are
isomorphic to their Gal(E/F)-conjugates.},
Key = {fds220702}
}

@article{fds218668,
Author = {J.R. Getz and E. Wambach},
Title = {Twisted relative trace formulae with a view towards unitary
groups},
Journal = {Amer. J. Math.},
Volume = {135},
Pages = {1-57},
Year = {2013},
url = {http://www.math.duke.edu/~jgetz/BCRT_Final_AJM.pdf},
Abstract = {We introduce a twisted relative trace formula which
simultaneously generalizes the twisted trace formula of
Langlands et. al. (in the quadratic case) and the relative
trace formula of Jacquet and Lai [JL]. Certain matching
statements relating this twisted relative trace formula to a
relative trace formula are also proven (including the
relevant fundamental lemma in the "biquadratic case"). Using
recent work of Jacquet, Lapid and their collaborators [J1]
and the Rankin-Selberg integral representation of the Asai
L-function (obtained by Flicker using the theory of Jacquet,
Piatetskii-Shapiro, and Shalika [Fl2]), we give the
following application: Let E/F be a totally real quadratic
extension, let U' be a quasi-split unitary group with
respect to a CM extension M/F, and let U := U'_E. Under
suitable local hypotheses, we show that a cuspidal
cohomological automorphic representation  of U whose Asai
L-function has a pole at the edge of the critical strip is
nearly equivalent to a cuspidal cohomological automorphic
representation 0 of U that is U'-distinguished in the
sense that there is a form in the space of 0 admitting a
nonzero period over U. This provides cohomologically
nontrivial cycles of middle dimension on unitary Shimura
varieties analogous to those on Hilbert modular surfaces
studied by Harder, Langlands, and Rapoport
[HLR].},
Key = {fds218668}
}

@article{fds219239,
Author = {J.R. Getz and J. Klassen},
Title = {Isolating Rankin-Selberg lifts},
Journal = {Proc. Amer. Math. Soc.},
Year = {2013},
Key = {fds219239}
}

%% Hahn, Heekyoung
@article{fds222818,
Author = {J. R. Getz and H. Hahn},
Title = {Algebraic cycles and Tate classes on Hilbert modular
varieties},
Journal = {Int. J. Number Theory},
Volume = {10},
Number = {1},
Pages = {161-176},
Year = {2014},
Key = {fds222818}
}

@article{fds223470,
Author = {J. R. Getz and H. Hahn},
Title = {A general simple relative trace formula and a relative Weyl
law},
Year = {2014},
Key = {fds223470}
}

@article{fds222461,
Author = {S. Akhtari and C. David and H. Hahn and L. Thompson},
Title = {Distribution of square-free values of sequences associated
with elliptic curves},
Journal = {Contemp. Math.},
Volume = {606},
Series = {Women in Numbers 2},
Pages = {171-188},
Publisher = {Amer. Math. Soc.},
Year = {2013},
Key = {fds222461}
}

%% Hain, Richard M
@article{fds223909,
Author = {Richard Hain},
Title = {Genus 3 Mapping Class Groups are not Kähler},
Journal = {Journal of Topology},
Year = {2014},
Month = {June},
ISSN = {1753-8416},
url = {http://arxiv.org/abs/1305.2052},
Key = {fds223909}
}

@article{fds223317,
Author = {Richard Hain},
Title = {The Hodge-de Rham theory of modular groups},
Year = {2014},
Month = {March},
url = {http://arxiv.org/abs/1403.6443},
Key = {fds223317}
}

@article{fds223449,
Author = {Alexandru Dimca and Richard Hain and Stefan Papadima},
Title = {The abelianization of the Johnson kernel},
Journal = {Journal of the European Mathematical Society},
Volume = {16},
Number = {4},
Pages = {805-822},
Year = {2014},
url = {http://www.ems-ph.org/journals/show_abstract.php?issn=1435-9855&vol=16&iss=4&rank=6},
Key = {fds223449}
}

@article{fds218754,
Author = {Richard Hain},
Title = {Notes on the Universal Elliptic KZB Equation},
Year = {2013},
Month = {September},
url = {http://arxiv.org/abs/1309.0580},
Key = {fds218754}
}

@article{fds217200,
Author = {Richard Hain},
Title = {Normal Functions and the Geometry of Moduli Spaces of
Curves},
Volume = {I},
Pages = {527-578},
Booktitle = {Handbook of Moduli},
Publisher = {International Press},
Editor = {Gavril Farkas and Ian Morrison},
Year = {2013},
Month = {March},
url = {http://arxiv.org/abs/1102.4031},
Key = {fds217200}
}

@book{fds212861,
Author = {Benson Farb and Richard Hain and Eduard Looijenga},
Title = {Moduli Spaces of Riemann Surfaces},
Series = {IAS/Park City Mathematics Series},
Publisher = {American Mathematical Society},
Year = {2013},
ISBN = {ISBN-13: 978-0-8218-9887-1},
url = {http://www.ams.org/bookstore-getitem/item=PCMS-20},
Key = {fds212861}
}

@article{fds217199,
Author = {Richard Hain},
Title = {Remarks on non-abelian cohomology of proalgebraic
groups},
Journal = {J. Algebraic Geom.},
Volume = {22},
Pages = {581-598},
Year = {2013},
url = {http://arxiv.org/abs/1009.3662},
Key = {fds217199}
}

%% Harer, John
@article{fds221198,
Author = {Katharine Turner and Yuriy Mileyko and Sayan Mukherjee and John
Harer},
Title = {Fréchet Means for Distributions of Persistence
diagrams},
Journal = {arXiv:1206.2790},
Year = {2013},
Abstract = {Given a distribution ρ on persistence diagrams and
observations X1,...Xn∼iidρ we introduce an algorithm in
this paper that estimates a Fr\'echet mean from the set of
diagrams X1,...Xn. If the underlying measure ρ is a
combination of Dirac masses ρ=1m∑mi=1δZi then we prove
the algorithm converges to a local minimum and a law of
large numbers result for a Fr\'echet mean computed by the
algorithm given observations drawn iid from ρ. We
illustrate the convergence of an empirical mean computed by
the algorithm to a population mean by simulations from
Gaussian random fields.},
Key = {fds221198}
}

@article{fds221199,
Author = {Elizabeth Munch and Paul Bendich and Katharine Turner and Sayan
Mukherjee, Jonathan Mattingly and John Harer},
Title = {Probabilistic Fréchet Means and Statistics on
Vineyards},
Year = {2013},
Abstract = {In order to use persistence diagrams as a true statistical
tool, it would be very useful to have a good notion of mean
and variance for a set of diagrams. Mileyko and his
collaborators made the first study of the properties of the
Fr\'{e}chet mean in (Dp,Wp), the space of persistence
diagrams equipped with the p-th Wasserstein metric. In
particular, they showed that the Fr\'{e}chet mean of a
finite set of diagrams always exists, but is not necessarily
unique. As an unfortunate consequence, one sees that the
means of a continuously-varying set of diagrams do not
themselves vary continuously, which presents obvious
problems when trying to extend the Fr\'{e}chet mean
definition to the realm of vineyards. We fix this problem by
altering the original definition of Fr\'{e}chet mean so that
it now becomes a probability measure on the set of
persistence diagrams; in a nutshell, the mean of a set of
diagrams will be a weighted sum of atomic measures, where
each atom is itself the (Fr\'{e}chet mean) persistence
diagram of a perturbation of the input diagrams. We show
that this new definition defines a (H\"older) continuous
map, for each k, from (Dp)k→P(Dp), and we present several
examples to show how it may become a useful statistic on
vineyards.},
Key = {fds221199}
}

@article{fds221210,
Author = {Jose Perea and J. Harer},
Title = {Sliding Windows and Persistence: An Application of
Topological Methods to Signal Analysis},
Journal = {arXiv:1307.6188},
Year = {2013},
Abstract = {We develop in this paper a theoretical framework for the
topological study of time series data. Broadly speaking, we
describe geometrical and topological properties of sliding
window (or time-delay) embeddings, as seen through the lens
of persistent homology. In particular, we show that maximum
persistence at the point-cloud level can be used to quantify
periodicity at the signal level, prove structural and
convergence theorems for the resulting persistence diagrams,
and derive estimates for their dependency on window size and
embedding dimension. We apply this methodology to
quantifying periodicity in synthetic data sets, and compare
the results with those obtained using state-of-the-art
methods in gene expression analysis. We call this new method
SW1PerS which stands for Sliding Windows and 1-dimensional
Persistence Scoring.},
Key = {fds221210}
}

@article{fds221197,
Author = {Christopher N Topp and Anjali S Iyer-Pascuzzi and Jill T Anderson and Cheng-Ruei Lee and Paul R Zurek and Olga Symonova and Ying Zheng and Alexander Bucksch and Yuriy Milyeko and Taras Galkovskyi and Brad
Moore, John Harer and Herbert Edelsbrunner and Thomas Mitchell
Olds and Joshua S Weitz and Philip N Benfey},
Title = {3-dimensional phenotyping of growing root systems combined
with QTL mapping identifies core regions of the rice genome
controlling root architecture},
Journal = {PNAS},
Year = {2013},
Abstract = {Identification of genes that control root system
architecture in crop plants requires innovations that enable
high-throughput and accurate measurements of root system
architecture through time. We demonstrate the ability of a
semiautomated 3D in vivo imaging and digital phenotyping
pipeline to interrogate the quantitative genetic basis of
root system growth in a rice biparental mapping population,
Bala × Azucena. We phenotyped >1,400 3D root models and
>57,000 2D images for a suite of 25 traits that quantified
the distribution, shape, extent of exploration, and the
intrinsic size of root networks at days 12, 14, and 16 of
growth in a gellan gum medium. From these data we identified
89 quantitative trait loci, some of which correspond to
those found previously in soil-grown plants, and provide
evidence for genetic tradeoffs in root growth allocations,
such as between the extent and thoroughness of exploration.
We also developed a multivariate method for generating and
mapping central root architecture phenotypes and used it to
identify five major quantitative trait loci (r2 = 24–37%),
two of which were not identified by our univariate analysis.
Our imaging and analytical platform provides a means to
identify genes with high potential for improving root traits
and agronomic qualities of crops.},
Key = {fds221197}
}

@article{fds221196,
Author = {Anastasia Deckard and Ron C. Anafi and John B. Hogenesch and Steven
B. Haase and John Harer},
Title = {Design and Analysis of Large-Scale Biological Rhythm
Studies: A Comparison of Algorithms for Detecting Periodic
Signals in Biological Data},
Journal = {PLOS Computational Biology},
Year = {2013},
Abstract = {The results of a major year-long DARPA funded project to
study the performance of a large collection of algorithms
for finding periodic gene expression.},
Key = {fds221196}
}

@article{fds221211,
Author = {J. Perea and A. Deckard and S. Haase and J. Harer},
Title = {Applications of SWiPerS to the discovery of periodic
genes},
Year = {2013},
Key = {fds221211}
}

@article{fds221202,
Author = {Sara Bristow and Laura A. Simmons Kovacs and Anastasia Deckard and John Harer and Steven B. Haase},
Title = {Checkpoint Pathways Couple the CDK-Independent
Transcriptional Oscillations to Cell Cycle
Progression},
Year = {2013},
Abstract = {A study of how checkpoint pathways control the yeast cell
cycle, derived from methods of finding periodic genes and
cell cycle experiments from the Haase Lab.},
Key = {fds221202}
}

%% Herschlag, Gregory
@article{fds220747,
Author = {G. Herschlag and G.J.M. Garcia and B. Button and R. Tarran and B.
Lindley, B. Reinhardt and T.C. Elston and M.G.
Forest},
Title = {A mechanochemical model for auto-regulation of lung airway
surface layer volume},
Journal = {Journal of Theoretical Biology},
Volume = {325},
Pages = {42-51},
Year = {2013},
Month = {May},
url = {http://www.sciencedirect.com/science/article/pii/S0022519313000489},
Abstract = {http://www.sciencedirect.com/science/article/pii/S0022519313000489},
Key = {fds220747}
}

%% Herzog, David P
@article{fds223339,
Author = {D.P. Herzog and J.C. Mattingly},
Title = {Noise-Induced Stabilization of Planar Flows
I},
Year = {2014},
Month = {April},
url = {http://arxiv.org/pdf/1404.0957v1.pdf},
Key = {fds223339}
}

@article{fds223340,
Author = {D.P. Herzog and J.C. Mattingly},
Title = {Noise-Induced Stabilization of Planar Flows
II},
Year = {2014},
Month = {April},
url = {http://arxiv.org/pdf/1404.0955v1.pdf},
Key = {fds223340}
}

@article{fds221189,
Author = {D.P. Herzog and Nathan Totz},
Title = {An extension of H\"{o}rmander's hypoellipticity
theorem},
Year = {2013},
Month = {February},
url = {http://arxiv.org/pdf/1312.3557v1.pdf},
Abstract = {Motivated by applications to stochastic differential
equations, an extension of H\"{o}rmander's hypoellipticity
theorem is proved for second-order degenerate elliptic
operators with non-smooth coefficients. The main results are
established using point-wise Bessel kernel estimates and a
weighted Sobolev inequality of Stein and Weiss. Of
particular interest is that our results apply to operators
with quite general first-order terms.},
Key = {fds221189}
}

@article{fds221190,
Author = {D.P. Herzog and Marc Ryser and David Sivakoff and Kevin McGoff and Evan
Myers},
Title = {Impact of coverage-dependent marginal costs on optimal HPV
vaccination strategies},
Year = {2013},
Month = {February},
Key = {fds221190}
}

%% Lawlor, David
@article{fds218102,
Author = {D. Lawlor and Y. Wang and A. Christlieb},
Title = {A Multiscale Sub-linear Time Fourier Algorithm for Noisy
Data},
Year = {2013},
Month = {Spring},
url = {http://arxiv.org/abs/1304.4517},
Abstract = {We extend the recent sparse Fourier algorithm of (Lawlor,
Christlieb, and Wang, 2013) to the noisy setting. We present
two such extensions, the second of which exhibits a novel
form of error-correction not unlike that of the
beta-encoders in analog-to-digital conversion (Daubechies et
al, 2006). The algorithm runs in time O(k log(k) log(N/k))
on average, provided the noise is not overwhelming. The
error-correction property allows the algorithm to outperform
FFTW over a wide range of sparsity and noise values, and is
to the best of our knowledge novel in the sparse Fourier
transform context.},
Key = {fds218102}
}

@article{fds220376,
Author = {D. Lawlor and Y. Wang and A. Christlieb},
Title = {Adaptive sub-linear Fourier algorithms},
Volume = {5},
Number = {1},
Publisher = {World Scientific},
Year = {2013},
Month = {January},
ISSN = {1793-5369},
url = {http://arxiv.org/abs/1207.6368},
Abstract = {We present a new deterministic algorithm for the sparse
Fourier transform problem, in which we seek to identify k <<
N significant Fourier coefficients from a signal of
bandwidth N. Previous deterministic algorithms exhibit
quadratic runtime scaling, while our algorithm scales
linearly with k in the average case. Underlying our
algorithm are a few simple observations relating the Fourier
coefficients of time-shifted samples to unshifted samples of
the input function. This allows us to detect when aliasing
between two or more frequencies has occurred, as well as to
determine the value of unaliased frequencies. We show that
empirically our algorithm is orders of magnitude faster than
competing algorithms.},
Key = {fds220376}
}

%% Layton, Anita T
@article{fds223269,
Author = {Aurelie Edwards and Anita T. Layton},
Title = {Calcium dynamics underlying the myogenic response of the
renal afferent arteriole},
Journal = {Am J Physiol Renal Physiol},
Volume = {306},
Number = {F34-F48},
Year = {2014},
Key = {fds223269}
}

@article{fds223975,
Author = {Ioannis Sgouralis and Anita T. Layton},
Title = {Theoretical assessment of renal autoregulatory
mechanisms},
Journal = {Am J Physiol Renal Physiol},
Volume = {306},
Pages = {F1357-F1371},
Year = {2014},
Key = {fds223975}
}

@article{fds222881,
Author = {Yi Li and Ioannis Sgouralis and Anita T. Layton},
Title = {Computing viscous flow in an elastic tube},
Journal = {Numer. Math. Theor. Meth. Appl., in press},
Year = {2014},
Key = {fds222881}
}

@article{fds223235,
Author = {Robert Moss and Anita T. Layton},
Title = {Dominant factors that govern pressure natriuresis in
diuresis and antidiuresis: a mathematical
model},
Journal = {Am J Physiol Renal Physiol, in press},
Year = {2014},
Key = {fds223235}
}

@article{fds224021,
Author = {Thomas L. Pannabecker and Anita T. Layton},
Title = {Targeted delivery of solutes and oxygen in the renal
medulla: role of microvessel architecture},
Journal = {Am J Physiol Renal Physiol, in press},
Year = {2014},
Key = {fds224021}
}

@article{fds223973,
Author = {Julia Arcerio and Laura Ellwein and Ashley N. Ford Versypt and Elizabeth Markride and Anita T. Layton},
Title = {Modeling blood flow in the kidney},
Journal = {IMA volume, submitted},
Year = {2014},
Key = {fds223973}
}

@article{fds223680,
Author = {Ioannis Sgouralis and Roger Evans and Bruce S. Gardiner and Julian A
Smith and Brendan C. Fry and Anita T. Layton},
Title = {Renal hemodynamics, function and oxygenation during cardiac
Surgery performed on cardiopulmonary bypass: A modeling
study},
Journal = {Am J Physiol Renal Physiol, submitted},
Year = {2014},
Key = {fds223680}
}

@article{fds223468,
Author = {Gregory J. Herschlag and Jian-Guo Liu and Anita T.
Layton},
Title = {An exact solution for Stokes flow in an in nite channel with
permeable walls},
Journal = {J Fluid Mech, submitted},
Year = {2014},
Key = {fds223468}
}

@article{fds223291,
Author = {Brendan C. Fry and Anita T. Layton},
Title = {Oxygen transport in a cross section of the rat inner
medulla: Impact of heterogeneous distribution of nephrons
and vessels},
Journal = {Math Biosci, submitted},
Year = {2014},
Key = {fds223291}
}

@article{fds223679,
Author = {Aurelie Edwards and Hayo Castrop and Kamel Laghmani and Volker
Vallon and Anita T. Layton},
Title = {Regulation of NKCC2 isoform expression and NaCl transport in
the thick ascending limb and macula densa
cells},
Journal = {Am J Physiol Renal Physiol, in press},
Year = {2014},
Key = {fds223679}
}

@book{fds223268,
Author = {Anita T. Layton and Sarah D. Olson},
Title = {Biological Fluid Dynamics: Modeling, Computation, and
Applications},
Journal = {AMS Contemporary Mathematics},
Year = {2014},
Key = {fds223268}
}

@article{fds223501,
Author = {Brendan C. Fry and Aurelie Edward and Ioannis Sgouralis and Anita
T. Layton},
Title = {Impact of renal medullary three-dimensional architecture on
oxygen transport},
Journal = {Am J Physiol Renal Physiol, in press},
Year = {2014},
Key = {fds223501}
}

@article{fds219930,
Author = {Anta T. Layton},
Title = {Mathematical modeling of urea transport in the
kidney},
Booktitle = {Urea Transporters, in press},
Publisher = {Springer},
Editor = {Baoxue Yang},
Year = {2013},
Key = {fds219930}
}

@article{fds214468,
Author = {Karin Leiderman and Elizabeth L. Bouzarth and Ricardo Cortez and Anita T. Layton},
Title = {A regularization method for the numerical solution of
periodic Stokes flow},
Journal = {J Comput Phys},
Volume = {236},
Number = {187-202},
Year = {2013},
Key = {fds214468}
}

@article{fds216651,
Author = {Aniel Nieves-Gonzalez and Chris Clausen and Anita .T. Layton and Harold E. Layton and Leon C. Moore},
Title = {Transport efficiency and workload distribution in a
mathematical model of the thick ascending
limb},
Journal = {Am J Physiol Renal Physiol},
Volume = {304},
Number = {F653-F664},
Year = {2013},
Key = {fds216651}
}

@article{fds216652,
Author = {Aniel Nieves-Gonzalez and Chris Clausen and Mariano Marcano and Anita
.T. Layton and Harold E. Layton and Leon C.
Moore},
Title = {Fluid dilution and efficiency of Na+ transport in a
mathematical model of a thick ascending limb
cell},
Journal = {Am J Physiol Renal Physiol},
Volume = {304},
Number = {F634-F652},
Year = {2013},
Key = {fds216652}
}

@article{fds218841,
Author = {Anita T. Layton and Lise Bankir},
Title = {Impacts of active urea secretion into pars recta on urine
concentrating mechanism},
Journal = {Physiol Report},
Volume = {1},
Number = {3},
Pages = {e00034},
Year = {2013},
Key = {fds218841}
}

@article{fds218844,
Author = {Hwayeon Ryu and Anita T. Layton},
Title = {Effect of tubular inhomogeneities on feedback-mediated
dynamics of a model of a thick ascending
limb},
Journal = {Med Math Biol},
Volume = {30},
Number = {191-212},
Year = {2013},
Key = {fds218844}
}

@article{fds219207,
Author = {William H. Dantzler and Anita T. Layton and Harold E. Layton and Thomas L. Pannabecker},
Title = {Urine concentrating mechanism in the inner medulla: function
of the thin limbs of Henle’s loops},
Journal = {Clin J Am Soc Nephrol},
Pages = {doi:10.2215/CJN.08750812},
Year = {2013},
Key = {fds219207}
}

@article{fds219490,
Author = {Yi Li and Sarah A. Williams and Anita T. Layton},
Title = {A hybrid immersed interface method for driven stokes flow in
an elastic tube},
Journal = {Numer. Math. Theor. Meth. Appl.},
Volume = {6},
Number = {4},
Pages = {600-616},
Year = {2013},
Key = {fds219490}
}

@article{fds223502,
Author = {Ioannis Sgouralis and Anita T. Layton},
Title = {Control and modulation of fluid flow in the rat
kidney},
Journal = {Bull Math Biol},
Volume = {75},
Pages = {2551-2574},
Year = {2013},
Key = {fds223502}
}

@article{fds223236,
Author = {Sarah D. Olson and Anita T. Layton},
Title = {Simulating Fluid-Structure Interactions --- A
Review},
Journal = {AMS Contemporary Mathematics, Biological Fluid Dynamics:
Modeling, Computations, and Applications, in
press},
Year = {2013},
Key = {fds223236}
}

@book{fds216729,
Author = {Anita T. Layton and Aurelie Edwards},
Title = {Mathematical Modeling of Renal Physiology},
Series = {Lecture Notes on Mathematical Modelling in the Life
Sciences},
Publisher = {Springer},
Editor = {Angela Stevens and Michael C. Mackey},
Year = {2013},
Key = {fds216729}
}

@article{fds218854,
Author = {Anita T. Layton},
Title = {Impacts of facilitated urea transporters on the urine
concentrating mechanism in the rat kidney},
Journal = {AMS Contemporary Mathematics, Biological Fluid Dynamics:
Modeling, Computations, and Applications, in
press},
Year = {2013},
Key = {fds218854}
}

@article{fds217955,
Author = {Hwayeon Ryu and Anita T. Layton},
Title = {Feedback-mediated dynamics in a model of coupled nephrons
with compliant short loop of Henle},
Journal = {AMS Contemporary Mathematics, Biological Fluid Dynamics:
Modeling, Computations, and Applications, in
press},
Year = {2013},
Key = {fds217955}
}

@article{fds219491,
Author = {Anita T. Layton},
Title = {Mathematical modeling of kidney transport},
Journal = {WIRESs Syst Biol Med},
Volume = {5},
Pages = {557-573},
Year = {2013},
Key = {fds219491}
}

@article{fds223498,
Author = {Hwayeon Ryu and Anita T. Layton},
Title = {Tubular fluid flow and distal NaCl delivery mediated by
tubuloglomerular feedback in the rat kidney},
Journal = {J Math Biol},
Volume = {68},
Number = {1023–1049},
Key = {fds223498}
}

%% Liao, Wenjing
@article{fds223442,
Author = {W. Liao and A. Fannjiang},
Title = {MUSIC for single-snapshot spectral estimation: stability and
super-resolution},
Year = {2014},
Key = {fds223442}
}

@article{fds223270,
Author = {A. Fannjiang and W. Liao},
Title = {Fourier phasing with phase-uncertain mask},
Journal = {Inverse problems},
Volume = {29},
Number = {12},
Year = {2013},
Key = {fds223270}
}

%% Lipnowski, Michael
@article{fds220725,
Author = {M. Lipnowski},
Title = {Equivariant Torsion and Base Change},
Year = {2013},
url = {http://arxiv.org/abs/1312.2540},
Key = {fds220725}
}

@article{fds220726,
Author = {M. Lipnowski},
Title = {The Equivariant Cheeger-Müller Theorem on Locally Symmetric
Spaces},
Year = {2013},
url = {http://arxiv.org/abs/1312.2543},
Key = {fds220726}
}

%% Liu, Jian-Guo
@article{fds220921,
Author = {S. Bian and J.-G. Liu and C. Zou},
Title = {Ultra-contractivity for Keller-Segel model with diffusion
exponent m>1-2/d},
Journal = {Kinetic and Related Models},
Volume = {7},
Pages = {9-28},
Year = {2014},
Key = {fds220921}
}

@article{fds220121,
Author = {Y. Duan and J.-G. Liu},
Title = {Convergence analysis of the vortex blob method for the
b-equation},
Journal = {Discrete Contin. Dyn. Syst. Ser. A},
Volume = {34},
Pages = {1995-2011},
Year = {2014},
Key = {fds220121}
}

@article{fds220922,
Author = {H. Johnston and C. Wang and J.-G. Liu},
Title = {A local pressure boundary condition spectral collocation
scheme for the three-dimensional Navier-Stokes
equations},
Journal = {J. Sci. Comput.},
Year = {2013},
Key = {fds220922}
}

@article{fds220114,
Author = {X. Chen and J.-G. Liu},
Title = {Global weak entropy solution to Doi-Saintillan-Shelley model
for active and passive rod-like and ellipsoidal particle
suspensions},
Journal = {J Diff Eqs},
Volume = {254},
Pages = {2764-2802},
Year = {2013},
Key = {fds220114}
}

@article{fds220115,
Author = {T. Goudon and S. Jin and J.-G. Liu and B. Yan},
Title = {Asymptotic-Preserving schemes for kinetic-fluid modeling of
disperse two-phase flows},
Journal = {J. Comput. Phy.},
Volume = {246},
Pages = {145-164},
Year = {2013},
Key = {fds220115}
}

@article{fds220116,
Author = {X. Chen and J.-G. Liu},
Title = {Analysis of polymeric flow models and related compactness
theorems in weighted spaces},
Journal = {SIAM J Math Anal},
Volume = {45},
Pages = {1179-1215},
Year = {2013},
Key = {fds220116}
}

@article{fds220117,
Author = {P. Degond and A. Frouvelle and J.-G. Liu and S Motsch and L
Navoret},
Title = {Macroscopic models of collective motion and
self-organization},
Journal = {Seminaire Laurent Schwartz -- EDP et applicatios},
Volume = {2012 - 2013},
Pages = {1-27},
Year = {2013},
Key = {fds220117}
}

@article{fds220118,
Author = {Y.L. Huang and J.-G. Liu and W.-C. Wang},
Title = {A generalized MAC scheme on curvilinear domains},
Journal = {SIAM J. Sci. Comput.},
Volume = {35},
Pages = {B953-B986},
Year = {2013},
Key = {fds220118}
}

@article{fds220119,
Author = {P. Degond and J.-G, Liu and S. Motsch and V. Panferov},
Title = {Hydrodynamic models of self-organized dynamics: derivation
and existence theory},
Journal = {Methods Anal. Appl.},
Volume = {20},
Pages = {89-114},
Year = {2013},
Key = {fds220119}
}

@article{fds220120,
Author = {S. Bian and J.-G. Liu},
Title = {Dynamic and steady states for multi-dimensional Keller-Segel
model with diffusion exponent m > 0},
Journal = {Comm Math Phy},
Volume = {323},
Pages = {1017-1070},
Year = {2013},
Key = {fds220120}
}

@article{fds220122,
Author = {D. Chae and P. Degond and J.-G. Liu},
Title = {Well-posedness for Hall-magnetohydrodynamics},
Journal = {Ann. I. H. Poincare, AN},
Year = {2013},
Key = {fds220122}
}

@article{fds220123,
Author = {P. Degond and A. Frouvelle and J.-G. Liu},
Title = {A note on phase transitions for the Smoluchowski equation
with dipolar potential},
Booktitle = {Proceedings of the Fourteenth International Conference on
Hyperbolic Problems: Theory, Numerics and
Application},
Year = {2013},
Key = {fds220123}
}

@article{fds220124,
Author = {X. Chen and X. Liu and J.-G. Liu},
Title = {Existence and uniqueness of global weak solution to a
kinetic model for the sedimentation of rod-like
particles},
Journal = {Commun. Math. Sci.},
Year = {2013},
Key = {fds220124}
}

@article{fds220126,
Author = {P. Degond and J.-G. Liu and C. Ringhofer},
Title = {Large-scale dynamics of Mean-Field Games driven by local
Nash equilibria},
Journal = {J Nonlinear Sci.},
Year = {2013},
Key = {fds220126}
}

@article{fds220127,
Author = {P. Degond and J.-G. Liu and C. Ringhofer},
Title = {Evolution of the distribution of wealth in an economic
environment driven by local Nash equilibria},
Journal = {J. Stat. Phys.},
Year = {2013},
Key = {fds220127}
}

@article{fds220128,
Author = {X. Chen and A. Jungel and J.-G. Liu},
Title = {A note on Aubin-Lions-Dubinskii lemmas},
Journal = {Acta Applicanda Mathematicae},
Year = {2013},
Key = {fds220128}
}

@article{fds220111,
Author = {P. Degond and A. Frouvell and J.-G. Liu},
Title = {Macroscopic limits and phase transition in a system of
self-propelled particles},
Journal = {J Nonlinear Sci.},
Volume = {23},
Pages = {427-456},
Year = {2013},
Key = {fds220111}
}

@article{fds220113,
Author = {S. Jin and J.-G. Liu and L. Wang},
Title = {A domain decomposition method for semilinear hyperbolic
systems with two-scale relaxations},
Journal = {Math. Comp.},
Volume = {82},
Pages = {749-779},
Year = {2013},
Key = {fds220113}
}

%% Lu, Jianfeng
@article{fds223301,
Author = {J. Lu and Lin Lin and Sihong Shao},
Title = {Analysis of the time reversible Born-Oppenheimer molecular
dynamics},
Journal = {Entropy},
Volume = {16},
Pages = {110-137},
Editor = {G. Ciccotti and M. Ferrario and Ch. Schuette},
Year = {2014},
url = {http://dx.doi.org/10.3390/e16010110},
Doi = {10.3390/e16010110},
Key = {fds223301}
}

@article{fds223588,
Author = {J. Lu and Robert V. Kohn and Ben Schweizer and Michael I.
Weinstein},
Title = {A variational perspective on cloaking by anomalous localized
resonance},
Journal = {Comm. Math. Phys.},
Volume = {328},
Number = {1},
Pages = {1-27},
Year = {2014},
url = {http://dx.doi.org/10.1007/s00220-014-1943-y},
Doi = {10.1007/s00220-014-1943-y},
Key = {fds223588}
}

@article{fds209290,
Author = {J. Lu and Felix Otto},
Title = {Nonexistence of minimizer for Thomas-Fermi-Dirac-von
Weizsacker model},
Journal = {Comm. Pure Appl. Math.},
Year = {2014},
Key = {fds209290}
}

@article{fds223239,
Author = {J. Lu and James Nolen},
Title = {Reactive trajectories and the transition path
processes},
Journal = {Probab. Theory Related Fields},
Year = {2014},
Key = {fds223239}
}

@article{fds223321,
Author = {J. Lu and Qin Li and Weiran Sun},
Title = {A convergent method for linear half-space kinetic
equation},
Year = {2014},
Key = {fds223321}
}

@article{fds223237,
Author = {J. Lu and Bin Hu},
Title = {Dynamic production capacity management with price
skimming},
Year = {2014},
Key = {fds223237}
}

@article{fds223256,
Author = {J. Lu and Rongjie Lai and Stanley Osher},
Title = {Density matrix minimization with $\ell_1$
regularization},
Year = {2014},
url = {http://arxiv.org/abs/1403.1525},
Key = {fds223256}
}

@article{fds223238,
Author = {J. Lu and Haizhao Yang and Lexing Ying},
Title = {Crystal image analysis using 2D synchrosqueezing
transforms},
Year = {2014},
url = {http://arxiv.org/abs/1402.1262},
Key = {fds223238}
}

@article{fds224003,
Author = {J. Lu and Weinan E},
Title = {Mathematical theory of solids: from quantum mechanics to
continuum models},
Journal = {Discret. Contin. Dyn. Sys.},
Volume = {34},
Pages = {5085-5097},
Year = {2014},
url = {http://dx.doi.org/10.3934/dcds.2014.34.5085},
Doi = {10.3934/dcds.2014.34.5085},
Key = {fds224003}
}

@article{fds224002,
Author = {J. Lu and Eric Vanden-Eijnden},
Title = {Exact dynamical coarse-graining without time-scale
separation},
Journal = {J. Chem. Phys.},
Year = {2014},
url = {http://arxiv.org/abs/1404.4225},
Key = {fds224002}
}

@article{fds223482,
Author = {J. Lu and Jingchen Liu and Xiang Zhou},
Title = {Efficient rare event simulation for failure problems in
random media},
Year = {2014},
url = {http://arxiv.org/abs/1404.4729},
Key = {fds223482}
}

@article{fds223674,
Author = {J. Lu and Vitaly Moroz and Cyrill B. Muratov},
Title = {Orbital-free density functional theory of out-of-plane
charge screening in graphene},
Year = {2014},
url = {http://arxiv.org/abs/1405.4949},
Key = {fds223674}
}

@article{fds223485,
Author = {J. Lu and Jeremy L. Marzuola},
Title = {Strang splitting methods for a quasilinear Schrodinger
equation - convergence, instability and dynamics},
Journal = {Commun. Math. Sci.},
Year = {2013},
Month = {May},
Key = {fds223485}
}

@article{fds223466,
Author = {J. Lu and Weinan E and Yuan Yao},
Title = {The Landscape of Complex Networks -- Critical Nodes and a
Hierarchical Decomposition},
Journal = {Methods Appl. Anal.},
Volume = {20},
Number = {4},
Pages = {383--404},
Year = {2013},
url = {http://dx.doi.org/10.4310/MAA.2013.v20.n4.a5},
Doi = {10.4310/MAA.2013.v20.n4.a5},
Key = {fds223466}
}

@article{fds223300,
Author = {J. Lu and Sergey Fomel and Xu Yang},
Title = {Seismic modeling using the frozen Gaussian
approximation},
Pages = {4677-4682},
Booktitle = {SEG Technical Program Expanded Abstracts
2013},
Year = {2013},
url = {http://arxiv.org/abs/1304.3542},
Key = {fds223300}
}

@article{fds211935,
Author = {J. Lu and Pingbing Ming},
Title = {Convergence of a force-based hybrid method for atomistic and
continuum models in three dimension},
Journal = {Comm. Pure Appl. Math.},
Volume = {66},
Pages = {83-108},
Year = {2013},
url = {http://dx.doi.org/10.1002/cpa.21429},
Doi = {10.1002/cpa.21429},
Key = {fds211935}
}

@article{fds211936,
Author = {J. Lu and Weinan E},
Title = {The Kohn-Sham equation for deformed crystals},
Journal = {Mem. Amer. Math. Soc.},
Volume = {221},
Number = {1040},
Year = {2013},
url = {http://dx.doi.org/10.1090/S0065-9266-2012-00659-9},
Doi = {10.1090/S0065-9266-2012-00659-9},
Key = {fds211936}
}

@article{fds215935,
Author = {J. Lu and Eric Vanden-Eijnden},
Title = {Infinite swapping replica exchange molecular dynamics leads
to a simple simulation patch using mixture
potentials},
Journal = {J. Chem. Phys.},
Volume = {138},
Pages = {084105},
Year = {2013},
url = {http://dx.doi.org/10.1063/1.4790706},
Doi = {10.1063/1.4790706},
Key = {fds215935}
}

@article{fds220491,
Author = {J. Lu and Weinan E and Xu Yang},
Title = {Asymptotic analysis of the quantum dynamics: Bloch-Wigner
transform and Bloch dynamics},
Journal = {Acta Math. Appl. Sin. Engl. Ser.},
Volume = {29},
Pages = {465--476},
Year = {2013},
url = {http://dx.doi.org/10.1007/s10255-011-0095-5},
Doi = {10.1007/s10255-011-0095-5},
Key = {fds220491}
}

%% Maggioni, Mauro
@article{fds221112,
Author = {M. Maggioni},
Title = {Geometric Estimation of Probability Measures in
High-Dimensions},
Journal = {Proc. IEEE Asilomar Conference},
Year = {2013},
Month = {November},
Key = {fds221112}
}

@article{fds221106,
Author = {M. Iwen and M. Maggioni},
Title = {Approximation of Points on Low-Dimensional Manifolds Via
Random Linear Projections},
Journal = {Inference & Information},
Volume = {2},
Year = {2013},
Month = {February},
url = {http://dx.doi.org/10.1093/imaiai/iat001},
Doi = {10.1093/imaiai/iat001},
Key = {fds221106}
}

@article{fds221105,
Author = {A. Coppola and B. Wenner and R. Stevens and O. Ilkayeva and M. Maggioni and T. Slotkin and E. Levin and C. Newgard},
Title = {Branched-chain amino acids alter neurobehavioral function in
rats},
Journal = {American Journal of Physiology - Endocrinology and
Metabolism},
Volume = {304},
Number = {4},
Year = {2013},
Month = {February},
url = {http://dx.doi.org/10.1152/ajpendo.00373.2012},
Doi = {10.1152/ajpendo.00373.2012},
Key = {fds221105}
}

@article{fds221113,
Author = {S. Gerber and M. Maggioni},
Title = {Multiscale dictionaries, transforms, and learning in
high-dimensions},
Journal = {Proc. SPIE 8858, Wavelets and Sparsity XV},
Year = {2013},
url = {http://dx.doi.org/10.1117/12.2021984},
Doi = {10.1117/12.2021984},
Key = {fds221113}
}

@article{fds221121,
Author = {Kalyani Krishnamurthy and Alex Mrozack and Mauro Maggioni and David Brady},
Title = {Multiscale, dictionary-based speckle denoising},
Booktitle = {Proc. Computational Optical Sensing and Imaging},
Year = {2013},
ISBN = {978-1-55752-975-6},
url = {http://dx.doi.org/http://dx.doi.org/10.1364/COSI.2013.CM2C.2},
Doi = {http://dx.doi.org/10.1364/COSI.2013.CM2C.2},
Key = {fds221121}
}

@article{fds221122,
Author = {G. Chen and A.V. Little and M. Maggioni},
Title = {Multi-Resolution Geometric Analysis for Data in High
Dimensions},
Volume = {1},
Booktitle = {Excursions in Harmonic Analysis},
Publisher = {Birkhaüser Boston},
Year = {2013},
ISBN = {978-0-8176-8375-7},
url = {http://dx.doi.org/10.1007/978-0-8176-8376-4_13},
Doi = {10.1007/978-0-8176-8376-4_13},
Key = {fds221122}
}

@inproceedings{MM:EEG,
Author = {E Causevic and R~R Coifman and R Isenhart and A Jacquin and E~R John and M Maggioni and L~S Prichep and F~J
Warner},
Title = {{QEEG}-based classification with wavelet packets and
microstate features for triage applications in the
{ER}},
Year = {2005},
Key = {MM:EEG}
}

@article{MRA_HRBF2004,
Author = {S. Ferrari and M. Maggioni and N. A. Borghese},
Title = {Multi-Scale Approximation with Hierarchical Radial Basis
Functions Networks,},
Journal = {IEEE Trans. on Neural Networks},
Volume = {15},
Number = {1},
Pages = {178--188},
Year = {2004},
Key = {MRA_HRBF2004}
}

@misc{PathNIH2004,
Author = {GL Davis and Mauro Maggioni and FJ Warner and FB Geshwind and AC Coppi and RA DeVerse and RR Coifman},
Title = {Hyper-spectral Analysis of normal and malignant colon tissue
microarray sections using a novel DMD system},
Year = {2004},
Key = {PathNIH2004}
}

@techreport{CMTech,
Author = {Ronald R Coifman and Mauro Maggioni},
Title = {Multiresolution Analysis associated to diffusion semigroups:
construction and fast algorithms},
Number = {YALE/DCS/TR-1289},
Organization = {Dept. Comp. Sci., Yale University},
Institution = {Dept. Comp. Sci., Yale University},
Year = {2004},
Key = {CMTech}
}

%% Mattingly, Jonathan C.
@article{fds223434,
Author = {J.C. Mattingly and David P. Herzog},
Title = {Noise-Induced Stabilization of Planar Flows
II},
Year = {2014},
Month = {April},
url = {http://arxiv.org/abs/1404.0955},
Key = {fds223434}
}

@article{fds223435,
Author = {J.C. Mattingly and David P. Herzog},
Title = {Noise-Induced Stabilization of Planar Flows
I},
Year = {2014},
Month = {April},
url = {http://arxiv.org/abs/1404.0957},
Key = {fds223435}
}

@article{fds224075,
Author = {J.C. Mattingly},
Title = {Regularity of invariant densities for 1D-systems with random
switching},
Year = {2014},
url = {http://arxiv.org/abs/1406.5425},
Abstract = {This is a detailed analysis of invariant measures for
one-dimensional dynamical systems with random switching. In
particular, we prove smoothness of the invariant densities
away from critical points and describe the asymptotics of
the invariant densities at critical points.},
Key = {fds224075}
}

@article{fds224076,
Author = {J.C. Mattingly and Sean D. Lawley and Michael C. Reed},
Title = {Stochastic switching in infinite dimensions with
applications to random parabolic PDEs},
Year = {2014},
url = {http://arxiv.org/abs/1407.2264},
Abstract = {We consider parabolic PDEs with randomly switching boundary
conditions. In order to analyze these random PDEs, we
consider more general stochastic hybrid systems and prove
convergence to, and properties of, a stationary
distribution. Applying these general results to the heat
equation with randomly switching boundary conditions, we
find explicit formulae for various statistics of the
solution and obtain almost sure results about its regularity
and structure. These results are of particular interest for
biological applications as well as for their significant
departure from behavior seen in PDEs forced by disparate
Gaussian noise. Our general results also have applications
to other types of stochastic hybrid systems, such as ODEs
with randomly switching right-hand sides.},
Key = {fds224076}
}

@article{fds224078,
Author = {Jonathan C. Mattingly and Etienne Pardoux},
Title = {Invariant measure selection by noise: An
Example},
Journal = {Discrete and Continuous Dynamical Systems. Series
A},
Volume = {34},
Number = {10},
Pages = {4223--4257},
Year = {2014},
url = {http://arxiv.org/abs/1403.3593},
Abstract = {We consider a deterministic system with two conserved
quantities and infinity many invariant measures. However the
systems possess a unique invariant measure when enough
stochastic forcing and balancing dissipation are added. We
then show that as the forcing and dissipation are removed a
unique limit of the deterministic system is selected. The
exact structure of the limiting measure depends on the
specifics of the stochastic forcing.},
Key = {fds224078}
}

@article{fds224074,
Author = {J.C. Mattingly and Sean D. Lawley and Michael C. Reed},
Title = {Sensitivity to switching rates in stochastically switched
ODEs},
Year = {2014},
url = {http://arxiv.org/abs/1310.2525},
Abstract = {We consider a stochastic process driven by a linear ordinary
differential equation whose right-hand side switches at
exponential times between a collection of different
matrices. We construct planar examples that switch between
two matrices where the individual matrices and the average
of the two matrices are all Hurwitz (all eigenvalues have
strictly negative real part), but nonetheless the process
goes to infinity at large time for certain values of the
switching rate. We further construct examples in higher
dimensions where again the two individual matrices and their
averages are all Hurwitz, but the process has arbitrarily
many transitions between going to zero and going to infinity
at large time as the switching rate varies. In order to
construct these examples, we first prove in general that if
each of the individual matrices is Hurwitz, then the process
goes to zero at large time for sufficiently slow switching
rate and if the average matrix is Hurwitz, then the process
goes to zero at large time for sufficiently fast switching
rate. We also give simple conditions that ensure the process
goes to zero at large time for all switching
rates.},
Key = {fds224074}
}

@article{fds224077,
Author = {Thomas Hotz and Sean Skwerer and Stephan Huckemann and Huiling Le and J.
S. Marron and Jonathan C. Mattingly and Ezra Miller and James Nolen and Megan Owen and Vic Patrangenaru},
Title = {Sticky central limit theorems on open books},
Journal = {Ann. Appl. Probab.},
Volume = {23},
Number = {6},
Pages = {2238--2258},
Year = {2013},
url = {http://arxiv.org/abs/1202.4267},
Abstract = {Given a probability distribution on an open book (a metric
space obtained by gluing a disjoint union of copies of a
half-space along their boundary hyperplanes), we define a
precise concept of when the Fr\'{e}chet mean (barycenter) is
sticky. This nonclassical phenomenon is quantified by a law
of large numbers (LLN) stating that the empirical mean
eventually almost surely lies on the (codimension 1 and
hence measure 0) spine that is the glued hyperplane, and a
central limit theorem (CLT) stating that the limiting
distribution is Gaussian and supported on the spine. We also
state versions of the LLN and CLT for the cases where the
mean is nonsticky (i.e., not lying on the spine) and partly
sticky (i.e., is, on the spine but not sticky).},
Key = {fds224077}
}

@article{fds221260,
Author = {Elizabeth Munch and Paul Bendich and Katharine Turner and Sayan
Mukherjee, Jonathan Mattingly and John Harer},
Title = {Probabilistic Fréchet Means and Statistics on
Vineyards},
Year = {2013},
url = {http://arxiv.org/abs/1307.6530},
Abstract = {In order to use persistence diagrams as a true statistical
tool, it would be very useful to have a good notion of mean
and variance for a set of diagrams. Mileyko and his
collaborators made the first study of the properties of the
Fr\'{e}chet mean in (Dp,Wp), the space of persistence
diagrams equipped with the p-th Wasserstein metric. In
particular, they showed that the Fr\'{e}chet mean of a
finite set of diagrams always exists, but is not necessarily
unique. As an unfortunate consequence, one sees that the
means of a continuously-varying set of diagrams do not
themselves vary continuously, which presents obvious
problems when trying to extend the Fr\'{e}chet mean
definition to the realm of vineyards. We fix this problem by
altering the original definition of Fr\'{e}chet mean so that
it now becomes a probability measure on the set of
persistence diagrams; in a nutshell, the mean of a set of
diagrams will be a weighted sum of atomic measures, where
each atom is itself the (Fr\'{e}chet mean) persistence
diagram of a perturbation of the input diagrams. We show
that this new definition defines a (H\"older) continuous
map, for each k, from (Dp)k→P(Dp), and we present several
examples to show how it may become a useful statistic on
vineyards.},
Key = {fds221260}
}

%% Miller, Ezra
@article{fds221013,
Author = {Sean Skwerer and Elizabeth Bullitt and Stephan Huckemann and Ezra
Miller, Ipek Oguz and Megan Owen and Vic Patrangenaru and Scott
Provan and J.S. Marron},
Title = {Tree-oriented analysis of brain artery structure},
Journal = {Journal of Mathematical Imaging and Vision},
Year = {2013},
Abstract = {Statistical analysis of magnetic resonance angiography (MRA)
brain artery trees is performed using two methods for
mapping brain artery trees to points in phylogenetic
treespace: cortical landmark correspondence and descendant
correspondence. The differences in end results based on
these mappings are highlighted to emphasize the importance
of correspondence in tree-oriented data analysis.
Representation of brain artery systems as points in
phylogenetic tree space, a mathematical space developed by
Billera, Holmes, and Vogtmann, facilitates this analysis.
Phylogenetic tree space is a rich setting for tree-oriented
data analysis. The Fréchet sample mean or an approximation
is reported. Multidimensional scaling is used to explore
structure in the data set based on pairwise distances
between data points. This analysis of MRA data shows a
statistically significant effect of age and sex on brain
artery structure. Variation in the proximity of brain
arteries to the cortical surface results in strong
statistical difference between sexes and statistically
significant age effect. That particular observation is
possible with cortical correspondence but did not appear in
the descendant correspondence.},
Key = {fds221013}
}

@article{fds220838,
Title = {Affine stratifications from finite misère
quotients},
Journal = {Journal of Algebraic Combinatorics},
Volume = {37},
Pages = {1-9},
Year = {2013},
url = {http://dx.doi.org/10.1007/s10801-012-0355-3},
Abstract = {Given a morphism from an affine semigroup Q to an arbitrary
commutative monoid, it is shown that every fiber possesses
an affine stratification: a partition into a finite disjoint
union of translates of normal affine semigroups. The proof
rests on mesoprimary decomposition of monoid congruences
[arXiv:1107.4699] and a novel list of equivalent conditions
characterizing the existence of an affine stratification.
The motivating consequence of the main result is a special
case of a conjecture due to Guo and the author
[arXiv:0908.3473, arXiv:1105.5420] on the existence of
affine stratifications for (the set of winning positions of)
any lattice game. The special case proved here assumes that
the lattice game has finite mis&egrave;re quotient, in the
sense of Plambeck and Siegel [arXiv:math/0501315,
arXiv:math/0609825v5].},
Key = {fds220838}
}

@article{fds220839,
Author = {First Miller and Alan Guo},
Title = {Algorithms for lattice games},
Journal = {International Journal of Game Theory},
Volume = {42},
Number = {4},
Pages = {777-788},
Year = {2013},
url = {http://dx.doi.org/10.1007/s00182-012-0319-9},
Abstract = {This paper provides effective methods for the polyhedral
formulation of impartial finite combinatorial games as
lattice games. Given a rational strategy for a lattice game,
a polynomial time algorithm is presented to decide (i)
whether a given position is a winning position, and to find
a move to a winning position, if not; and (ii) to decide
whether two given positions are congruent, in the sense of
misère quotient theory. The methods are based on the theory
of short rational generating functions.},
Key = {fds220839}
}

@article{fds220949,
Author = {First Miller and Thomas Hotz and Stephan Huckemann and Huiling Le and J. S. Marron and Jonathan C. Mattingly and James Nolen and Megan Owen and Vic
Patrangenaru and Sean Skwerer},
Title = {Sticky central limit theorems on open books},
Journal = {Annals of Applied Probability},
Volume = {23},
Number = {6},
Pages = {2238-2258},
Year = {2013},
url = {http://dx.doi.org/10.1214/12-AAP899},
Abstract = {Given a probability distribution on an open book (a metric
space obtained by gluing a disjoint union of copies of a
half-space along their boundary hyperplanes), we define a
precise concept of when the Fr&eacute;chet mean (barycenter)
is <i>sticky</i>. This non-classical phenomenon is
quantified by a law of large numbers (LLN) stating that the
empirical mean eventually almost surely lies on the
(codimension 1 and hence measure 0) <i>spine</i> that is the
glued hyperplane, and a central limit theorem (CLT) stating
that the limiting distribution is Gaussian and supported on
the spine. We also state versions of the LLN and CLT for the
cases where the mean is nonsticky (that is, not lying on the
spine) and partly sticky (that is, on the spine but not
sticky).},
Key = {fds220949}
}

@article{fds220950,
Author = {First Miller and Manoj Gopalkrishnan and Anne Shiu},
Title = {A projection argument for differential inclusions, with
applications to persistence of mass-action
kinetics},
Journal = {SIGMA (Symmetry, Integrability, and Geometry: Methods and
Applications)},
Volume = {9},
Year = {2013},
url = {http://dx.doi.org/10.3842/SIGMA.2013.025},
Abstract = {Motivated by questions in mass-action kinetics, we introduce
the notion of <i>vertexical family</i> of differential
inclusions. Defined on open hypercubes, these families are
characterized by particular good behavior under projection
maps. The motivating examples are certain families of
reaction networks&mdash;including reversible, weakly
reversible, endotactic, and <i>strongly endotactic</i>
reaction networks&mdash;that give rise to vertexical
families of mass-action differential inclusions. We prove
that vertexical families are amenable to structural
induction. Consequently, a trajectory of a vertexical family
approaches the boundary if and only if either the trajectory
approaches a vertex of the hypercube, or a trajectory in a
lower-dimensional member of the family approaches the
boundary. With this technology, we make progress on the
global attractor conjecture, a central open problem
concerning mass-action kinetics systems. Additionally, we
phrase mass-action kinetics as a functor on reaction
networks with variable rates.},
Key = {fds220950}
}

@article{fds221011,
Author = {First Miller and Manoj Gopalkrishnan and Anne Shiu},
Title = {A geometric approach to the Global Attractor
Conjecture},
Journal = {SIADS (SIAM Journal on Applied Dynamical
Systems)},
Year = {2013},
url = {http://arxiv.org/abs/math/1305.5303},
Abstract = {This paper introduces the class of "strongly endotactic
networks", a subclass of the endotactic networks introduced
by G. Craciun, F. Nazarov, and C. Pantea. The main result
states that the global attractor conjecture holds for
complex-balanced systems that are strongly endotactic: every
trajectory with positive initial condition converges to the
unique positive equilibrium allowed by conservation laws.
This extends a recent result by D. F. Anderson for systems
where the reaction diagram has only one linkage class
(connected component). The results here are proved using
differential inclusions, a setting that includes power-law
systems. The key ideas include a perspective on reaction
kinetics in terms of combinatorial geometry of reaction
diagrams, a projection argument that enables analysis of a
given system in terms of systems with lower dimension, and
an extension of Birch's theorem, a well-known result about
intersections of affine subspaces with manifolds
parameterized by monomials.},
Key = {fds221011}
}

%% Minsker, Stanislav
@article{fds220272,
Author = {S. Minsker},
Title = {Estimation of Extreme Values and Associated Level Sets of a
Regression Function via Selective Sampling},
Journal = {In Proceedings of the Conference on Learning Theory (COLT
2013)},
Pages = {105-121},
Year = {2013},
url = {http://jmlr.org/proceedings/papers/v30/Minsker13.html},
Abstract = {We propose a new method for estimating the locations and the
value of an absolute maximum (minimum) of a function from
the observations contaminated by random noise. Our goal is
to solve the problem under minimal regularity and shape
constraints. In particular, we do not assume
differentiability of a function nor that its maximum is
attained at a single point. We provide tight upper and lower
bounds for the performance of proposed estimators. Our
method is adaptive with respect to the unknown parameters of
the problem over a large class of underlying
distributions.},
Key = {fds220272}
}

@article{fds220270,
Author = {V. Koltchinskii and S. Minsker},
Title = {L1-Penalization in Functional Linear Regression with
Subgaussian Design},
Journal = {Submitted},
Year = {2013},
url = {http://arxiv.org/abs/1307.8137},
Abstract = {We study functional regression with random subgaussian
design and real-valued response. The focus is on the
problems in which the regression function can be well
approximated by a functional linear model with the slope
function being "sparse" in the sense that it can be
represented as a sum of a small number of well separated
"spikes". This can be viewed as an extension of now
classical sparse estimation problems to the case of infinite
dictionaries. We study an estimator of the regression
function based on penalized empirical risk minimization with
quadratic loss and the complexity penalty defined in terms
of L1-norm (a continuous version of LASSO). The main goal is
to introduce several important parameters characterizing
sparsity in this class of problems and to prove sharp oracle
inequalities showing how the L2-error of the continuous
LASSO estimator depends on the underlying sparsity of the
problem.},
Key = {fds220270}
}

@article{fds220271,
Author = {S. Minsker},
Title = {Geometric Median and Robust Estimation in Banach
Spaces},
Year = {2013},
url = {http://arxiv.org/abs/1308.1334},
Abstract = {In many real-world applications, collected data is
contaminated by the noise with heavy-tailed distribution and
might contain outliers of large magnitude. In this
situation, it is necessary to apply methods which produce
reliable outcomes even if the input contains corrupted
measurements. We describe a general method which allows one
to obtain estimators with tight concentration around the
true parameter of interest taking values in a Banach space.
Suggested construction relies on the fact that the geometric
median of a collection of independent "weakly concentrated"
estimators satisfies a much stronger deviation bound than
each individual element in the collection. Our approach is
illustrated through several examples, including sparse
linear regression and low-rank matrix recovery
problems.},
Key = {fds220271}
}

%% Moss, Robert
@article{fds219949,
Author = {R. Moss and S. R. Thomas},
Title = {Hormonal regulation of salt and water excretion: a
mathematical model of whole-kidney function and
pressure-natriuresis},
Journal = {AJP Renal Physiol},
Year = {2013},
url = {http://ajprenal.physiology.org/content/early/2013/10/03/ajprenal.00089.2013},
Abstract = {We present a lumped-nephron model that explicitly represents
the main features of the underlying physiology,
incorporating the major hormonal regulatory effects on both
tubular and vascular function, and which accurately
simulates hormonal regulation of renal salt and water
excretion. This is the first model to explicitly couple
glomerulovascular and medullary dynamics, and it is much
more detailed in structure than existing whole-organ models
and renal portions of multi-organ models. In contrast to
previous medullary models, which have only considered the
antidiuretic state, our model is able to regulate water and
sodium excretion over a variety of experimental conditions
in good agreement with data from experimental studies of the
rat. Since the properties of the vasculature and epithelia
are explicitly represented, they can be altered to simulate
pathophysiological conditions and pharmacological
interventions. The model serves as an appropriate starting
point for simulations of physiological, pathophysiological
and pharmacological renal conditions, and for exploring the
relationship between the extra-renal environment and renal
excretory function in physiological and pathophysiological
contexts.},
Doi = {10.1152/ajprenal.00089.2013},
Key = {fds219949}
}

%% Ng, Lenhard L
@article{fds223315,
Author = {L. Ng},
Title = {A topological introduction to knot contact
homology},
Booktitle = {Contact and Symplectic Topology},
Editor = {F. Bourgeois and V. Colin and A. Stipsicz},
Year = {2014},
ISBN = {978-3-319-02035-8},
url = {http://dx.doi.org/10.1007/978-3-319-02036-5_10},
Doi = {10.1007/978-3-319-02036-5_10},
Key = {fds223315}
}

@article{fds218592,
Author = {T. Ekholm and L. Ng},
Title = {Legendrian contact homology in the boundary of a subcritical
Weinstein 4-manifold},
Year = {2013},
url = {http://arxiv.org/abs/1307.8436},
Key = {fds218592}
}

@article{fds218591,
Author = {L. Ng and D. Rutherford},
Title = {Satellites of Legendrian knots and representations of the
Chekanov-Eliashberg algebra},
Journal = {Algebraic & Geometric Topology},
Volume = {13},
Number = {5},
Pages = {3047–3097},
Year = {2013},
url = {http://dx.doi.org/10.2140/agt.2013.13.3047},
Doi = {10.2140/agt.2013.13.3047},
Key = {fds218591}
}

@article{fds217173,
Author = {W. Chongchitmate and L. Ng},
Title = {An atlas of Legendrian knots},
Journal = {Experimental Mathematics},
Volume = {22},
Number = {1},
Pages = {26-37},
Year = {2013},
url = {http://dx.doi.org/10.1080/10586458.2013.750221},
Doi = {10.1080/10586458.2013.750221},
Key = {fds217173}
}

@article{fds217174,
Author = {J. Etnyre and L. Ng and V. Vertesi},
Title = {Legendrian and transverse twist knots},
Journal = {Journal of the European Mathematical Society},
Volume = {15},
Number = {3},
Pages = {451-512},
Year = {2013},
url = {http://dx.doi.org/10.4171/JEMS/383},
Doi = {10.4171/JEMS/383},
Key = {fds217174}
}

@article{fds217175,
Author = {T. Ekholm and J. Etnyre and L. Ng and M. Sullivan},
Title = {Filtrations on the knot contact homology of transverse
knots},
Journal = {Mathematische Annalen},
Volume = {355},
Number = {4},
Pages = {1561-1691},
Year = {2013},
url = {http://dx.doi.org/10.1007/s00208-012-0832-y},
Doi = {10.1007/s00208-012-0832-y},
Key = {fds217175}
}

@article{fds217177,
Author = {T. Ekholm and J. Etnyre and L. Ng and M. Sullivan},
Title = {Knot contact homology},
Journal = {Geometry & Topology},
Volume = {17},
Pages = {975-1112},
Year = {2013},
url = {http://dx.doi.org/10.2140/gt.2013.17.975},
Doi = {10.2140/gt.2013.17.975},
Key = {fds217177}
}

@article{fds218616,
Author = {M. Aganagic and T. Ekholm and L. Ng and C. Vafa},
Title = {Topological strings, D-model, and knot contact
homology},
Year = {2013},
url = {http://arxiv.org/abs/1304.5778},
Key = {fds218616}
}

@article{fds223316,
Author = {R. Lipshitz and L. Ng and S. Sarkar},
Title = {On transverse invariants from Khovanov homology},
Journal = {Quantum Topology},
Year = {2013},
url = {http://arxiv.org/abs/1303.6371},
Key = {fds223316}
}

%% Nolen, James
@article{fds223681,
Author = {J. Lu and J. Nolen},
Title = {Reactive trajectories and the transition path
process.},
Journal = {Probability Theory and Related Fields},
Year = {2014},
Month = {January},
url = {http://arxiv.org/abs/1303.1744},
Doi = {10.1007/s00440-014-0547-y},
Key = {fds223681}
}

@article{fds218100,
Author = {J. Nolen},
Title = {Normal approximation for a random elliptic
equation},
Journal = {Probability Theory and Related Fields},
Volume = {159},
Number = {3},
Pages = {661-700},
Year = {2014},
url = {http://math.duke.edu/~nolen/preprints/ellipfluctper_rev.pdf},
Doi = {10.1007/s00440-013-0517-9},
Key = {fds218100}
}

@article{fds223716,
Author = {J. Nolen},
Title = {Normal approximation for the net flux through a random
conductor},
Year = {2014},
url = {http://arxiv.org/abs/1406.2186},
Key = {fds223716}
}

@article{fds216732,
Author = {F. Hamel and J. Nolen and J.-M. Roquejoffre and L.
Ryzhik},
Title = {A short proof of the logarithmic Bramson correction in
Fisher-KPP equations},
Journal = {Networks and Heterogeneous Media},
Volume = {8},
Number = {1},
Pages = {275-289},
Year = {2013},
url = {http://math.duke.edu/~nolen/preprints/hnrr1_submit.pdf},
Doi = {doi:10.3934/nhm.2013.8.275},
Key = {fds216732}
}

@article{fds219489,
Author = {T. Hotz and S. Huckemann and H. Le and J. Marron and J. Mattingly and E.
Miller, J. Nolen and M. Owen and V. Patrangenaru and S.
Skwere},
Title = {Sticky central limit theorem on open books},
Journal = {Annals of Applied Probability},
Volume = {23},
Number = {6},
Pages = {2238-2258},
Year = {2013},
url = {http://arxiv.org/abs/1202.4267},
Doi = {doi:10.1214/12-AAP899},
Key = {fds219489}
}

@article{fds217615,
Author = {J. Nolen and J.-M. Roqujoffre and L. Ryzhik},
Title = {Power-like delay in time inhomogeneous Fisher-KPP
equations},
Year = {2013},
url = {http://math.duke.edu/~nolen/preprints/bigdelay-draft.pdf},
Key = {fds217615}
}

@article{fds215981,
Author = {S. Bhamidi and J. Hannig and C. Lee and J. Nolen},
Title = {The importance sampling technique for understanding rare
events in Erdős-Rényi random graphs},
Year = {2013},
url = {http://arxiv.org/abs/1302.6551},
Key = {fds215981}
}

%% Patel, Mainak
@article{fds218652,
Author = {M. Patel and B. Joshi},
Title = {Decoding synchronized oscillations within the brain:
Phase-delayed inhibition provides a robust mechanism for
creating a sharp synchrony filter},
Journal = {Journal of Theoretical Biology},
Volume = {334C},
Pages = {13-25},
Year = {2013},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23747525},
Abstract = {The widespread presence of synchronized neuronal
oscillations within the brain suggests that a mechanism must
exist that is capable of decoding such activity. Two
realistic designs for such a decoder include: (1) a read-out
neuron with a high spike threshold, or (2) a phase-delayed
inhibition network motif. Despite requiring a more elaborate
network architecture, phase-delayed inhibition has been
observed in multiple systems, suggesting that it may provide
inherent advantages over simply imposing a high spike
threshold. In this work, we use a computational and
mathematical approach to investigate the efficacy of the
phase-delayed inhibition motif in detecting synchronized
oscillations. We show that phase-delayed inhibition is
capable of creating a synchrony detector with sharp
synchrony filtering properties that depend critically on the
time course of inputs. Additionally, we show that
phase-delayed inhibition creates a synchrony filter that is
far more robust than that created by a high spike
threshold.},
Key = {fds218652}
}

@article{fds218653,
Author = {M. Patel and B. Joshi},
Title = {Switching mechanisms and bout times in a pair of
reciprocally inhibitory neurons},
Journal = {Journal of Computational Neuroscience [ePub ahead of
print]},
Year = {2013},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23820857},
Abstract = {Within the appropriate parameter regime, a deterministic
model of a pair of mutually inhibitory neurons receiving
excitatory driving currents exhibits bistability-each of the
two stable states corresponds to one neuron being active and
the other being quiescent. The presence of noise in the
driving currents results in a system that randomly switches
back and forth between these two states, causing alternating
bouts of spiking activity. In this work, we examine the
random bout durations of the two neurons and dependence on
system parameters. We find that bout durations of each
neuron are exponentially distributed, with changes in system
parameters altering only the mean of the distribution.
Synaptic inhibition independently controls the bout
durations of the two neurons-the mean bout time of a neuron
is a function of efferent (or outgoing) inhibition, and is
independent of afferent (or incoming) inhibition.
Furthermore, we find that the mean bout time of a neuron
exhibits a critical dependence on the time course (rather
than amplitude) of efferent inhibition-mean bout time of a
neuron grows exponentially with the time course of efferent
inhibition, and the growth rate of this exponential function
depends only on the excitatory driving current to that
neuron (and not on any other system parameters). We discuss
the relevance of our results to the regulation of sleep-wake
cycling by medullary and pontine structures within the
brain.},
Key = {fds218653}
}

@article{fds217324,
Author = {M. Patel},
Title = {Stimulus encoding within the barn owl optic tectum using
gamma oscillations vs. spike rate: A modeling
approach.},
Journal = {Network},
Volume = {24},
Number = {2},
Pages = {52-74},
Year = {2013},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23406211},
Abstract = {The optic tectum of the barn owl is a multimodal structure
with multiple layers, with each layer topographically
organized according to spatial receptive field. The response
of a site to a stimulus can be measured as either spike rate
or local field potential (LFP) gamma (25-90 Hz) power;
within superficial layers, spike rate and gamma power
spatial tuning curves are narrow and contrast-response
functions rise slowly. Within deeper layers, however, spike
rate tuning curves broaden and gamma power contrast-response
functions sharpen. In this work, we employ a computational
model to describe the inputs required to generate these
transformations from superficial to deep layers and show
that gamma power and spike rate can act as parallel
information processing streams.},
Key = {fds217324}
}

@article{fds217323,
Author = {B. Joshi and M. Patel},
Title = {Encoding with synchrony: Phase-delayed inhibition allows for
reliable and specific stimulus detection.},
Journal = {Journal of Theoretical Biology},
Volume = {328},
Pages = {26-32},
Year = {2013},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23524360},
Abstract = {Synchronized oscillations are observed in a diverse array of
neuronal systems, suggesting that synchrony represents a
common mechanism used by the brain to encode and relay
information. Coherent population activity can be deciphered
by a decoder neuron with a high spike threshold or by a
decoder using phase-delayed inhibition. These two mechanisms
are fundamentally different - a high spike threshold detects
a minimum number of synchronous input spikes (absolute
synchrony), while phase-delayed inhibition requires a fixed
fraction of incoming spikes to be synchronous (relative
synchrony). We show that, in a system with noisy encoders
where stimuli are encoded through synchrony, phase-delayed
inhibition enables the creation of a decoder that can
respond both reliably and specifically to a stimulus, while
a high spike threshold does not.},
Key = {fds217323}
}

@article{fds217322,
Author = {M. Patel and AV Rangan and D Cai},
Title = {Coding of odors by temporal binding within a model network
of the locust antennal lobe.},
Journal = {Frontiers in Computational Neuroscience},
Volume = {7},
Pages = {50-67},
Year = {2013},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23630495},
Abstract = {The locust olfactory system interfaces with the external
world through antennal receptor neurons (ORNs), which
represent odors in a distributed, combinatorial manner. ORN
axons bundle together to form the antennal nerve, which
relays sensory information centrally to the antennal lobe
(AL). Within the AL, an odor generates a dynamically
evolving ensemble of active cells, leading to a
stimulus-specific temporal progression of neuronal spiking.
This experimental observation has led to the hypothesis that
an odor is encoded within the AL by a dynamically evolving
trajectory of projection neuron (PN) activity that can be
decoded piecewise to ascertain odor identity. In order to
study information coding within the locust AL, we developed
a scaled-down model of the locust AL using
Hodgkin-Huxley-type neurons and biologically realistic
connectivity parameters and current components. Using our
model, we examined correlations in the precise timing of
spikes across multiple neurons, and our results suggest an
alternative to the dynamic trajectory hypothesis. We propose
that the dynamical interplay of fast and slow inhibition
within the locust AL induces temporally stable correlations
in the spiking activity of an odor-dependent neural subset,
giving rise to a temporal binding code that allows rapid
stimulus detection by downstream elements.},
Key = {fds217322}
}

%% Perea, Jose A.
@article{fds223841,
Author = {Jose A. Perea and Anastasia Deckard and Steve B. Haase and John
Harer},
Title = {SW1PerS: Sliding Windows and 1-Persistence Scoring;
Discovering Periodicity in Gene Expression Time Series
Data},
Year = {2014},
Month = {June},
Key = {fds223841}
}

@article{fds223454,
Author = {Jose A. Perea and John Harer},
Title = {Sliding Windows and Persistence: An Application of
Topological Methods to Signal Analysis},
Journal = {Foundations of Computational Mathematics},
Year = {2014},
Month = {May},
ISSN = {1615-3375},
url = {http://dx.doi.org/10.1007/s10208-014-9206-z},
Doi = {10.1007/s10208-014-9206-z},
Key = {fds223454}
}

@article{fds223453,
Author = {Jose A. Perea and Gunnar Carlsson},
Title = {A Klein-Bottle-Based Dictionary for Texture
Representation},
Journal = {International Journal of Computer Vision},
Volume = {107},
Number = {1},
Pages = {75-97},
Year = {2014},
Month = {March},
ISSN = {0920-5691},
url = {http://dx.doi.org/10.1007/s11263-013-0676-2},
Doi = {10.1007/s11263-013-0676-2},
Key = {fds223453}
}

%% Petters, Arlie O
@book{fds15387,
Author = {A. O. Petters and M. C. Werner},
Title = {Gravitational Lensing and Black Holes},
Publisher = {Springer, in preparation},
Year = {2015},
Month = {July},
Key = {fds15387}
}

@book{fds51036,
Author = {A. O. Petters and X. Dong},
Title = {Mathematical Finance with Applications: Understanding and
Buiding Financial Intuition},
Series = {SUMAT},
Publisher = {Springer, in preparation},
Year = {2014},
Month = {July},
Key = {fds51036}
}

%% Reed, Michael C
@article{fds221130,
Author = {L. Rios-Avila and H. F. Nijhout and M. C. Reed and H. S. Sitren and J.
F. Gregory III},
Title = {A mathematical model of tryptophan metabolism via the
kynurenine pathway provides insights into the effects of
tryptophan 2,3-dioxygenase on tryptophan
metabolites},
Journal = {J. Nutrition},
Volume = {143},
Pages = {1509-1519},
Year = {2013},
Key = {fds221130}
}

@article{fds221131,
Author = {M. Reed and H. F. Nijhout and J. Best},
Title = {Computational studies of the role of serotonin in the basal
ganglia},
Journal = {Frontiers in Integrative Neuroscience},
Volume = {7},
Pages = {1-8},
Year = {2013},
Key = {fds221131}
}

@article{fds221133,
Author = {T. Duncan and M. Reed and H. F. Nijhout},
Title = {A population model of folate-mediated one-carbon
metabolism},
Journal = {Nutrients},
Volume = {5},
Pages = {2457-2474},
Year = {2013},
Key = {fds221133}
}

@article{fds221135,
Author = {M. Reed and H. F. Nijhout and J. Best},
Title = {Projecting biochemistry over long distances},
Journal = {Math. Models Natural Phenomena},
Year = {2013},
Key = {fds221135}
}

@article{fds221136,
Author = {S. Lawley and J. Mattingly and M. Reed},
Title = {Sensitivity to switching rates on stochastically switched
ODEs},
Year = {2013},
Key = {fds221136}
}

@article{fds212606,
Author = {T. Duncan and M. Reed and H. F. Nijhout},
Title = {The relationship between intracellular and plasma levels of
folate and metabolites in the methionine cycle: A
model},
Journal = {Mol. Food Nutr. Res.},
Volume = {DOI 10.1002/mnfr.201200125},
Pages = {628-636},
Year = {2013},
Key = {fds212606}
}

@article{fds221124,
Author = {R. Ben-Shachar and Y, Chen and S. Luo and C. Hartman and M. Reed and H. F.
Nijhout},
Title = {The biochemistry of acetaminophen hepatotoxicity and rescue:
a mathematical model},
Journal = {Theoretical Biology and Medical Modeling},
Volume = {9},
Pages = {1-22},
Year = {2013},
Key = {fds221124}
}

@article{fds221127,
Author = {M. Patel and M. Reed},
Title = {Stimulus Encoding Within the Barn Owl Optic Tectum Using
Gamma Oscillations versus Spike Rate: A Modeling
Approach.},
Journal = {Network},
Volume = {24},
Pages = {52-74},
Year = {2013},
Key = {fds221127}
}

%% Ryser, Marc D
@article{fds221213,
Author = {S. Payne and B. Li and Y. Cao and D. Schaeffer and M.D. Ryser and L.
You},
Title = {Temporal control of self-organized pattern formation without
Journal = {Molecular Systems Biology},
Volume = {9},
Number = {697},
Year = {2013},
Key = {fds221213}
}

@article{fds221214,
Author = {J. Foo and K. Leder and M.D. Ryser},
Title = {Multifocality and recurrence risk: a quantitative model of
field cancerization},
Year = {2013},
Key = {fds221214}
}

@article{fds221216,
Author = {M.D. Ryser and K. McGoff and D. Herzog and D. Sivakoff and E.
Myers},
Title = {Impact of coverage-dependent marginal costs on optimal HPV
vaccination strategies},
Year = {2013},
Key = {fds221216}
}

@book{fds215731,
Author = {M.D. Ryser and S.V. Komarova},
Title = {Mathematical modeling of cancer metastases},
Booktitle = {Computational Bioengineering},
Publisher = {CRC/Taylor & Francis},
Key = {fds215731}
}

@article{fds218712,
Author = {C. Schoen},
Title = {Invariants of regular models of the product of two elliptic
curves at a place of multiplicative reduction},
Series = {Fields Institute Communications 67},
Pages = {461-487},
Booktitle = {Arithmetic and Geometry of K3 surfaces and Calabi-Yau
Threefolds},
Publisher = {Springer},
Editor = {Laza, R. and Schuett, M and and Yui, N.},
Year = {2013},
ISBN = {978-1-4614-6402-0},
Key = {fds218712}
}

@article{fds215558,
Author = {C. Schoen},
Title = {The geometric genus of a desingularized fiber product of
elliptic surfaces},
Journal = {Proceedings of the American Mathematical
Society},
Volume = {141},
Number = {3},
Pages = {745-752},
Year = {2013},
Key = {fds215558}
}

@article{fds216477,
Author = {C. Schoen},
Title = {Torsion in the Cohomology of Desingularized Fiber Products
of Elliptic Surfaces},
Journal = {Michigan Math. J.},
Volume = {62},
Pages = {81-115},
Year = {2013},
Key = {fds216477}
}

%% Schott, Sarah
@article{fds220537,
Author = {Mark Huber, and Sarah Schott},
Title = {Random Construction of Interpolating Sets for High
Dimensional Integration},
Journal = {Journal of Applied Probability},
Year = {2013},
Key = {fds220537}
}

%% Stern, Mark A
@article{fds219287,
Author = {Anda Degeratu and M.A. Stern},
Title = {Witten spinors on nonspin manifolds},
Journal = {Communications of Mathematical Physics 2013},
Year = {2013},
Month = {October},
url = {http://xxx.lanl.gov/abs/1112.0194},
Abstract = {Motivated by Witten's spinor proof of the positive mass
theorem, we analyze asymptotically constant harmonic spinors
on complete asymptotically flat nonspin manifolds with
nonnegative scalar curvature.},
Key = {fds219287}
}

@article{fds199121,
Author = {B. Charbonneau and M. Stern},
Title = {Asymptotic Hodge Theory of Vector Bundles},
Journal = {Communications in Analysis and Geometry},
Year = {2013},
Month = {August},
url = {http://xxx.lanl.gov/abs/1111.0591},
Abstract = {We introduce several families of filtrations on the space of
vector bundles over a smooth projective variety. These
filtrations are defined using the large k asymptotics of the
kernel of the Dolbeault Dirac operator on a bundle twisted
by the kth power of an ample line bundle. The filtrations
measure the failure of the bundle to admit a holomorphic
structure. We study compatibility under the Chern
isomorphism of these filtrations with the Hodge filtration
on cohomology.},
Key = {fds199121}
}

%% Strawn, Nathaniel K
@article{fds220457,
Author = {J. Cahill and D. Mixon and N. Strawn},
Title = {Connectivity and Irreducibility of Algebraic Varieties of
Finite Unit Norm Tight Frames},
Year = {2013},
Key = {fds220457}
}

@article{fds220455,
Author = {A. Armagan and D. Dunson and J. Lee and W. Bajwa and N.
Strawn},
Title = {Posterior consistency in linear models under shrinkage
priors},
Journal = {Biometrika},
Year = {2013},
Key = {fds220455}
}

%% Thompson, Andrew
@article{fds220947,
Author = {C. Cartis and A. Thompson},
Title = {An exact tree projection algorithm for wavelets},
Journal = {IEEE Signal Processing Letters},
Volume = {20},
Number = {11},
Pages = {1028-1031},
Year = {2013},
Key = {fds220947}
}

%% Trangenstein, John
@article{3547392,
Author = {Trangenstein, J.A. and Bell, J.B.},
Title = {Mathematical structure of compositional reservoir
simulation},
Journal = {SIAM J. Sci. Stat. Comput. (USA)},
Volume = {10},
Number = {5},
Pages = {817 - 45},
Keywords = {chemical technology;numerical methods;petroleum
industry;two-phase flow;},
Abstract = {Multicomponent two-phase isothermal fluid flow in petroleum
reservoirs is described. The fluid-flow model consists of
component conservation equations. Darcy's law for the
volumetric flow rates, balance between the fluid volume and
the rock void, and the conditions of thermodynamic
equilibrium that determine the distribution of the chemical
components into phases. Thermodynamic equilibrium is
described by means of a mathematical model for the chemical
potentials of each component in each phase of the fluid. The
flow equations are manipulated to form a pressure equation
and a modified component-conservation equation: these form
the basis for the sequential method. It is shown that the
pressure equation is parabolic under reasonable assumptions
on the thermodynamic equilibrium model, and that the
component-conservation equations are hyperbolic in the
absence of diffusive forces such as capillary pressure and
mixing. A numerical method based on the sequential
formulation of the flow equations is outlined and used to
illustrate the kinds of flow behavior that occur during
miscible gas injection},
Key = {3547392}
}

%% Venakides, Stephanos
@article{fds220956,
Author = {Oscar P. Bruno and Stephen P. Shipman and Catalin Turc and Stephanos
Venakides},
Title = {Efficient Evaluation of Doubly Periodic Green Functions in
3D Scattering, Including Wood Anomaly Frequencies},
Journal = {ArXiv>Mathematics > Analysis of PDEs},
Year = {2013},
Month = {July},
url = {http://arxiv.org/abs/1307.1176},
Abstract = {We present efficient methods for computing wave scattering
by diffraction gratings that exhibit two-dimensional
periodicity in three dimensional (3D) space. Applications
include scattering in acoustics, electromagnetics and
elasticity. Our approach uses boundary-integral equations.
The quasi-periodic Green function is a doubly infinite sum
of scaled 3D free-space outgoing Helmholtz Green functions.
Their source points are located at the nodes of a
periodicity lattice of the grating. For efficient numerical
computation of the lattice sum, we employ a smooth
truncation. Super-algebraic convergence to the Green
function is achieved as the truncation radius increases,
except at frequency-wavenumber pairs at which a Rayleigh
wave is at exactly grazing incidence to the grating. At
these "Wood frequencies", the term in the Fourier series
representation of the Green function that corresponds to the
grazing Rayleigh wave acquires an infinite coefficient and
the lattice sum blows up. At Wood frequencies, we modify the
Green function by adding two types of terms to it. The first
type adds weighted spatial shifts of the Green function to
itself with singularities below the grating; this yields
algebraic convergence. The second-type terms are
quasi-periodic plane wave solutions of the Helmholtz
equation. They reinstate (with controlled coefficients) the
grazing modes, effectively eliminated by the terms of first
type. These modes are needed in the Green function for
guaranteeing the well-posedness of the boundary-integral
equation that yields the scattered field. We apply this
approach to acoustic scattering by a doubly periodic 2D
grating near and at Wood frequencies and scattering by a
doubly periodic array of scatterers away from Wood
frequencies.},
Key = {fds220956}
}

@article{fds221201,
Author = {Jackson AD and Huang D and Gauthier DJ and Venakides
S.},
Title = {Destructive impact of imperfect beam collimation in
extraordinary optical transmission.},
Journal = {J. Opt. Soc. Am A},
Volume = {30},
Number = {6},
Pages = {1281-1290},
Year = {2013},
Month = {June},
Abstract = {We investigate the difference between analytic predictions,
numerical simulations, and experiments measuring the
transmission of energy through subwavelength, periodically
arranged holes in a metal film. At normal incidence, theory
predicts a sharp transmission minimum when the wavelength is
equal to the periodicity, and sharp transmission maxima at
one or more nearby wavelengths. In experiments, the sharpest
maximum from the theory is not observed, while the others
appear less sharp. In numerical simulations using commercial
electromagnetic field solvers, we find that the sharpest
maximum appears and approaches our predictions as the
computational resources are increased. To determine possible
origins of the destruction of the sharp maximum, we
incorporate additional features in our model. Incorporating
imperfect conductivity and imperfect periodicity in our
model leaves the sharp maximum intact. Imperfect
collimation, on the other hand, incorporated into the model
causes the destruction of the sharp maximum as happens in
experiments. We provide analytic support through an
asymptotic calculation for both the existence of the sharp
maximum and the destructive impact of imperfect collimation.
© 2013 Optical Society of America},
Key = {fds221201}
}

@article{fds220953,
Author = {S. Belov and S. Venakides},
Title = {Smooth parametric dependence of asymptotics of the
semiclassical focusing NLS},
Journal = {APDE (Analysis and PDE)},
Year = {2013},
Abstract = {We consider the one dimensional focusing (cubic) Nonlinear
Schrodinger equation (NLS) in the semiclassical limit with
a one parameter family of exponentially decaying in absolute
value initial conditions. We prove smooth parametric
dependence of the asymptotic solution on the parameter
utilizing the Riemann-Hilbert approach. Nu- merical
computations supporting our estimates of important
quantities are presented.},
Key = {fds220953}
}

%% Wang, Yi (Grace)
@article{fds221742,
Author = {Y. Wang},
Title = {K mappings and regression trees},
Year = {2013},
Month = {October},
Key = {fds221742}
}

%% Witelski, Thomas P.
@article{fds222260,
Author = {T.P. Witelski and L.N. Virgin and C. George},
Title = {A driven system of impacting pendulums: Experiments and
simulations},
Journal = {Journal of Sound and Vibration},
Volume = {333},
Number = {6},
Pages = {1734-1753},
Year = {2014},
Month = {March},
url = {http://dx.doi.org/10.1016/j.jsv.2013.11.004},
Doi = {10.1016/j.jsv.2013.11.004},
Key = {fds222260}
}

@article{fds215741,
Author = {S.J.Chapman, P.H.Trinh and T.P. Witelski},
Title = {Exponential asymptotics for thin film rupture},
Journal = {SIAM Journal on Applied Mathematics},
Volume = {73},
Number = {1},
Pages = {232-253},
Year = {2013},
url = {http://dx.doi.org/10.1137/120872012},
Doi = {10.1137/120872012},
Key = {fds215741}
}

@article{fds218639,
Author = {L.B.Smolka and T.P. Witelski},
Title = {Biaxial extensional motion of an inertially driven
Journal = {Physics of Fluids},
Volume = {25},
Number = {062105},
Year = {2013},
url = {http://dx.doi.org/10.1063/1.4811389},
Doi = {10.1063/1.4811389},
Key = {fds218639}
}



dept@math.duke.edu
ph: 919.660.2800
fax: 919.660.2821

Mathematics Department
Duke University, Box 90320
Durham, NC 27708-0320