%% Papers Published
@article{fds329938,
Author = {Motta, FC},
Title = {Topological Data Analysis: Developments and
Applications},
Pages = {369-391},
Booktitle = {Advances in Nonlinear Geosciences},
Publisher = {Springer},
Editor = {Tsonis, A},
Year = {2017},
Month = {November},
ISBN = {3319588958},
Abstract = {Topological Data Analysis (TDA) and its mainstay
computational device, persistent homology (PH), has
established a strong track record of providing researchers
across the data-driven sciences with new insights and
methodologies by characterizing low-dimensional geometric
structures in high-dimensional data. When combined with
machine learning (ML) methods, PH is valued as a
discriminating-feature extraction tool. This work highlights
many of the recent successes at the intersection of TDA and
ML, introduces some of the foundational mathematics
underpinning TDA, and summarizes the efforts to strengthen
the bridge between TDA and ML. Thus, this document is a
launching point for experimentalists and theoreticians to
consider what can be learned from the shape of their
data.},
Key = {fds329938}
}
@article{fds318325,
Author = {F.C. Motta and Pearson, DA and Bradley, RM and Motta, FC and Shipman,
PD},
Title = {Producing nanodot arrays with improved hexagonal order by
patterning surfaces before ion sputtering.},
Journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter
Physics},
Volume = {92},
Number = {6},
Pages = {062401},
Year = {2015},
Month = {December},
url = {http://http://dx.doi.org/10.1103/PhysRevE.92.062401},
Abstract = {When the surface of a nominally flat binary material is
bombarded with a broad, normally incident ion beam,
disordered hexagonal arrays of nanodots can form. Shipman
and Bradley have derived equations of motion that govern the
coupled dynamics of the height and composition of such a
surface [Shipman and Bradley, Phys. Rev. B 84, 085420
(2011)]. We investigate the influence of initial conditions
on the hexagonal order yielded by integration of those
equations of motion. The initial conditions studied are
hexagonal and sinusoidal templates, straight scratches, and
nominally flat surfaces. Our simulations indicate that both
kinds of templates lead to marked improvements in the
hexagonal order if the initial wavelength is approximately
equal to or double the linearly selected wavelength.
Scratches enhance the hexagonal order in their vicinity if
their width is close to or less than the linearly selected
wavelength. Our results suggest that prepatterning a binary
material can dramatically increase the hexagonal order
achieved at large ion fluences.},
Doi = {10.1103/physreve.92.062401},
Key = {fds318325}
}
@article{fds300025,
Author = {F.C. Motta and S.R. Fassnacht and I. Oprea and P.D. Shipman and J. Kirkpatrick and G.
Borleske and D. Kamin},
Title = {Geometric methods to describe snow surface
roughness},
Journal = {35th Annual American Geophysical Union Hydrology
Days},
Year = {2015},
Month = {March},
url = {http://hydrologydays.colostate.edu/Papers_15/Fassnacht_paper.pdf},
Key = {fds300025}
}
@article{fds300014,
Author = {F.C. Motta and P.D. Shipman and B. D. Springer},
Title = {A Point of Tangency Between Combinatorics and Differential
Geometry},
Journal = {The American Mathematical Monthly},
Volume = {122},
Number = {1},
Pages = {52-55},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.4169/amer.math.monthly.122.01.52},
Key = {fds300014}
}
%% Papers Accepted
@article{fds329101,
Author = {Cho, C-Y and Motta, FC and Kelliher, CM and Deckard, A and Haase,
SB},
Title = {Reconciling conflicting models for global control of
cell-cycle transcription.},
Journal = {Cell Cycle},
Volume = {16},
Number = {20},
Pages = {1965-1978},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1080/15384101.2017.1367073},
Abstract = {Models for the control of global cell-cycle transcription
have advanced from a CDK-APC/C oscillator, a transcription
factor (TF) network, to coupled CDK-APC/C and TF networks.
Nonetheless, current models were challenged by a recent
study that concluded that the cell-cycle transcriptional
program is primarily controlled by a CDK-APC/C oscillator in
budding yeast. Here we report an analysis of the
transcriptome dynamics in cyclin mutant cells that were not
queried in the previous study. We find that B-cyclin
oscillation is not essential for control of phase-specific
transcription. Using a mathematical model, we demonstrate
that the function of network TFs can be retained in the face
of significant reductions in transcript levels. Finally, we
show that cells arrested at mitotic exit with
non-oscillating levels of B-cyclins continue to cycle
transcriptionally. Taken together, these findings support a
critical role of a TF network and a requirement for CDK
activities that need not be periodic.},
Doi = {10.1080/15384101.2017.1367073},
Key = {fds329101}
}
@article{fds329102,
Author = {Burris, CS and Motta, FC and Shipman, PD},
Title = {An Unoriented Variation on de Bruijn Sequences},
Journal = {Graphs and Combinatorics},
Volume = {33},
Number = {4},
Pages = {845-858},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.1007/s00373-017-1793-4},
Doi = {10.1007/s00373-017-1793-4},
Key = {fds329102}
}
@article{fds318324,
Author = {F.C. Motta and Francis C. Motta, and Patrick D. Shipman, and Bethany D.
Springer},
Title = {Optimally Topologically Transitive Orbits in Discrete
Dynamical Systems},
Journal = {American Mathematical Monthly},
Volume = {123},
Number = {2},
Pages = {115-115},
Year = {2016},
url = {http://dx.doi.org/10.4169/amer.math.monthly.123.2.115},
Doi = {10.4169/amer.math.monthly.123.2.115},
Key = {fds318324}
}
%% Papers Submitted
@article{fds300026,
Author = {F.C. Motta and H. Adams and S. Chepushtanova and T. Emerson and E. Hanson and M. Kirby and R. Neville and C. Peterson and P.D. Shipman and L.
Ziegelmeier},
Title = {Persistent images: a stable vector representation of
persistent homology},
Year = {2015},
Month = {December},
Key = {fds300026}
}
@article{fds300024,
Author = {F.C. Motta and H. Adams and M. Adamaszek},
Title = {Random cyclic dynamical systems},
Year = {2015},
Month = {November},
url = {http://arxiv.org/abs/1511.07832},
Key = {fds300024}
}
@article{fds300020,
Author = {F.C. Motta and P.D. Shipman},
Title = {Sharpening the defect of complex Hadamards with a
flow},
Year = {2015},
Key = {fds300020}
}
@article{fds300021,
Author = {F.C. Motta and P.D. Shipman and C. Burris},
Title = {An unoriented variation on de Bruijn sequences},
Year = {2015},
Key = {fds300021}
}
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Mathematics Department