|
| Applied Math : Publications since January 2023
List all publications in the database. :chronological alphabetical combined listing:
%% Harer, John
@article{fds371293,
Author = {Motta, FC and McGoff, K and Moseley, RC and Cho, C-Y and Kelliher, CM and Smith, LM and Ortiz, MS and Leman, AR and Campione, SA and Devos, N and Chaorattanakawee, S and Uthaimongkol, N and Kuntawunginn, W and Thongpiam, C and Thamnurak, C and Arsanok, M and Wojnarski, M and Vanchayangkul, P and Boonyalai, N and Smith, PL and Spring, MD and Jongsakul, K and Chuang, I and Harer, J and Haase,
SB},
Title = {The parasite intraerythrocytic cycle and human circadian
cycle are coupled during malaria infection.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {120},
Number = {24},
Pages = {e2216522120},
Year = {2023},
Month = {June},
url = {http://dx.doi.org/10.1073/pnas.2216522120},
Abstract = {During infections with the malaria parasites <i>Plasmodium
vivax</i>, patients exhibit rhythmic fevers every 48 h.
These fever cycles correspond with the time the parasites
take to traverse the intraerythrocytic cycle (IEC). In other
<i>Plasmodium</i> species that infect either humans or mice,
the IEC is likely guided by a parasite-intrinsic clock
[Rijo-Ferreira<i>et al.</i>, <i>Science</i> <b>368</b>,
746-753 (2020); Smith <i>et al</i>., <i>Science</i>
<b>368</b>, 754-759 (2020)], suggesting that intrinsic clock
mechanisms may be a fundamental feature of malaria
parasites. Moreover, because <i>Plasmodium</i> cycle times
are multiples of 24 h, the IECs may be coordinated with the
host circadian clock(s). Such coordination could explain the
synchronization of the parasite population in the host and
enable alignment of IEC and circadian cycle phases. We
utilized an ex vivo culture of whole blood from patients
infected with <i>P. vivax</i> to examine the dynamics of the
host circadian transcriptome and the parasite IEC
transcriptome. Transcriptome dynamics revealed that the
phases of the host circadian cycle and the parasite IEC are
correlated across multiple patients, showing that the cycles
are phase coupled. In mouse model systems, host-parasite
cycle coupling appears to provide a selective advantage for
the parasite. Thus, understanding how host and parasite
cycles are coupled in humans could enable antimalarial
therapies that disrupt this coupling.},
Doi = {10.1073/pnas.2216522120},
Key = {fds371293}
}
%% Maggioni, Mauro
@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}
}
@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{fds361709,
Author = {Earle, G and Mattingly, JC},
Title = {Convergence of stratified MCMC sampling of non-reversible
dynamics},
Journal = {Stochastics and Partial Differential Equations: Analysis and
Computations},
Year = {2024},
Month = {January},
url = {http://dx.doi.org/10.1007/s40072-024-00325-0},
Abstract = {We present a form of stratified MCMC algorithm built with
non-reversible stochastic dynamics in mind. It can also be
viewed as a generalization of the exact milestoning method
or form of NEUS. We prove the convergence of the method
under certain assumptions, with expressions for the
convergence rate in terms of the process’s behavior within
each stratum and large-scale behavior between strata. We
show that the algorithm has a unique fixed point which
corresponds to the invariant measure of the process without
stratification. We will show how the convergence speeds of
two versions of the algorithm, one with an extra eigenvalue
problem step and one without, related to the mixing rate of
a discrete process on the strata, and the mixing probability
of the process being sampled within each stratum. The
eigenvalue problem version also relates to local and global
perturbation results of discrete Markov chains, such as
those given by Van Koten, Weare et. al.},
Doi = {10.1007/s40072-024-00325-0},
Key = {fds361709}
}
@article{fds371623,
Author = {Autry, E and Carter, D and Herschlag, GJ and Hunter, Z and Mattingly,
JC},
Title = {METROPOLIZED FOREST RECOMBINATION FOR MONTE CARLO SAMPLING
OF GRAPH PARTITIONS},
Journal = {SIAM Journal on Applied Mathematics},
Volume = {83},
Number = {4},
Pages = {1366-1391},
Publisher = {Society for Industrial & Applied Mathematics
(SIAM)},
Year = {2023},
Month = {August},
url = {http://dx.doi.org/10.1137/21M1418010},
Abstract = {We develop a new Markov chain on graph partitions that makes
relatively global moves yet is computationally feasible to
be used as the proposal in the Metropolis-Hastings method.
Our resulting algorithm is able to sample from a specified
measure on partitions or spanning forests. Being able to
sample from a specified measure is a requirement of what we
consider as the gold standard in quantifying the extent to
which a particular map is a gerrymander. Our proposal chain
modifies the recently developed method called recombination
(ReCom), which draws spanning trees on joined partitions and
then randomly cuts them to repartition. We improve the
computational efficiency by augmenting the statespace from
partitions to spanning forests. The extra information
accelerates the computation of the forward and backward
proposal probabilities which are required for the
Metropolis-Hastings algorithm. We demonstrate this method by
sampling redistricting plans on several measures of interest
and find promising convergence results on several key
observables of interest. We also explore some limitations in
the measures that are efficient to sample from and
investigate the feasibility of using parallel tempering to
extend this space of measures.},
Doi = {10.1137/21M1418010},
Key = {fds371623}
}
@article{fds361536,
Author = {Herzog, DP and Mattingly, JC and Nguyen, HD},
Title = {Gibbsian dynamics and the generalized Langevin
equation},
Journal = {Electronic Journal of Probability},
Volume = {28},
Year = {2023},
Month = {January},
url = {http://dx.doi.org/10.1214/23-EJP904},
Abstract = {We study the statistically invariant structures of the
nonlinear generalized Langevin equation (GLE) with a
power-law memory kernel. For a broad class of memory
kernels, including those in the subdiffusive regime, we
construct solutions of the GLE using a Gibbsian framework,
which does not rely on existing Markovian approximations.
Moreover, we provide conditions on the decay of the memory
to ensure uniqueness of statistically steady states,
generalizing previous known results for the GLE under
particular kernels as a sum of exponentials.},
Doi = {10.1214/23-EJP904},
Key = {fds361536}
}
%% Witelski, Thomas P.
@article{fds376241,
Author = {Ji, H and Witelski, TP},
Title = {COARSENING OF THIN FILMS WITH WEAK CONDENSATION},
Journal = {SIAM Journal on Applied Mathematics},
Volume = {84},
Number = {2},
Pages = {362-386},
Publisher = {Society for Industrial & Applied Mathematics
(SIAM)},
Year = {2024},
Month = {January},
url = {http://dx.doi.org/10.1137/23M1559336},
Abstract = {A lubrication model can be used to describe the dynamics of
a weakly volatile viscous fluid layer on a hydrophobic
substrate. Thin layers of the fluid are unstable to
perturbations and break up into slowly evolving interacting
droplets. A reduced-order dynamical system is derived from
the lubrication model based on the nearest-neighbor droplet
interactions in the weak condensation limit. Dynamics for
periodic arrays of identical drops and pairwise droplet
interactions are investigated, providing insights into the
coarsening dynamics of a large droplet system. Weak
condensation is shown to be a singular perturbation,
fundamentally changing the long-time coarsening dynamics for
the droplets and the overall mass of the fluid in two
additional regimes of long-time dynamics.},
Doi = {10.1137/23M1559336},
Key = {fds376241}
}
@article{fds371622,
Author = {Chapman, SJ and Dallaston, MC and Kalliadasis, S and Trinh, PH and Witelski, TP},
Title = {The role of exponential asymptotics and complex
singularities in self-similarity, transitions, and branch
merging of nonlinear dynamics},
Journal = {Physica D: Nonlinear Phenomena},
Volume = {453},
Year = {2023},
Month = {November},
url = {http://dx.doi.org/10.1016/j.physd.2023.133802},
Abstract = {We study a prototypical example in nonlinear dynamics where
transition to self-similarity in a singular limit is
fundamentally changed as a parameter is varied. Here, we
focus on the complicated dynamics that occur in a
generalised unstable thin-film equation that yields
finite-time rupture. A parameter, n, is introduced to model
more general disjoining pressures. For the standard case of
van der Waals intermolecular forces, n=3, it was previously
established that a countably infinite number of self-similar
solutions exist leading to rupture. Each solution can be
indexed by a parameter, ϵ=ϵ1>ϵ2>⋯>0, and the prediction
of the discrete set of solutions requires examination of
terms beyond-all-orders in ϵ. However, recent numerical
results have demonstrated the surprising complexity that
exists for general values of n. In particular, the
bifurcation structure of self-similar solutions now exhibits
branch merging as n is varied. In this work, we shall
present key ideas of how branch merging can be interpreted
via exponential asymptotics.},
Doi = {10.1016/j.physd.2023.133802},
Key = {fds371622}
}
@article{fds370567,
Author = {Bowen, M and King, JR and Witelski, TP},
Title = {CAUCHY-DIRICHLET PROBLEMS FOR THE POROUS MEDIUM
EQUATION},
Journal = {Discrete and Continuous Dynamical Systems- Series
A},
Volume = {43},
Number = {3-4},
Pages = {1143-1174},
Publisher = {American Institute of Mathematical Sciences
(AIMS)},
Year = {2023},
Month = {March},
url = {http://dx.doi.org/10.3934/dcds.2022182},
Abstract = {We consider the porous medium equation subject to
zero-Dirichlet conditions on a variety of two-dimensional
domains, namely strips, slender domains and sectors,
allowing us to capture a number of different classes of
behaviours. Our focus is on intermediate-asymptotic
descriptions, derived by formal arguments and validated
against numerical computations. While our emphasis is on
non-negative solutions to the slow-diffusion case, we also
derive a number of results for sign-change solutions and for
fast diffusion. Self-similar solutions of various kinds play
a central role, alongside the identification of suitable
conserved quantities. The characterisation of domains
exhibiting infinite-time hole closure is a particular upshot
and we highlight a number of open problems.},
Doi = {10.3934/dcds.2022182},
Key = {fds370567}
}
|
