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Spatial extent is a complicating factor in mathematical biology. The possibility that an action at point A cannot immediately affect what happens at point B creates the opportunity for spatial nonuniformity. This nonuniformity must change…
Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an…
This paper presents two different evolutionary systems - Evolutionary Programming Network (EPNet) and Novel Evolutions Strategy (NES) Algorithm. EPNet does both training and architecture evolution simultaneously, whereas NES does a fixed…
Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This faster-X effect can arise either as a consequence of hemizygosity, which leads to…
Five distinct full-length mineralocorticoid receptor (MR) genes have been identified in humans. These human MRs can be distinguished by the presence or absence of an in-frame insertion of 12 base pairs coding for Lys, Cys, Ser, Trp (KCSW)…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
In Parts I and II of this series, we established isomorphisms between ant colony decision-making and two major families of ensemble learning: random forests (parallel, variance reduction) and boosting (sequential, bias reduction). Here we…
We report two-dimensional electronic spectroscopy (2DES) experiments on the bacterial reaction center (BRC) from purple bacteria, revealing hidden excitonic and vibronic structure. Through analysis of the coherent dynamics of the BRC we…
Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change. Theoretical work and empirical…
Ultraluminous X-ray sources (ULXs) represent an extreme class of accreting compact objects: from the identification of some of the accretors as neutron stars to the detection of powerful winds travelling at 0.1-0.2 c, the increasing…
The dipole response of a nuclear system, characterized by its photon strength function (PSF), is a key ingredient of many applications of nuclear structure, ranging from nuclear reactor design and nuclear waste transmutation to…
Emerin, a nuclear membrane protein with important biological roles in mechanotransduction and nuclear shape adaptation, self-assembles into nanometer-size domains at the inner nuclear membrane. The size and emerin occupancy of these…
Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggested that the position of a protein in the network determines its evolutionary rate but there has been considerable…
We present a detailed study of the exact-exchange (EXX) kernel of time-dependent density functional theory with an emphasis on its discontinuity at integer particle numbers. It was recently found that this exact property leads to sharp…
The endoplasmic reticulum (ER) is the largest continuous membrane-bound organelle in the cell and plays a central role in the synthesis and turnover of many lipids and proteins. It connects directly to the nucleus through specialized…
In our previous work, we studied an interconnected bursting neuron model for insect locomotion, and its corresponding phase oscillator model, which at high speed can generate stable tripod gaits with three legs off the ground simultaneously…
I have carried out a project to study the eccentric neutron-star binary Circinus X-1 through an extensive series of observational studies with the Rossi X-ray Timing Explorer satellite and through theoretical computer models I developed to…
A central goal in ecology is to understand how biodiversity is maintained. Previous theoretical works have employed the rock-paper-scissors (RPS) game as a toy model, demonstrating that population mobility is crucial in determining the…
We develop a mathematical model to capture the web dynamics of slingshot spiders (Araneae: Theridiosomatidae), which utilize a tension line to deform their orb webs into conical springs to hunt flying insects. Slingshot spiders are…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…