Physical Sciences and Mathematics Commons^™

Synchrony In A Boolean Network Of The L-Arabinose Operon In Escherichia Coli, Andy Jenkins, Matthew Macauley

Publications

The lactose operon in Escherichia coli was the first known gene regulatory network, and it is frequently used as a prototype for new modeling paradigms. Historically, many of these modeling frameworks use differential equations. More recently, Stigler and Veliz-Cuba proposed a Boolean network model that captures the bistability of the system and all of the biological steady states. In this paper, we model the well-known arabinose operon in E. coli with a Boolean network. This has several complex features not found in the lac operon, such as a protein that is both an activator and repressor, a DNA looping mechanism …

Noncrossing Partitions, Toggles, And Homomesies, David Einstein, Miriam Farber, Emily Gunawan, Michael Joseph, Matthew Macauley, James Propp, Simon Rubinstein-Salzedo

Publications

We introduce n(n−1)/2 natural involutions (“toggles”) on the set S of noncrossing partitions π of size n, along with certain composite operations obtained by composing these involutions. We show that for many operations T of this kind, a surprisingly large family of functions f on S (including the function that sends π to the number of blocks of π) exhibits the homomesy phenomenon: the average of f over the elements of a T -orbit is the same for all T -orbits. We can apply our method of proof more broadly to toggle operations back on the collection of independent sets …

Cytoplasmic Dynein Binding, Run Length, And Velocity Are Guided By Long-Range Electrostatic Interactions, Lin Li, Joshua Alper, Emil Alexov

Publications

Dyneins are important molecular motors involved in many essential biological processes, including cargo transport along microtubules, mitosis, and in cilia. Dynein motility involves the coupling of microtubule binding and unbinding to a change in the configuration of the linker domain induced by ATP hydrolysis, which occur some 25 nm apart. This leaves the accuracy of dynein stepping relatively inaccurate and susceptible to thermal noise. Using multi-scale modeling with a computational focusing technique, we demonstrate that the microtubule forms an electrostatic funnel that guides the dynein’s microtubule binding domain (MTBD) as it finally docks to the precise, keyed binding location on …

Morphisms And Order Ideals Of Toric Posets, Matthew Macauley

Publications

Toric posets are in some sense a natural “cyclic” version of finite posets in that they capture the fundamental features of a partial order but without the notion of minimal or maximal elements. They can be thought of combinatorially as equivalence classes of acyclic orientations under the equivalence relation generated by converting sources into sinks, or geometrically as chambers of toric graphic hyperplane arrangements. In this paper, we define toric intervals and toric order-preserving maps, which lead to toric analogues of poset morphisms and order ideals. We develop this theory, discuss some fundamental differences between the toric and ordinary cases, …

Local Standards For Sample Size At Chi, Kelly Caine

Publications

We describe the primary ways researchers can determine the size of a sample of research participants, present the benefits and drawbacks of each of those methods, and focus on improving one method that could be useful to the CHI community: local standards. To determine local standards for sample size within the CHI community, we conducted an analysis of all manuscripts published at CHI2014. We find that sample size for manuscripts published at CHI ranges from 1 -- 916,000 and the most common sample size is 12. We also find that sample size differs based on factors such as study setting …

Ion Transport Through Macrocapillaries – Oscillations Due To Charge Patch Formation, Dhruva Kulkarni, L.A.M. Lyle, Chad E. Sosolik

Publications

We present results on ion transport through large bore capillaries (macrocapillaries) that probe both the geometric and ion-guided aspects of this ion delivery mechanism. We have demonstrated that guiding in macrocapillaries exhibits position- and angle-dependent transmission properties which are directly related to the capillary material (either metal or insulator) and geometry. Specifically, we have passed 1 keV Rb⁺ ions through glass and metal macrocapillaries, and have observed oscillations for the transmitted ion current passing through the insulating capillaries. Straightforward calculations show that these oscillations can be attributed to beam deflections from charge patches that form on the interior walls …

What Moser Could Have Asked: Counting Hamilton Cycles In Tournaments, Neil J. Calkin, Beth Novick, Hayato Ushijima-Mwesigwa

Publications

Moser asked for a construction of explicit tournaments on n vertices having at least Hamilton cycles. We show that he could have asked rather more.

Relaxations And Discretizations For The Pooling Problem, Akshay Gupte, Shabbir Ahmed, Santanu S. Dey, Myun Seok Cheon

Publications

The pooling problem is a folklore NP-hard global optimization problem that finds applications in industries such as petrochemical refining, wastewater treatment and mining. This paper assimilates the vast literature on this problem that is dispersed over different areas and gives new insights on prevalent techniques. We also present new ideas for computing dual bounds on the global optimum by solving high-dimensional linear programs. Finally, we propose discretization methods for inner approximating the feasible region and obtaining good primal bounds. Valid inequalities are derived for the discretized models, which are formulated as mixed integer linear programs. The strength of our relaxations …

Factors Associated With Anaplasma Spp. Seroprevalence Among Dogs In The United States, Christopher S. Mcmahan, Dongmei Wang, Melissa J. Beall, Dwight D. Bowman, Susan E. Little, Patrick O. Pithua, Julia L. Sharp, Roger W. Stich, Michael J. Yabsley, Robert B. Lund

Publications

Background

Dogs in the United States are hosts to a diverse range of ticks and tick-borne pathogens, including A. phagocytophilum, an important emerging canine and human pathogen. Previously, a Companion Animal Parasite Council (CAPC)-sponsored workshop proposed factors purported to be associated with the infection risk for tick-transmitted pathogens in dogs in the United States, including climate conditions, socioeconomic characteristics, local topography, and vector distribution.

Methods

Approximately four million test results from routine veterinary diagnostic tests from 2011–2013, which were collected on a county level across the contiguous United States, are statistically analyzed with the proposed factors via logistic regression …

Performance Considerations Of Network Functions Virtualization Using Containers, Jason Anderson, Udit Agarwal, Hongda Li, Hongxin Hu, Craig Lowery, Amy W. Apon

Publications

The network performance of virtual machines plays a critical role in Network Functions Virtualization (NFV), and several technologies have been developed to address hardware-level virtualization shortcomings. Recent advances in operating system level virtualization and deployment platforms such as Docker have made containers an ideal candidate for high performance application encapsulation and deployment. However, Docker and other solutions typically use lower-performing networking mechanisms. In this paper, we explore the feasibility of using technologies designed to accelerate virtual machine networking with containers, in addition to quantifying the network performance of container-based VNFs compared to the state-of-the-art virtual machine solutions. Our results show …

A Revision Of Megalocraerus Lewis, 1902 (Coleoptera, Histeridae: Exosternini), Michael S. Caterino, Alexey K. Tishechkin

Publications

The formely monotypic Neotropical genus Megalocraerus Lewis is revised to include five species, known from southeastern Brazil to Costa Rica: M. rubricatus Lewis, M. mandibularis sp. n., M. chico sp. n., M. madrededios sp. n., and M. tiputini sp. n. We describe the species, map their distributions, and provide a key for their identification. Their subcylindrical body form and emarginate mesosternum have previously hindered placement to tribe, although their curent assignment to Exosternini now appears well supported by morphological evidence. Nothing is known of the natural history of the species.