A Novice's Process of Object-Oriented Programming

Exposing students to the process of programming is merely implied but not explicitly addressed in texts on programming which appear to deal with 'program' as a noun rather than as a verb.We present a set of principles and techniques as well as an informal but systematic process of decomposing a programming problem. Two examples are used to demonstrate the application of process and techniques.The process is a carefully down-scaled version of a full and rich software engineering process particularly suited for novices learning object-oriented programming. In using it, we hope to achieve two things: to help novice programmers learn faster and better while at the same time laying the foundation for a more thorough treatment of the aspects of software engineering

\u3ci\u3eTiphia Vernalis\u3c/i\u3e (Hymenoptera: Tiphiidae) Parasitizing Oriental Beetle, \u3ci\u3eAnomala Orientalis\u3c/i\u3e (Coleoptera: Scarabaeidae) in a Nursery

(excerpt) Tiphia vernalis Rohwer is native to China, Japan, and Korea where it is an external parasite of Popillia spp. (King 1931). It was released into the United States from China and Korea during the mid-1920s through early 30s (Fleming 1968). After it became established in the United States, releases were made from domestic sources beginning in 1931 (King et al. 1951). Tiphia vernalis was released into Ohio sporadically during 1936-1953 (King et al.1951). Tiphia vernalis has been reported parasitizing Popillia spp. (P. quadriguttata (Fabricius) in Korea; P. chinensis (Frivaldsky) and P. formosana (Arrow) in China; and P. japonica Newman in Japan) exclusively in the field (Balock 1934, Fleming 1968). It accepted Anomala (=Exomala) orientalis Waterhouse (oriental beetle) as a host in the laboratory and cocoons were obtained (King et al.1927, Balock 1934), but there are no previously published reports of T. vernalis parasitizing A. orientalis in the field

Computing Optimal Morse Matchings

Morse matchings capture the essential structural information of discrete Morse functions. We show that computing optimal Morse matchings is NP-hard and give an integer programming formulation for the problem. Then we present polyhedral results for the corresponding polytope and report on computational results

Ligand Binding, Protein Fluctuations, and Allosteric Free Energy

Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between protein conformational distributions before and after ligand binding was proposed as a means of quantifying allosteric effects in proteins. Here, previous applications of Dx to methods for analysis and simulation of proteins are first reviewed, and their implications for understanding aspects of protein function and protein evolution are discussed. Next, equations for Dx suggest that k_{B}TDx should be interpreted as an allosteric free energy -- the free energy associated with changing the ligand-free protein conformational distribution to the ligand-bound conformational distribution. This interpretation leads to a thermodynamic model of allosteric transitions that unifies existing perspectives on the relation between ligand binding and changes in protein conformational distributions. The definition of Dx is used to explore some interesting mathematical relations among commonly recognized thermodynamic and biophysical quantities, such as the total free energy change upon ligand binding, and ligand-binding affinities for individual protein conformations. These results represent the beginnings of a theoretical framework for considering the full protein conformational distribution in modeling allosteric transitions. Early applications of the framework have produced results with implications both for methods for coarsed-grained modeling of proteins, and for understanding the relation between ligand binding and protein dynamics.Comment: 18 pages; 7 figures; Second International Congress of the Biocomputing and Physics of Complex Systems Research Institute, Zaragoza, Spain, 8-11 Feb 2006; increase breadth of review of methods for analysis of allosteric mechanisms; Add AIP in press; fix missing kTs in equation

Set systems without a 3-simplex

A 3-simplex is a collection of four sets A_1,...,A_4 with empty intersection such that any three of them have nonempty intersection. We show that the maximum size of a set system on n elements without a 3-simplex is $2^{n-1} + \binom{n-1}{0} + \binom{n-1}{1} + \binom{n-1}{2}$ for all $n \ge 1$, with equality only achieved by the family of sets either containing a given element or of size at most 2. This extends a result of Keevash and Mubayi, who showed the conclusion for n sufficiently large.Comment: 5 page