Assessing Students’ Object-Oriented Programming Skills with Java: The “Department-Employee” Project

Java is arguably today’s most popular and widely used object-oriented programming language. Learning Java is a daunting task for students, and teaching it is a challenging undertaking for instructors. To assess students’ object-oriented programming skills with Java, we developed the “Department-Employee” project. In this article, we review the history of object-oriented programming and provide an overview of object-oriented programming with Java. We also provide the project specification as well as the course background, grading rubric, and score reports. Survey data are presented on students’ backgrounds, as well as students’ perceptions regarding the project. Results from the instructor score reports and student perceptions show that the “Department-Employee” project was effective in assessing students’ object-oriented programming skills with Java

Teaching Introductory Programming from A to Z: Twenty-Six Tips from the Trenches

A solid foundation in computer programming is critical for students to succeed in advanced computing courses, but teaching such an introductory course is challenging. Therefore, it is important to develop better approaches in order to improve teaching effectiveness and enhance student learning. In this paper, we present 26 tips for teaching introductory programming drawn from the experiences of four well-qualified college professors. It is our hope that our peers can pick up some tips from this paper, apply them in their own classroom, improve their teaching effectiveness, and ultimately enhance student learning

Central extension of the reflection equations and an analog of Miki's formula

Two different types of centrally extended quantum reflection algebras are introduced. Realizations in terms of the elements of the central extension of the Yang-Baxter algebra are exhibited. A coaction map is identified. For the special case of $U_q(\hat{sl_2})$, a realization in terms of elements satisfying the Zamolodchikov-Faddeev algebra - a `boundary' analog of Miki's formula - is also proposed, providing a free field realization of $O_q(\hat{sl_2})$ (q-Onsager) currents.Comment: 11 pages; two references added; to appear in J. Phys.

Model morphing and sequence assignment after molecular replacement.

A procedure termed `morphing' for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package

The Erd\H{o}s-Ko-Rado theorem for twisted Grassmann graphs

We present a "modern" approach to the Erd\H{o}s-Ko-Rado theorem for Q-polynomial distance-regular graphs and apply it to the twisted Grassmann graphs discovered in 2005 by van Dam and Koolen.Comment: 5 page

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement.

An approach is presented for addressing the challenge of model rebuilding after molecular replacement in cases where the placed template is very different from the structure to be determined. The approach takes advantage of the observation that a template and target structure may have local structures that can be superimposed much more closely than can their complete structures. A density-guided procedure for deformation of a properly placed template is introduced. A shift in the coordinates of each residue in the structure is calculated based on optimizing the match of model density within a 6 Å radius of the center of that residue with a prime-and-switch electron-density map. The shifts are smoothed and applied to the atoms in each residue, leading to local deformation of the template that improves the match of map and model. The model is then refined to improve the geometry and the fit of model to the structure-factor data. A new map is then calculated and the process is repeated until convergence. The procedure can extend the routine applicability of automated molecular replacement, model building and refinement to search models with over 2 Å r.m.s.d. representing 65-100% of the structure

From critters to cancers: bridging comparative and clinical research on oxygen sensing, HIF signaling, and adaptations towards hypoxia

The objective of this symposium at the First International Congress of Respiratory Biology (ICRB) was to enhance communication between comparative biologists and cancer researchers working on O2 sensing via the HIF pathway. Representatives from both camps came together on August 13-16, 2006, in Bonn, Germany, to discuss molecular adaptations that occur after cells have been challenged by a reduced (hypoxia) or completely absent (anoxia) supply of oxygen. This brief "critters-to-cancer” survey discusses current projects and new directions aimed at improving understanding of hypoxic signaling and developing therapeutic intervention

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence

Ethylene-Vinyl Acetate Potential Problems for Photovoltaic Packaging: Preprint

Photovoltaic (PV) devices are typically encapsulated using ethylene-vinyl acetate (EVA) to provide mechanical support, optical coupling, electrical isolation, and protection against environmental exposure. Under exposure to atmospheric water and/or ultraviolet radiation, EVA will decompose to produce acetic acid, lowering the pH and increasing the surface corrosion rates of embedded devices. Even though acetic acid is produced at a very slow rate, it may not take much to catalyze reactions that lead to rapid module deterioration. Another consideration is that the glass transition of EVA, as measured using dynamic mechanical analysis, begins at temperatures of about ?15 C. Temperatures lower than this can be reached for extended periods of time in some climates. Because of increased moduli below the glass transition temperature, a module may be more vulnerable to damage if a mechanical load is applied by snow or wind at low temperatures. Modules using EVA should not be rated for use at such low temperatures without additional low-temperature mechanical testing beyond the scope of UL 1703