Popular Mechanics Research Articles

Image Text Ithaca

ITHACA COLLEGE ITHACA, NEW YORK JULY 9-10, 2015 The second annual Image Text Ithaca (ITI) symposium brought together thirteen ITI workshop fellows and several invited guests for public presentations on campus of Ithaca College over course of one evening and next day, following a workshop during which this year's fellows worked on new image and text projects. The brief public event began with a talk by Jason Fulford, a fellow from 2014 workshop, and Tamara Shopsin. They shared individually produced works such as Fulford's photo book Hotel Oracle (2013) and Shopsin's illustration work for New York Times, as well as inspirations (which range from semiotics to poetic ambiguity) for joint book projects including absorbing image-only monograph This Equals That (2014). Other invited speakers included Federica Chiocchetti, who spoke about website she founded, The Photocaptionist, on which are paired visual and text-based works (either found or commissioned) to promote the practice of concubinage between photography and literature, images and words. Chiocchetti also shared several projects she has worked on for Victoria and Albert Museum. Maria Damon of Pratt Institute offered a hypnotic essay moving between cross-stitching, alphabetics, and novels of Kathy Acker, weaving a linguistic thread through a rich cultural history. Matvei Yankelevich, another 2014 fellow, utilizing images and found text from throughout twentieth century (from works by poet Laura Riding to writings by philosopher Vilem Flusser), examined foundational space and structure of books and their elements, recommending how they should be read. This year's ITI fellows (five senior fellows and eight junior fellows) participated in a four-day workshop in days preceding symposium. Since most came from either photography or writing backgrounds, this was first time many had worked in image and text combinations. Daniel Augscholl and Anya Jasbar, cofounders of Ahorn Magazine, an online publication dedicated to contemporary photography, presented a photo essay on theme of desire, combining text and landscape photographs. Photographer Ben Alper presented a screening and audio performance of a project he began during this year's workshop session and had wrapped up that very morning (Thursday). Titled In event of misinterpretation or human error, piece uses found text and photographs from decades-old Popular Mechanics magazines to explore meaning within randomness. Writer Christine Hume used same source material, commenting on white privilege by augmenting text, which she read aloud as images she had selected from magazines were projected. On Friday, Hume presented an original spoken text with an underlayer of found audio of a 911 call and supplemental stressed breathing to heighten tension. Photographer Andre Bradley shared a photographic project with a spoken personal narrative about history, memory, learning, and identity. [Ed. note: See Bradley's Portfolio in this issue of Afterimage.] Author John Keene read text from two short projects, one about online dating (with facially redacted profile photographs culled by ITI co-director Nicholas Muellner from gay online dating archives) and other concerning slavery and based on work of Kara Walker. …

Design Principles for Serious Video Games in Mathematics Education: From Theory to Practice

There is growing interest in the employment of serious video games in science education, but there are no clear design principles. After surveying previous work in serious video game design, we highlighted the following design principles: 1) engage the students with narrative (hero, story), 2) employ familiar gameplay mechanics from popular video games, 3) engage students into constructive trial and error game-play and 4) situate collaborative learning. As illustrated examples we designed two math video games targeted to primary education students. The gameplay of the math video games embeds addition operations in a seamless way, which has been inspired by that of classic platform games. In this way, the students are adding numbers as part of popular gameplay mechanics and as a means to reach the video game objective, rather than as an end in itself. The employment of well-defined principles in the design of math video games should facilitate the evaluation of learning effectiveness by researchers. Moreover, educators can deploy alternative versions of the games in order to engage students with diverse learning styles. For example, some students might be motived and benefited by narrative, while others by collaboration, because it is unlikely that one type of serious video game might fit all learning styles. The proposed principles are not meant to be an exhaustive list, but a starting point for extending the list and applying them in other cases of serious video games beyond mathematics and learning.

Multipolar electrostatics.

Atomistic simulation of chemical systems is currently limited by the elementary description of electrostatics that atomic point-charges offer. Unfortunately, a model of one point-charge for each atom fails to capture the anisotropic nature of electronic features such as lone pairs or π-systems. Higher order electrostatic terms, such as those offered by a multipole moment expansion, naturally recover these important electronic features. The question remains as to why such a description has not yet been widely adopted by popular molecular mechanics force fields. There are two widely-held misconceptions about the more rigorous formalism of multipolar electrostatics: (1) Accuracy: the implementation of multipole moments, compared to point-charges, offers little to no advantage in terms of an accurate representation of a system's energetics, structure and dynamics. (2) Efficiency: atomistic simulation using multipole moments is computationally prohibitive compared to simulation using point-charges. Whilst the second of these may have found some basis when computational power was a limiting factor, the first has no theoretical grounding. In the current work, we disprove the two statements above and systematically demonstrate that multipole moments are not discredited by either. We hope that this perspective will help in catalysing the transition to more realistic electrostatic modelling, to be adopted by popular molecular simulation software.

What Makes an Orc? Racial Cosmos and Emergent Narrative in World of Warcraft

This article offers a new method of reading racial narrative in massive multiplayer online games. Rather than looking to the game text or the behaviors of individual players, it focuses on collective emergent behavior and demographics. From this perspective, the various racial group in World of Warcraft (WoW) take on their on unique characteristics that inform the broader WoW narrative. These differences result from the collective playing decisions of millions of gamers, influenced by the text, and also popular culture, game mechanics, and innumerable other factors.

Mechanized Harvest of Southern Highbush Blueberries for the Fresh Market: An Introduction and Overview of the Workshop Proceedings

T he development of mechanical devices to assist in harvesting cultivated blueberries (Vaccinium species and hybrids) began in the late 1950s. In 1958, U.S. Department of Agriculture engineers located at Michigan State University developed handheld shakers that were used with fabric-lined catch frames as aids for harvesting processed blueberries (Hedden et al., 1959; Monroe and Levin, 1966). These devices substantially increased worker productivity and reduced harvest costs by 55% (Monroe and Levin, 1966). By 1963, 35% of the Michigan crop and 20% of the New Jersey crop were harvested in this fashion. Later Monroe and Levin (1966) described their early attempts to develop a continuous over-the-row blueberry harvester, which required a driver and two additional workers. Testing of over-the-row harvesters began in the late 1950s and by 1966 over-the-row harvesters were available commercially in the United States. Eck (1988) reported that over 100 such machines were in use in the United States by 1971. One of the earliest commercial models, the Harvey Harvester, was featured in an article entitled ‘‘Fantastic New Farm Machines’’ in Popular Mechanics in 1970 (Lamm, 1970). Over time, various harvesters were developed that used different methods to remove ripe berries from canes and they were generally classified as slappers, sway shakers, and rotary shakers (Brown et al., 1996; Mainland, 1993). In their review, Dale et al. (1994) provide a detailed account of blueberry harvester designs up through the early 1990s. Over-the-row harvesters were reported to increase worker productivity by almost 60 times and reduce the cost of harvesting by up to 85% (Brown et al., 1996). However, numerous problems were soon identified with harvesting blueberries mechanically. The primary ones were 1) ground loss of otherwise marketable fruit, 2) detachment of immature berries, 3) reduced berry firmness and quality, and 4) increased postharvest decay and reduced storage life. Machine harvest necessitates increased handling of fruit during grading and sorting, and on blueberries most postharvest decay occurs at the detachment point—the newly exposed stem scar (Ballinger et al., 1978). When both fungal spores and moisture are present on packing lines, this extra handling can greatly increase postharvest decay caused by fungi (Alternaria, Colletotrichum) due to the exposure (rolling) of berries over contaminated surfaces (Cline, 1996). In the first comprehensive report directly comparing the effects of machine and hand harvesting on highbush blueberry (V. corymbosum), Mainland et al. (1975) found that losses of marketable fruit of ‘Wolcott’, ‘Jersey’, ‘Morrow’, and ‘Murphy’ were from 19% to 44% greater for machine harvesting than for hand harvesting. Machine-harvested fruit were 10% to 38% softer than hand-harvested fruit, and soft berries were difficult to identify and remove during grading. Moreover, after 7 d of storage at 21 C, there was 11% to 41% more postharvest decay for the machine-harvested fruit. They concluded that the inability to remove bruised fruit during grading and sorting presented serious problems for maintaining quality during storage. Similar reductions in marketable yield from mechanical harvesting were reported in Michigan by Howell et al. (1976). In general, increased berry softening and decay during storage have been widely reported in association with mechanical blueberry harvesting (Ceponis and Cappellini, 1979; Dale et al., 1994; Howell et al., 1976; Mainland et al., 1971, 1975; Milholland and Jones, 1972). Ballinger et al. (1973) studied factors affecting blueberry firmness and emphasized the importance of careful harvesting and handling procedures, noting that blueberries are easily bruised, leading to softening and subsequent decay during storage. In a review of the literature, Morris (1983) stated that ‘‘decay of machineharvested blueberries during postharvest holding is perhaps the biggest problem of the industry.’’ Reductions in berry firmness and marketable yield were also found for machine-harvested rabbiteye blueberry (V. virgatum). Using the rabbiteye blueberry cultivar Tifblue, Austin and Williamson (1977) reported increased ground loss of marketable fruit, reduced fruit firmness, and more than twice the amount of unmarketable fruit from machine harvesting vs. hand harvesting. Increased berry softening following machine harvesting was also noted for ‘Climax’ and ‘Woodard’ (Miller and Smittle, 1987) and ‘Brightwell’ (NeSmith et al., 2002), although depending on cultivar, the softer machine-harvested fruit may still be considered marketable as fresh fruit. NeSmith et al. (2002) proportionally attributed the causes of ‘Brightwell’ rabbiteye berry softening to the following harvest activities: 20% to 30% loss of firmness due to

We Used to Win, We Used to Lose, We Used to Play: Simulacra, Hypo-Ludicity and the Lost Art of Losing

This article is concerned with the modern design of digital games, in particular their formulation as experiences for consumers rather than players. Utilizing Baudrillard’s concept of the simulacra as an analytical probe, this article discusses the simulations of winning, losing and playing evident in today’s digital game products. Building upon the author’s previous work, which introduced the twin concepts of hyper- and contra-ludicity to game studies, this article argues that the recent invasion of hypo-ludicity into game design sets a dangerous precedent for digital games as games as opposed to entertainment media. While hyper-ludicity empowers and contra-ludicity challenges, hypoludicity is characterized by its emptiness; of empowerment, of challenge, of agency. Anchoring the discussion in analyses of popular game systems, design features and mechanics, the article ultimately illustrates the prevalence of simulacra within today’s digital game products, and how this undermines the very notion of winning, losing and even playing.

The Maker Movement

word “inventor”—most people just don’t identify themselves that way. “Maker,” on the other hand, describes each one of us, no matter how we live our lives or what our goals might be. We all are makers: as cooks preparing food for our families, as gardeners, as knitters. Although this view may not be part of mainstream thought, there once was a time when most Americans commonly thought of themselves as tinkerers. Tinkering used to be a basic skill, and you could get a little bit more out of life than the average person if you had good tinkering skills—if you could fix your own car, for example, or improve your home or make your own clothes. I think we lost some of that over the decades, but I also think it is coming back, for a lot of reasons. While people today may not treasure this ability out of the same sense of necessity as they once did, they are finding their lives enriched by creating something new and learning new skills. Make magazine, which I founded in 2005, harkens back to the magazines that hit their peak in the mid-20th century, like Popular Mechanics, which had the attitude, if it’s fun, why not do it? Such publications often helped people to start a hobby and learn new skills. Moreover, they helped the new hobbyist find a community of likeminded tinkerers to talk with about it. Maker Faire, which started in the Bay Area in 2006, a year after the magazine, expanded this idea of learning and community and created a space where readers of the magazine could get together to extend the conversation. At the Faire, a maker could put an object they created up on a table and have people ask them about it. Having that kind of conversation with a range of people is the essence of the magazine, of the Faires—and perhaps of the whole movement. The excitement of making things extends to kids as well. Many begin at a young age to explore and develop things they really care about, so we have made the Faires a family-oriented event that features many exhibits by younger makers. We also hold workshops and competitions for people of all ages. Since the first Maker Faire held in San Mateo, California, we have held Faires in Austin, Texas; Detroit, Michigan; and New York City. The most recent New York City event, the World Maker Faire, attracted over 100,000 attendees. In response to requests from fans, we have begun to hold mini-Maker Faires in cities around North America.

Origin of Decrease in Potency of Darunavir and Two Related Antiviral Inhibitors against HIV-2 Compared to HIV-1 Protease

Acquired immune deficiency syndrome (AIDS) is caused by the human immunodeficiency virus (HIV) type 1 and 2 (HIV-1 and HIV-2). HIV-1 is observed worldwide while HIV-2 though prevalent in West Africa is persistently spreading to other parts of the world. An important target for AIDS treatment is the use of HIV protease (PR) inhibitors preventing the replication of the virus. In this work, the popular molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method has been used to investigate the effectiveness of the HIV-1 PR inhibitors darunavir, GRL-06579A, and GRL-98065 against HIV-2 and HIV-1 protease. The affinity of the inhibitors for both HIV-1 and HIV-2 PR decreases in the order GRL-06579A > darunavir > GRL-98065, in accordance with experimental data. On the other hand, our results show that all these inhibitors bind less strongly to HIV-2 than to HIV-1 protease, again in agreement with experimental findings. The decrease in binding affinity for HIV-2 relative to HIV-1 PR is found to arise from an increase in the energetic penalty from the desolvation of polar groups (DRV) or a decrease in the size of the electrostatic interactions between the inhibitor and the PR (GRL-06579A and GRL-98065). For GRL-98065, also a decrease in the magnitude of the van der Waals interactions contributes to the reduction in binding affinity. A detailed understanding of the molecular forces governing binding and drug resistance might assist in the design of efficient inhibitors against HIV-2 protease.

Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir

Amprenavir (APV) is a high affinity (0.15 nM) HIV-1 protease (PR) inhibitor. However, the affinities of the drug resistant protease variants V32I, I50V, I54V, I54M, I84V and L90M to amprenavir are decreased 3 to 30-fold compared to the wild-type. In this work, the popular molecular mechanics Poisson-Boltzmann surface area method has been used to investigate the effectiveness of amprenavir against the wild-type and these mutated protease variants. Our results reveal that the protonation state of Asp25/Asp25' strongly affects the dynamics, the overall affinity and the interactions of the inhibitor with individual residues. We emphasize that, in contrast to what is often assumed, the protonation state may not be inferred from the affinities but requires pK(a) calculations. At neutral pH, Asp25 and Asp25' are ionized or protonated, respectively, as suggested from pK(a) calculations. This protonation state was thus mainly considered in our study. Mutation induced changes in binding affinities are in agreement with the experimental findings. The decomposition of the binding free energy reveals the mechanisms underlying binding and drug resistance. Drug resistance arises from an increase in the energetic contribution from the van der Waals interactions between APV and PR (V32I, I50V, and I84V mutant) or a rise in the energetic contribution from the electrostatic interactions between the inhibitor and its target (I54M and I54V mutant). For the V32I mutant, also an increased free energy for the polar solvation contributes to the drug resistance. For the L90M mutant, a rise in the van der Waals energy for APV-PR interactions is compensated by a decrease in the polar solvation free energy such that the net binding affinity remains unchanged. Detailed understanding of the molecular forces governing binding and drug resistance might assist in the design of new inhibitors against HIV-1 PR variants that are resistant against current drugs.

WebWatch

BioTechniquesVol. 51, No. 1 WebWatchOpen AccessWebWatchKevin AhernKevin Ahern*E-mail Address: ahernk@orst.eduSearch for more papers by this authorPublished Online:3 Apr 2018https://doi.org/10.2144/000113698AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail The Green SceneIn contrast to what happens in nature, urban forests don't evolve from natural selection. Rather, they are carefully planned from square one, often using sophisticated computer software. The Urban Forest Management Plan (UFMP) Toolkit web site is aimed at today's “urban foresters” to help them develop appropriate plans for their areas. The Toolkit includes (i) a framework for a management plan, (ii) an organizing process design, and (iii) an online work plan tool. The site's step-by-step organization guides users through the process of making a plan and organizes everything into a check-listed outline that facilitates easy tracking of the project. If you or someone you know needs help managing trees in a concrete jungle, the UFMP is a great place to start.[http://ufmptoolkit.com]Bio-DirtLooking for the latest “gossip” on the biotechnology industry? Then you need to direct your browser to the address below. The site hosted there, Biofind, has several interesting sections including the under-used “Blogs” area, a vibrant news segment, and a collection of press releases. Probably most noteworthy is the section called Rumor Mill, which is packed with juicy tidbits about all of the major players in bioindustry: Novartis, Pfizer, Roche, Beckman, and more. Visitors should recognize, of course, that rumors are just that and the anonymous postings and comments are sometimes as beneficial for spreading misinformation as they are for uncovering company truths. But the breadth of commentary is impressive: some posts have over 1200 replies, and it is in this feedback that the truth may be found.[www.biofind.com]Comparative GenomicsThe field of comparative genomics is an extension of the attempts to understand the evolutionary relationships among organisms based on protein sequences. The wrinkle here is that entire genomes constitute the datasets. Enter the Microbial Genome Databa se for Comparative Analysis (MBGD), a website that can generate homologous gene cluster tables, dynamically create orthologous cluster tables using precomputed homology data, and also enable users to create their own groupings. Multiple genomes can be analyzed using global map comparisons, local map comparisons, multiple sequence alignments, and phylogenetic trees can be constructed. Over 500 genomes are currently available.[http://mbgd.genome.ad.jp]Pest QuestIf you're not an entomologist, you may not be interested in insects unless they're chewing, biting, buzzing, infesting, or stinging you, or damaging your property. There are, of course, notable exceptions, but for the most part, people don't tend to pay attention to the tiny varmints until they cause problems. At Iowa State University, the Department of Entomology hosts an outstanding, informative set of pages that assist in identification and management of pests, as well as educational materials (Horticulture and Home Pest News) and a guide to insects relevant to soybeans. Topic areas include everything from bird mites to earwigs to mold mites. There's even an Insect Zoo outreach program that can travel all over Iowa (Have Bugs, Will Travel?).[www.ent.iastate.edu]Spined soldier bug (Podisus maculiventris).© 2010 John VanDyk.Related SystersIdentifying the relationships between protein sequences is also the aim of the Systers database system. Starting with the Swiss-Prot and TrEMBL database proteins, Systers performs large scale clustering based on sequence similarity. Single linkage trees of protein clusters are generated based on pairwise E-values, followed by construction of distance graphs for every superfamily. Families are then categorized according to their cluster characteristics: Perfect (all sequences connected to all other sequences), Single (a perfect cluster), Nested (at least one sequence connected to all others), and Overlapping (no sequence connected to all others). The current Systers release (4.0) identifies over 158,000 such clusters that can be retrieved by protein ID, keyword, gene name, organism/taxon, Pfam domain, or protein family ID. BlastP and BlastX search options are also available.[http://systers.molgen.mpg.de/index.html]The Popsci GenerationAlong with Popular Mechanics, Popular Science is one of the two iconic science/engineering publications from the “New Math” era of science that was tremendously inspirational to budding, young scientists. Now in the information era, its online progeny www.popsci.com aims to do the same with an entirely new online audience. While that's a pretty tall order, it is well on its way to meeting the challenge. It has a rock-solid collection of fun to read articles on various science topics, and visitors may browse by way of links to five central areas of interest: gadgets, cars, science, technology, and do-it-yourself. Impressively, the entire 138-year archive of Popular Science is searchable in an instant. On-the-go options are available for reading on tablets and mobile devices, and up-to- the-minute updates are available via its Twitter feed.[www.popsci.com]FiguresReferencesRelatedDetails Vol. 51, No. 1 Follow us on social media for the latest updates Metrics Downloaded 152 times History Published online 3 April 2018 Published in print July 2011 Information© 2011 Author(s)PDF download

The Public Health Implications of Consumers' Environmental Concern and Their Willingness to Pay for an Eco-Friendly Product

Environmental concern has been an important topic for more than 40 years and has recently become even more critical with today's concerns about creating a sustainable and healthy environment. This research examines factors affecting an individual's willingness to pay more for an environmentally friendly product. Our results show that willingness to pay more differs across demographic groups. We also find that individuals who rate concern for waste as highly important are willing to spend more money on an eco-friendly product. Consequently, our findings provide insight into the development of appropriate educational strategies for different consumer groups to encourage consumers to purchase eco-friendly products, with a goal of creating a healthier environment for current and future generations. ********** challenge of healthier communities begins with environmental concern and collective adoption of eco-friendly behaviors, because the choices consumers make with regard to the environment influence the health and quality of life for both current and future generations. In general terms, environmental concern is a concept that can refer to feelings [consumers have] about many different green (Zimmer, Stafford, and Stafford 1994, p. 64). topic became an important one in 1962 when Rachel Carson's Silent Spring was published and has recently become even more critical with today's concerns about creating a sustainable and healthy environment. Trends show a remarkable increase in consumer worry about environmental problems (e.g., Gallup Poll 2009) and continued support for alternative forms of energy generation (Pew 2010) and other sustainable initiatives. Interest in environmental issues has also triggered rapid growth and enrollment in environmental courses offered in colleges and universities (Fuller 2010). In the corporate world, environmentalism has moved to the boardroom (Hanas 2007), while at the lay level, magazines such as Popular Mechanics feature articles related to global warming (http://www.popularmechanics.com 2010). In addition, a recent blog points out that popular media incorporate environmental messages into their programming: The powers that be at NBC Universal started going green and making the environment a priority, using a tactic called 'behavior placement' to weave subtle eco-friendly messages into the scripts of some of the network's most popular daytime and prime time programs (http://www.environment.about.com 2010). Although the environmental movement can be traced back to the nineteenth century, the modern iteration of environmental concern as an issue of critical interest began about four decades ago. Most recently, this concern has reappeared in the academic, scientific and popular press in terms of issues related to sustainability and renewable resources (e.g., Gallup 2009; Pew 2009, 2010). For example, a major initiative in the National Science Foundation's proposed 2011 budget is expanded support for climate research activities, designed to address challenges in sustainability, energy research and education (http://www.nsf.gov 2010). latest approach to understanding and researching sustainability and environmental concepts spans several disciplines including marketing, public policy and public health, among others. In particular, sustainability is recognized as a major public health issue of the twenty-first century (American Public Health Association 2007). Health concerns are a primary component of overall environmental concern because physical surroundings (air quality, water protection and even the availability of health care alternatives) directly affect human survival and quality of life (Zimmer, Stafford, and Stafford 1994), and individuals who practice environmental behaviors will promote healthier communities, via improved quality of air, water and physical health (Patz and Olson 2006). Consequently, understanding environmental concern among consumers can have an important influence on public health. …

Exploring Newtonian mechanics in a conceptually-integrated digital game: Comparison of learning and affective outcomes for students in Taiwan and the United States

This study investigates the potential of a digital game that overlays popular game-play mechanics with formal physics representations and terminology to support explicit learning and exploration of Newtonian mechanics. The analysis compares test data, survey data, and observational data collected during implementations in Taiwan and the United States with students in grades 7–9. Results demonstrate learning on some core disciplinary measures and high levels of learner engagement, indicating the potential benefits of this genre of conceptually-integrated games, but also suggesting that further research and development will be needed to more fully harness this potential. Encouragingly, striking similarities were observed across the two countries in terms of learning and engagement, suggesting that this genre of learning games may prove suitable for engaging students in active exploration of core science concepts across multiple countries.

Molecular simulation of absolute hydration Gibbs energies of polar compounds

In this work, we present simulation-based predictions of the absolute hydration energy for several simple polar molecules with different functional groups, as well as for more complex multifunctional molecules. Our calculations were performed using the thermodynamic integration methodology where electrostatic and non-polar interactions were treated separately, allowing for a stable transition path between the end-points of the integration. An appropriate methodology for the analytical integration of the simulation data was applied. We compare the performance of three popular molecular mechanics force fields: TraPPE, Gromos and OPLS-AA for the description of solute atoms in MSPC/E water. It is observed that these force fields generally perform well for the simpler molecules, but are less accurate when multifunctional molecules are considered.

Evaluation of density functionals, SCC-DFTB, neglect of diatomic differential overlap (NDDO) models and molecular mechanics methods for prolyl-leucyl-glycinamide (PLG) and structural analogs

Prolyl-leucyl-glycinamide (PLG) is a unique endogenous peptide that modulates dopamine receptor subtypes of the D 2 receptor family within the CNS. We seek to elucidate the structural basis and molecular mechanism by which PLG and its analogs modulate dopamine receptors, toward the development of new therapeutics to treat Parkinson’s disease, tardive dyskinesia and schizophrenia. As a first step toward establishing a validated protocol for accurate computational modeling of PLG and associated peptidomimetic analogs, we evaluated the accuracy of density functional theory (DFT), wave function theory (WFT), and molecular mechanics (MM) calculations for PLG and for a library of structurally related small molecules. We first tested 12 local and nonlocal density functionals, Hartree–Fock (HF) theory, four “semiempirical” methods of the neglect of diatomic differential overlap (NDDO) type, and one self-consistent-charge nonorthogonal tight-binding (SCC-DFTB) method as implemented in two software suites, against coupled-cluster benchmark geometries for 4-methylthiazolidine, a small molecule that comprises key structural features present in our PLG-analog library. DFT and HF calculations were done with the MG3S augmented polarized triple-zeta basis set. We find that for 4-methylthiazolidine bond distances, DFT significantly outperforms NDDO, and both SCC-DFTB versions we evaluated perform worse than HF theory and are less accurate than 83% of the density functionals tested. The top five functionals for 4-methylthiazolidine were M05-2X, mPW1PW, B97-2, M06-2X, and PBEh, with mean unsigned errors (MUEs) in bond length of 0.0017, 0.0020, 0.0023, 0.0025 and 0.0027 Å, respectively. The widely used B3LYP functional ranked 11th out of 12 functionals evaluated, slightly below SCC-DFTB, and is significantly less accurate for 4-methylthiazolidine bond distances (MUE = 0.0095 Å) than the best local functional (M06-L, MUE = 0.0030 Å), which is far less computationally costly. Based on that initial analysis, we obtained new M05-2X benchmark geometric parameters for PLG and a library of 11 peptidomimetic derivatives, which we in turn used to examine the accuracy of thirty-four popular molecular mechanics (MM) force fields, four NDDO approaches, and SCC-DFTB for the full compound structures. Here, we found that ∼70% of the MM force fields tested superior to the best semiempirical and SCC-DFTB codings. Moreover, AMBER-type force fields proved most accurate among MM methods for this class of small-molecule peptidomimetics; the AMBER-type methods comprised eight out of the top 10 molecular mechanics options we tested.

Developing Improved Charge Sets for the Modeling of the KcsA K(+) Channel Using QM/MM Electrostatic Potentials.

The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside the selectivity filter of the KcsA potassium channel. A comparison is made with the result of classical electrostatic calculations with nonpolarizable MM force fields (AMBER, CHARMM, and GROMOS). An effective procedure is proposed to improve force field charges by performing a fit on the electrostatic potential computed along QM/MM simulations, using a dynamical electrostatic potential derived charge set. The optimized charge set is able to reproduce the QM/MM electrostatic potentials along the channel axis within 1-2 kcal/mol, which represents an improvement relative to the corresponding electrostatic potentials obtained with popular MM force fields. By providing quantum mechanical benchmark charges and energies for the KcsA selectivity filter, we hope to facilitate developments toward the modeling of ion channels by providing an objective test as to whether a given implementation of a new, polarizable, model represents a real improvement over existing fixed point charge models.

Watching giants: the secret lives of whales

Acknowledgments Introduction 1. Extreme Motherhood 2. A Sea of Milk 3. Looking for Whales in All the Wrong Places 4. Resident Aliens? 5. How to Make a Really Rich Sea 6. Popular Mechanics: What Chimpanzees and Dolphins Can Teach Us about Tools 7. Mirror, Mirror on the Wall, Who's the Smartest One of All? 8. Building Nets from Bubbles and Other Mysterious Talents of Humpback Whales 9. Do Baby Sperm Whales Suck Milk through Their Noses? 10. Deep Culture 11. What's the Use of Granny? 12. Dolphin Snatchers 13. Friendly Mothers, Friendly Calves? 14. The War on Fish 15. Why Blue Whales Gotta Be Big 16. What You Can See by Listening 17. What You Can Learn from the Dead 18. Let's Talk about Sex, Baby 19. Missing Meat 20. Shifting Scale Notes Index

A New Method to Determine Adhesion of Cantilever Beams Using Beam Height Experimental Data

A new method for calculating the apparent work of adhesion of microfabricated cantilever beams is presented and validated. This technique, based on popular beam mechanics, directly utilizes interferometrically produced deflection experimental data. The data are analyzed based on an energy minimization approach along the lines of a previous methodology. However, the new technique differs in that it does not rely on a priori knowledge of the shape of cantilever beams to evaluate work of adhesion. In order to validate the new method, both synthetic and empirical cantilever beam data were examined. The results show that apparent work of adhesion values calculated using this method agree well with values determined using a technique previously developed and widely accepted.

Why a curveball curves: the incredible science of sports

Sports get the blood pumping and hearts racing. Fans scream and cheer as their favourite athletes run, throw, pedal, dive, or swing their way to victory. But what makes an athlete successful? do some players excel when others fall behind? In Why a Curveball Curves, the experts at Popular Mechanics, along with top athletes, coaches and sports journalists, explore the science behind sports. Fluid dynamics, biomechanics and technology determine everything from speed in cycling and protection in football to performance measurement in all sports. This book is designed for both the player and the fan, helping athletes become better-prepared and giving enthusiasts a more complete understanding and appreciation of the subtle nuances of competition. The explanations are clear, entertaining and written by people who really love and understand their game.

“Taking Hell's Measurements”: Popular Science and Popular Mechanics Magazines and the Atomic Bomb from Hiroshima to Bikini

The Journal of Popular CultureVolume 41, Issue 4 p. 695-711 “Taking Hell's Measurements”: Popular Science and Popular Mechanics Magazines and the Atomic Bomb from Hiroshima to Bikini SCOTT C. ZEMAN, SCOTT C. ZEMAN New Mexico TechSearch for more papers by this author SCOTT C. ZEMAN, SCOTT C. ZEMAN New Mexico TechSearch for more papers by this author First published: 15 July 2008 https://doi.org/10.1111/j.1540-5931.2008.00543.xCitations: 2Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Citing Literature Volume41, Issue4August 2008Pages 695-711 RelatedInformation

Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets

It has been suggested that the computational cost of correlated ab initio calculations could be reduced efficiently by using truncated basis sets on hydrogen atoms (Mintz et al., J Chem Phys 2004, 121, 5629). We now explore this proposal in the context of conformational analysis of small molecules, such as hydrogen peroxide, dimethyl ether, ethyl methyl ether, formic acid, methyl formate, and several small alcohols. It is found that truncated correlation consistent basis sets that lack certain higher angular momentum functions on hydrogen atoms offer accuracy similar to traditional Dunning's basis sets for conformational analysis. Combination of such basis sets with the basis set extrapolation technique to estimate Hartree-Fock and Møller-Plesset second order energies provides composite extrapolation model chemistries that are significantly more accurate and faster than analogous single point calculations with traditional correlation consistent basis sets. Root mean square errors of best composite extrapolation model chemistries on the used set of molecules are within 0.03 kcal/mol of traditional focal point conformational energies. The applicability of composite extrapolation methods is illustrated by performing conformational analysis of tert-butanol and cyclohexanol. For comparison, conformational energies calculated with popular molecular mechanics force fields are also given.