Jarzynski's equality, fluctuation theorems, and variance reduction: Mathematical analysis and numerical algorithms

In this paper, we study Jarzynski's equality and fluctuation theorems for diffusion processes. While some of the results considered in the current work are known in the (mainly physics) literature, we review and generalize these nonequilibrium theorems using mathematical arguments, therefore enabling further investigations in the mathematical community. On the numerical side, variance reduction approaches such as importance sampling method are studied in order to compute free energy differences based on Jarzynski's equality.Comment: journal versio

Influence of pH and sequence in peptide aggregation via molecular simulation

We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to correctly account for the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.Comment: 21 pages, 4 figure

pH-dependent coarse-grained model of peptides

We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving interactions. We use reference data from atomistic simulations and experimental databases and transfer its main physical features to the coarse-grained resolution according the principle of "consistency across the scales". The coarse-grained model is refined by finding a set of parameters that, when applied to peptides with different sequences and experimental properties, reproduces the experimental and atomistic data of reference. We use the such parameterized model for performing several numerical tests to check its transferability to other systems and to prove the universality of the related modeling strategy. We have tried systems with rather different response to pH variations, showing a highly satisfactory performance of the model.Comment: accepted for publication in Soft Matte

Researching the Historical Representations of Ancient Egypt in Trade Books

State and national education initiatives require that historical information be introduced in the classroom through the utilization of multiple diverse texts. The role of non-fiction in the English/language arts classroom, as well as informational texts in the history/social studies classroom, increased considerably. The use of trade books allows teachers to connect the two curricula, while also meeting the standards. Primary sources can assist in filling the informational gap left by trade books and textbooks, which allow students to gain a more balanced view of historical events. Teachers, however, are not given direction as to which specific curricular materials are most appropriate. My research empirically evaluated how ancient Egypt is represented in trade books, a curricular topic that appears in world history. I reported misrepresentations that were found to be present within the data pool. My findings can direct classroom teachers in selecting appropriate literature about ancient Egypt

A WIND CONDUCTOR’S GUIDE: JAMES BARNES’S TRAIL OF TEARS, CHARLES IVES’S OLD HOME DAYS: SUITE FOR BAND, AND DAVID MASLANKA’S GOLDEN LIGHT

AN ABSTRACT OF THE RESEARCH PAPER OF Melanie K. Schuette, for the Master of Music degree in Music, presented on April 1, 2019, at Southern Illinois University Carbondale. TITLE: A WIND CONDUCTOR’S GUIDE: JAMES BARNES’S TRAIL OF TEARS, CHARLES IVES’S OLD HOME DAYS: SUITE FOR BAND, AND DAVID MASLANKA’S GOLDEN LIGHT MAJOR PROFESSOR: Dr. Christopher Morehouse The scope of this paper is to provide an analysis of three wind band/ensemble works performed as part of the graduate recital of Melanie Schuette. Each chapter is divided into four categories; biography, background, analysis, and rehearsal considerations from the viewpoint of the conductor. The repertoire includes James Barnes’s Trail of Tears, Charles Ives’s Old Home Days: Suite for Band, and David Maslanka’s Golden Light

15. The Conservation Significance of Prairie Remnants in Missouri

How to conserve the great biodiversity of the prairie resource is a question of continuous debate. In Missouri the estimated 6,070,284 ha (15 million acres) of prairie at the time of Euro-American settlement has been reduced to an estimated 20,234–24,281 ha (50,000–60,000 acres) today, with 8,093 ha (20,000 acres) in conservation ownership. This valuable resource is rare now and is continuing to disappear. The Missouri Prairie Foundation (MPF), a nongovernmental organization celebrating its 50th anniversary in 2016, has acquired and protects 22 tracts that cover more than 1,335 ha (3,300 acres), comprised mostly of original unplowed prairie. These parcels, though limited in size, constitute a system of high quality native remnants. MPF has recently embarked on several surveys to document the biodiversity of these prairies. As funding and opportunity have allowed, surveys were conducted of flora, floristic integrity, bryophytes, soil biota, birds, pollinators, ants, lepidopterans, and odonates. These surveys are demonstrating that even relatively small remnants are supporting and perpetuating high levels of conservative and rare species and providing exciting new discoveries. Protecting remnant prairies, large and not so large, before they disappear is MPF’s approach to conserving prairie biodiversity in Missouri and is an essential practice that needs to be included in any state’s prairie conservation strategy

A Comparative Study Analyzing Undergraduate Internship Participation and the Impact on Retention and Timely Degree Completion at a Four-Year, Private, Midwest Institution

Declining enrollments, rising costs and increasing student debt have caused college administrators, potential students, and outside stakeholders to focus on certain student outcomes, including retention and timely degree completion. Colleges and universities are not only collecting data in these two areas, they are searching for strategies, which might have a positive effect. Research has provided a variety of factors, which contribute to retention and timely degree completion. High-impact practices, such as service learning, student faculty research and internships featured several characteristics that may contribute to retention and timely degree completion. Internships offer several advantages, such as preparation for future careers and skill development. The purpose of this mixed-methods study was to compare undergraduate students who completed internships and those not completing internships to corresponding retention and graduation rates. The quantitative research analyzed the impact of internship participation on retention and timely degree completion. The research question provided insight into the perceptions of internship participants and the connection between their internship experience and retention and timely degree completion. The statistical analysis found that internship participants are more likely to stay at the institution and to complete their degree. However, the analysis did not prove that internship participation influenced four, five, or six-year graduation rates. The survey of internship participants revealed that students do not view their internship experience as a reason for remaining enrolled at the university or for graduating in four years. Further recommendations for college and university administrators, as well as additional research, were made in regards to internship programs