Pray for the People Who Feed You : Voices of Pauper Children in the Industrial Age

Following the Industrial Revolution in the late nineteenth and early twentieth centuries, countries such as the United States and England experienced a widening gap between the rich industrialists and the impoverished working class. As a result, poverty quickly shifted from a localized problem to a national epidemic. Each country was faced with the challenges of addressing and alleviating poverty on a national scale. With a limited amount of resources, questions arose about who should receive relief. What should it look like? How should it be administered? And how would poverty and policy affect political, economic, social and familial structures? [excerpt]https://cupola.gettysburg.edu/artcatalogs/1016/thumbnail.jp

Ab Initio Molecular Dynamics Study of Aqueous Solvation of Ethanol and Ethylene

The structure and dynamics of aqueous solvation of ethanol and ethylene are studied by DFT-based Car-Parrinello molecular dynamics. We did not find an enhancement of the structure of the hydrogen bonded network of hydrating water molecules. Both ethanol and ethylene can easily be accommodated in the hydrogen-bonded network of water molecules without altering its structure. This is supports the conclusion from recent neutron diffraction experiments that there is no hydrophobic hydration around small hydrophobic groups. Analysis of the electronic charge distribution using Wannier functions shows that the dipole moment of ethanol increases from 1.8 D to 3.1 D upon solvation, while the apolar ethylene molecule attains an average dipole moment of 0.5 D. For ethylene, we identified configurations with $\pi$-H bonded water molecules, that have rare four-fold hydrogen-bonded water coordination, yielding instantaneous dipole moments of ethylene of up to 1 D. The results provide valuable information for the improvement of empirical force fields, and point out that for an accurate description of the aqueous solvation of ethanol, and even of the apolar ethylene, polarizable force fields are required.Comment: 15 pages, 10 figures, 4 tables, revtex4, submitted to J. Chem. Phy

Efficiency analysis of reaction rate calculation methods using analytical models I: The 2D sharp barrier

We analyze the efficiency of different methods for the calculation of reaction rates in the case of two simple analytical benchmark systems. Two classes of methods are considered: the first are based on the free energy calculation along a reaction coordinate and the calculation of the transmission coefficient, the second on the sampling of dynamical pathways. We give scaling rules for how this efficiency depends on barrier height and width, and we hand out simple optimization rules for the method-specific parameters. We show that the path sampling methods, using the transition interface sampling technique, become exceedingly more efficient than the others when the reaction coordinate is not the optimal one.Comment: 22 pages, 5 figure

Reaction rate calculation by parallel path swapping

The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we have devised a new algorithmic procedure based on the transition interface sampling technique. In the same spirit of parallel tempering, paths between different ensembles are swapped, but the role of temperature is here played by the interface position. We have tested the method on the denaturation transition of DNA using the Peyrard-Bishop-Dauxois model. We find that the new algorithm gives a reduction of the computational cost by a factor 20.Comment: 5 pages, 3 figure

Feasibility investigation of a low-temperature, variable infrared source. Horizon definition study

Feasibility of low temperature, variable infrared source - calibration of instrumentation used in defining earth horizo

Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants.

De novo genetic variants are an important source of causative variation in complex genetic disorders. Many methods for variant discovery rely on mapping reads to a reference genome, detecting numerous inherited variants irrelevant to the phenotype of interest. To distinguish between inherited and de novo variation, sequencing of families (parents and siblings) is commonly pursued. However, standard mapping-based approaches tend to have a high false-discovery rate for de novo variant prediction. Kevlar is a mapping-free method for de novo variant discovery, based on direct comparison of sequences between related individuals. Kevlar identifies high-abundance k-mers unique to the individual of interest. Reads containing these k-mers are partitioned into disjoint sets by shared k-mer content for variant calling, and preliminary variant predictions are sorted using a probabilistic score. We evaluated Kevlar on simulated and real datasets, demonstrating its ability to detect both de novo single-nucleotide variants and indels with high accuracy

The Future of Civil War History

In March 2013, hundreds of academics, preservationists, consultants, historical interpreters, museum professionals, living historians, students, K-12 teachers, and new media specialists gathered in Gettysburg, Pennsylvania to assess the state and potential future of the study of the American Civil War. The essays in this special issue build on the themes of that conference: embracing the democratic and civic potential of historical thinking; reaffirming the power of place and the importance of specific, focused stories; integrating military, political, social, cultural, and gender history; and encouraging collaboration among historians working in different settings. Our three guest editors offer their own thoughts about the state and potential future of Civil War history. [excerpt

Direct Transient Analysis of a Fuze Assembly by Axisymmetric Solid Elements

A fuze assembly, which consists of three major parts, nose, collar and sleeve, was designed to survive severe transverse impact giving a maximum base acceleration of 20.000 G. It is shown that hoop failure occurred in the collar after the impact. They also showed that by bonding the collar to the nose, the collar was able to survive the same impact. To find out the effectiveness of the bonding quantitatively, axisymmetric solid elements TRAPAX and TRIAAX were used in modelling the fuze and direct transient analysis was performed. The dynamic stresses in selected elements on the bonded and unbonded collars were compared. The peak hoop stresses in the unbonded collar were found to be up to three times higher than those in the bonded collar. The NASTRAN results explained the observed hoop failure in the unbonded collar. In addition, static and eigenvalue runs were performed as checks on the models prior to the transient runs. The use of the MPCAX cards and the existence and contributors of the calculated first several nearly identical natural frequencies are addressed

Rate constants for diffusive processes by partial path sampling

We introduce a path sampling method for the computation of rate constants for systems with a highly diffusive character. Based on the recently developed algorithm of transition interface sampling (TIS) this procedure increases the efficiency by sampling only parts of complete transition trajectories confined within a certain region. The algorithm assumes the loss of memory for highly diffusive progression along the reaction coordinate. We compare the new technique to the TIS method for a simple diatomic system and show that the computation time of the new method scales linearly, instead of quadraticaly, with the length of the diffusive barrier. The validity of the memory loss assumption is also discussed.Comment: 12 pages, including 8 figures, RevTeX

A Novel Path Sampling Method for the Calculation of Rate Constants

We derive a novel efficient scheme to measure the rate constant of transitions between stable states separated by high free energy barriers in a complex environment within the framework of transition path sampling. The method is based on directly and simultaneously measuring the fluxes through many phase space interfaces and increases the efficiency with at least a factor of two with respect to existing transition path sampling rate constant algorithms. The new algorithm is illustrated on the isomerization of a diatomic molecule immersed in a simple fluid.Comment: 14 pages, including 13 figures, RevTeX