Symplectic quaternion scheme for biophysical molecular dynamics

Massively parallel biophysical molecular dynamics simulations, coupled with efficient methods, promise to open biologically significant time scales for study. In order to promote efficient fine-grained parallel algorithms with low communication overhead, the fast degrees of freedom in these complex systems can be divided into sets of rigid bodies. Here, a novel Hamiltonian form of a minimal, nonsingular representation of rigid body rotations, the unit quaternion, is derived, and a corresponding reversible, symplectic integrator is presented. The novel technique performs very well on both model and biophysical problems in accord with a formal theoretical analysis given within, which gives an explicit condition for an integrator to possess a conserved quantity, an explicit expression for the conserved quantity of a symplectic integrator, the latter following and in accord with Calvo and Sanz-Sarna, Numerical Hamiltonian Problems (1994), and extension of the explicit expression to general systems with a flat phase space

Dietary Methionine Restriction Regulates Liver Protein Synthesis and Gene Expression Independently of Eukaryotic Initiation Factor 2 Phosphorylation in Mice

Background: The phosphorylation of eukaryotic initiation factor 2 (p-eIF2) during dietary amino acid insufficiency reduces protein synthesis and alters gene expression via the integrated stress response (ISR).Objective: We explored whether a Met-restricted (MR) diet activates the ISR to reduce body fat and regulate protein balance.Methods: Male and female mice aged 3-6 mo with either whole-body deletion of general control nonderepressible 2 (Gcn2) or liver-specific deletion of protein kinase R-like endoplasmic reticulum kinase (Perk) alongside wild-type or floxed control mice were fed an obesogenic diet sufficient in Met (0.86%) or an MR (0.12% Met) diet for ≤5 wk. Ala enrichment with deuterium was measured to calculate protein synthesis rates. The guanine nucleotide exchange factor activity of eIF2B was measured alongside p-eIF2 and hepatic mRNA expression levels at 2 d and 5 wk. Metabolic phenotyping was conducted at 4 wk, and body composition was measured throughout. Results were evaluated with the use of ANOVA (P < 0.05).Results: Feeding an MR diet for 2 d did not increase hepatic p-eIF2 or reduce eIF2B activity in wild-type or Gcn2-/- mice, yet many genes transcriptionally regulated by the ISR were altered in both strains in the same direction and amplitude. Feeding an MR diet for 5 wk increased p-eIF2 and reduced eIF2B activity in wild-type but not Gcn2-/- mice, yet ISR-regulated genes altered in both strains similarly. Furthermore, the MR diet reduced mixed and cytosolic but not mitochondrial protein synthesis in both the liver and skeletal muscle regardless of Gcn2 status. Despite the similarities between strains, the MR diet did not increase energy expenditure or reduce body fat in Gcn2-/- mice. Finally, feeding the MR diet to mice with Perk deleted in the liver increased hepatic p-eIF2 and altered body composition similar to floxed controls.Conclusions: Hepatic activation of the ISR resulting from an MR diet does not require p-eIF2. Gcn2 status influences body fat loss but not protein balance when Met is restricted

Tracking the Legacy of Inner-City Catholic Schools: An Analysis of U.S. Elementary Catholic School Organizational and Demographic Data

Over the past twenty years, Catholic elementary schools that self-identify as “inner-city” have closed at a higher rate than Catholic schools in other locations. These schools have also long been associated with a legacy of effectively serving low-income students, students of color, and recent immigrant students, suggesting that the persistent closure of these schools may have a negative impact on these communities. In this paper, we set out to assess the extent to which there have been demographic or organizational changes over the past twenty years in these “inner-city” schools. We found that while these schools do still serve higher proportions of students of color than Catholic schools nationally, there are distinct organizational and demographic trends that have developed in these schools that merit additional analysis or investigation. We conclude this paper with several suggestions for how to build a research agenda around this up-to-date demographic and organizational analysis of this segment of U.S. Catholic elementary schools

Tracking the Legacy of Inner-City Catholic Schools: An Analysis of U.S. Elementary Catholic School Organizational and Demographic Data

Over the past twenty years, Catholic elementary schools that self identify as “inner-city” have closed at a higher rate than Catholic schools in other locations. These schools have also long been associated with a legacy of effectively serving low-income students, students of color, and recent immigrant students, suggesting that the persistent closure of these schools may have a negative impact on these communities. In this paper, we set out to assess the extent to which there have been demographic or organizational changes over the past twenty years in these “inner-city” schools. We found that while these schools do still serve higher proportions of students of color than Catholic schools nationally, there are distinct organizational and demographic trends that have developed in these schools that merit additional analysis or investigation. We conclude this paper with several suggestions for how to build a research agenda around this up-to-date demographic and organizational analysis of this segment of U.S. Catholic elementary schools

Nuclear Magnetic Resonance and Hyperfine Structure

Contains reports on five research projects

Effective Symmetries of the Minimal Supermultiplet of N = 8 Extended Worldline Supersymmetry

A minimal representation of the N = 8 extended worldline supersymmetry, known as the `ultra-multiplet', is closely related to a family of supermultiplets with the same, E(8) chromotopology. We catalogue their effective symmetries and find a Spin(4) x Z(2) subgroup common to them all, which explains the particular basis used in the original construction. We specify a constrained superfield representation of the supermultiplets in the ultra-multiplet family, and show that such a superfield representation in fact exists for all adinkraic supermultiplets. We also exhibit the correspondences between these supermultiplets, their Adinkras and the E(8) root lattice bases. Finally, we construct quadratic Lagrangians that provide the standard kinetic terms and afford a mixing of an even number of such supermultiplets controlled by a coupling to an external 2-form of fluxes.Comment: 13 Figure

On the cosmic ray bound for models of extragalactic neutrino production

We obtain the maximum diffuse neutrino intensity predicted by hadronic photoproduction models of the type which have been applied to the jets of active galactic nuclei or gamma ray bursts. For this, we compare the proton and gamma ray fluxes associated with hadronic photoproduction in extragalactic neutrino sources with the present experimental upper limit on cosmic ray protons and the extragalactic gamma ray background, employing a transport calculation of energetic protons traversing cosmic photon backgrounds. We take into account the effects of the photon spectral shape in the sources on the photoproduction process, cosmological source evolution, the optical depth for cosmic ray ejection, and discuss the possible effects of magnetic fields in the vicinity of the sources. For photohadronic neutrino sources which are optically thin to the emission of neutrons we find that the cosmic ray flux imposes a stronger bound than the extragalactic gamma ray background in the energy range between 10^5 GeV and 10^11 GeV, as previously noted by Waxman & Bahcall (1999). We also determine the maximum contribution from the jets of active galactic nuclei, using constraints set to their neutron opacity by gamma-ray observations. This present upper limit is consistent with the jets of active galactic nuclei producing the extragalactic gamma ray background hadronically, but we point out future observations in the GeV-to-TeV regime could lower this limit. We also briefly discuss the contribution of gamma ray bursts to ultra-high energy cosmic rays as it can be inferred from possible observations or limits on their correlated neutrino fluxes.Comment: 16 pages, includes 7 figures, using REVtex3.1, accepted for publication in Phys.Rev.D after minor revision

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology

The dynamical Green's function and an exact optical potential for electron-molecule scattering including nuclear dynamics

We derive a rigorous optical potential for electron-molecule scattering including the effects of nuclear dynamics by extending the common many-body Green's function approach to optical potentials beyond the fixed-nuclei limit for molecular targets. Our formalism treats the projectile electron and the nuclear motion of the target molecule on the same footing whereby the dynamical optical potential rigorously accounts for the complex many-body nature of the scattering target. One central result of the present work is that the common fixed-nuclei optical potential is a valid adiabatic approximation to the dynamical optical potential even when projectile and nuclear motion are (nonadiabatically) coupled as long as the scattering energy is well below the electronic excitation thresholds of the target. For extremely low projectile velocities, however, when the cross sections are most sensitive to the scattering potential, we expect the influences of the nuclear dynamics on the optical potential to become relevant. For these cases, a systematic way to improve the adiabatic approximation to the dynamical optical potential is presented that yields non-local operators with respect to the nuclear coordinates.Comment: 22 pages, no figures, accepted for publ., Phys. Rev.