Absolute binding free energies for octa-acids and guests in SAMPL₅

As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid (OAMe). We use the double decoupling method via thermodynamic integration (TI) or Hamiltonian replica exchange in connection with the Bennett acceptance ratio (HREM-BAR). We produce the binding poses either through manual docking or by using GalaxyDock-HG, a docking software developed specifically for this study. The root mean square deviations for our most accurate predictions are 1.4 kcal mol−1 for OAH with TI and 1.9 kcal mol−1 for OAMe with HREM-BAR. Our best results for OAMe were obtained for systems with ionic concentrations corresponding to the ionic strength of the experimental solution. The most problematic system contains a halogenated guest. Our attempt to model the σ-hole of the bromine using a constrained off-site point charge, does not improve results. We use results from molecular dynamics simulations to argue that the distinct binding affinities of this guest to OAH and OAMe are due to a difference in the flexibility of the host. We believe that the results of this extensive analysis of host-guest complexes will help improve the protocol used in predicting binding affinities for larger systems, such as protein-substrate compounds

RADIOCARBON AND STABLE ISOTOPE EVIDENCE OF DIETARY CHANGE FROM THE MESOLITHIC TO THE MIDDLE AGES IN THE IRON GATES: NEW RESULTS FROM LEPENSKI VIR

This is the published version, also available here: https://journals.uair.arizona.edu/index.php/radiocarbon/article/view/4269.A previous radiocarbon dating and stable isotope study of directly associated ungulate and human bone samples from Late Mesolithic burials at Schela Cladovei in Romania established that there is a freshwater reservoir effect of approximately 500 yr in the Iron Gates reach of the Danube River valley in southeast Europe. Using the d15N values as an indicator of the percentage of freshwater protein in the human diet, the 14C data for 24 skeletons from the site of Lepenski Vir were corrected for this reservoir effect. The results of the paired 14C and stable isotope measurements provide evidence of substantial dietary change over the period from about 9000 BP to about 300 BP. The data from the Early Mesolithic to the Chalcolithic are consistent with a 2-component dietary system, where the linear plot of isotopic values reflects mixing between the 2 end-members to differing degrees. Typically, the individuals of Mesolithic age have much heavier d15N signals and slightly heavier d13C, while individuals of Early Neolithic and Chalcolithic age have lighter d15N and d13C values. Contrary to our earlier suggestion, there is no evidence of a substantial population that had a transitional diet midway between those that were characteristic of the Mesolithic and Neolithic. However, several individuals with Final Mesolithic 14C ages show d15N and d13C values that are similar to the Neolithic dietary pattern. Provisionally, these are interpreted either as incomers who originated in early farming communities outside the Iron Gates region or as indigenous individuals representing the earliest Neolithic of the Iron Gates. The results from Roman and Medieval age burials show a deviation from the linear function, suggesting the presence of a new major dietary component containing isotopically heavier carbon. This is interpreted as a consequence of the introduction of millet into the human food chain

Neurophysiology

Contains reports on eight research projects.Bell Telephone Laboratories, Inc.Teagle Foundation, Inc.National Science Foundation (Grant GP-2495)National Institutes of Health (Grants MH-04737-04)National Institutes of Health (NB-04985-01)U. S. Air Force. Aeronautical Systems Division (Contract AF 33(615)-1747)U. S. Air Force. Cambridge Research Laboratories (Contract AF19(628)-3807)U. S. Air Force. Electronic Systems Division (Contract AF19(628)-4147)National Aeronautics and Space Administration (Grant NsG-496

A Composite HST Spectrum of Quasars

We construct a composite quasar spectrum from 284 HST FOS spectra of 101 quasars with redshifts z > 0.33. The spectrum covers the wavelengths between 350 and 3000 A in the rest frame. There is a significant steepening of the continuum slope around 1050 A. The continuum between 1050 and 2200 A can be modeled as a power law with alpha = -0.99. For the full sample the power-law index in the extreme ultraviolet (EUV) between 350 and 1050 A is alpha = -1.96. The continuum flux in the wavelengths near the Lyman limit shows a depression of about 10 percent. The break in the power-law index and the slight depression of the continuum near the Lyman limit are features expected in Comptonized accretion-disk spectra.Comment: 10 figures To appear in the February 1, 1997, issue of the Ap.

Ab initio Random Structure Searching

It is essential to know the arrangement of the atoms in a material in order to compute and understand its properties. Searching for stable structures of materials using first-principles electronic structure methods, such as density functional theory (DFT), is a rapidly growing field. Here we describe our simple, elegant and powerful approach to searching for structures with DFT which we call ab initio random structure searching (AIRSS). Applications to discovering structures of solids, point defects, surfaces, and clusters are reviewed. New results for iron clusters on graphene, silicon clusters, polymeric nitrogen, hydrogen-rich lithium hydrides, and boron are presented.Comment: 44 pages, 23 figure

The monomer-dimer problem and moment Lyapunov exponents of homogeneous Gaussian random fields

We consider an "elastic" version of the statistical mechanical monomer-dimer problem on the n-dimensional integer lattice. Our setting includes the classical "rigid" formulation as a special case and extends it by allowing each dimer to consist of particles at arbitrarily distant sites of the lattice, with the energy of interaction between the particles in a dimer depending on their relative position. We reduce the free energy of the elastic dimer-monomer (EDM) system per lattice site in the thermodynamic limit to the moment Lyapunov exponent (MLE) of a homogeneous Gaussian random field (GRF) whose mean value and covariance function are the Boltzmann factors associated with the monomer energy and dimer potential. In particular, the classical monomer-dimer problem becomes related to the MLE of a moving average GRF. We outline an approach to recursive computation of the partition function for "Manhattan" EDM systems where the dimer potential is a weighted l1-distance and the auxiliary GRF is a Markov random field of Pickard type which behaves in space like autoregressive processes do in time. For one-dimensional Manhattan EDM systems, we compute the MLE of the resulting Gaussian Markov chain as the largest eigenvalue of a compact transfer operator on a Hilbert space which is related to the annihilation and creation operators of the quantum harmonic oscillator and also recast it as the eigenvalue problem for a pantograph functional-differential equation.Comment: 24 pages, 4 figures, submitted on 14 October 2011 to a special issue of DCDS-

Choice in the context of informal care-giving

Extending choice and control for social care service users is a central feature of current English policies. However, these have comparatively little to say about choice in relation to the informal carers of relatives, friends or older people who are disabled or sick. To explore the realities of choice as experienced by carers, the present paper reviews research published in English since 1985 about three situations in which carers are likely to face choices: receiving social services; the entry of an older person to long-term care; and combining paid work and care. Thirteen electronic databases were searched, covering both the health and social care fields. Databases included: ASSIA; IBSS; Social Care Online; ISI Web of Knowledge; Medline; HMIC Sociological Abstracts; INGENTA; ZETOC; and the National Research Register. The search strategy combined terms that: (1) identified individuals with care-giving responsibilities; (2) identified people receiving help and support; and (3) described the process of interest (e.g. choice, decision-making and self-determination). The search identified comparatively few relevant studies, and so was supplemented by the findings from another recent review of empirical research on carers' choices about combining work and care. The research evidence suggests that carers' choices are shaped by two sets of factors: one relates to the nature of the care-giving relationship; and the second consists of wider organisational factors. A number of reasons may explain the invisibility of choice for carers in current policy proposals for increasing choice. In particular, it is suggested that underpinning conceptual models of the relationship between carers and formal service providers shape the extent to which carers can be offered choice and control on similar terms to service users. In particular, the exercise of choice by carers is likely to be highly problematic if it involves relinquishing some unpaid care-giving activities

Neurophysiology

Contains research objectives and reports on three research projects.National Aeronautics and Space Administration (Grant NsG-496)U.S. Air Force (Aeronautical Systems Division) under Contract AF33 (616)-7783The Teagle Foundation, Inc.National Institutes of Health (Grant MH-04737-03)National Institutes of Health (Grant NB-04897-01)National Science Foundation (Grant G-16526)Bell Telephone Laboratories, Inc

Underground railroads: citizen entitlements and unauthorized mobility in the antebellum period and today

In recent years, some scholars and prominent political figures have advocated the deepening of North American integration on roughly the European Union model, including the creation of new political institutions and the free movement of workers across borders. The construction of such a North American Union, if it included even a very thin trans-state citizenship regime, could represent the most significant expansion of individual entitlements in the region since citizenship was extended to former slaves in the United States. With such a possibility as its starting point, this article explores some striking parallels between the mass, legally prohibited movement across boundaries by fugitive slaves in the pre-Civil War period, and that by current unauthorized migrants to the United States. Both were, or are, met on their journeys by historically parallel groups of would-be helpers and hinderers. Their unauthorized movements in both periods serve as important signals of incomplete entitlements or institutional protections. Most crucially, moral arguments for extending fuller entitlements to both groups are shown here to be less distinct than may be prima facie evident, reinforcing the case for expanding and deepening the regional membership regime