Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples.

The distribution of fitness effects (DFE) has considerable importance in population genetics. To date, estimates of the DFE come from studies using a small number of individuals. Thus, estimates of the proportion of moderately to strongly deleterious new mutations may be unreliable because such variants are unlikely to be segregating in the data. Additionally, the true functional form of the DFE is unknown, and estimates of the DFE differ significantly between studies. Here we present a flexible and computationally tractable method, called Fit∂a∂i, to estimate the DFE of new mutations using the site frequency spectrum from a large number of individuals. We apply our approach to the frequency spectrum of 1300 Europeans from the Exome Sequencing Project ESP6400 data set, 1298 Danes from the LuCamp data set, and 432 Europeans from the 1000 Genomes Project to estimate the DFE of deleterious nonsynonymous mutations. We infer significantly fewer (0.38-0.84 fold) strongly deleterious mutations with selection coefficient |s| > 0.01 and more (1.24-1.43 fold) weakly deleterious mutations with selection coefficient |s| < 0.001 compared to previous estimates. Furthermore, a DFE that is a mixture distribution of a point mass at neutrality plus a gamma distribution fits better than a gamma distribution in two of the three data sets. Our results suggest that nearly neutral forces play a larger role in human evolution than previously thought

Finite-volume two-pion energies and scattering in the quenched approximation

We investigate how L\"uscher's relation between the finite-volume energy of two pions at rest and pion scattering lengths has to be modified in quenched QCD. We find that this relation changes drastically, and in particular, that ``enhanced finite-volume corrections" of order $L^0=1$ and $L^{-2}$ occur at one loop ($L$ is the linear size of the box), due to the special properties of the $\eta'$ in the quenched approximation. We define quenched pion scattering lengths, and show that they are linearly divergent in the chiral limit. We estimate the size of these various effects in some numerical examples, and find that they can be substantial.Comment: 22 pages, uuencoded, compressed postscript fil

Quenched Chiral Perturbation Theory for Heavy-light Mesons

We formulate quenched chiral perturbation theory for heavy-light mesons coupled to pions, and calculate the one-loop chiral logarithmic corrections to $f_B$, $f_{B_{s}}$, $B_B$ and $B_{B_{s}}$. We also calculate these corrections for ``partially quenched'' theories. In both theories, the chiral logarithms diverge in the chiral limit, indicating that (partially) quenched theories should not be used to study this limit. Comparing the chiral logarithms to those in QCD, we estimate the errors caused by (partial) quenching. By forming suitable ratios, we can reduce the uncertainties in our estimates.Comment: 22 pages, revtex format, 5 Postscript figure

Thermodynamics of Lattice QCD with Chiral 4-Fermion Interactions

We have studied lattice QCD with an additional, irrelevant 4-fermion interaction having a U(1)xU(1) chiral symmetry, at finite temperatures. Adding this 4-fermion term allowed us to work at zero quark mass, which would have otherwise been impossible. The theory with 2 massless staggered quark flavours appears to have a first order finite temperature phase transition at N_t=4 for the value of 4-fermion coupling we have chosen, in contrast to what is expected for 2-flavour QCD. The pion screening mass is seen to vanish below this transition, only to become massive and degenerate with the sigma (f_0) above this transition where the chiral symmetry is restored, as is seen by the vanishing of the chiral condensate.Comment: 23 pages, 11 figure

Chiral Logs in Quenched QCD

The quenched chiral logs are examined on a $16^3 \times 28$ lattice with Iwasaki gauge action and overlap fermions. The pion decay constant $f_{\pi}$ is used to set the lattice spacing, $a = 0.200(3) {\rm fm}$. With pion mass as low as $\sim 180 {\rm MeV}$, we see the quenched chiral logs clearly in $m_{\pi}^2/m$ and $f_P$, the pseudoscalar decay constant. We analyze the data to determine how low the pion mass needs to be in order for the quenched one-loop chiral perturbation theory ($\chi$PT) to apply. With the constrained curve-fitting method, we are able to extract the quenched chiral log parameter $\delta$ together with other low-energy parameters. Only for $m_{\pi} \leq 300 {\rm MeV}$ do we obtain a consistent and stable fit with a constant $\delta$ which we determine to be 0.24(3)(4) (at the chiral scale $\Lambda_{\chi}=0.8 {\rm GeV}$). By comparing to the $12^3 \times 28$ lattice, we estimate the finite volume effect to be about 2.7% for the smallest pion mass. We also fitted the pion mass to the form for the re-summed cactus diagrams and found that its applicable region is extended farther than the range for the one-loop formula, perhaps up to $m_{\pi} \sim 500-600$ MeV. The scale independent $\delta$ is determined to be 0.20(3) in this case. We study the quenched non-analytic terms in the nucleon mass and find that the coefficient $C_{1/2}$ in the nucleon mass is consistent with the prediction of one-loop $\chi$PT\@. We also obtain the low energy constant $L_5$ from $f_{\pi}$. We conclude from this study that it is imperative to cover only the range of data with the pion mass less than $\sim 300 {\rm MeV}$ in order to examine the chiral behavior of the hadron masses and decay constants in quenched QCD and match them with quenched one-loop $\chi$PT\@.Comment: 37 pages and 24 figures, pion masses are fitted to the form for the re-summed cactus diagrams, figures added, to appear in PR

Chiral perturbation theory calculation for pn -> dpipi at threshold

We investigate the reaction pn -> dpipi in the framework of Chiral Perturbation Theory. For the first time a complete calculation of the leading order contributions is presented. We identify various diagrams that are of equal importance as compared to those recognized in earlier works. The diagrams at leading order behave as expected by the power counting. Also for the first time the nucleon-nucleon interaction in the initial, intermediate and final state is included consistently and found to be very important. This study provides a theoretical basis for a controlled evaluation of the non-resonant contributions in two-pion production reactions in nucleon-nucleon collisions.Comment: 24 pages, 3 figures, 3 table

A Lattice Study of the Nucleon Excited States with Domain Wall Fermions

We present results of our numerical calculation of the mass spectrum for isospin one-half and spin one-half non-strange baryons, i.e. the ground and excited states of the nucleon, in quenched lattice QCD. We use a new lattice discretization scheme for fermions, domain wall fermions, which possess almost exact chiral symmetry at non-zero lattice spacing. We make a systematic investigation of the negative-parity $N^*$ spectrum by using two distinct interpolating operators at $\beta=6/g^2=6.0$ on a $16^3 \times 32 \times 16$ lattice. The mass estimates extracted from the two operators are consistent with each other. The observed large mass splitting between this state, $N^*(1535)$, and the positive-parity ground state, the nucleon N(939), is well reproduced by our calculations. We have also calculated the mass of the first positive-parity excited state and found that it is heavier than the negative-parity excited state for the quark masses studied.Comment: 46 pages, REVTeX, 11 figures included, revised version accepted for publication in Phys. Rev.

Monte Carlo study of the hull distribution for the q=1 Brauer model

We study a special case of the Brauer model in which every path of the model has weight q=1. The model has been studied before as a solvable lattice model and can be viewed as a Lorentz lattice gas. The paths of the model are also called self-avoiding trails. We consider the model in a triangle with boundary conditions such that one of the trails must cross the triangle from a corner to the opposite side. Motivated by similarities between this model, SLE(6) and critical percolation, we investigate the distribution of the hull generated by this trail (the set of points on or surrounded by the trail) up to the hitting time of the side of the triangle opposite the starting point. Our Monte Carlo results are consistent with the hypothesis that for system size tending to infinity, the hull distribution is the same as that of a Brownian motion with perpendicular reflection on the boundary.Comment: 21 pages, 9 figure

Exact Large Deviation Function in the Asymmetric Exclusion Process

By an extension of the Bethe ansatz method used by Gwa and Spohn, we obtain an exact expression for the large deviation function of the time averaged current for the fully asymmetric exclusion process in a ring containing $N$ sites and $p$ particles. Using this expression we easily recover the exact diffusion constant obtained earlier and calculate as well some higher cumulants. The distribution of the deviation $y$ of the average current is, in the limit $N \to \infty$, skew and decays like $\exp - (A y^{5/2})$ for $y \to + \infty$ and $\exp - (A' |y|^{3/2})$ for $y \to -\infty$. Surprisingly, the large deviation function has an expression very similar to the pressure (as a function of the density) of an ideal Bose or Fermi gas in $3d$.Comment: 8 pages, in ReVTeX, e-mail addresses: [email protected] and [email protected]

Physical Properties of Giant Molecular Clouds in the Large Magellanic Cloud

The Magellanic Mopra Assessment (MAGMA) is a high angular resolution CO mapping survey of giant molecular clouds (GMCs) in the Large and Small Magellanic Clouds using the Mopra Telescope. Here we report on the basic physical properties of 125 GMCs in the LMC that have been surveyed to date. The observed clouds exhibit scaling relations that are similar to those determined for Galactic GMCs, although LMC clouds have narrower linewidths and lower CO luminosities than Galactic clouds of a similar size. The average mass surface density of the LMC clouds is 50 Msol/pc2, approximately half that of GMCs in the inner Milky Way. We compare the properties of GMCs with and without signs of massive star formation, finding that non-star-forming GMCs have lower peak CO brightness than star-forming GMCs. We compare the properties of GMCs with estimates for local interstellar conditions: specifically, we investigate the HI column density, radiation field, stellar mass surface density and the external pressure. Very few cloud properties demonstrate a clear dependence on the environment; the exceptions are significant positive correlations between i) the HI column density and the GMC velocity dispersion, ii) the stellar mass surface density and the average peak CO brightness, and iii) the stellar mass surface density and the CO surface brightness. The molecular mass surface density of GMCs without signs of massive star formation shows no dependence on the local radiation field, which is inconsistent with the photoionization-regulated star formation theory proposed by McKee (1989). We find some evidence that the mass surface density of the MAGMA clouds increases with the interstellar pressure, as proposed by Elmegreen (1989), but the detailed predictions of this model are not fulfilled once estimates for the local radiation field, metallicity and GMC envelope mass are taken into account.Comment: 28 pages, 10 figures, accepted by MNRA