Some comments on Monte Carlo and molecular dynamics methods

We highlight some links between molecular dynamics and Monte Carlo algorithms used to simulate condensed matter systems. Special attention is paid to the question of sampling the desired statistical ensemble

Canadian City Housing Prices and Urban Market Segmentation

The authors provide a detailed empirical analysis of Canadian city housing prices. They examine the long-run relationship between city house prices in Canada from 1981 to 2005 as well as idiosyncratic relations between city prices and city-specific variables. The results suggest that city house prices are only weakly correlated in the long run, and that there is a disconnect between house prices and interest rates. City-specific variables such as union wage levels, new-housing prices, and the issuance of building permits tend to be positively related to city existing-house prices. Surprisingly, there is mixed evidence with respect to standard measures of economic activity, such as labour force and per capita GDP.Regional economic developments

Folding kinetics of a polymer [corrigendum]

In our original article (Phys. Chem. Chem. Phys., 2012, 14, 60446053) a convergence problem resulted in an averaging error in computing the entropy from a set of Wang-Landau Monte-Carlo simulations. Here we report corrected results for the freezing temperature of the homopolymer chain as a function of the range of the non-bonded interaction. We find that the previously reported forward-flux sampling (FFS) and brute-force (BF) simulation results are in agreement with the revised Wang-Landau (WL) calculations. This confirms the utility of FFS for computing crystallisation rates in systems of this kind.Comment: 2 pages, 4 figure

Murine terminal deoxynucleotidyl transferase: cellular distribution and response to cortisone

The mouse thymus contains two forms of terminal deoxynucleotidyl transferase (TdT) which are distinguishable by the salt concentration necessary to elute them from a phosphocellulose column, by their distrubtion among the thymocyte subpopulations, and by their sensitivity to cortisone treatment. In the whole thymus the later eluting peak (peak II) is the predominant one with about 3-10% of the total activity appearing in peak I. Both peak I and peak II activities are most sensitively assayed by the polymerization of dGMP onto an oligo(dA) primer. The minor population of thymocytes which is less dense and cortisone-resistant contains a higher specific activity of peak I TdT. The majority of TdT activity is, however, found in the major population of thymocytes which occurs in the center region of a bovine serum albumin gradient and is cortisone-sensitive. A very low level of an activity indistinguishable from peak II TdT activity is also detected in the mouse bone marrow. Other tissues, such as spleen, liver, heart, and brain lack detectable amounts of TdT activity

A Multi-Factor Analysis of AREIT Returns

Since 1990, the Australian Real Estate Investment Trust (AREIT) sector has experienced substantial growth and popularity. While the AREIT sector had benefit from the increased flow of funds from institutional investors during the 1997 Asian financial crisis, the recent impact of the 2008 global financial crisis has been a negative one. In this paper, we examine the sensitivities of annualised AREIT returns against a set of seven firm-specific variables and four market-wide risk variables. Balanced and unbalanced panel regressions are conducted on three sub-periods during 1990 - 2008 corresponding to the major phases in evolution of the AREIT sector. Our regression results find that size has a negative impact on returns, and this effect has been diminishing over time. Overall market risk was also found to be significant and positive only since 2003, suggesting that recently AREITs behave more like stocks and less like defensive assets. The relationship with exchange rate risk has been positive in recent years, due to more AREITs choosing to diversify internationally, particularly in the U.S. property markets. Our findings on the relationship between market-to-book ratios and AREIT returns depart from standard finance literature. In comparison to REITs in other countries, AREITs have shifted their preferences away from property-type diversification and into more specialised investment strategies. We also find contrasting evidence on the impact of international diversification, and that domestic AREITs provide better returns than internationally diversified counterparts. The relationship between returns and short term interest rates was found to be positive and significant prior to 2002, and the relationship with long-term interest rates was found to be negative and significant since 2003, suggesting that AREITs exhibit less bond-like characteristics in the past five years.AREITs, AREIT returns, Property-type diversification, International diversification, Panel regressions

Coarse-grained simulation of amphiphilic self-assembly

We present a computer simulation study of amphiphilic self assembly performed using a computationally efficient single-site model based on Gay-Berne and Lennard-Jones particles. Molecular dynamics simulations of these systems show that free self-assembly of micellar, bilayer and inverse micelle arrangements can be readily achieved for a single model parameterisation. This self-assembly is predominantly driven by the anisotropy of the amphiphile-solvent interaction, amphiphile-amphiphile interactions being found to be of secondary importance. While amphiphile concentration is the main determinant of phase stability, molecular parameters such as headgroup size and interaction strength also have measurable affects on system properties. </p

Cloning of terminal transferase cDNA by antibody screening

A cDNA library was prepared from a terminal deoxynucleotidyltransferase-containing thymoma in the phage vector λgt11. By screening plaques with anti-terminal transferase antibody, positive clones were identified of which some had β-galactosidase-cDNA fusion proteins identifiable after electrophoretic fractionation by immunoblotting with anti-terminal transferase antibody. The predominant class of cross-hybridizing clones was determined to represent cDNA for terminal transferase by showing that one representative clone hybridized to a 2200-nucleotide mRNA in close-matched enzyme-positive but not to enzyme-negative cells and that the cDNA selected a mRNA that translated to give a protein of the size and antigenic characteristics of terminal transferase. Only a small amount of genomic DNA hybridized to the longest available clone, indicating that the sequence is virtually unique in the mouse genome

Sperm mobility: mechanisms of fertilizing efficiency, genetic variation and phenotypic relationship with male status in the domestic fowl, Gallus gallus domesticus

When females are sexually promiscuous, sexual selection continues after insemination through sperm competition and cryptic female choice, and male traits conveying an advantage in competitive fertilization are selected for. Although individual male and ejaculate traits are known to influence paternity in a competitive scenario, multiple mechanisms co-occur and interact to determine paternity. The way in which different traits interact with each other and the mechanisms through which their heritability is maintained despite selection remain unresolved. In the promiscuous fowl, paternity is determined by the number of sperm inseminated into a female, which is mediated by male social dominance, and by the quality of the sperm inseminated, measured as sperm mobility. Here we show that: (i) the number of sperm inseminated determines how many sperm reach the female sperm-storage sites, and that sperm mobility mediates the fertilizing efficiency of inseminated sperm, mainly by determining the rate at which sperm are released from the female storage sites, (ii) like social status, sperm mobility is heritable, and (iii) subdominant males are significantly more likely to have higher sperm mobility than dominant males. This study indicates that although the functions of social status and sperm mobility are highly interdependent, the lack of phenotypic integration of these traits may maintain the variability of male fitness and heritability of fertilizing efficiency