A contact cavity-biased method for grand canonical Monte Carlo simulations

A modification of the cavity-biased grand canonical Monte Carlo (GCMC) proposed by Mezei is introduced here. Instead of on a fixed grid, test points of cavities are generated at the contact positions around the centers of existing particles. The increase in the probability or bias of finding a cavity is related to the radial distribution function and can hence be corrected. With this new cavity-biased implementation, an improved convergence to equihbrium is demonstrated and higher densities can be attained. Comparisons with the standard GCMC method, and the original cavity-biased scheme of Mezei are made. © 1994 American Institute of Physics.published_or_final_versio

Logarithmic interaction under periodic boundary conditions: Closed form formulas for energy and forces

A method is given to obtain closed form formulas for the energy and forces for an aggregate of charges interacting via a logarithmic interaction under periodic boundary conditions. The work done here is a generalization of Glasser's results [M. L. Glasser, J. Math. Phys. 15, 188 (1974)] and is obtained with a different and simpler method than that by Stremler [M. A. Stremler, J. Math. Phys. 45, 3584 (2004)]. The simplicity of the formulas derived here makes them extremely convenient in a computer simulation

Yukawa potentials in systems with partial periodic boundary conditions II : Lekner sums for quasi-two dimensional systems

Yukawa potentials may be long ranged when the Debye screening length is large. In computer simulations, such long ranged potentials have to be taken into account with convenient algorithms to avoid systematic bias in the sampling of the phase space. Recently, we have provided Ewald sums for quasi-two dimensional systems with Yukawa interaction potentials [M. Mazars, {\it J. Chem. Phys.}, {\bf 126}, 056101 (2007) and M. Mazars, {\it Mol. Phys.}, Paper I]. Sometimes, Lekner sums are used as an alternative to Ewald sums for Coulomb systems. In the present work, we derive the Lekner sums for quasi-two dimensional systems with Yukawa interaction potentials and we give some numerical tests for pratical implementations. The main result of this paper is to outline that Lekner sums cannot be considered as an alternative to Ewald sums for Yukawa potentials. As a conclusion to this work : Lekner sums should not be used for quasi-two dimensional systems with Yukawa interaction potentials.Comment: 25 pages, 5 figures and 1 tabl

Yukawa potentials in systems with partial periodic boundary conditions I : Ewald sums for quasi-two dimensional systems

Yukawa potentials are often used as effective potentials for systems as colloids, plasmas, etc. When the Debye screening length is large, the Yukawa potential tends to the non-screened Coulomb potential ; in this small screening limit, or Coulomb limit, the potential is long ranged. As it is well known in computer simulation, a simple truncation of the long ranged potential and the minimum image convention are insufficient to obtain accurate numerical data on systems. The Ewald method for bulk systems, i.e. with periodic boundary conditions in all three directions of the space, has already been derived for Yukawa potential [cf. Y., Rosenfeld, {\it Mol. Phys.}, \bm{88}, 1357, (1996) and G., Salin and J.-M., Caillol, {\it J. Chem. Phys.}, \bm{113}, 10459, (2000)], but for systems with partial periodic boundary conditions, the Ewald sums have only recently been obtained [M., Mazars, {\it J. Chem. Phys.}, {\bf 126}, 056101 (2007)]. In this paper, we provide a closed derivation of the Ewald sums for Yukawa potentials in systems with periodic boundary conditions in only two directions and for any value of the Debye length. A special attention is paid to the Coulomb limit and its relation with the electroneutrality of systems.Comment: 40 pages, 5 figures and 4 table

Morphine induces preconditioning via activation of mitochondrial KCa channels

PURPOSE: Mitochondrial calcium sensitive potassium (mK(Ca)) channels are involved in cardioprotection induced by ischemic preconditioning. In the present study we investigated whether morphine-induced preconditioning also involves activation of mK(Ca) channels. METHODS: Isolated rat hearts (six groups; each n = 8) underwent global ischemia for 30 min followed by a 60-min reperfusion. Control animals were not further treated. Morphine preconditioning (MPC) was initiated by two five-minute cycles of morphine 1 muM infusion with one five-minute washout and one final ten-minute washout period before ischemia. The mK(Ca) blocker, paxilline 1 muM, was administered, with and without morphine administration (MPC + Pax and Pax). As a positive control, we added an ischemic preconditioning group (IPC) alone and combined with paxilline (IPC + Pax). At the end of reperfusion, infarct sizes were determined by triphenyltetrazoliumchloride staining. RESULTS: Infarct size was (mean +/- SD) 45 +/- 9% of the area at risk in the Control group. The infarct size was less in the morphine or ischemic preconditioning groups (MPC: 23 +/- 8%, IPC: 20 +/- 5%; each P < 0.05 vs Control). Infarct size reduction was abolished by paxilline (MPC + Pax: 37 +/- 7%, P < 0.05 vs MPC and IPC + Pax: 36 +/- 6%, P < 0.05 vs IPC), whereas paxilline alone had no effect (Pax: 46 +/- 7%, not significantly different from Control). CONCLUSION: Cardioprotection by morphine-induced preconditioning is mediated by activation of mK(Ca) channel

De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam

Autism spectrum disorder (ASD) is a developmental disorder with a prevalence of around 1% children worldwide and characterized by patient behaviour (communication, social interaction, and personal development). Data on the efficacy of diagnostic tests using copy number variations (CNVs) in candidate genes in ASD is currently around 10% but it is overrepresented by patients of Caucasian background. We report here that the diagnostic success of de novo candidate CNVs in Vietnamese ASD patients is around 6%. We recruited one hundred trios (both parents and a child) where the child was clinically diagnosed with ASD while the parents were not affected. We performed genetic screening to exclude RETT syndrome and Fragile X syndrome and performed genome-wide DNA microarray (aCGH) on all probands and their parents to analyse for de novo CNVs. We detected 1708 non-redundant CNVs in 100 patients and 118 (7%) of them were de novo. Using the filter for known CNVs from the Simons Foundation Autism Research Initiative (SFARI) database, we identified six CNVs (one gain and five loss CNVs) in six patients (3 males and 3 females). Notably, 3 of our patients had a deletion involving the SHANK3 gene–which is the highest compared to previous reports. This is the first report of candidate CNVs in ASD patients from Vietnam and provides the framework for building a CNV based test as the first tier screening for clinical management

Development and Notch Signaling Requirements of the Zebrafish Choroid Plexus

The choroid plexus (CP) is an epithelial and vascular structure in the ventricular system of the brain that is a critical part of the blood-brain barrier. The CP has two primary functions, 1) to produce and regulate components of the cerebral spinal fluid, and 2) to inhibit entry into the brain of exogenous substances. Despite its importance in neurobiology, little is known about how this structure forms.Here we show that the transposon-mediated enhancer trap zebrafish line Et(Mn16) expresses green fluorescent protein within a population of cells that migrate toward the midline and coalesce to form the definitive CP. We further demonstrate the development of the integral vascular network of the definitive CP. Utilizing pharmacologic pan-notch inhibition and specific morpholino-mediated knockdown, we demonstrate a requirement for Notch signaling in choroid plexus development. We identify three Notch signaling pathway members as mediating this effect, notch1b, deltaA, and deltaD.This work is the first to identify the zebrafish choroid plexus and to characterize its epithelial and vasculature integration. This study, in the context of other comparative anatomical studies, strongly indicates a conserved mechanism for development of the CP. Finally, we characterize a requirement for Notch signaling in the developing CP. This establishes the zebrafish CP as an important new system for the determination of key signaling pathways in the formation of this essential component of the vertebrate brain

Positive and Negative Regulation of Gli Activity by Kif7 in the Zebrafish Embryo

Loss of function mutations of Kif7, the vertebrate orthologue of the Drosophila Hh pathway component Costal2, cause defects in the limbs and neural tubes of mice, attributable to ectopic expression of Hh target genes. While this implies a functional conservation of Cos2 and Kif7 between flies and vertebrates, the association of Kif7 with the primary cilium, an organelle absent from most Drosophila cells, suggests their mechanisms of action may have diverged. Here, using mutant alleles induced by Zinc Finger Nuclease-mediated targeted mutagenesis, we show that in zebrafish, Kif7 acts principally to suppress the activity of the Gli1 transcription factor. Notably, we find that endogenous Kif7 protein accumulates not only in the primary cilium, as previously observed in mammalian cells, but also in cytoplasmic puncta that disperse in response to Hh pathway activation. Moreover, we show that Drosophila Costal2 can substitute for Kif7, suggesting a conserved mode of action of the two proteins. We show that Kif7 interacts with both Gli1 and Gli2a and suggest that it functions to sequester Gli proteins in the cytoplasm, in a manner analogous to the regulation of Ci by Cos2 in Drosophila. We also show that zebrafish Kif7 potentiates Gli2a activity by promoting its dissociation from the Suppressor of Fused (Sufu) protein and present evidence that it mediates a Smo dependent modification of the full length form of Gli2a. Surprisingly, the function of Kif7 in the zebrafish embryo appears restricted principally to mesodermal derivatives, its inactivation having little effect on neural tube patterning, even when Sufu protein levels are depleted. Remarkably, zebrafish lacking all Kif7 function are viable, in contrast to the peri-natal lethality of mouse kif7 mutants but similar to some Acrocallosal or Joubert syndrome patients who are homozygous for loss of function KIF7 alleles