On Stochastic Error and Computational Efficiency of the Markov Chain Monte Carlo Method

In Markov Chain Monte Carlo (MCMC) simulations, the thermal equilibria quantities are estimated by ensemble average over a sample set containing a large number of correlated samples. These samples are selected in accordance with the probability distribution function, known from the partition function of equilibrium state. As the stochastic error of the simulation results is significant, it is desirable to understand the variance of the estimation by ensemble average, which depends on the sample size (i.e., the total number of samples in the set) and the sampling interval (i.e., cycle number between two consecutive samples). Although large sample sizes reduce the variance, they increase the computational cost of the simulation. For a given CPU time, the sample size can be reduced greatly by increasing the sampling interval, while having the corresponding increase in variance be negligible if the original sampling interval is very small. In this work, we report a few general rules that relate the variance with the sample size and the sampling interval. These results are observed and confirmed numerically. These variance rules are derived for the MCMC method but are also valid for the correlated samples obtained using other Monte Carlo methods. The main contribution of this work includes the theoretical proof of these numerical observations and the set of assumptions that lead to them

Dispersal of larval and juvenile seabream: Implications for Mediterranean marine protected areas

In the marine context, information about dispersal is essential for the design of networks of marine protected areas (MPAs). Generally, most of the dispersal of demersal fishes is thought to be driven by the transport of eggs and larvae in currents, with the potential contribution of dispersal in later life stages relatively minimal.Using otolith chemistry analyses, we estimate dispersal patterns across a spatial scale of approximately 180. km at both propagule (i.e. eggs and larvae) and juvenile (i.e. between settlement and recruitment) stages of a Mediterranean coastal fishery species, the two-banded seabream Diplodus vulgaris. We detected three major natal sources of propagules replenishing local populations in the entire study area, suggesting that propagule dispersal distance extends to at least 90. km. For the juvenile stage, we detected dispersal of up to 165. km. Our work highlights the surprising and significant role of dispersal during the juvenile life stages as an important mechanism connecting populations. Such new insights are crucial for creating effective management strategies (e.g. MPAs and MPA networks) and to gain support from policymakers and stakeholders, highlighting that MPA benefits can extend well beyond MPA borders, and not only via dispersal of eggs and larvae, but also through movement by juveniles

Patterns of variability in early life traits of a Mediterranean coastal fish

Spawning dates and pelagic larval duration (PLD) are early life traits (ELT) crucial for understanding life cycles, properly assessing patterns of connectivity and gathering indications about patchiness or homogeneity of larval pools. Considering that little attention has been paid to spatial variability in these traits, we investigated variability of ELT from the analysis of otolith microstructure in the common two-banded sea bream Diplodus vulgaris. In the southwestern Adriatic Sea, along ~200 km of coast (∼1° in latitude, 41.2° to 40.2°N), variability of ELT was assessed at multiple spatial scales. Overall, PLD (ranging from 25 to 61 d) and spawning dates (October 2009 to February 2010) showed significant variability at small scales (i.e. <6 km), but not at larger scales. These outcomes suggest patchiness of the larval pool at small spatial scales. Multiple causal processes underlying the observed variability are discussed, along with the need to properly consider spatial variability in ELT, for example when delineating patterns of connectivity. Copyright © 2013 Inter-Research

Genetic improvement for crossbreeding in table grape varieties

Genetic improvement by crossbreeding of table grape varieties was realized at the Istituto Sperimentale per la Viticoltura for the achievement of the following main targets: early species, seedless species, species with high content of fructose in grapes and, at the same time, a research concerning the hereditary transmission of these features. The results are the followings: Registration in the National Catalogue of the varieties of 4 new table grape varieties that are interesting for their ripening (IC. 199, LC. 218, IC. 120, IC. 213).Information concerning the heritability of earliness, average weight of grape and bunch for the varieties examined.Achievement of varieties that have a ratio between the two monosaccharides considerably tending towards fructose. This feature remains constant throughout the years

Restrictions in model reduction for polymer chain models in Dissipative Particle Dynamics

We model high molecular weight homopolymers in semidilute concentration via Dissipative Particle Dynamics (DPD). We show that in model reduction methodologies for polymers it is not enough to preserve system properties (i.e., density ñ, pressure p, temperature T, radial distribution function g(r)) but preserving also the characteristic shape and length scale of the polymer chain model is necessary. In this work we apply a DPD-model-reduction methodology for linear polymers recently proposed; and demonstrate why the applicability of this methodology is limited upto certain maximum polymer length, and not suitable for solvent coarse graining. © The Authors. Published by Elsevier B.V

Expressive Policy Analysis with Enhanced System Dynamicity

Despite several research studies, the effective analysis of policy based systems remains a significant challenge. Policy analysis should at least (i) be expressive (ii) take account of obligations and authorizations, (iii) include a dynamic system model, and (iv) give useful diagnostic information. We present a logic-based policy analysis framework which satisfies these requirements, showing how many significant policy-related properties can be analysed, and we give details of a prototype implementation. Copyright 2009 ACM

Correlation of vulnerability and damage between artistic assets and structural elements: The DataBAES archive for the conservation planning of CH masonry buildings in seismic areas

Historical buildings in seismic hazard-prone regions need specific measures in safety protection, largely due to the presence of artistic assets and/or decorations, both movable (e.g., statues, pinnacles, etc.) and unmovable (e.g., frescoes, valuable plasters or wall paintings, mosaics, and stuccoes). A correlation of damage between structural systems and artworks is fundamental for defining limit states, which can identify the proper conditions for interventions. Nevertheless, several vulnerability aspects can be identified before a seismic event occurs, the study of which can provide the basic dataset for setting up preventive measures in conservation programs. In this paper, the vulnerability and damage conditions related to structural elements (SE) and unmovable artistic assets (AA) belonging to historical masonry buildings are analysed. Optimized survey forms for the onsite detection of either intrinsic (e.g., compositional) defects or deterioration phenomena for both materials and structure are proposed, and results are provided in a web data system (called DataBAES). This enables us to compare the current levels of vulnerability and damage of AA and SE on a scale of five increasing grades. This procedure has been validated on a series of buildings struck by earthquakes in Italy and can be used for correlations of the seismic behaviour of SE and AA in predictive analyses