Histogram Reweighting Method for Dynamic Properties

The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from Molecular Dynamics simulations. The theory presented here is based on the fact that the correlation functions in systems in thermodynamic equilibrium are averages over initial conditions of functions of the trajectory of the system in phase-space, the latter depending on the volume, the total number of particles and the classical Hamiltonian. Thus, the well-known histogram reweighting method can almost straightforwardly be applied to reconstruct the probability distribution of initial states at different thermodynamic conditions, without extra computational effort. Correlation functions and transport coefficients are obtained with this method from few simulation data sets.Comment: 4 pages, 3 figure

Near Critical Coexistence for an AUA Model of Thiophenes

Near critical coexistence has been determined by means of parallel tempering coupled with grand canonical Monte Carlo simulations which were later recombined by using histogram reweighting techniques. The data collected during the simulations is not only useful to determine accurately the critical point but also to provide estimates for the coexistence density jump between the phases in equilibrium. A recently introduced algorithm by Kim [Kim Y.C. (2005) Phys. Rev. 71, 051501; Kim Y.C. (2005) Comput. Phys. Commun. 169, 295], based on the scaling of the positions of the different minima found for the Binder parameter, has been applied to the case of a realistic model of thiophene consisting of different Lennard Jones sites. Contrary to the case of the Hard Core Square Well (HCSW) and Restricted Primitive Model (RPM) systems, significant corrections to scaling are found in this case. By readapting the algorithm we are able to calculate the coexistence in the critical region

Sketching a Portrait of the Optimal Adsorbent for CO 2 Separation by Pressure Swing Adsorption

International audienceIn silico screening of CO2 adsorbents is a very powerful method for preselecting the most promising porous solids for experimental studies. Because of increased computational power, it is now possible to investigate a large number of adsorbents in a fairly short time. However, it remains difficult to rationalize structure–performance correlations because the complexity of such porous materials cannot be reduced to a few simple descriptors. In this paper, we present a different approach that was applied to the design of an optimal adsorbent for CO2 separation from gas mixtures. A CO2–CH4 mixture was used as the feed. We constructed a simplified model of the porous material by adopting a spherical pore geometry. From the dispersion–repulsion point of view, the spherical pore was modeled by homogeneously distributed Lennard-Jones sites. Besides, a charge distribution was introduced to mimic the electrostatic behavior. The selected charge distribution is constituted of negative charges homogeneously distributed over the surface of the pore. The total negative charge is counterbalanced by eight positive discrete charges placed on the corners of the cube inscribed in the sphere. This model can be characterized by two main descriptors: the pore size and the cation charge. For this model, the adsorbate–adsorbent interaction potential due to electrostatic and dispersion–repulsion interactions was determined. Then, the Henry constants of CO2 and CH4 are calculated from statistical thermodynamics and substituted in the Ruthven statistical model, which allows calculation of the binary adsorption isotherms. Finally, the adsorbed quantities are used to estimate the performance indexes of the pressure swing adsorption (PSA) process, such as the working capacity and separation factor. We show how these two parameters depend on the pore size and cation charge. For a medium-pressure PSA process, the optimal adsorbent has a large pore volume and is highly charged, which provides high working capacity and selectivity. The high cationic charge allows one to efficiently fill the large pore volume and assures high CO2 selectivity

Role of structure and chemistry in controlling separations of CO ₂/CH₄ and CO₂/CH₄/CO mixtures over honeycomb MOFs with coordinatively unsaturated metal sites

A systematic study of the effect of coordinatively unsaturated sites (cus) in the separation of CO2/CH4 and CO/CO2/CH 4 mixtures on CPO-27-M (M = Ni, Co, and Zn) and STA-12-Ni metal-organic frameworks was carried out using gravimetric and breakthrough experiments. The separation selectivity and the working capacity of these structures were evaluated as important performance indicators for CO2 separations by PSA. The results demonstrate a remarkable influence of coordinatively unsaturated sites on the selectivity and the working capacity. Particularly, the high affinity of CPO-27-Ni and CPO-27-Co for CO2 leads to a low working capacity for CO2 (because regeneration of the adsorbents is difficult) but a high CO2/CH4 selectivity. With a ternary CO/CO2/CH4 feed mixture, CPO-27-Ni and -Co prefer the adsorption of CO over CO2 due to the strong specific interaction of CO with cus. Surprisingly, STA-12-Ni does not exhibit the same behavior: it is selective for the adsorption of CO2 in a ternary mixture, just like CPO-27-Zn. Among the four MOFs tested in this study, CPO-27-Zn presents the best compromise between the working capacity and the CO2/CH4 and CO2/CO selectivities. The results are discussed in terms of the coordination chemistry of the coordinatively unsaturated metal sites, their acid-base properties, and their accessibility.</p

Immunological and pathological status of gilthead sea bream (Sparus aurata L.) under different long-term feeding regimes

The possible influence of the feeding regime (FR) on the immune system and pathological status of gilthead sea bream was studied. Two growth trials were performed starting at different seasons (trial 1 = March; trial 2 = June) under controlled experimental conditions. In both trials, FR-1 groups received a restricted amount of food, whereas FR-2 groups were fed to visual satiety. The pathology study included parasitological and bacteriological examination, and the immunological traits analysed were respiratory burst activity of head kidney leucocytes, serum lysozyme and alternative pathway complement activity (ACH50). The immunological status of gilthead sea bream not only was not impaired by the restricted feeding regime, but also seemed to be enhanced in some aspects, as the respiratory burst of FR-1 fish of trial 2 was significantly higher. No differences in the bacterial isolates were detected between the two feeding regimes, and Vibrio harveyi was the most prevalent species in both cases, especially in warm months. Also, fish under FR-1 regimes had significantly lower mortality, lower prevalence of infection of all the parasites except Cryptosporidium molnari, and less histopathological alterations in liver and intestine than those under FR-2 regimes. © 2003 Elsevier Science B.V. All rights reserved.This work was supported by research grants from the Spanish Ministerio de Educación, Cultura y Deporte under FEDER Program no. 1FD97-979-C02. M. Mingarro was recipient of a fellowship from the Diputación de Castellón. We are thankful to M.L. Alonso, M.A. González and G. Sanza for technical assistance in the samplings, and to J. Montfort for the histological processing

Bacterial and parasitic pathogens in cultured common dentex, Dentex dentex L.

A bacteriological and parasitological study on cultured common dentex, Dentex dentex L., was conducted in a 2-year survey. Two different groups of fish were studied: (1) sampled only when mortalities occurred; and (2) sampled periodically from 10 days post-hatch until the juvenile stage. In both groups, peaks of mortalities coincided with high water temperatures. The same parasites were detected in both groups, except Ichthyophonus sp., which was identified only in the trunk kidney of fish from group 1. Two myxosporeans, Ceratomyxa sp. and Lepthotheca sp., were found in the bile and the trunk kidney, respectively. Epitheliocystis infection was also very frequent in the gills. An unidentified microsporidium, which was found in the liver, occurred very infrequently. Vibrio harveyi was dominant in samples from diseased animals (79%) and clearly associated with mortalities. It was not detected in water or larval homogenates. A high percentage (60%) of the isolates of this species were sorbitol positive. Other less frequently occurring bacteria were V. alginolyticus and Photobacterium (V.) damselae. The disease conditions found in common dentex were considered to be multifactorial in origin.This work was supported by research grants from Generalitat Valenciana and the Spanish Ministry of EducaciÓn y Cultura (PETRI 95-0183-OP). Theauthors want to thank J. Monfort and M. J. San Cleto for histological processin

Bacteria associated with winter mortalities in laboratory-reared common dentex (Dentex dentex L.)

A pathological study was conducted on laboratory-reared juvenile common dentex (Dentex dentex) suffering trickling and continuous mortalities. During a 3-month period (October-December), water temperature, clinical signs and mortalities were recorded. Moribund or dead fish were examined for bacteria and parasites. Bacteria were isolated from head kidney and external ulcers, and samples from the gills, intestine, stomach, trunk kidney, gall bladder and liver were taken for histology. Cumulative mortality reached 73%, and 80% of fish examined were positive for bacteria (102 isolates). Vibrio splendidus was the most prevalent in head kidney (59.7%) and ulcers (88.9%), and it was frequently isolated as pure culture (74.7% and 100% respectively). This is the first report of this bacterium in association with mortality in common dentex. Vibrio scophthalmi was the second most prevalent bacterium (29.2%) and accounted for 63.6% of the mixed infections with V. splendidus, V. harveyi, Pseudoalteromonas spp. and other species were rarely isolated. No parasites were found in histological sections. Bacteria were frequently observed in the lumen of the intestine and stomach, destroying the epithelium. A cellular reaction was suggested by the high numbers of rodlet cells (RC) in the intestinal epithelium, and the abundance of eosinophilic granular cells (EGC) in the intestinal lamina propria. In the stomach, vacuolized cells containing unidentified debris, sometimes of crystalloid appearance, were very common. The high prevalence of V. splendidus in pure cultures and the absence of other aetiological agents suggest that V. splendidus is substantially involved in the registered mortalities, although the implication of V. scophthalmi and even of some nutritional factors cannot be discounted.Funding for this study was provided by JACUMAR-Generalitat Valenciana (project no. GCI 0870/2002).The authors are grateful to P. Cabrera for excellent as-sistance in pathogen isolation and to J. Monfort forhistological processing at IATS. The authors are in-debted to Dr A. Estevez (Centre d’Aquicultura, IRTA,Tarragona) for providing animals

Virulence and molecular typing of Vibrio harveyi strains isolated from cultured dentex, gilthead sea bream and European sea bass

Vibrio harveyi was isolated from internal organs or ulcers of diseased and apparently healthy gilthead sea bream (Sparus aurata) and European sea bass (Dicentrarchus labrax) cultured in several fish farms located on the Spanish Mediterranean coast. The prevalence of the bacterium was significantly higher in European sea bass than in gilthead sea bream, and was closely related to the season in both fish species, occurring almost exclusively on warm months (June to November). After phenotypic characterization, a selection of forty five isolates from gilthead sea bream, sea bass, and several isolates previously obtained from common dentex (Dentex dentex) of the same area, were molecularly typed by automated ribotyping and random amplified polymorphic DNA (RAPD) analysis. Cluster analysis of data established 8 RAPD types and 13 ribotypes among wild isolates, and the combination of both techniques allowed to define fourteen different groups and a clear discrimination of all outbreaks and samplings. Several strains isolated from diseased gilthead sea bream and sea bass and also from asymptomatic sea bream, were tested for virulence in both fish species by intracoelomic injection. All the isolates (11) were pathogenic for sea bass, with nine out of the eleven LD50 values ranging from 1.5 × 105 to 1.6 × 106 cfu/fish. Gilthead sea bream was unaffected by the seven tested strains, even by those more virulent for sea bass, and only one strain caused a 10% mortality at 4.2 × 107 cfu/fish. This is the first report on virulence of V. harveyi for sea bass.This work was supported by research grants from the Spanish Ministerio de Educación, Cultura y Deporte MAR-98/1000 C02 and FEDER Program 1FD97-979-C02. We are thankful to M.L. Alonso for technical assistance in the samplings