On the absorption spectrum and stability of Ag32+ in aqueous solution

Pulse radiolysis results suggest that the very first steps of silver aggregation in water involve the formation of Ag32+. The authors present a mixed classical quantum simulation of the absorption spectrum of this aggregate which is in agreement with the exptl. spectrum. The formation and structure of this aggregate are discussed with the help of addnl. Monte Carlo and ab initio calcns. The results tend to confirm the formation of Ag32+

The many facets of polyelectrolytes and oppositely charged macroions complex formation

A review. Various models of the complex formation between polyelectrolyte chains and oppositely charged macroions are reviewed. In recent years, a great deal of knowledge of the multitude of possible polyelectrolyte conformations at the macroion surface has been accumulated, which consequently has led to increasing interest in using such complexes in the design of nanomaterials. This review focuses on key studies relating to the effects of various physico-chem. parameters on complex formation and areas for future research are identified

A novel approach to find the missing links in genome-scale metabolic models: The BridgeIt mrthod

Genome-scale metabolic reconstructions (GSMRs) are valuable resources in the analysis and understanding of cellular metabolism. They are based on genome sequence and annotation, and they are to develop bottom-up mathematical models of metabolic networks. These models are used in a wide variety of studies ranging from metabolic engineering to evolutionary studies. However, there are incomplete pathways and orphan metabolites in all GSMRs, even for the most well studied organisms. These knowledge gaps are due to the lack of experimental or homologous information, as current methods rely on a database of known reactions to generate possible pathways for bridging these gaps, and they fall short when there is no sequence homology. We present a novel computational framework called BridgIT that is able to generate hypothetical reactions and pathways that bridge gaps in reconstructed pathways. The novel reactions generated are based the third level of enzyme commission classification system (EC), which is consistent with known biochemical reactions, protein structures, genomic sequences, and enzyme properties that follow the EC classification. Within the BridgIT framework, we generate all biochemically plausible reactions and pathways, which can link two or more metabolites. These pathways are then ranked according to their length, thermodynamic feasibility, and network feasibility. We next use chemical similarity metrics to link the generated hypothetical reactions with known reactions through their substrate and product similarity. The protein and gene sequences of the linked known reactions are used to identify possible sequences within the GSMR to further refine and improve the annotation of the existing GSMR. We demonstrate the ability of this method to identify gaps that can be easily filled by known reactions and also gaps that require novel reactions which existing methods fail to do so

Dielectric discontinuity effects on the adsorption of a linear polyelectrolyte at the surface of a neutral nanoparticle

The formation of complexes between nanoparticles and polyelectrolytes is a key process for the control of the reactivity of manufd. nanoparticles and rational design of core shell nanostructures. In this work, we investigate the influence of the nanoparticle dielec. const. on the adsorption of a linear charged polymer (polyelectrolyte) at the surface of a neutral nanoparticle. The polyelectrolyte linear charge d., as well as the image charges in the nanoparticle due to the dielec. discontinuity, is taken into account. Monte Carlo simulations are used to predict the adsorption/desorption limits and system properties. Effects of the nanoparticle size and polyelectrolyte length are also investigated. The polyelectrolyte is found adsorbed on the nanoparticle when the dielec. const. of the nanoparticle is greater than the dielec. const. of the medium. Attractive interactions induced by the presence of opposite sign image charges are found strong enough to adsorb the polyelectrolyte showing that the reaction field contribution has to be considered. The affinity between the polyelectrolyte and the nanoparticle is found to increase in magnitude by increasing the nanoparticle size and dielec. const. The reaction field magnitude is also found to depend in a nonlinear way from the polyelectrolyte length

Effects of surface site distribution and dielectric discontinuity on the charging behavior of nanoparticles. A grand canonical Monte Carlo study

The surface site distribution and the dielec. discontinuity effects on the charging process of a spherical nanoparticle (NP) have been investigated. It is well known that electrostatic repulsion between charges on neighboring sites tends to decrease the effective charge of a NP. The situation is more complicated close to a dielec. breakdown, since here a charged site is not only interacting with its neighbors but also with its own image charge and the image charges of all its neighbors. Coexistence of opposite charges, titrn. sites positions, and pH dependence are systematically studied using a grand canonical Monte Carlo method. A Tanford and Kirkwood approach has been applied to describe the interaction potentials between explicit discrete ampholytic charging sites. Homogeneous, heterogeneous and patch site distributions were considered to reproduce the titrn. site distribution at the solid/soln. interface of natural NPs. Results show that the charging process is controlled by the balance between Coulomb interactions and the reaction field through the solid-liq. interface. They also show that the site distribution plays a crucial role in the charging process. In patch distributions, charges accumulate at the perimeter of each patch due to finite size effects. When homogeneous and heterogeneous distributions are compared, three different charging regimes are obtained. In homogeneous and heterogeneous (with quite low polydispersity indexes) distributions, the effects of the NP dielec. const. on Coulomb interactions are counterbalanced by the reaction field and in this case, the dielec. breakdown has no significant effect on the charging process. This is not the case in patch distributions, where the dielec. breakdown plays a crucial role in the charging process

C9ORF72 repeat expansion in Australian and Spanish frontotemporal dementia patients

A hexanucleotide repeat expansion in C9ORF72 has been established as a common cause of frontotemporal dementia (FTD). However, the minimum repeat number necessary for disease pathogenesis is not known. The aims of our study were to determine the frequency of the C9ORF72 repeat expansion in two FTD patient collections (one Australian and one Spanish, combined n = 190), to examine C9ORF72 expansion allele length in a subset of FTD patients, and to examine C9ORF72 allele length in ‘non-expansion’ patients (those with <30 repeats). The C9ORF72 repeat expansion was detected in 5–17% of patients (21–41% of familial FTD patients). For one family, the expansion was present in the proband but absent in the mother, who was diagnosed with dementia at age 68. No association was found between C9ORF72 non-expanded allele length and age of onset and in the Spanish sample mean allele length was shorter in cases than in controls. Southern blotting analysis revealed that one of the nine ‘expansion-positive’ patients examined, who had neuropathologically confirmed frontotemporal lobar degeneration with TDP-43 pathology, harboured an ‘intermediate’ allele with a mean size of only ~65 repeats. Our study indicates that the C9ORF72 repeat expansion accounts for a significant proportion of Australian and Spanish FTD cases. However, C9ORF72 allele length does not influence the age at onset of ‘non-expansion’ FTD patients in the series examined. Expansion of the C9ORF72 allele to as little as ~65 repeats may be sufficient to cause disease.Carol Dobson-Stone, Marianne Hallupp, Clement T. Loy, Elizabeth M. Thompson, Eric Haan, Carolyn M. Sue, Peter K. Panegyres, Cristina Razquin, Manuel Seijo-Martínez, Ramon Rene, Jordi Gascon, Jaume Campdelacreu, Birgit Schmoll, Alexander E. Volk, William S. Brooks, Peter R. Schofield, Pau Pastor, John B. J. Kwo

Modeling the surface charge behavior and dynamic processes of colloidal particles: Application to components found in natural waters

L'agrégation ou non des collïdes aquatiques détermine le transport des polluants et des composés vitaux au sein des systèmes aquatiques. Le but de cette thèse est de mieux décrire les caractéristiques des colloïdes ainsi que leurs processus d'agrégations par simulation numériques. Un premier modèle Monte Carlo-Métropolis a été développé afin de mieux comprendre les processus de chargement des colloïdes inorganiques en tenant compte du pH, de la concentration ionique du milieu considéré, de la discontinuité diélectrique entre le colloïde et l'eau, de la répartition ainsi que des propriétés ampholytiques des sites de surface. Un second modèle Monte Carlo-Métropolis a été créé afin de mieux comprendre le rôle de la discontinuité diélectrique dans l'agrégation entre un biopolymère rigide chargé et un colloïde neutre. Un modèle de dynamique Brownienne a été créé afin de mieux comprendre les processus d'agrégation entre les colloïdes inorganiques, les acides fulviques et les biopolymères rigides

Explicit Simulations of Parameters Impacting Nanoparticles Transport in Saturated Soils: Monte Carlo Approach

The production and worldwide market of manufactured nanoparticles (NPs) are steadily growing past years. They open new opportunities for many industrial applications such as agriculture, pharmaceutical components or even everyday products. Proportionally, release of NPs in the environment is increasing drastically: Release in environment can be intentional (e.g., fertilizers, nanopesticides) or non-intentional due to products' alteration, degradation, recycling etc. Then, concerns on the environmental fate and toxicity of NPs are rising. All environmental compartments are concerned: air, water and soil. Soil is a critical environmental compartment due to the potential NPs ecotoxicity on soil organisms, groundwater contamination, etc. Understanding NPs transport processes in soils is a complex topic owing to the number of influencing factors and interactions: Computer simulations can help in addressing this issue. To get further insight into mechanisms and processes controlling NPs transport in soils, such as NPs and soil matrix interactions, soil porosity, etc. we present a new and original Monte Carlo approach: Based on an explicit (off lattice) representation of NPs and soil grains, simulations and NPs transport in porous matrices are performed by considering attachment/detachment efficiencies of NPs with soil grains, putting in front the impact of soil porosities. As highlighted by Cornelis et al.1 and Bradford et al.2, specific and detailed interactions between NPs and soils are crucial points to consider. With the explicit representation of soil grains and NPs, we investigate the impact of size exclusion of NPs and aggregates in pores (straining effects), as well as surface affinity of NPs to soil grains/soil surface. The reversibility of NPs adsorption, i.e. NPs detachment, which has been shown experimentally to be a key process, is also considered. All these parameters, including NPs aggregation, are systematically explored and their effect on breakthrough curves investigated. 1-Cornelis, G.; Hund-Rinke, K.; Kuhlbusch, T.; Brink, N. van den; Nickel, C. Fate and Bioavailability of Engineered Nanoparticles in Soils: A Review. Critical Reviews in Environmental Science and Technology 2014, 44 (24), 2720–2764. 2-Bradford, S. A.; Simunek, J.; Bettahar, M.; van Genuchten, M. T.; Yates, S. R. Modeling Colloid Attachment, Straining, and Exclusion in Saturated Porous Media. Environ. Sci. Technol. 2003, 37 (10), 2242–2250

Effect of deposition, detachment and aggregation processes on nanoparticle transport in porous media using Monte Carlo simulations

A novel off-lattice three-dimensional coarse-grained Monte Carlo model is developed to study engineered nanoparticle (ENP) behavior in porous media. Based on individual particle tracking and on the assumption that different physicochemical processes may occur with different probabilities, our model is used to independently evaluate the influence of homoaggregation, attachment and detachment processes on ENP transport and retention inside porous media made of colloidal collectors. The possibility of straining, i.e. trapping of ENPs or aggregates that are too large to pass pore necks, is also included in the model. The overall probability of ENP retention as a function of the above mentioned processes is quantified using functional tests in the form of a alpha(global)(t(ref)) retention parameter. High alpha(global)(t(ref)) values were obtained for moderate probabilities of homoaggregation between ENPs (alpha(ENP-ENP)) and very small probabilities of attachment between ENPs and collectors (alpha(att)), thus indicating the important role of homoaggregation and attachment in ENP retention. Moreover, attaching ENPs and large aggregates was found to cause pore neck enclosure and thus largely contributed to the straining of unbound ENPs. An analysis of depth distribution of retained ENPs revealed that, depending on the dominating conditions, the number of ENPs was decreasing monotonously or exponentially with depth. The introduction of the ENP detachment probability (alpha(det)) from collectors resulted in an increased ENP occurrence at the porous media matrix outlet. It was also found that different sets of alpha(det) and alpha(att) values, reflecting different ENPs and collector physicochemical properties and inter-particle forces, lead to identical alpha(global)(t(ref)) values. This constitutes an important outcome indicating that alpha(global)(t(ref)) values determined from functional tests are not mechanistic but operationally defined parameters and thus cannot be deemed predictive beyond these tests