The structure and organization within the membrane of the helices composing the pore-forming domain of Bacillus thuringiensis δ-endotoxin are consistent with an “umbrella-like” structure of the pore

The aim of this study was to elucidate the mechanism of membrane insertion and the structural organization of pores formed by Bacillus thuringiensis δ-endotoxin. We determined the relative affinities for membranes of peptides corresponding to the seven helices that compose the toxin pore-forming domain, their modes of membrane interaction, their structures within membranes, and their orientations relative to the membrane normal. In addition, we used resonance energy transfer measurements of all possible combinatorial pairs of membrane-bound helices to map the network of interactions between helices in their membrane-bound state. The interaction of the helices with the bilayer membrane was also probed by a Monte Carlo simulation protocol to determine lowest-energy orientations. Our results are consistent with a situation in which helices α4 and α5 insert into the membrane as a helical hairpin in an antiparallel manner, while the other helices lie on the membrane surface like the ribs of an umbrella (the “umbrella model”). Our results also support the suggestion that α7 may serve as a binding sensor to initiate the structural rearrangement of the pore-forming domain.

Characteristic temperatures of folding of a small peptide

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the folding of a small peptide is a multistage process associated with two characteristic temperatures, the collapse temperature Tθ and the folding temperature Tƒ. Our results give supporting evidence for the energy landscape picture and funnel concept. These ideas were previously developed in the context of studies of simplified protein models, and here are checked in an all-atom Monte Carlo simulation.

Cooperative enhancement of specificity in a lattice of T cell receptors

Two of the most important models to account for the specificity and sensitivity of the T cell receptor (TCR) are the kinetic proofreading and serial ligation models. However, although kinetic proofreading provides a means for individual TCRs to measure accurately the length of time they are engaged and signal appropriately, the stochastic nature of ligand dissociation means the kinetic proofreading model implies that at high concentrations the response of the cell will be relatively nonspecific. Recent ligand experiments have revealed the phenomenon of both negative and positive crosstalk among neighboring TCRs. By using a Monte Carlo simulation of a lattice of TCRs, we integrate receptor crosstalk with the kinetic proofreading and serial ligation models and discover that receptor cooperativity can enhance T cell specificity significantly at a very modest cost to the sensitivity of the response.

Modeling and optimization of populations subject to time-dependent mutation.

It has become clear that many organisms possess the ability to regulate their mutation rate in response to environmental conditions. So the question of finding an optimal mutation rate must be replaced by that of finding an optimal mutation schedule. We show that this task cannot be accomplished with standard population-dynamic models. We then develop a "hybrid" model for populations experiencing time-dependent mutation that treats population growth as deterministic but the time of first appearance of new variants as stochastic. We show that the hybrid model agrees well with a Monte Carlo simulation. From this model, we derive a deterministic approximation, a "threshold" model, that is similar to standard population dynamic models but differs in the initial rate of generation of new mutants. We use these techniques to model antibody affinity maturation by somatic hypermutation. We had previously shown that the optimal mutation schedule for the deterministic threshold model is phasic, with periods of mutation between intervals of mutation-free growth. To establish the validity of this schedule, we now show that the phasic schedule that optimizes the deterministic threshold model significantly improves upon the best constant-rate schedule for the hybrid and Monte Carlo models.

Numerical test of the Cardy-Jacobsen conjecture in the site-diluted Potts model in three dimensions

We present a microcanonical Monte Carlo simulation of the site-diluted Potts model in three dimensions with eight internal states, partly carried out on the citizen supercomputer Ibercivis. Upon dilution, the pure model’s first-order transition becomes of the second order at a tricritical point. We compute accurately the critical exponents at the tricritical point. As expected from the Cardy-Jacobsen conjecture, they are compatible with their random field Ising model counterpart. The conclusion is further reinforced by comparison with older data for the Potts model with four states.

Análise da dinâmica e quantificação metabólica de imagens de medicina nuclear na modalidade PET/CT.

A presença da Medicina Nuclear como modalidade de obtenção de imagens médicas é um dos principais procedimentos utilizados hoje nos centros de saúde, tendo como grande vantagem a capacidade de analisar o comportamento metabólico do paciente, traduzindo-se em diagnósticos precoces. Entretanto, sabe-se que a quantificação em Medicina Nuclear é dificultada por diversos fatores, entre os quais estão a correção de atenuação, espalhamento, algoritmos de reconstrução e modelos assumidos. Neste contexto, o principal objetivo deste projeto foi melhorar a acurácia e a precisão na análise de imagens de PET/CT via processos realísticos e bem controlados. Para esse fim, foi proposta a elaboração de uma estrutura modular, a qual está composta por um conjunto de passos consecutivamente interligados começando com a simulação de phantoms antropomórficos 3D para posteriormente gerar as projeções realísticas PET/CT usando a plataforma GATE (com simulação de Monte Carlo), em seguida é aplicada uma etapa de reconstrução de imagens 3D, na sequência as imagens são filtradas (por meio do filtro de Anscombe/Wiener para a redução de ruído Poisson caraterístico deste tipo de imagens) e, segmentadas (baseados na teoria Fuzzy Connectedness). Uma vez definida a região de interesse (ROI) foram produzidas as Curvas de Atividade de Entrada e Resultante requeridas no processo de análise da dinâmica de compartimentos com o qual foi obtida a quantificação do metabolismo do órgão ou estrutura de estudo. Finalmente, de uma maneira semelhante imagens PET/CT reais fornecidas pelo Instituto do Coração (InCor) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP) foram analisadas. Portanto, concluiu-se que a etapa de filtragem tridimensional usando o filtro Anscombe/Wiener foi relevante e de alto impacto no processo de quantificação metabólica e em outras etapas importantes do projeto em geral.

Background Measurement Techniques and Sensitivity Studies for the SNO+ Neutrinoless Double Beta Decay Search

The control of radioactive backgrounds will be key in the search for neutrinoless double beta decay at the SNO+ experiment. Several aspects of the SNO+ back- grounds have been studied. The SNO+ tellurium purification process may require ultra low background ethanol as a reagent. A low background assay technique for ethanol was developed and used to identify a source of ethanol with measured 238U and 232Th concentrations below 2.8 10^-13 g/g and 10^-14 g/g respectively. It was also determined that at least 99:997% of the ethanol can be removed from the purified tellurium using forced air ow in order to reduce 14C contamination. In addition, a quality-control technique using an oxygen sensor was studied to monitor 222Rn contamination due to air leaking into the SNO+ scintillator during transport. The expected sensitivity of the technique is 0.1mBq/L or better depending on the oxygen sensor used. Finally, the dependence of SNO+ neutrinoless double beta decay sensitivity on internal background levels was studied using Monte Carlo simulation. The half-life limit to neutrinoless double beta decay of 130Te after 3 years of operation was found to be 4.8 1025 years under default conditions.

The burden of major depression avoidable by longer-term treatment strategies

Background: Major depression is the largest single cause of nonfatal disease burden in Australia. Effective drug and psychological treatments exist, yet are underused. Objective: To quantify the burden of disease currently averted in people seeking care for major depression and the amount of disease burden that could be averted in these people under optimal episodic and maintenance treatment strategies. Design: Modeling impact of current and optimal treatment strategies based on secondary analysis of mental health survey data, studies of the natural history of major depression, and meta-analyses of effectiveness data. Monte Carlo simulation of uncertainty in the model. Setting: The cohort of Australian adults experiencing an episode of major depression in 2000 are modeled through "what if" scenarios of no treatment, current treatment, and optimal treatment strategies with cognitive behavioral therapy or antidepressant drug treatment. Main Outcome Measure: Disability-Adjusted Life Year. Results: Current episodic treatment averts 9% (95% uncertainty interval, 6%-12%) of the disease burden of major depression in Australian adults. Optimal episodic treatment with cognitive behavioral therapy could avert 28% (95% uncertainty interval, 19%-39%) of this disease burden, and with drugs 24% (95% uncertainty interval, 19%-30%) could be averted. During the 5 years after an episode of major depression, current episodic treatment patterns would avert 13% (95% uncertainty interval, 10%-17%) of Disability-Adjusted Life Years, whereas maintenance drug treatment could avert 50% (95% uncertainty interval, 40%-60%) and maintenance cognitive behavioral therapy could avert 52% (95% uncertainty interval, 42%-64%), even if adherence of around 60% is taken into account. Conclusions: Longer-term maintenance drug or psychological treatment strategies are required to make significant inroads into the large disease burden associated with major depression in the Australian population.

Colorectal cancer screening in Australia: an economic evaluation of a potential biennial screening program using faecal occult blood tests

Objective: To evaluate whether the introduction of a national, co-ordinated screening program using the faecal occult blood test represents 'value-for-money' from the perspective of the Australian Government as third-party funder. Methods: The annual equivalent costs and consequences of a biennial screening program in 'steady-state' operation were estimated for the Australian population using 1996 as the reference year. Disability-adjusted life years (DALYs) and the years of life lost (YLLs) averted, and the health service costs were modelled, based on the epidemiology and the costs of colorectal cancer in Australia together with the mortality reduction achieved in randomised controlled trials. Uncertainty in the model was examined using Monte Carlo simulation methods. Results: We estimate a minimum or 'base program' of screening those aged 55 to 69 years could avert 250 deaths per annum (95% uncertainty interval 99-400), at a gross cost of $A55 million (95% UI $A46 million to $A96 million) and a gross incremental cost-effectiveness ratio of $A17,000/DALY (95% UI $A13,000/DALY to $A52,000/DALY). Extending the program to include 70 to 74-year-olds is a more effective option (cheaper and higher health gain) than including the 50 to 54-year-olds. Conclusions: The findings of this study support the case for a national program directed at the 55 to 69-year-old age group with extension to 70 to 74-year-olds if there are sufficient resources. The pilot tests recently announced in Australia provide an important opportunity to consider the age range for screening and the sources of uncertainty, identified in the modelled evaluation, to assist decisions on implementing a full national program.

Prediction of high-pressure adsorption equilibrium of supercritical gases using density functional theory

In this paper, we present the results of the prediction of the high-pressure adsorption equilibrium of supercritical. gases (Ar, N-2, CH4, and CO2) on various activated carbons (BPL, PCB, and Norit R1 extra) at various temperatures using a density-functional-theory-based finite wall thickness (FWT) model. Pore size distribution results of the carbons are taken from our recent previous work 1,2 using this approach for characterization. To validate the model, isotherms calculated from the density functional theory (DFT) approach are comprehensively verified against those determined by grand canonical Monte Carlo (GCMC) simulation, before the theoretical adsorption isotherms of these investigated carbons calculated by the model are compared with the experimental adsorption measurements of the carbons. We illustrate the accuracy and consistency of the FWT model for the prediction of adsorption isotherms of the all investigated gases. The pore network connectivity problem occurring in the examined carbons is also discussed, and on the basis of the success of the predictions assuming a similar pore size distribution for accessible and inaccessible regions, it is suggested that this is largely related to the disordered nature of the carbon.

Process systems modelling and applications in granulation: A review

Granulation is one of the fundamental operations in particulate processing and has a very ancient history and widespread use. Much fundamental particle science has occurred in the last two decades to help understand the underlying phenomena. Yet, until recently the development of granulation systems was mostly based on popular practice. The use of process systems approaches to the integrated understanding of these operations is providing improved insight into the complex nature of the processes. Improved mathematical representations, new solution techniques and the application of the models to industrial processes are yielding better designs, improved optimisation and tighter control of these systems. The parallel development of advanced instrumentation and the use of inferential approaches provide real-time access to system parameters necessary for improvements in operation. The use of advanced models to help develop real-time plant diagnostic systems provides further evidence of the utility of process system approaches to granulation processes. This paper highlights some of those aspects of granulation. (c) 2005 Elsevier Ltd. All rights reserved.

Modelling nucleation in wet granulation

Nucleation is the first stage in any granulation process where binder liquid first comes into contact with the powder. This paper investigates the nucleation process where binder liquid is added to a fine powder with a spray nozzle. The dimensionless spray flux approach of Hapgood et al. (Powder Technol. 141 (2004) 20) is extended to account for nonuniform spray patterns and allow for overlap of nuclei granules rather than spray drops. A dimensionless nuclei distribution function which describes the effects of the design and operating parameters of the nucleation process (binder spray characteristics, the nucleation area ratio between droplets and nuclei and the powder bed velocity) on the fractional surface area coverage of nuclei on a moving powder bed is developed. From this starting point, a Monte Carlo nucleation model that simulates full nuclei size distributions as a function of the design and operating parameters that were implemented in the dimensionless nuclei distribution function is developed. The nucleation model was then used to investigate the effects of the design and operating parameters on the formed nuclei size distributions and to correlate these effects to changes of the dimensionless nuclei distribution function. Model simulations also showed that it is possible to predict nuclei size distributions beyond the drop controlled nucleation regime in Hapgood's nucleation regime map. Qualitative comparison of model simulations and experimental nucleation data showed similar shapes of the nuclei size distributions. In its current form, the nucleation model can replace the nucleation term in one-dimensional population balance models describing wet granulation processes. Implementation of more sophisticated nucleation kinetics can make the model applicable to multi-dimensional population balance models.

Application of density functional theory to equilibrium adsorption of argon and nitrogen on amorphous silica surface

We present a new version of non-local density functional theory (NL-DFT) adapted to description of vapor adsorption isotherms on amorphous materials like non-porous silica. The novel feature of this approach is that it accounts for the roughness of adsorbent surface. The solid–fluid interaction is described in the same framework as in the case of fluid–fluid interactions, using the Weeks–Chandler–Andersen (WCA) scheme and the Carnahan–Starling (CS) equation for attractive and repulsive parts of the Helmholtz free energy, respectively. Application to nitrogen and argon adsorption isotherms on non-porous silica LiChrospher Si-1000 at their boiling points, recently published by Jaroniec and co-workers, has shown an excellent correlative ability of our approach over the complete range of pressures, which suggests that the surface roughness is mostly the reason for the observed behavior of adsorption isotherms. From the analysis of these data, we found that in the case of nitrogen adsorption short-range interactions between oxygen atoms on the silica surface and quadrupole of nitrogen molecules play an important role. The approach presented in this paper may be further used in quantitative analysis of adsorption and desorption isotherms in cylindrical pores such as MCM-41 and carbon nanotubes.

Effects of potential models in the vapor-liquid equilibria and adsorption of simple gases on graphitized thermal carbon black

In this paper, we investigate the effects of various potential models in the description of vapor–liquid equilibria (VLE) and adsorption of simple gases on highly graphitized thermal carbon black. It is found that some potential models proposed in the literature are not suitable for the description of VLE (saturated gas and liquid densities and the vapor pressure with temperature). Simple gases, such as neon, argon, krypton, xenon, nitrogen, and methane are studied in this paper. To describe the isotherms on graphitized thermal carbon black correctly, the surface mediation damping factor introduced in our recent publication should be used to calculate correctly the fluid–fluid interaction energy between particles close to the surface. It is found that the damping constant for the noble gases family is linearly dependent on the polarizability, suggesting that the electric field of the graphite surface has a direct induction effect on the induced dipole of these molecules. As a result of this polarization by the graphite surface, the fluid–fluid interaction energy is reduced whenever two particles are near the surface. In the case of methane, we found that the damping constant is less than that of a noble gas having the similar polarizability, while in the case of nitrogen the damping factor is much greater and this could most likely be due to the quadrupolar nature of nitrogen.

Modeling nitrogen adsorption in spherical pores of siliceous materials by density functional theory

Adsorption of nitrogen in spherical pores of FDU-1 silica at 77 K is considered by means of a nonlocal density functional theory (NLDFT) accounting for a disordered structure of pore walls. Pore size distribution analysis of various FDU-1 samples subject to different temperatures of calcination revealed three distinct groups of pores. The principal group of pores is identified as ordered spherical mesopores connected with each other by smaller interconnecting pores and irregular micropores present in the mesopore walls. To account for the entrances (connecting pores) into spherical mesopores, a concept of solid mass distribution with respect to the apparent density was introduced. It is shown that the introduction of the aforementioned distribution was sufficient to quantitatively describe experimental adsorption isotherms over the entire range of relative pressures spanning six decades.