RNA packaging motor: From structure to quantum mechanical modelling and sequential-stochastic mechanism

The bacteriophages of the Cystoviridae family package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate, i.e. the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum-chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work

Structural sizing considerations for large space structures

A number of missions for the space shuttle were proposed which involve placing large truss platforms on-orbit. These platforms range in size from tens of meters in span for reflector application to several thousand meters for solar power collector application. These proposed sizes and the operational requirements considered are unconventional in comparison to Earthbound structures and little information exists concerning efficient proportions of the structural elements forming the framework of the platforms. Such proportions are of major concern because they have a strong influence on the packaging efficiency and, thus, the transportation effectiveness of the shuttle. The present study is undertaken to: (1) identify efficient ranges of application of deployable and erectable platforms configured for shuttle transport to orbit, and (2) determine sensitivity to key parameters of minimum mass deployable and erectable platform designs

Effect of the green-emitting CaF2:Ce3+,Tb3+ phosphor particles’ size on color rendering index and color quality scale of the in-cup packaging multichip white LEDs

In this paper, we investigate the effect of the green-emitting CaF2:Ce (3+), Tb (3+) phosphor particle's size on the color rendering index (CRI) and the color quality scale (CQS) of the in-cup packaging multichip white LEDs (MCW-LEDs). For this purpose, 7000K and 8500K in-cup packaging MCW-LEDs is simulated by the commercial software Light Tools. Moreover, scattering process in the phosphor layers is investigated by using Mie Theory with Mat Lab software. Finally, the research results show that the green-emitting CaF2: Ce (3+), Tb (3+) phosphor's size crucially influences on the CRI and CQS. From that point of view, CaF2: Ce (3+), Tb (3+) can be proposed as a potential practical direction for manufacturing the in-cup packaging phosphor WLEDs.Web of Science13235134

Stability, Causality, and Passivity in Electrical Interconnect Models

Modern packaging design requires extensive signal integrity simulations in order to assess the electrical performance of the system. The feasibility of such simulations is granted only when accurate and efficient models are available for all system parts and components having a significant influence on the signals. Unfortunately, model derivation is still a challenging task, despite the extensive research that has been devoted to this topic. In fact, it is a common experience that modeling or simulation tasks sometimes fail, often without a clear understanding of the main reason. This paper presents the fundamental properties of causality, stability, and passivity that electrical interconnect models must satisfy in order to be physically consistent. All basic definitions are reviewed in time domain, Laplace domain, and frequency domain, and all significant interrelations between these properties are outlined. This background material is used to interpret several common situations where either model derivation or model use in a computer-aided design environment fails dramatically.We show that the root cause for these difficulties can always be traced back to the lack of stability, causality, or passivity in the data providing the structure characterization and/or in the model itsel

The integrated use of enterprise and system dynamics modelling techniques in support of business decisions

Enterprise modelling techniques support business process re-engineering by capturing existing processes and based on perceived outputs, support the design of future process models capable of meeting enterprise requirements. System dynamics modelling tools on the other hand are used extensively for policy analysis and modelling aspects of dynamics which impact on businesses. In this paper, the use of enterprise and system dynamics modelling techniques has been integrated to facilitate qualitative and quantitative reasoning about the structures and behaviours of processes and resource systems used by a Manufacturing Enterprise during the production of composite bearings. The case study testing reported has led to the specification of a new modelling methodology for analysing and managing dynamics and complexities in production systems. This methodology is based on a systematic transformation process, which synergises the use of a selection of public domain enterprise modelling, causal loop and continuous simulationmodelling techniques. The success of the modelling process defined relies on the creation of useful CIMOSA process models which are then converted to causal loops. The causal loop models are then structured and translated to equivalent dynamic simulation models using the proprietary continuous simulation modelling tool iThink

Co-doping red-emitting Sr2Si5N8:Eu2+ into yellow-emitting phosphor-packaging for enhancing the optical properties of the 8500 K remote-phosphor packaging wleds

In the last decades, WLEDs attract more and more consideration in both academic and industrial purposes because of its advantages such as fast response time, environment friendliness, small size, long lifetime, and high efficiency. In this research, by doping the red-emitting Sr2Si5N8:Eu2+ phosphor particles into yellow-emitting YAG:Ce phosphor-packaging, a new recommendation for enhancing the optical properties (color uniformity, color rendering index, and lumen output) of the 8500 K remote-phosphor packaging WLEDs is presented, investigated, and demonstrated. By using Mat Lab and Light Tools software based on Mie Theory, the obtained results show that the optical properties of the 8500 K remote-phosphor packaging WLEDs significantly depended on Sr2Si5N8:Eu2+ concentration. The results have provided a potential practical recommendation for manufacturing remote-phosphor W-LEDs.Web of Science1341034102

Transpiration and moisture evolution in packaged fresh horticultural produce and the role of integrated mathematical models: A review

Transpiration has various adverse effects on postharvest quality and the shelf-life of fresh fruit and vegetables (FFV). If not controlled, the water released through this process results in direct mass loss and moisture condensation inside packaged FFV. Condensation represents a threat to the product quality as water may accumulate on the product surface and/or packaging system, causing defects in external appearance and promoting growth of spoilage microorganisms. Thus, moisture regulation is extremely important for extending FFV shelf-life. This review focuses on transpiration phenomenon and moisture evolution in packaged fresh horticultural produce. It provides recent information on various moisture control strategies suitable for packaging of fresh horticultural produce. It also provides an evaluation on the role and application of integrative mathematical modelling in describing water relations of FFV for packaging design, as well as, an overview of models reported in literature

Packaging signals in single-stranded RNA viruses: nature’s alternative to a purely electrostatic assembly mechanism

The formation of a protective protein container is an essential step in the life-cycle of most viruses. In the case of single-stranded (ss)RNA viruses, this step occurs in parallel with genome packaging in a co-assembly process. Previously, it had been thought that this process can be explained entirely by electrostatics. Inspired by recent single-molecule fluorescence experiments that recapitulate the RNA packaging specificity seen in vivo for two model viruses, we present an alternative theory, which recognizes the important cooperative roles played by RNA–coat protein interactions, at sites we have termed packaging signals. The hypothesis is that multiple copies of packaging signals, repeated according to capsid symmetry, aid formation of the required capsid protein conformers at defined positions, resulting in significantly enhanced assembly efficiency. The precise mechanistic roles of packaging signal interactions may vary between viruses, as we have demonstrated for MS2 and STNV. We quantify the impact of packaging signals on capsid assembly efficiency using a dodecahedral model system, showing that heterogeneous affinity distributions of packaging signals for capsid protein out-compete those of homogeneous affinities. These insights pave the way to a new anti-viral therapy, reducing capsid assembly efficiency by targeting of the vital roles of the packaging signals, and opens up new avenues for the efficient construction of protein nanocontainers in bionanotechnology

Optimising economic, environmental, and social objectives: a goal-programming approach in the food sector

The business-decision environment is increasingly complicated by the emergence of competing economic, environmental, and social goals, a notion typified by the current pressures of global economic instability and climate-change targets. Trade-offs are often unclear and contributions by different actors and stakeholders in the supply chain may be unequal but, due to the interdependencies between businesses and stakeholders in relation to total environmental or social impact, a whole chain, simultaneous, and strategic approach is required. After a review of relevant literature and the identification of knowledge gaps, the author introduces and illustrates the use of goal programming as a technique that could facilitate this approach and uses real case evidence for alternative food supply chain strategies, at local, regional, and national levels. It is shown that the method can simplify a complex simultaneous decision situation into a useful and constructive decision and planning framework. Results show how a priori beliefs may be challenged and how operational and resource efficiency could be improved through the use of such a model, which enables a broad stakeholder appreciation and the opportunity to explore and test new environmental or social challenges