Algorithmic Models of Biochemical Dynamics

The paper presents the main ideas about MP grammars, a discrete formalism for describing and deducing dynamical systems, that combines ideas from formal language theory (P systems), recurrent equations, linear algebra and statistical regression. In this framework, some synthetic oscillators are presented which illustrate, in a simple manner, the expressive power of MP grammars in the analysis of interesting phenomena that are crucial in biochemical and biological contexts.

Emerging Exposure Risks and Ethics of the Nanotechnology Workplace

As the applications of nanotechnology continue to span various industries, the number of workers who may be in regular contact with nanomaterials correspondingly expand. The excitement associated with the promise of opportunities to create revolutionary advances in product development using nanotechnology must be moderated with the fact that there is a paucity of empirical data about the potential health effects of exposure to nanoparticles. This lack of exposure data hinders the development of nanotechnology health and safety guidelines (Murashov, 2009). Nanotechnology is science at the size of individual atoms and molecules. At that size scale, materials have different chemical and physical properties than those of the same materials in bulk. With the current state of knowledge in this field, there are unanswered questions about the impacts of nanomaterials and nanoproducts on human health and the environment. This paper reviews the state-of the-science, exposure assessment and mitigation, and potential macro ethical issues that must be considered to mitigate risk implications this emerging technology, nanotechnology.

Trends in Nanotechnology Knowledge Creation and Dissemination

This article explores trends in nanotechnology knowledge creation across scientific disciplines and technology domains, and helps to understand the dissemination of nanotechnology knowledge. In relation to intense global competition in nanotechnology, this study exhibits a forward-looking approach in characterizing nanotechnology research and development trajectories. This research adopts hybrid research methodology, including both quantitative and qualitative methods. The findings imply that nanotechnology knowledge creation and dissemination trends have appeared to bridge divergent disciplines, emphasizing the importance of collaborative research networks among scientists to co-create, share and disseminate nano-knowledge across groups, institutions and borders.

Nanotechnology and Microelectronics

For many centuries, the gross world product was flat. But as technology penetrated many economies, over time, the world economy has expanded. Technology will continue to shape the future of commerce, industry and culture with likes of nanotechnology and microelectronics directly or indirectly playing major roles in redesigning the global economic structures. These technologies will drive other industries and will be central to a new international economy where technology capability will determine national competitiveness. Technology-intensive firms will emerge and new innovations will evolve a new dawn in wealth creation. Nations that create or adopt and then diffuse these technologies will profit. Those that fail to use technology as a means to compete internationally will find it difficult to progress economically. This article provides insights on global technology diffusion, the drivers and impacts with specific focus on nanotechnology and microelectronics. It also discusses the science of these technologies along with the trends, realities and possibilities, and the barriers which must be overcome for higher global penetration rates.

Towards the Sixth Kondratieff Cycle of Nano Revolution

Nanotechnology is currently seen as a paradigm shift towards scientific revolution or ‘nano revolution. This article discusses the nano revolution within the global context. It is interesting to see that the governments around the world have formulated policies to manage the research and development (R&D) efforts and exploit the potential of nanotechnology to increase industry's ability in the global economy. The article analyses the successive waves of technological change based on Kuhn's model of scientific change and Schumpeter's model of Kondratieff cycles. As nanotechnology would have significant impacts on virtually every commercial sector, many countries commit to foster nanotechnology developments. This article will focus on nanotechnology framework policy recommendations. The policies and research activities of the most preeminent nations discussed in this article represent global research trend towards nano revolution in the next decades.

Citrate Stabilized Silver Nanoparticles

Citrate stabilized silver (Ag) colloidal solution were synthesized and characterized for crystallographic and surface properties by using transmission electron microscopy (TEM) and zeta potential measurement techniques. TEM investigation depicted the size of Ago ranges from 5 to 50 nm with smaller particles having single crystal structure while larger particles with structural defects (such as multiply twinned, high coalescence and Moire patterns). ?-potential measurement confirms the presence of Ag+ in nAg stock solution. The shift in ?-potential measurement by +25.1 mV in the filtered solution suggests the presence of Ag+ in Ago nanoparticles.

On the Internalisation, Intraplasmodial Carriage and Excretion of Metallic Nanoparticles in the Slime Mould, Physarum Polycephalum

The plasmodium of Physarum polycephalum is a large single cell visible with the naked eye. When inoculated on a substrate with attractants and repellents the plasmodium develops optimal networks of protoplasmic tubes which span sites of attractants (i.e. nutrients) yet avoid domains with a high nutrient concentration. It should therefore be possible to program the plasmodium towards deterministic adaptive transformation of internalised nano- and micro-scale materials. In laboratory experiments with magnetite nanoparticles and glass micro-spheres coated with silver metal the authors demonstrate that the plasmodium of P. polycephalum can propagate the nano-scale objects using a number of distinct mechanisms including endocytosis, transcytosis and dragging. The results of the authors’ experiments could be used in the development of novel techniques targeted towards the growth of metallised biological wires and hybrid nano- and micro-circuits.

Sequential Voronoi Diagram Calculations using Simple Chemical Reactions

In the authors’ recent paper (de Lacy Costello et al., 2010) the authors described the formation of complex tessellations of the plane arising from the various reactions of metal salts with potassium ferricyanide and ferrocyanide loaded gels. In addition to producing colourful tessellations these reactions are naturally computing generalised Voronoi diagrams of the plane. The reactions reported previously were capable of the calculation of three distinct Voronoi diagrams of the plane. As diffusion coupled with a chemical reaction is responsible for the calculation then this is achieved in parallel. Thus an increase in the complexity of the data input does not utilise additional computational resource. Additional benefits of these chemical reactions are that a permanent record of the Voronoi diagram calculation (in the form of precipitate free bisectors) is achieved, so there is no requirement for further processing to extract the calculation results. Previously it was assumed that the permanence of the results was also a potential drawback which limited reusability. This paper presents new data which shows that sequential Voronoi diagram calculations can be performed on the same chemical substrate. This is dependent on the reactivity of the original reagent and the cross reactivity of the secondary reagent with the primary product. The authors present the results from a number of binary combinations of metal salts on both potassium ferricyanide and potassium ferrocyanide substrates. The authors observe three distinct mechanisms whereby secondary sequential Voronoi diagrams can be calculated. In most cases the result was two interpenetrating permanent Voronoi diagrams. This is interesting from the perspective of mapping the capability of unconventional computing substrates. But also in the study of natural pattern formation per se.

Geometric Approaches to Gibbs Energy Landscapes and DNA Oligonucleotide Design

DNA codeword design has been a fundamental problem since the early days of DNA computing. The problem calls for finding large sets of single DNA strands that do not crosshybridize to themselves, to each other or to others' complements. Such strands represent so-called domains, particularly in the language of chemical reaction networks (CRNs). The problem has shown to be of interest in other areas as well, including DNA memories and phylogenetic analyses because of their error correction and prevention properties. In prior work, a theoretical framework to analyze this problem has been developed and natural and simple versions of Codeword Design have been shown to be NP-complete using any single reasonable metric that approximates the Gibbs energy, thus practically making it very difficult to find any general procedure for finding such maximal sets exactly and efficiently. In this framework, codeword design is partially reduced to finding large sets of strands maximally separated in DNA spaces and, therefore, the size of such sets depends on the geometry of these spaces. Here, the authors describe in detail a new general technique to embed them in Euclidean spaces in such a way that oligonucleotides with high (low, respectively) hybridization affinity are mapped to neighboring (remote, respectively) points in a geometric lattice. This embedding materializes long-held metaphors about codeword design in analogies with error-correcting code design in information theory in terms of sphere packing and leads to designs that are in some cases known to be provably nearly optimal for small oligonucleotide sizes, whenever the corresponding spherical codes in Euclidean spaces are known to be so. It also leads to upper and lower bounds on estimates of the size of optimal codes of size under 20-mers, as well as to a few infinite families of DNA strand lengths, based on estimates of the kissing (or contact) number for sphere codes in high-dimensional Euclidean spaces. Conversely, the authors show how solutions to DNA codeword design obtained by experimental or other means can also provide solutions to difficult spherical packing geometric problems via these approaches. Finally, the reduction suggests a tool to provide some insight into the approximate structure of the Gibbs energy landscapes, which play a primary role in the design and implementation of biomolecular programs.

Robust Computation through Percolation

This paper proposes a probabilistic framework for digital computation with lattices of nanoscale switches based on the mathematical phenomenon of percolation. With random connectivity, percolation gives rise to a sharp non-linearity in the probability of global connectivity as a function of the probability of local connectivity. This phenomenon is exploited to compute Boolean functions robustly in the presence of defects. It is shown that the margins, defined in terms of the steepness of the non-linearity, translate into the degree of defect tolerance. Achieving good margins entails a mapping problem. Given a target Boolean function, the problem is how to assign literals to regions of the lattice such that no diagonal paths of 1’s exist in any assignment that evaluates to 0. Assignments with such paths result in poor error margins due to stray, random connections that can form across the diagonal. A necessary and sufficient condition is formulated for a mapping strategy that preserves good margins: the top-to-bottom and left-to-right connectivity functions across the lattice must be dual functions. Based on lattice duality, an efficient algorithm to perform the mapping is proposed. The algorithm optimizes the lattice area while meeting prescribed worst-case margins. Its effectiveness is demonstrated on benchmark circuits.