Quantum fluctuations and life

There have been many claims that quantum mechanics plays a key role in the origin and/or operation of biological organisms, beyond merely providing the basis for the shapes and sizes of biological molecules and their chemical affinities. These range from the suggestion by Schrodinger that quantum fluctuations produce mutations, to the conjecture by Hameroff and Penrose that quantum coherence in microtubules is linked to consciousness. I review some of these claims in this paper, and discuss the serious problem of decoherence. I advance some further conjectures about quantum information processing in bio-systems. Some possible experiments are suggested.Comment: 10 pages, no figures, conference pape

Fault-tolerant complexes

Fault-tolerant complexes describe surface-code fault-tolerant protocols from a single geometric object. We first introduce fusion complexes that define a general family of fusion-based quantum computing (FBQC) fault-tolerant quantum protocols based on surface codes. We show that any 3-dimensional cell complex where each edge has four incident faces gives a valid fusion complex. This construction enables an automated search for fault tolerance schemes, allowing us to identify 627 examples within a moderate search time. We implement this using the open-source software tool Gavrog and present threshold results for a variety of schemes, finding fusion networks with higher erasure and Pauli thresholds than those existing in the literature. We then define more general structures we call fault-tolerant complexes that provide a homological description of fault tolerance from a large family of low-level error models, which include circuit-based computation, floquet-based computation, and FBQC with multi-qubit measurements. This extends the applicability of homological descriptions of fault tolerance, and enables the generation of many new schemes which have not been previously identified. We also define families of fault-tolerant complexes for color codes and 3d single-shot subsystem codes, which enables similar constructive methods, and we present several new examples of each

A novel graph-based method for targeted ligand-protein fitting

A thesis submitted to the Faculty of Creative Arts, Technologies & Science, University of Bedfordshire, in partial & fulfilment of the requirements for the degree of Master of Philosophy.The determination of protein binding sites and ligand -protein fitting are key to understanding the functionality of proteins, from revealing which ligand classes can bind or the optimal ligand for a given protein, such as protein/ drug interactions. There is a need for novel generic computational approaches for representation of protein-ligand interactions and the subsequent prediction of hitherto unknown interactions in proteins where the ligand binding sites are experimentally uncharacterised. The TMSite algorithms read in existing PDB structural data and isolate binding sites regions and identifies conserved features in functionally related proteins (proteins that bind the same ligand). The Boundary Cubes method for surface representation was applied to the modified PDB file allowing the creation of graphs for proteins and ligands that could be compared and caused no loss of geometric data. A method is included for describing binding site features of individual ligands conserved in terms of spatial relationships allowed identification of 3D motifs, named fingerprints, which could be searched for in other protein structures. This method combine with a modification of the pocket algorithm allows reduced search areas for graph matching. The methods allow isolation of the binding site from a complexed protein PDB file, identification of conserved features among the binding sites of individual ligand types, and search for these features in sequence data. In terms of spatial conservation create a fingerprint ofthe binding site that can be sought in other proteins of/mown structure, identifYing putative binding sites. The approach offers a novel and generic method for the identification of putative ligand binding sites for proteins for which there is no prior detailed structural characterisation of protein/ ligand interactions. It is unique in being able to convert PDB data into graphs, ready for comparison and thus fitting of ligand to protein with consideration of chemical charge and in the future other chemica! properties

On Two Families of Multiset Tree Automata

The relation between the membrane structures of P systems and an extension of tree automata which introduces multisets in the transition function has been proposed in previous works. Here we propose two features of tree automata which have been previously studied (namely, reversibility and local testability) in order to extend them to multiset tree automata. The characterization of these families will introduce a new characterization of membrane structures defined by the set of rules used for membrane creation and deletion

Measuring telomere length and telomere dynamics in evolutionary biology and ecology

Telomeres play a fundamental role in the protection of chromosomal DNA and in the regulation of cellular senescence. Recent work in human epidemiology and evolutionary ecology suggests adult telomere length (TL) may reflect past physiological stress and predict subsequent morbidity and mortality, independent of chronological age. Several different methods have been developed to measure TL, each offering its own technical challenges. The aim of this review is to provide an overview of the advantages and drawbacks of each method for researchers, with a particular focus on issues that are likely to face ecologists and evolutionary biologists collecting samples in the field or in organisms that may never have been studied in this context before. We discuss the key issues to consider and wherever possible try to provide current consensus view regarding best practice with regard to sample collection and storage, DNA extraction and storage, and the five main methods currently available to measure TL. Decisions regarding which tissues to sample, how to store them, how to extract DNA, and which TL measurement method to use cannot be prescribed, and are dependent on the biological question addressed and the constraints imposed by the study system. What is essential for future studies of telomere dynamics in evolution and ecology is that researchers publish full details of their methods and the quality control thresholds they employ

A grammatical evolution approach to the automatic inference of P systems

P systems are a bio-inspired framework for defining parallel models of computation. Despite their relevance for both theoretical and application scenarios, the design and the identification of P systems remain tedious and demanding tasks, requiring considerable time and expertise. In this work, we try to address these problems by proposing an automated methodology based on Grammatical Evolution (GE)—an evolutionary computation technique—which does not require any domain knowledge. We consider a setting where observations of successive configurations of a P system are available, and we rely on GE for automatically inferring the P system, i.e., its ruleset. Such approach directly addresses the identification problem, but it can also be employed for automated design, requiring the designer to simply express the configurations of the P system rather than its full ruleset. We assess the practicability of the proposed method on six problems of various difficulties and evaluate its behavior in terms of inference capability and time consumption. Experimental results confirm our approach is a viable strategy for small problem sizes, where it achieves perfect inference in a few seconds without any human intervention. Moreover, we also obtain promising results for larger problem sizes in a human-aided context, paving the way for fully- or partially-automated design of P systems

Computational models in the age of large datasets.

Technological advances in experimental neuroscience are generating vast quantities of data, from the dynamics of single molecules to the structure and activity patterns of large networks of neurons. How do we make sense of these voluminous, complex, disparate and often incomplete data? How do we find general principles in the morass of detail? Computational models are invaluable and necessary in this task and yield insights that cannot otherwise be obtained. However, building and interpreting good computational models is a substantial challenge, especially so in the era of large datasets. Fitting detailed models to experimental data is difficult and often requires onerous assumptions, while more loosely constrained conceptual models that explore broad hypotheses and principles can yield more useful insights.Charles A King TrustThis is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.conb.2015.01.00

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 335)

This bibliography lists 143 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during March, 1990. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance