Temporal Correlations and Persistence in the Kinetic Ising Model: the Role of Temperature

We study the statistical properties of the sum $S_t=\int_{0}^{t}dt' \sigma_{t'}$, that is the difference of time spent positive or negative by the spin $\sigma_{t}$, located at a given site of a $D$-dimensional Ising model evolving under Glauber dynamics from a random initial configuration. We investigate the distribution of $S_{t}$ and the first-passage statistics (persistence) of this quantity. We discuss successively the three regimes of high temperature ($T>T_{c}$), criticality ($T=T_c$), and low temperature ($T<T_{c}$). We discuss in particular the question of the temperature dependence of the persistence exponent $\theta$, as well as that of the spectrum of exponents $\theta(x)$, in the low temperature phase. The probability that the temporal mean $S_t/t$ was always larger than the equilibrium magnetization is found to decay as $t^{-\theta-\frac12}$. This yields a numerical determination of the persistence exponent $\theta$ in the whole low temperature phase, in two dimensions, and above the roughening transition, in the low-temperature phase of the three-dimensional Ising model.Comment: 21 pages, 11 PostScript figures included (1 color figure

When the path is never shortest: a reality check on shortest path biocomputation

Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems such as route optimisation and labyrinth navigation, but their outputs are typically difficult to reproduce and somewhat abstract in nature, suggesting that both experimental design and analysis in the field require standardising. This chapter details laboratory experimental data which probe the path finding process in two single-celled protistic model organisms, Physarum polycephalum and Paramecium caudatum, comprising a shortest path problem and labyrinth navigation, respectively. The results presented illustrate several of the key difficulties that are encountered in categorising biological behaviours in the language of computing, including biological variability, non-halting operations and adverse reactions to experimental stimuli. It is concluded that neither organism examined are able to efficiently or reproducibly solve shortest path problems in the specific experimental conditions that were tested. Data presented are contextualised with biological theory and design principles for maximising the usefulness of experimental biocomputer prototypes.Comment: To appear in: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

Geometric quantum computation using fictitious spin- 1/2 subspaces of strongly dipolar coupled nuclear spins

Geometric phases have been used in NMR, to implement controlled phase shift gates for quantum information processing, only in weakly coupled systems in which the individual spins can be identified as qubits. In this work, we implement controlled phase shift gates in strongly coupled systems, by using non-adiabatic geometric phases, obtained by evolving the magnetization of fictitious spin-1/2 subspaces, over a closed loop on the Bloch sphere. The dynamical phase accumulated during the evolution of the subspaces, is refocused by a spin echo pulse sequence and by setting the delay of transition selective pulses such that the evolution under the homonuclear coupling makes a complete $2\pi$ rotation. A detailed theoretical explanation of non-adiabatic geometric phases in NMR is given, by using single transition operators. Controlled phase shift gates, two qubit Deutsch-Jozsa algorithm and parity algorithm in a qubit-qutrit system have been implemented in various strongly dipolar coupled systems obtained by orienting the molecules in liquid crystal media.Comment: 37 pages, 17 figure

Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation.

Aim: To determine whether dynamic DNA methylation changes in the human placenta can be used to predict gestational age. Materials & methods: Publicly available placental DNA methylation data from 12 studies, together with our own dataset, using Illumina Infinium Human Methylation BeadChip arrays. Results & conclusion: We developed an accurate tool for predicting gestational age of placentas using 62 CpG sites. There was a higher predicted gestational age for placentas from early onset preeclampsia cases, but not term preeclampsia, compared with their chronological age. Therefore, early onset preeclampsia is associated with placental aging. Gestational age acceleration prediction from DNA methylation array data may provide insight into the molecular mechanisms of pregnancy disorders.Benjamin T Mayne, Shalem Y Leemaqz, Alicia K Smith, James Breen, Claire T Roberts, Tina Bianco-Miott

Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans

The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analyzed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes), followed by the heart (375 genes), kidney (224 genes), colon (218 genes), and thyroid (163 genes). More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs, and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.Benjamin T. Mayne, Tina Bianco-Miotto, Sam Buckberry, James Breen, Vicki Clifton, Cheryl Shoubridge and Claire T. Robert

Toxicity and Applications of Internalised Magnetite Nanoparticles Within Live Paramecium caudatum Cells

© 2017, The Author(s). The nanotechnology revolution has allowed us to speculate on the possibility of hybridising nanoscale materials with live substrates, yet significant doubt still remains pertaining to the effects of nanomaterials on biological matter. In this investigation, we cultivate the ciliated protistic pond-dwelling microorganism Paramecium caudatum in the presence of excessive quantities of magnetite nanoparticles in order to deduce potential beneficial applications for this technique, as well as observe any deleterious effects on the organisms’ health. Our findings indicate that this variety of nanoparticle is well-tolerated by P. caudatum cells, who were observed to consume them in quantities exceeding 5–12% of their body volume: cultivation in the presence of magnetite nanoparticles does not alter P. caudatum cell volume, swimming speed, growth rate or peak colony density and cultures may persist in nanoparticle-contaminated media for many weeks. We demonstrate that P. caudatum cells ingest starch-coated magnetite nanoparticles which facilitates their being magnetically immobilised whilst maintaining apparently normal ciliary dynamics, thus demonstrating that nanoparticle biohybridisation is a viable alternative to conventional forms of ciliate quieting. Ingested magnetite nanoparticle deposits appear to aggregate, suggesting that (a) the process of being internalised concentrates and may therefore detoxify (i.e. render less reactive) nanomaterial suspensions in aquatic environments, and (b) P. caudatum is a candidate organism for programmable nanomaterial manipulation and delivery

Cellular automata modelling of slime mould actin network signalling

© 2016, The Author(s). Actin is a cytoskeletal protein which forms dense, highly interconnected networks within eukaryotic cells. A growing body of evidence suggests that actin-mediated intra- and extracellular signalling is instrumental in facilitating organism-level emergent behaviour patterns which, crucially, may be characterised as natural expressions of computation. We use excitable cellular automata modelling to simulate signal transmission through cell arrays whose topology was extracted from images of Watershed transformation-derived actin network reconstructions; the actin networks sampled were from laboratory experimental observations of a model organism, slime mould Physarum polycephalum. Our results indicate that actin networks support directional transmission of generalised energetic phenomena, the amplification and trans-network speed of which of which is proportional to network density (whose primary determinant is the anatomical location of the network sampled). Furthermore, this model also suggests the ability of such networks for supporting signal-signal interactions which may be characterised as Boolean logical operations, thus indicating that a cell’s actin network may function as a nanoscale data transmission and processing network. We conclude by discussing the role of the cytoskeleton in facilitating intracellular computing, how computation can be implemented in such a network and practical considerations for designing ‘useful’ actin circuitry