Collective transport in the discrete Frenkel-Kontorova model

Through multiscale analysis of the adjoint Fokker-Planck equation, strict bounds are derived for the center of mass diffusivity of an overdamped harmonic chain in a periodic potential, often known as the discrete Frenkel-Kontorova model. Significantly, it is shown that the free energy barrier is a lower bound to the true finite temperature migration barrier for this general and popular system. Numerical simulation confirms the analysis, whilst effective migration potentials implied by the bounds are employed to give a surprisingly accurate prediction of the non-linear response.Comment: 7 pages, 3 figures, submitte

The phonon drag force acting on a mobile crystal defect: full treatment of discreteness and non-linearity

Phonon scattering calculations predict the drag force acting on defects and dislocations rises linearly with temperature, in direct contradiction with molecular dynamics simulations that often finds the drag force to be independent of temperature. Using the Mori-Zwanzig projection technique, with no recourse to elasticity or scattering theories, we derive a general Langevin equation for a crystal defect, with full treatment of discreteness and non-linearity in the defect core. We obtain an analytical expression for the drag force that is evaluated in molecular statics and molecular dynamics, extracting the force on a defect directly from the inter-atomic forces. Our results show that a temperature independent drag force arises because vibrations in a discrete crystal are never independent of the defect motion, an implicit assumption in any phonon-based approach. This effect remains even when the Peierls barrier is effectively zero, invalidating qualitative explanations involving the radiation of phonons. We apply our methods to an interstitial defect in tungsten and solitons in the Frenkel-Kontorova model, finding very good agreement with trajectory-based estimations of the thermal drag force.Comment: 20 pages, 8 figure

Imperfect identity

Questions of identity over time are often hard to answer. A long tradition has it that such questions are somehow soft: they have no unique, determinate answer, and disagreements about them are merely verbal. I argue that this claim is not the truism it is taken to be. Depending on how it is understood, it turns out either to be false or to presuppose a highly contentious metaphysical claim

Theory and Simulation of the diffusion of kinks on dislocations in bcc metals

Isolated kinks on thermally fluctuating (1/2) screw, edge and (1/2) edge dislocations in bcc iron are simulated under zero stress conditions using molecular dynamics (MD). Kinks are seen to perform stochastic motion in a potential landscape that depends on the dislocation character and geometry, and their motion provides fresh insight into the coupling of dislocations to a heat bath. The kink formation energy, migration barrier and friction parameter are deduced from the simulations. A discrete Frenkel-Kontorova-Langevin (FKL) model is able to reproduce the coarse grained data from MD at a fraction of the computational cost, without assuming an a priori temperature dependence beyond the fluctuation-dissipation theorem. Analytic results reveal that discreteness effects play an essential r\^ole in thermally activated dislocation glide, revealing the existence of a crucial intermediate length scale between molecular and dislocation dynamics. The model is used to investigate dislocation motion under the vanishingly small stress levels found in the evolution of dislocation microstructures in irradiated materials

Against the complex versus simple distinction

This paper examines three proposals on the difference between complex and simple views about personal identity: Parfit’s original introduction of the distinction, Gasser and Stefan’s definition and Noonan’s recent proposal. I argue that the first two classify the paradigm cases of simplicity as complex, while Noonan’s proposal makes simplicity and complexity turn on features whose relevance for the distinction is questionable. Given these difficulties, I examine why we should be interested in whether a position is complex or simple. I describe two purposes of having a distinction, and show that extant accounts of the complex vs. simple distinction fail to serve these. I argue that unless we find a satisfying account of the difference between complex and simple positions, we should not frame discourses on personal identity in these terms.Publisher PDFPeer reviewe

Evidence for intron length conservation in a set of mammalian genes associated with embryonic development

<p>Abstract</p> <p>Background</p> <p>We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals.</p> <p>Results</p> <p>Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns.</p> <p>Conclusions</p> <p>Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.</p

Can discrete time make continuous space look discrete?

Van Bendegem has recently offered an argument to the effect that, if time is discrete, then there should exist a correspondence between the motions of massive bodies and a discrete geometry. On this basis, he concludes that, even if space is continuous, it should nonetheless appear discrete. This paper examines the two possible ways of making sense of that correspondence, and shows that in neither case van Bendegem's conclusion logically follows

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Background: Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results: Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion: We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution

Lived religion: Rethinking human nature in a neoliberal age

This article considers the relationship between philosophy of religion and an approach to the study of religion, which prioritises the experience of lived religion. Considering how individuals and communities live out their faith challenges some of the assumptions of analytic philosophers of religion regarding the position the philosopher should adopt when approaching the investigation of religion. If philosophy is understood principally as a means for analysing belief, it will have little space for an engagement with what it feels like to live out one’s faith