Thermally-activated Non-Schmid Glide of Screw Dislocations in W using Atomistically-informed Kinetic Monte Carlo Simulations

Thermally-activated \small{\nicefrac{1}{2}} screw dislocation motion is the controlling plastic mechanism at low temperatures in body-centered cubic (bcc) crystals. Motion proceeds by the nucleation and propagation of atomic-sized kink pairs susceptible of being studied using molecular dynamics (MD). However, MD's natural inability to properly sample thermally-activated processes as well as to capture $\{110\}$ screw dislocation glide calls for the development of other methods capable of overcoming these limitations. Here we develop a kinetic Monte Carlo (kMC) approach to study single screw dislocation dynamics from room temperature to $0.5T_m$ and at stresses $0<\sigma<0.9\sigma_P$, where $T_m$ and $\sigma_P$ are the melting point and the Peierls stress. The method is entirely parameterized with atomistic simulations using an embedded atom potential for tungsten. To increase the physical fidelity of our simulations, we calculate the deviations from Schmid's law prescribed by the interatomic potential used and we study single dislocation kinetics using both projections. We calculate dislocation velocities as a function of stress, temperature, and dislocation line length. We find that considering non-Schmid effects has a strong influence on both the magnitude of the velocities and the trajectories followed by the dislocation. We finish by condensing all the calculated data into effective stress and temperature dependent mobilities to be used in more homogenized numerical methods

LINK and the dynamics of utterance interpretation.

The operation allows the derivation of inferential units as the result of syntactic processing. The same operation derives structure across a diffuse range of data; the differences between these are attributable to lexical information and the dynamics of the process. The thesis examines a range of data where clauses depend on some element in the main clause for interpretation. These are assigned structure as LINK trees in the framework of Labelled Deductive Systems for Natural Language outlined in Kempson, Meyer-Viol & Gabbay, (Dynamic Syntax: the Deductive Flow of Natural Language, in prep.). I describe the approach to utterance interpretation this proposes: linguistic structure is built incrementally according to lexically encoded procedural instructions and rules of construction constrained by pragmatic principles. This allows a perspective where problems previously divided between syntax, semantics and pragmatics can be addressed in a more unified manner. 1 outline the operation as it has been developed for relative clauses. This allows several trees to be built for the same utterance which are connected by a having a node description in common. I argue that this operation can be extended to cover the following data: extraposed relative clauses, reduced relative clauses, adjunct predicates and parenthetical constituents. To this end I introduce type (p) into the framework, which allows the representation of non-tensed propositions and I modify the operation to allow the creation of trees from discontinuous input. I develop context-dependent lexical rules to capture the difference between modifying and predicative uses of lexical items. The interaction of processing tasks, compilation and lexical information determines the precise nature of the structures which are built. The update procedure I develop allows a uniform characterisation of the way structure is derived across different contexts, shedding new light on the dynamics of building interpretation

Future Contingents and the Logic of Temporal Omniscience

At least since Aristotle’s famous 'sea-battle' passages in On Interpretation 9, some substantial minority of philosophers has been attracted to the doctrine of the open future--the doctrine that future contingent statements are not true. But, prima facie, such views seem inconsistent with the following intuition: if something has happened, then (looking back) it was the case that it would happen. How can it be that, looking forwards, it isn’t true that there will be a sea battle, while also being true that, looking backwards, it was the case that there would be a sea battle? This tension forms, in large part, what might be called the problem of future contingents. A dominant trend in temporal logic and semantic theorizing about future contingents seeks to validate both intuitions. Theorists in this tradition--including some interpretations of Aristotle, but paradigmatically, Thomason (1970), as well as more recent developments in Belnap, et. al (2001) and MacFarlane (2003, 2014)--have argued that the apparent tension between the intuitions is in fact merely apparent. In short, such theorists seek to maintain both of the following two theses: (i) the open future: Future contingents are not true, and (ii) retro-closure: From the fact that something is true, it follows that it was the case that it would be true. It is well-known that reflection on the problem of future contingents has in many ways been inspired by importantly parallel issues regarding divine foreknowledge and indeterminism. In this paper, we take up this perspective, and ask what accepting both the open future and retro-closure predicts about omniscience. When we theorize about a perfect knower, we are theorizing about what an ideal agent ought to believe. Our contention is that there isn’t an acceptable view of ideally rational belief given the assumptions of the open future and retro-closure, and thus this casts doubt on the conjunction of those assumptions

A synthetic low-frequency mammalian oscillator

Circadian clocks have long been known to be essential for the maintenance of physiological and behavioral processes in a variety of organisms ranging from plants to humans. Dysfunctions that subvert gene expression of oscillatory circadian-clock components may result in severe pathologies, including tumors and metabolic disorders. While the underlying molecular mechanisms and dynamics of complex gene behavior are not fully understood, synthetic approaches have provided substantial insight into the operation of complex control circuits, including that of oscillatory networks. Using iterative cycles of mathematical model-guided design and experimental analyses, we have developed a novel low-frequency mammalian oscillator. It incorporates intronically encoded siRNA-based silencing of the tetracycline-dependent transactivator to enable the autonomous and robust expression of a fluorescent transgene with periods of 26 h, a circadian clock-like oscillatory behavior. Using fluorescence-based time-lapse microscopy of engineered CHO-K1 cells, we profiled expression dynamics of a destabilized yellow fluorescent protein variant in single cells and real time. The novel oscillator design may enable further insights into the system dynamics of natural periodic processes as well as into siRNA-mediated transcription silencing. It may foster advances in design, analysis and application of complex synthetic systems in future gene therapy initiatives

Femtosecond quantification of void evolution during rapid material failure

Understanding high-velocity impact, and the subsequent high strain rate material deformation and potential catastrophic failure, is of critical importance across a range of scientific and engineering disciplines that include astrophysics, materials science, and aerospace engineering. The deformation and failure mechanisms are not thoroughly understood, given the challenges of experimentally quantifying material evolution at extremely short time scales. Here, copper foils are rapidly strained via picosecond laser ablation and probed in situ with femtosecond x-ray free electron (XFEL) pulses. Small-angle x-ray scattering (SAXS) monitors the void distribution evolution, while wide-angle scattering (WAXS) simultaneously determines the strain evolution. The ability to quantifiably characterize the nanoscale during high strain rate failure with ultrafast SAXS, complementing WAXS, represents a broadening in the range of science that can be performed with XFEL. It is shown that ultimate failure occurs via void nucleation, growth, and coalescence, and the data agree well with molecular dynamics simulations

A Genome Scan for Positive Selection in Thoroughbred Horses

Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1) deviations from expected heterozygosity (Ewens-Watterson test) in Thoroughbred (n = 112) and (2) global differentiation among four geographically diverse horse populations (FST). We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; P<0.01), insulin receptor signalling (5.0-fold enrichment; P<0.01) and lipid transport (2.2-fold enrichment; P<0.05) genes. We found a significant overrepresentation of sarcoglycan complex (11.1-fold enrichment; P<0.05) and focal adhesion pathway (1.9-fold enrichment; P<0.01) genes highlighting the role for muscle strength and integrity in the Thoroughbred athletic phenotype. We report for the first time candidate athletic-performance genes within regions targeted by selection in Thoroughbred horses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1), ACTA1 (actin, alpha 1, skeletal muscle), ACTN2 (actinin, alpha 2), ADHFE1 (alcohol dehydrogenase, iron containing, 1), MTFR1 (mitochondrial fission regulator 1), PDK4 (pyruvate dehydrogenase kinase, isozyme 4) and TNC (tenascin C). Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes within the complex molecular networks underlying obesity and its consequential pathologies, such as type 2 diabetes. Therefore, we propose Thoroughbred as a novel in vivo large animal model for understanding molecular protection against metabolic disease