Quasi one dimensional 4^4He inside carbon nanotubes

We report results of diffusion Monte Carlo calculations for both $^4$He absorbed in a narrow single walled carbon nanotube (R = 3.42 \AA) and strictly one dimensional $^4$He. Inside the tube, the binding energy of liquid $^4$He is approximately three times larger than on planar graphite. At low linear densities, $^4$He in a nanotube is an experimental realization of a one-dimensional quantum fluid. However, when the density increases the structural and energetic properties of both systems differ. At high density, a quasi-continuous liquid-solid phase transition is observed in both cases.Comment: 11 pages, 3ps figures, to appear in Phys. Rev. B (RC

Vibrations of a chain of Xe atoms in a groove of carbon nanotube bundle

We present a lattice dynamics study of the vibrations of a linear chain of Xe adsorbates in groove positions of a bundle of carbon nanotubes. The characteristic phonon frequencies are calculated and the adsorbate polarization vectors discussed. Comparison of the present results with the ones previously published shows that the adsorbate vibrations cannot be treated as completely decoupled from the vibrations of carbon nanotubes and that a significant hybridization between the adsorbate and the tube modes occurs for phonons of large wavelengths.Comment: 3 PS figure

Aberrant behaviours of reaction diffusion self-organisation models on growing domains in the presence of gene expression time delays

Turing’s pattern formation mechanism exhibits sensitivity to the details of the initial conditions suggesting that, in isolation, it cannot robustly generate pattern within noisy biological environments. Nonetheless, secondary aspects of developmental self-organisation, such as a growing domain, have been shown to ameliorate this aberrant model behaviour. Furthermore, while in-situ hybridisation reveals the presence of gene expression in developmental processes, the influence of such dynamics on Turing’s model has received limited attention. Here, we novelly focus on the Gierer–Meinhardt reaction diffusion system considering delays due the time taken for gene expression, while incorporating a number of different domain growth profiles to further explore the influence and interplay of domain growth and gene expression on Turing’s mechanism. We find extensive pathological model behaviour, exhibiting one or more of the following: temporal oscillations with no spatial structure, a failure of the Turing instability and an extreme sensitivity to the initial conditions, the growth profile and the duration of gene expression. This deviant behaviour is even more severe than observed in previous studies of Schnakenberg kinetics on exponentially growing domains in the presence of gene expression (Gaffney and Monk in Bull. Math. Biol. 68:99–130, 2006). Our results emphasise that gene expression dynamics induce unrealistic behaviour in Turing’s model for multiple choices of kinetics and thus such aberrant modelling predictions are likely to be generic. They also highlight that domain growth can no longer ameliorate the excessive sensitivity of Turing’s mechanism in the presence of gene expression time delays. The above, extensive, pathologies suggest that, in the presence of gene expression, Turing’s mechanism would generally require a novel and extensive secondary mechanism to control reaction diffusion patterning

Interval Logics and Their Decision Procedures - Part II: A Real-Time Interval Logic

In a companion paper, we presented an interval logic, and showed that it is elementarily decidable. In this paper we extend the logic to allow reasoning about real-time properties of concurrent systems; we call this logic Real-Time Future Interval Logic (RTFIL). We model time by the real numbers, and allow our syntax to state the bounds on the duration of an interval. RTFIL possesses the "real-time interpolation property," which appears to be the natural quantitative counterpart of invariance under finite stuttering. As the main result of this paper, we show that RTFIL is decidable; the decision algorithm is slightly more expensive than for the untimed logic. Our decidability proof is based on the reduction of the satisfiability problem for the logic to the emptiness problem for timed Buchi automata. The latter problem was shown decidable by Alur and Dill in a landmark paper, in which this real-time extension of !-automata was introduced. Finally, we consider an extension of the logic ..

Axiomatizations of Interval Logics

Interval logic has been introduced as a temporal logic that provides higher-level constructs and an intuitive graphical representation, making it easier in interval logic than in other temporal logics to specify and reason about concurrency in software and hardware designs. In this paper we present axiomatizations for two propositional interval logics and relate these logics to Until Temporal Logic. All of these logics are discrete linear-time temporal logics with no next operator. The next operator obstructs the use of hierarchical abstraction and refinement, and makes reasoning about concurrency difficult. 1 Introduction Although temporal logic has been widely recognized as an appropriate logic for reasoning about the relative ordering of events in concurrent systems, ordinary programmers and system designers have found temporal logic unintuitive and difficult to use. The difficulty stems mainly from the need to establish temporal contexts within which requirements apply. Interval ..

Visual Specifications for Temporal Reasoning

Graphical Interval Logic (GIL) is a visual temporal logic in which formulas resemble the informal timing diagrams familiar to system designers and software engineers. It provides an intuitive and natural visual notation in which to express specifications for concurrent systems and retains the benefits of a formal notation. A visual editor permits GIL specifications to be easily constructed, and to be stored in and retrieved from files. The editor interfaces with a proof checker and model generator, which permit verification of temporal inferences. The paper shows how graphical specifications are created and used to reason about temporal properties of systems. It shows how pictures that formalize temporal arguments enhance understanding and help motivate successful proof strategies. 1 Introduction Temporal logic [7] provides a rigorous framework for expressing temporal properties of concurrent systems and has been a focus of much research activity in the last decade. Temporal logic spe..

A Graphical Environment for Design of Concurrent Real-Time Systems

ion, Composition, and Refinement In RTGIL, as well as in other logics [Abadi and Lamport 1995], composition is represented by the conjunction of specifications. A primary concern when composing specifications is that the set of specifications may be inconsistent, i.e., their conjunction may be equivalent to false, from which anything can be demonstrated. To ensure that a set of specifications is consistent, it suffices to show that at least one model, or computation, exists for their conjunction, i.e., that the conjunction is satisfiable. For example, the two specifications a a b b b a A Graphical Environment for Design of Concurrent Real-Time Systems \Delta 9 are each individually consistent, but together they are inconsistent, i.e., their conjunction is unsatisfiable. The RTGIL environment can be used to demonstrate satisfiability and thus consistency of specifications. In general, however, a demonstration of satisfiability must consider the entire set of specifications and can ea..

Supplementary Material for: A Mechanistic Study of the Effect of Doxorubicin/Adriamycin on the Estrogen Response in a Breast Cancer Model

<strong><em>Objective:</em></strong> Estrogen treatment limits the cytotoxic effects of chemotherapy in estrogen receptor-positive (ER+) breast cancer cell lines, suggesting that estrogen pathway signaling may confer chemotherapeutic resistance. This study investigates the molecular responses of ER+ breast cancer cell lines to the chemotherapeutic agent, doxorubicin, in the presence or absence of estrogen. <b><i>Methods:</i></b> ER+ MCF-7 and T47-D cells were cultured in hormone-starved or estrogen-containing media with or without doxorubicin at concentrations mimicking the low concentrations seen in plasma and tumor microenvironments in humans following typical bolus administration. Protein levels, phosphorylations, and interactions of estrogen-signaling molecules were assessed following these treatments, as well the effects of ER signaling inhibitors on cell proliferation. <b><i>Results:</i></b> Surprisingly, estrogen and doxorubicin co-treatment markedly induced pro-growth alterations compared to doxorubicin alone and modestly enhanced estrogen alone-induced changes. Several inhibitors suppressed cell proliferation in the presence of doxorubicin and estrogen. <b><i>Conclusions:</i></b> These findings demonstrate that molecular changes caused by doxorubicin in ER+ breast cancer cells can be reversed by estrogen, providing molecular evidence for the poorer responses of ER+ tumors to doxorubicin in the presence of physiologic estrogen levels. Our results also suggest that the addition of drugs targeting the ER, EGFR, the SFKs, MEK, PI3K, and/or the MMP proteins to a conventional chemotherapy regimen may improve chemosensitivity