TumorML: Concept and requirements of an in silico cancer modelling markup language

This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification

Determination of the number of atoms trapped in an optical cavity

The number of atoms trapped within the mode of an optical cavity is determined in real time by monitoring the transmission of a weak probe beam. Continuous observation of atom number is accomplished in the strong coupling regime of cavity quantum electrodynamics and functions in concert with a cooling scheme for radial atomic motion. The probe transmission exhibits sudden steps from one plateau to the next in response to the time evolution of the intracavity atom number, from Ngreater than or equal to 3 to N=2-->1-->0 atoms, with some trapping events lasting over 1 s

Cavity QED "By The Numbers"

The number of atoms trapped within the mode of an optical cavity is determined in real time by monitoring the transmission of a weak probe beam. Continuous observation of atom number is accomplished in the strong coupling regime of cavity quantum electrodynamics and functions in concert with a cooling scheme for radial atomic motion. The probe transmission exhibits sudden steps from one plateau to the next in response to the time evolution of the intracavity atom number, from N >= 3 to N = 2 to 1 to 0, with some trapping events lasting over 1 second.Comment: 5 pages, 4 figure

Object-Oriented Paradigms for Modelling Vascular\ud Tumour Growth: a Case Study

Motivated by a family of related hybrid multiscale models, we have built an object-oriented framework for developing and implementing multiscale models of vascular tumour growth. The models are implemented in our framework as a case study to highlight how object-oriented programming techniques and good object-oriented design may be used effectively to develop hybrid multiscale models of vascular tumour growth. The intention is that this paper will serve as a useful reference for researchers modelling complex biological systems and that these researchers will employ some of the techniques presented herein in their own projects

Cavity QED with Single Atoms and Photons

Recent experimental advances in the field of cavity quantum electrodynamics (QED) have opened new possibilities for control of atom-photon interactions. A laser with "one and the same atom" demonstrates the theory of laser operation pressed to its conceptual limit. The generation of single photons on demand and the realization of cavity QED with well defined atomic numbers N = 0, 1, 2,... both represent important steps toward realizing diverse protocols in quantum information science. Coherent manipulation of the atomic state via Raman transitions provides a new tool in cavity QED for in situ monitoring and control of the atom-cavity system. All of these achievements share a common point of departure: the regime of strong coupling. It is thus interesting to consider briefly the history of the strong coupling criterion in cavity QED and to trace out the path that research has taken in the pursuit of this goal

Collective Oscillations of an Imbalanced Fermi Gas: Axial Compression Modes and Polaron Effective Mass

We investigate the low-lying compression modes of a unitary Fermi gas with imbalanced spin populations. For low polarization, the strong coupling between the two spin components leads to a hydrodynamic behavior of the cloud. For large population imbalance we observe a decoupling of the oscillations of the two spin components, giving access to the effective mass of the Fermi polaron, a quasi-particle composed of an impurity dressed by particle-hole pair excitations in a surrounding Fermi sea. We find $m^*/m=1.17(10)$, in agreement with the most recent theoretical predictions.Comment: 4 pages, 4 figures, submitted to PR

Dynamics of a tunable superfluid junction

We study the population dynamics of a Bose-Einstein condensate in a double-well potential throughout the crossover from Josephson dynamics to hydrodynamics. At barriers higher than the chemical potential, we observe slow oscillations well described by a Josephson model. In the limit of low barriers, the fundamental frequency agrees with a simple hydrodynamic model, but we also observe a second, higher frequency. A full numerical simulation of the Gross-Pitaevskii equation giving the frequencies and amplitudes of the observed modes between these two limits is compared to the data and is used to understand the origin of the higher mode. Implications for trapped matter-wave interferometers are discussed.Comment: 8 pages, 7 figures; v3: Journal reference added, minor changes to tex

Fast and Automated Peak Bagging with DIAMONDS (FAMED)

Stars of low and intermediate mass that exhibit oscillations may show tens of detectable oscillation modes each. Oscillation modes are a powerful to constrain the internal structure and rotational dynamics of the star, hence tool allowing one to obtain an accurate stellar age. The tens of thousands of solar-like oscillators that have been discovered thus far are representative of the large diversity of fundamental stellar properties and evolutionary stages available. Because of the wide range of oscillation features that can be recognized in such stars, it is particularly challenging to properly characterize the oscillation modes in detail, especially in light of large stellar samples. Overcoming this issue requires an automated approach, which has to be fast, reliable, and flexible at the same time. In addition, this approach should not only be capable of extracting the oscillation mode properties of frequency, linewidth, and amplitude from stars in different evolutionary stages, but also able to assign a correct mode identification for each of the modes extracted. Here we present the new freely available pipeline FAMED (Fast and AutoMated pEak bagging with DIAMONDS), which is capable of performing an automated and detailed asteroseismic analysis in stars ranging from the main sequence up to the core-Helium-burning phase of stellar evolution. This, therefore, includes subgiant stars, stars evolving along the red giant branch (RGB), and stars likely evolving toward the early asymptotic giant branch. In this paper, we additionally show how FAMED can detect rotation from dipolar oscillation modes in main sequence, subgiant, low-luminosity RGB, and core-Helium-burning stars. FAMED can be downloaded from its public GitHub repository (https://github.com/EnricoCorsaro/FAMED).Comment: 46 pages, 19 figures, 4 tables. Accepted for publication in A&