On-lattice agent-based simulation of populations of cells within the open-source chaste framework

Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors and ordinary differential equations (ODEs) for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here we report on the creation of an agent-based multiscale environment amalgamating the characteristics of these models within a Virtual Pysiological Human (VPH) Exemplar Project. This project enables re-use, integration, expansion and sharing of the model and relevant data. The agent-based and reactiondiffusion parts of the multiscale model have been implemented and are available for download as part of the latest public release of Chaste (“Cancer, Heart and Soft Tissue Environment”), (http://www.cs.ox.ac.uk/chaste/) version 3.1, part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the “what if” scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia. We conclude our work by summarising the future steps for the expansion of the current system

Superconductivity in 2-2-3 system Y2Ba2Cu2O(8+delta)

Researchers synthesized a new high T(sub c) 2-2-3 superconductor Y2Ba2Cu3O(8+delta) by a special preparation technique and characterized it by ac-susceptibility measurements. Diamagnetism and Meissner effect sets in at low fields and superconducting transition onsets at 90 K. The systematic investigation of the real and imaginary components of ac-susceptibility as a function of temperature and applied ac magnetic field reveals that the magnetic behavior is that of a granular type superconductor

Intertwined Functions of Separase and Caspase in Cell Division and Programmed Cell Death.

Timely sister chromatid separation, promoted by separase, is essential for faithful chromosome segregation. Separase is a member of the CD clan of cysteine proteases, which also includes the pro-apoptotic enzymes known as caspases. We report a role for the C. elegans separase SEP-1, primarily known for its essential activity in cell division and cortical granule exocytosis, in developmentally programmed cell death when the predominant pro-apoptotic caspase CED-3 is compromised. Loss of SEP-1 results in extra surviving cells in a weak ced-3(-) mutant, and suppresses the embryonic lethality of a mutant defective for the apoptotic suppressor ced-9/Bcl-2 implicating SEP-1 in execution of apoptosis. We also report apparent non-apoptotic roles for CED-3 in promoting germ cell proliferation, meiotic chromosome disjunction, egg shell formation, and the normal rate of embryonic development. Moreover, loss of the soma-specific (CSP-3) and germline-specific (CSP-2) caspase inhibitors result in CED-3-dependent suppression of embryonic lethality and meiotic chromosome non-disjunction respectively, when separase function is compromised. Thus, while caspases and separases have evolved different substrate specificities associated with their specialized functions in apoptosis and cell division respectively, they appear to have retained the residual ability to participate in both processes, supporting the view that co-option of components in cell division may have led to the innovation of programmed cell suicide early in metazoan evolution

Exotic attractors of the non-equilibrium Rabi-Hubbard model

We explore the phase diagram of the dissipative Rabi-Hubbard model, as could be realized by a Raman-pumping scheme applied to a coupled cavity array. There exist various exotic attractors, including ferroelectric, antiferroelectric, and inccomensurate fixed points, as well as regions of persistent oscillations. Many of these features can be understood analytically by truncating to the two lowest lying states of the Rabi model on each site. We also show that these features survive beyond mean-field, using Matrix Product Operator simulations.Comment: 5pages, 3 figures, plus supplementary material. Final version, as publishe

On the Role of Initial Data in the Gravitational Collapse of Inhomogeneous Dust

We consider here the gravitational collapse of a spherically symmetric inhomogeneous dust cloud described by the Tolman-Bondi models. By studying a general class of these models, we find that the end state of the collapse is either a black hole or a naked singularity, depending on the parameters of the initial density distribution, which are $\rho_{c}$, the initial central density of the massive body, and $R_0$, the initial boundary. The collapse ends in a black hole if the dimensionless quantity $\beta$ constructed out of this initial data is greater than 0.0113, and it ends in a naked singularity if $\beta$ is less than this number. A simple interpretation of this result can be given in terms of the strength of the gravitational potential at the starting epoch of the collapse.Comment: Original title changed, numerical range of naked singularity corrected. Plain Tex File. 14 pages. To appear in Physical Review

Singular normal form for the Painlev\'e equation P1

We show that there exists a rational change of coordinates of Painlev\'e's P1 equation $y''=6y^2+x$ and of the elliptic equation $y''=6y^2$ after which these two equations become analytically equivalent in a region in the complex phase space where $y$ and $y'$ are unbounded. The region of equivalence comprises all singularities of solutions of P1 (i.e. outside the region of equivalence, solutions are analytic). The Painlev\'e property of P1 (that the only movable singularities are poles) follows as a corollary. Conversely, we argue that the Painlev\'e property is crucial in reducing P1, in a singular regime, to an equation integrable by quadratures