Epigenetic Landscape of Interacting Cells: A Model Simulation for Developmental Process

We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape epigenetically and the differentiation in developmental process is understood as a self-organization. The effect of the regulation by gene expression which is a key ingredient in development is renormalized into the interaction and the environment. At earlier stage of the development the energy landscape of the model is rugged with small amplitude. The state of cells in such a landscape is susceptible to fluctuations and not uniquely determined. These cells are regarded as stem cells. At later stage of the development the landscape has a funnel-like structure corresponding to the canalization in differentiation. The rewinding or stability of the differentiation is also demonstrated by substituting test cells into the time sequence of the model development.Comment: The discussion, in terms of our model, on the recently reported context-dependent behavior of STAP cells [Nature 505, 641-647 (2014)] has been added in Appendi

SFLM: A mix of a Functional Linear Model and of a Spatial Autoregressive Model for spatially correlated functional data

International audienc

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

http://dx.doi.org/10.1093/bib/bbn026Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. Here we provide a general introduction to the field of formal modelling, which emphasizes the intuitive biochemical basis of the modelling process, but is also accessible for an audience with a background in computing science and/or model engineering. We show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach { Qualitative Petri nets, and quantitative approaches { Continuous Petri Nets and Ordinary Differential Equations. We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building, and present ..

Probing the A1 to L10 Transformation in FeCuPt Using the First Order Reversal Curve Method

The A1- L10 phase transformation has been investigated in (001) FeCuPt thin films prepared by atomic-scale multilayer sputtering and rapid thermal annealing (RTA). Traditional x-ray diffraction is not always applicable in generating a true order parameter, due to non-ideal crystallinity of the A1 phase. Using the first-order reversal curve (FORC) method, the A1 and L10 phases are deconvoluted into two distinct features in the FORC distribution, whose relative intensities change with the RTA temperature. The L10 ordering takes place via a nucleation-and-growth mode. A magnetization-based phase fraction is extracted, providing a quantitative measure of the L10 phase homogeneity.Comment: 17 pages, 5 figures, 4 page supplementary material (4 figures

Precipitating Ordered Skyrmion Lattices from Helical Spaghetti

Magnetic skyrmions have been the focus of intense research due to their potential applications in ultra-high density data and logic technologies, as well as for the unique physics arising from their antisymmetric exchange term and topological protections. In this work we prepare a chiral jammed state in chemically disordered (Fe, Co)Si consisting of a combination of randomly-oriented magnetic helices, labyrinth domains, rotationally disordered skyrmion lattices and/or isolated skyrmions. Using small angle neutron scattering, (SANS) we demonstrate a symmetry-breaking magnetic field sequence which disentangles the jammed state, resulting in an ordered, oriented skyrmion lattice. The same field sequence was performed on a sample of powdered Cu2OSeO3 and again yields an ordered, oriented skyrmion lattice, despite relatively non-interacting nature of the grains. Micromagnetic simulations confirm the promotion of a preferred skyrmion lattice orientation after field treatment, independent of the initial configuration, suggesting this effect may be universally applicable. Energetics extracted from the simulations suggest that approaching a magnetic hard axis causes the moments to diverge away from the magnetic field, increasing the Dzyaloshinskii-Moriya energy, followed subsequently by a lattice re-orientation. The ability to facilitate an emergent ordered magnetic lattice with long-range orientation in a variety of materials despite overwhelming internal disorder enables the study of skyrmions even in imperfect powdered or polycrystalline systems and greatly improves the ability to rapidly screen candidate skyrmion materials

Momentum space imaging of Cooper pairing in a half-Dirac-gas topological superconductor (a helical 2D topological superconductor)

Superconductivity in Dirac electrons has recently been proposed as a new platform between novel concepts in high-energy and condensed matter physics. It has been proposed that supersymmetry and exotic quasiparticles, both of which remain elusive in particle physics, may be realized as emergent particles in superconducting Dirac electron systems. Using artificially fabricated topological insulator-superconductor heterostructures, we present direct spectroscopic evidence for the existence of Cooper pairing in a half Dirac gas 2D topological superconductor. Our studies reveal that superconductivity in a helical Dirac gas is distinctly different from that of in an ordinary two-dimensional superconductor while considering the spin degrees of freedom of electrons. We further show that the pairing of Dirac electrons can be suppressed by time-reversal symmetry breaking impurities removing the distinction. Our demonstration and momentum-space imaging of Cooper pairing in a half Dirac gas and its magnetic behavior taken together serve as a critically important 2D topological superconductor platform for future testing of novel fundamental physics predictions such as emergent supersymmetry and quantum criticality in topological systems.Comment: Submitted June'14; Accepted to NaturePhysics, to appear AOP (2014