12,157 research outputs found
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
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
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 ..
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
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