Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo

Mammalian embryogenesis is a dynamic process involving gene expression and mechanical forces between proliferating cells. The exact nature of these interactions, which determine the lineage patterning of the trophectoderm and endoderm tissues occurring in a highly regulated manner at precise periods during the embryonic development, is an area of debate. We have developed a computational modeling framework for studying this process, by which the combined effects of mechanical and genetic interactions are analyzed within the context of proliferating cells. At a purely mechanical level, we demonstrate that the perpendicular alignment of the animal-vegetal (a-v) and embryonic-abembryonic (eb-ab) axes is a result of minimizing the total elastic conformational energy of the entire collection of cells, which are constrained by the zona pellucida. The coupling of gene expression with the mechanics of cell movement is important for formation of both the trophectoderm and the endoderm. In studying the formation of the trophectoderm, we contrast and compare quantitatively two hypotheses: (1) The position determines gene expression, and (2) the gene expression determines the position. Our model, which couples gene expression with mechanics, suggests that differential adhesion between different cell types is a critical determinant in the robust endoderm formation. In addition to differential adhesion, two different testable hypotheses emerge when considering endoderm formation: (1) A directional force acts on certain cells and moves them into forming the endoderm layer, which separates the blastocoel and the cells of the inner cell mass (ICM). In this case the blastocoel simply acts as a static boundary. (2) The blastocoel dynamically applies pressure upon the cells in contact with it, such that cell segregation in the presence of differential adhesion leads to the endoderm formation. To our knowledge, this is the first attempt to combine cell-based spatial mechanical simulations with genetic networks to explain mammalian embryogenesis. Such a framework provides the means to test hypotheses in a controlled in silico environment

Time reversal in thermoacoustic tomography - an error estimate

The time reversal method in thermoacoustic tomography is used for approximating the initial pressure inside a biological object using measurements of the pressure wave made on a surface surrounding the object. This article presents error estimates for the time reversal method in the cases of variable, non-trapping sound speeds.Comment: 16 pages, 6 figures, expanded "Remarks and Conclusions" section, added one figure, added reference

Mathematical Modelling of Optical Coherence Tomography

In this chapter a general mathematical model of Optical Coherence Tomography (OCT) is presented on the basis of the electromagnetic theory. OCT produces high resolution images of the inner structure of biological tissues. Images are obtained by measuring the time delay and the intensity of the backscattered light from the sample considering also the coherence properties of light. The scattering problem is considered for a weakly scattering medium located far enough from the detector. The inverse problem is to reconstruct the susceptibility of the medium given the measurements for different positions of the mirror. Different approaches are addressed depending on the different assumptions made about the optical properties of the sample. This procedure is applied to a full field OCT system and an extension to standard (time and frequency domain) OCT is briefly presented.Comment: 28 pages, 5 figures, book chapte

Flow-induced dynamic surface tension effects at nanoscale

The aim of this study is to investigate flow-induced dynamic surface tension effects, similar to the well-known Marangoni phenomena, but solely generated by the nanoscale topography of the substrates. The flow-induced surface tension effects are examined on the basis of a sharp interface theory. It is demonstrated how nanoscale objects placed at the boundary of the flow domain result in the generation of substantial surface forces acting on the bulk flow

General Spectral Flow Formula for Fixed Maximal Domain

We consider a continuous curve of linear elliptic formally self-adjoint differential operators of first order with smooth coefficients over a compact Riemannian manifold with boundary together with a continuous curve of global elliptic boundary value problems. We express the spectral flow of the resulting continuous family of (unbounded) self-adjoint Fredholm operators in terms of the Maslov index of two related curves of Lagrangian spaces. One curve is given by the varying domains, the other by the Cauchy data spaces. We provide rigorous definitions of the underlying concepts of spectral theory and symplectic analysis and give a full (and surprisingly short) proof of our General Spectral Flow Formula for the case of fixed maximal domain. As a side result, we establish local stability of weak inner unique continuation property (UCP) and explain its role for parameter dependent spectral theory.Comment: 22 page

Transition between nuclear and quark-gluon descriptions of hadrons and light nuclei

We provide a perspective on studies aimed at observing the transition between hadronic and quark-gluonic descriptions of reactions involving light nuclei. We begin by summarizing the results for relatively simple reactions such as the pion form factor and the neutral pion transition form factor as well as that for the nucleon and end with exclusive photoreactions in our simplest nuclei. A particular focus will be on reactions involving the deuteron. It is noted that a firm understanding of these issues is essential for unraveling important structure information from processes such as deeply virtual Compton scattering as well as deeply virtual meson production. The connection to exotic phenomena such as color transparency will be discussed. A number of outstanding challenges will require new experiments at modern facilities on the horizon as well as further theoretical developments.Comment: 37 pages, 17 figures, submitted to Reports on Progress in Physic

Q^2 Evolution of Chiral-Odd Twist-3 Distributions h_L(x, Q^2) and e(x, Q^2) in Large-N_c QCD

We prove that the twist-3 chiral-odd parton distributions obey simple Gribov-Lipatov-Altarelli-Parisi evolution equations in the limit $N_c\to\infty$ and give analytic results for the corresponding anomalous dimensions. To this end we introduce an evolution equation for the corresponding three-particle twist-3 parton correlation functions and find an exact analytic solution. For large values of n (operator dimension) we are further able to collect all corrections subleading in N_c, so our final results are valid to $O(1/N_c^2\cdot \ln(n)/n)$ accuracy.Comment: 10 pages, 1 Postscript figure, revte

Energy Dependence of Nuclear Transparency in C(p,2p) Scattering

The transparency of carbon for (p,2p) quasi-elastic events was measured at beam energies ranging from 6 to 14.5 GeV at 90 degrees c.m. The four momentum transfer squared q*q ranged from 4.8 to 16.9 (GeV/c)**2. We present the observed energy dependence of the ratio of the carbon to hydrogen cross sections. We also apply a model for the nuclear momentum distribution of carbon to normalize this transparency ratio. We find a sharp rise in transparency as the beam energy is increased to 9 GeV and a reduction to approximately the Glauber level at higher energies.Comment: 4 pages, 2figures, submitted to PR

Band Calculations for Ce Compounds with AuCu3_{3}-type Crystal Structure on the basis of Dynamical Mean Field Theory I. CePd3_{3} and CeRh3_{3}

Band calculations for Ce compounds with the AuCu$_{3}$-type crystal structure were carried out on the basis of dynamical mean field theory (DMFT). The auxiliary impurity problem was solved by a method named NCA$f^{2}$vc (noncrossing approximation including the $f^{2}$ state as a vertex correction). The calculations take into account the crystal-field splitting, the spin-orbit interaction, and the correct exchange process of the $f^{1} \rightarrow f^{0},f^{2}$ virtual excitation. These are necessary features in the quantitative band theory for Ce compounds and in the calculation of their excitation spectra. The results of applying the calculation to CePd$_{3}$ and CeRh$_{3}$ are presented as the first in a series of papers. The experimental results of the photoemission spectrum (PES), the inverse PES, the angle-resolved PES, and the magnetic excitation spectra were reasonably reproduced by the first-principles DMFT band calculation. At low temperatures, the Fermi surface (FS) structure of CePd$_{3}$ is similar to that of the band obtained by the local density approximation. It gradually changes into a form that is similar to the FS of LaPd$_{3}$ as the temperature increases, since the $4f$ band shifts to the high-energy side and the lifetime broadening becomes large.}Comment: 12 pasges, 13 figure

Wilson Lines off the Light-cone in TMD PDFs

Transverse Momentum Dependent (TMD) parton distribution functions (PDFs) also take into account the transverse momentum ($p_T$) of the partons. The $p_T$-integrated analogues can be linked directly to quark and gluon matrix elements using the operator product expansion in QCD, involving operators of definite twist. TMDs also involve operators of higher twist, which are not suppressed by powers of the hard scale, however. Taking into account gauge links that no longer are along the light-cone, one finds that new distribution functions arise. They appear at leading order in the description of azimuthal asymmetries in high-energy scattering processes. In analogy to the collinear operator expansion, we define a universal set of TMDs of definite rank and point out the importance for phenomenology.Comment: 12 pages, presented by the first author at the Light-Cone Conference 2013, May 20-24, 2013, Skiathos, Greece. To be published in Few Body System