Discrete Formulation for the dynamics of rods deforming in space

We describe the main ingredients needed to create, from the smooth lagrangian density, a variational principle for discrete motions of a discrete rod, with corresponding conserved Noether currents. We describe all geometrical objects in terms of elements on the linear Atiyah bundle, using a reduced forward difference operator. We show how this introduces a discrete lagrangian density that models the discrete dynamics of a discrete rod. The presented tools are general enough to represent a discretization of any variational theory in principal bundles, and its simplicity allows to perform an iterative integration algorithm to compute the discrete rod evolution in time, starting from any predefined configurations of all discrete rod elements at initial times

Emitter-site selective photoelectron circular dichroism of trifluoromethyloxirane

The angle-resolved inner-shell photoionization of R-trifluoromethyloxirane, C3H3F3O, is studied experimentally and theoretically. Thereby, we investigate the photoelectron circular dichroism (PECD) for nearly-symmetric O 1s and F 1s electronic orbitals, which are localized on different molecular sites. The respective dichroic $\beta_{1}$ and angular distribution $\beta_{2}$ parameters are measured at the photoelectron kinetic energies from 1 to 16 eV by using variably polarized synchrotron radiation and velocity map imaging spectroscopy. The present experimental results are in good agreement with the outcome of ab initio electronic structure calculations. We report a sizable chiral asymmetry $\beta_{1}$ of up to about 9% for the K-shell photoionization of oxygen atom. For the individual fluorine atoms, the present calculations predict asymmetries of similar size. However, being averaged over all fluorine atoms, it drops down to about 2%, as also observed in the present experiment. Our study demonstrates a strong emitter- and site-sensitivity of PECD in the one-photon inner-shell ionization of this chiral molecule

A New Biology: A Modern Perspective on the Challenge of Closing the Gap between the Islands of Knowledge

This paper discusses the rebirth of the old quest for the principles of biology along the discourse line of machine-organism disanalogy and within the context of biocomputation from a modern perspective. It reviews some new attempts to revise the existing body of research and enhance it with new developments in some promising fields of mathematics and computation. The major challenge is that the latter are expected to also answer the need for a new framework, a new language and a new methodology capable of closing the existing gap between the different levels of complex system organization

Groupoids and Wreath Products of Musical Transformations: a Categorical Approach from poly-Klumpenhouwer Networks

Transformational music theory, pioneered by the work of Lewin, shifts the music-theoretical and analytical focus from the "object-oriented" musical content to an operational musical process, in which transformations between musical elements are emphasized. In the original framework of Lewin, the set of transformations often form a group, with a corresponding group action on a given set of musical objects. Klumpenhouwer networks have been introduced based on this framework: they are informally labelled graphs, the labels of the vertices being pitch classes, and the labels of the arrows being transformations that maps the corresponding pitch classes. Klumpenhouwer networks have been recently formalized and generalized in a categorical setting, called poly-Klumpenhouwer networks. This work proposes a new groupoid-based approach to transformational music theory, in which transformations of PK-nets are considered rather than ordinary sets of musical objects. We show how groupoids of musical transformations can be constructed, and an application of their use in post-tonal music analysis with Berg's Four pieces for clarinet and piano, Op. 5/2. In a second part, we show how groupoids are linked to wreath products (which feature prominently in transformational music analysis) through the notion of groupoid bisectionsComment: 16 pages, 9 figures; comments welcom

MacDowell-Mansouri gravity and Cartan geometry

The geometric content of the MacDowell-Mansouri formulation of general relativity is best understood in terms of Cartan geometry. In particular, Cartan geometry gives clear geometric meaning to the MacDowell-Mansouri trick of combining the Levi-Civita connection and coframe field, or soldering form, into a single physical field. The Cartan perspective allows us to view physical spacetime as tangentially approximated by an arbitrary homogeneous "model spacetime", including not only the flat Minkowski model, as is implicitly used in standard general relativity, but also de Sitter, anti de Sitter, or other models. A "Cartan connection" gives a prescription for parallel transport from one "tangent model spacetime" to another, along any path, giving a natural interpretation of the MacDowell-Mansouri connection as "rolling" the model spacetime along physical spacetime. I explain Cartan geometry, and "Cartan gauge theory", in which the gauge field is replaced by a Cartan connection. In particular, I discuss MacDowell-Mansouri gravity, as well as its more recent reformulation in terms of BF theory, in the context of Cartan geometry.Comment: 34 pages, 5 figures. v2: many clarifications, typos correcte

Hyper-domains in exchange bias micro-stripe pattern

A combination of experimental techniques, e.g. vector-MOKE magnetometry, Kerr microscopy and polarized neutron reflectometry, was applied to study the field induced evolution of the magnetization distribution over a periodic pattern of alternating exchange bias (EB) stripes. The lateral structure is imprinted into a continuous ferromagnetic/antiferromagnetic EB bilayer via laterally selective exposure to He-ion irradiation in an applied field. This creates an alternating frozen-in interfacial EB field competing with the external field in the course of the re-magnetization. It was found that in a magnetic field applied at an angle with respect to the EB axis parallel to the stripes the re-magnetization process proceeds via a variety of different stages. They include coherent rotation of magnetization towards the EB axis, precipitation of small random (ripple) domains, formation of a stripe-like alternation of the magnetization, and development of a state in which the magnetization forms large hyper-domains comprising a number of stripes. Each of those magnetic states is quantitatively characterized via the comprehensive analysis of data on specular and off-specular polarized neutron reflectivity. The results are discussed within a phenomenological model containing a few parameters, which can readily be controlled by designing systems with a desired configuration of magnetic moments of micro- and nano-elements

Mutation Symmetries in BPS Quiver Theories: Building the BPS Spectra

We study the basic features of BPS quiver mutations in 4D $\mathcal{N}=2$ supersymmetric quantum field theory with $G=ADE$ gauge symmetries.\ We show, for these gauge symmetries, that there is an isotropy group $\mathcal{G}_{Mut}^{G}$ associated to a set of quiver mutations capturing information about the BPS spectra. In the strong coupling limit, it is shown that BPS chambers correspond to finite and closed groupoid orbits with an isotropy symmetry group $\mathcal{G}_{strong}^{G}$ isomorphic to the discrete dihedral groups $Dih_{2h_{G}}$ contained in Coxeter$(G)$ with $$ the Coxeter number of G. These isotropy symmetries allow to determine the BPS spectrum of the strong coupling chamber; and give another way to count the total number of BPS and anti-BPS states of $\mathcal{N}=2$ gauge theories. We also build the matrix realization of these mutation groups $\mathcal{G}_{strong}^{G}$ from which we read directly the electric-magnetic charges of the BPS and anti-BPS states of $\mathcal{N}=2$ QFT$_{4}$ as well as their matrix intersections. We study as well the quiver mutation symmetries in the weak coupling limit and give their links with infinite Coxeter groups. We show amongst others that $\mathcal{G}_{weak}^{su_{2}}$ is contained in ${GL}({2,}\mathbb{Z})$; and isomorphic to the infinite Coxeter ${I_{2}^{\infty}}$. Other issues such as building $\mathcal{G}$ and $\mathcal{G}_{weak}^{su_{3}}$ are also studied.Comment: LaTeX, 98 pages, 18 figures, Appendix I on groupoids adde

Observation of enhanced chiral asymmetries in the inner-shell photoionization of uniaxially oriented methyloxirane enantiomers

Most large molecules are chiral in their structure: they exist as two enantiomers, which are mirror images of each other. Whereas the rovibronic sublevels of two enantiomers are almost identical, it turns out that the photoelectric effect is sensitive to the absolute configuration of the ionized enantiomer - an effect termed Photoelectron Circular Dichroism (PECD). Our comprehensive study demonstrates that the origin of PECD can be found in the molecular frame electron emission pattern connecting PECD to other fundamental photophysical effects as the circular dichroism in angular distributions (CDAD). Accordingly, orienting a chiral molecule in space enhances the PECD by a factor of about 10

Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses