Understanding the Changes in the Circular Dichroism of Light Harvesting Complex II upon Varying Its Pigment Composition and Organization

In this work we modeled the circular dichroism (CD) spectrum of LHCII, the main light harvesting antenna of photosystem II of higher plants. Excitonic calculations are performed for a monomeric subunit, taken from the crystal structure of trimeric LHCII from spinach. All of the major features of the CD spectrum above 450 nm are satisfactorily reproduced, and possible orientations of the Chl and carotenoid transition dipole moments are identified. The obtained modeling parameters are used to simulate the CD spectra of two complexes with altered pigment composition: a mutant lacking Chls a 611-612 and a complex lacking the carotenoid neoxanthin. By removing the relevant pigment(s) from the structure, we are able to reproduce their spectra, which implies that the alteration does not disturb the overall structure. The CD spectrum of trimeric LHCII shows a reversed relative intensity of the two negative bands around 470 and 490 nm as compared to monomeric LHCII. The simulations reproduce this reversal, indicating that it is mainly due to interactions between chromophores in different monomeric subunits, and the trimerization does not induce observable changes in the monomeric structure. Our simulated spectrum resembles one of two different trimeric CD spectra reported in literature. We argue that the differences in the experimental trimeric CD spectra are caused by changes in the strength of the monomer-monomer interactions due to the differences in detergents used for the purification of the complexes.

Geometric Optimization Methods for Mobile Systems

When studying robot systems, it is common to ask about optimal approaches to accomplish a given task. In the context of mobile systems, particularly biomimetic systems, optimization tasks are closely related to the relevant dynamics of locomotion. In this thesis, building on prior work from the geometric mechanics community, we introduce several methods for optimization in the context of mobile systems. Each topic is covered in a separate manuscript: in the first manuscript, we investigate how error accrues when using second order displacement approximations for planar mobile systems, and how coordinate optimization reduces error by accounting for higher order error effects. In the second manuscript, we extend planar coordinate optimization to the group of 3D rotations, clarifying methods presented in prior work. Contributions introduced here further reduce error inherent to displacement approximations. In the third and final manuscript, we use recent robot gait optimization methods to perform dimensionality reduction on robot shape spaces, respecting useful dynamics. The resulting 2D shape spaces have useful topological and geometric properties, and could act as a building block for more general robot dimensionality reduction. Finally, the conclusion summarizes the shared themes of the included papers, and discusses in general the potential of geometric mechanics in future robotics work

Second-order finite volume with hydrostatic reconstruction for tsunami simulation

Tsunami modeling commonly accepts the shallow water system as governing equations where the major difficulty is the correct treatment of the nonconservative term due to bathymetry variations. The finite volume method for solving the shallow water equations with such source terms has received great attention in the two last decades. The built-in conservation property, the capacity to correctly treat discontinuities, and the ability to handle complex bathymetry configurations preserving some steady state configurations (well-balanced scheme) make the method very efficient. Nevertheless, it is still a challenge to build an efficient numerical scheme, with very few numerical artifacts (e.g., small numerical diffusion, correct propagation of the discontinuities, accuracy, and robustness), to be used in an operational environment, and that is able to better capture the dynamics of the wet-dry interface and the physical phenomena that occur in the inundation area. In the first part of this paper, we present a new second-order finite volume code. The code is developed for the shallow water equations with a nonconservative term based on the hydrostatic reconstruction technology to achieve a well-balanced scheme and an adequate dry/wet interface treatment. A detailed presentation of the numerical method is given. In the second part of the paper, we highlight the advantages of the new numerical technique. We benchmark the numerical code against analytical, experimental, and field results to assess the robustness and the accuracy of the numerical code. Finally, we use the 28 February 1969 North East Atlantic tsunami to check the performance of the code with real data.Historical data for Cascais and Lagos (1969 Lisbon Tsunami) are available at http://www.dgterritorio.pt/cartografia_e_geodesia/geodesia/redes_geodesicas/rede_maregrafica/. The tagus estuary data (typewriter document) are available at the Dom Luiz Institute library http://idl.ul.pt/node/33. This work is funded by the Portugal-France research agreement, through the research project GEONUM FCT-ANR/MAT-NAN/0122/2012. This research was financed by Portuguese Funds through FCT-Fundacao para a Ciencia e a Tecnologia, within the Project UID/MAT/00013/2013

Truth and Speed-Up

In this paper, we investigate the phenomenon of speed-up in the context of theories of truth. We focus on axiomatic theories of truth extending Peano arithmetic. We are particularly interested on whether conservative extensions of PA have speed-up and on how this relates to a deflationist account. We show that disquotational theories have no significant speed-up, in contrast to some compositional theories, and we briefly assess the philosophical implications of these results

Hyperbolic Conservation Laws

[no abstract available

The control of particles in the Stokes limit

There are numerous ways to control objects in the Stokes regime, with microscale examples ranging from the use of optical tweezers to the application of external magnetic fields. In contrast, there are relatively few explorations of theoretical controllability, which investigate whether or not refined and precise control is indeed possible in a given system. In this work, seeking to highlight the utility and broad applicability of such rigorous analysis, we recount and illustrate key concepts of geometric control theory in the context of multiple particles in Stokesian fluids interacting with each other, such that they may be readily and widely applied in this largely unexplored fluid-dynamical setting. Motivated both by experimental and abstract questions of control, we exemplify these techniques by explicit and detailed application to multiple problems concerning the control of two particles, such as the motion of tracers in flow and the guidance of one sphere by another. Further, we showcase how this analysis of controllability can directly lead to the construction of schemes for control, in addition to facilitating explorations of mechanical efficiency and contributing to our overall understanding of non-local hydrodynamic interactions in the Stokes limit

Supervenience, Dependence, Disjunction

This paper explores variations on and connections between the topics mentioned in its title, using as something of an anchor the discussion in Valentin Goranko and Antti Kuusisto’s “Logics for propositional determinacy and independence”, a venture into what the authors call the logic of determinacy, which they contrast with (a demodalized version of) Jouko Väänänen’s modal dependence logic. As they make clear in their discussion, these logics are closely connected with the topics of noncontingency and supervenience. Two opening sections of the present paper address some of these connections, including related earlier logical work by the present author as well as very recent work by Jie Fan. The Väänänen-inspired treatment is presented in a third section, and then, in Sections 4 and 5, as a kind of centerpiece for the discussion, we follow Goranko and Kuusisto in elaborating one principal reason offered for preferring their own approach over that treatment, which concerns some anomalies over the behaviour of disjunction in the latter treatment. Sections 6 and 7 look at dependence and (several different versions of) disjunction in inquisitive logic, especially as presented by Ivano Ciardelli. Section 8 revisits the less formal property-supervenience literature with issues from the first two sections of the paper in mind, and we conclude with a Postscript addressing a further conceptual issue pertaining to the relation between modal and quantificational dependence logics