## Recursos de colección

#### Sapientia Repositório Institucional Universidade do Algarve (29.729 recursos)

O Repositório Institucional da Universidade do Algarve desenvolvido no âmbito do projecto RCAAP.

FCT1-Artigos

1. #### An invariant for stallings manifolds from a TQFT

SemiÃ£o, Paulo
We will present our construction of a class of effectively calculable, isomorphism invariants for Stallings [1] manifolds by constructing a class of Topological Quantum Field Theories (TQFT's) [2] for these manifolds. Given a $2$-dimensional oriented manifold without boundary, $S$, and an orientation-preserving automorphism $\varphi :S\rightarrow S$, the self-gluing of the cylinder $S\times I$, where $I$ is the standard closed unit interval, is a $3$-dimensional manifold $S_{\varphi }:=\frac{S\times I}{\sim _{\varphi }}$ known as a Stallings manifold, where $\sim _{\varphi }$ is the relation generated by the relation $\left(x,0\right) \sim \left( \varphi (x),1\right)$. A fundamental feature of TQFT is the gluing...

2. #### TQFT - a new direction in algebraic topology

Picken, Roger; SemiÃ£o, Paulo
We give an introduction for the non-expert to TQFT (Topological Quantum Field Theory), focussing especially on its role in algebraic topology. We compare the Atiyah axioms for TQFT with the Eilenberg Steenrod axioms for homology, give a few simple examples of TQFTs, and discuss some other approaches that have been taken to defining TQFT. We then propose a new formulation of TQFT, which is closer in spirit to the way conventional functors of algebraic topology, like homology, are presented. In this approach the fundamental operation of gluing is incorporated through the notion of a gluing morphism, which we define. It...

3. #### Strategies for a web-based mathematics course

Semião, Paulo
In this paper we will describe the main aspects and strategies for the implementation, development, and deployment of an on-line mathematics course. We also point out some key issues of the infrastructure needed for creating and operating this kind of system. Although this is a huge subject and has many aspects to cover we sketch some guidelines that will help anyone in the implementation of a project with these features. The main topics for such a course will range from basic to advance and are given through a gradually process.

4. #### A descriptive e-learning environment for mathematics

SemiÃ£o, Paulo
This article is focused in the creation of descriptive processes for subjects of mathematics in an elearning environment. The main idea is for some chosen mathematical contents try to implement processes that go beyond the binomial question-answer. The system pretends to give step-by-step solutions of questions and is intended to work with any kind of mathematics. We had tried to drawn up explanations of questions as much detailed as possible, so that each learner can progress without skilled help. Our experience tells us that the combination of lectures and session problems turn out to be much more productive and successful.

5. #### A conic asssociated with Euler Lines

SemiÃ£o, Paulo; Rodriguez, Juan; Manuel, Paula
We study the locus of a point C for which the Euler line of triangle ABC with given A and B has a given slope m. This is a conic through A and B, and with center (if it exists) at the midpoint of AB. The main properties of such an Euler conic are described. We also give a construction of a point C for which triangle ABC, with A and B fixed, has a prescribed Euler line.

6. #### An interactive evaluation system for learning mathematics

SemiÃ£o, Paulo
We present an interactive evaluation system for mathematics in the e-learning Moodle environment. One of the most important aspects of the teaching-learning process is to check the acquired knowledge and to achieve this goal we submit the students to questions, tests, and exams in their course materials. In this article we present a system which makes possible to choose a subject from a given list, in some area of mathematics, and the tool generates a test or exam for that subject. The kind of questions which are available are not only the usual multiple-choice questions but it is also possible to give short-answer questions. The system...

7. #### A topological framework for interactive queries on 3D models in the web

Figueiredo, Mauro; Rodrigues, J. I.; Silvestre, Ivo; Veiga-Pires, C.
Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the...

8. #### Functional modifications associated with gastrointestinal tract organogenesis during metamorphosis in Atlantic halibut (Hippoglossus hippoglossus)

Gomes, Ana S.; Kamisaka, Y.; Harboe, Torstein; Power, Deborah; Rønnestad, I.
Background: Flatfish metamorphosis is a hormone regulated post-embryonic developmental event that transforms a symmetric larva into an asymmetric juvenile. In altricial-gastric teleost fish, differentiation of the stomach takes place after the onset of first feeding, and during metamorphosis dramatic molecular and morphological modifications of the gastrointestinal (GI-) tract occur. Here we present the functional ontogeny of the developing GI-tract from an integrative perspective in the pleuronectiforme Atlantic halibut, and test the hypothesis that the multiple functions of the teleost stomach develop synchronously during metamorphosis. Results: Onset of gastric function was determined with several approaches (anatomical, biochemical, molecular and in vivo observations)....

9. #### On the possibility of electric transport mediated by long living intrinsic localized solectron modes

Cantu Ros, O. G.; Cruzeiro, Leonor; Velarde, M. G.; Ebeling, W.
We consider a polaron Hamiltonian in which not only the lattice and the electron-lattice interactions, but also the electron hopping term is affected by anharmonicity. We find that the one-electron ground states of this system are localized in a wide range of the parameter space. Furthermore, low energy excited states, generated either by additional momenta in the lattice sites or by appropriate initial electron conditions, lead to states constituted by a localized electron density and an associated lattice distortion, which move together through the system, at subsonic or supersonic velocities. Thus we investigate here the localized states above the ground state...

10. #### Erratum: Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helix [Phys. Rev. B 82, 174308 (2010)]

Freedman, Holly; Martel, Paulo; Cruzeiro, Leonor
In the GROMACS codemodifications, instead of the nanometer unit for the distance that is standard in GROMACS, a unit of 1 °A was previously assumed. This led to dipole-dipole interactions between amide I vibrations at different sites and the interaction energies of the amide I vibration with the protein hydrogen bonds being overestimated, respectively, by three orders and by one order of magnitude.

11. #### Quartic lattice interactions, soliton-like excitations, and electron pairing in one-dimensional anharmonic crystals

Velarde, M. G.; Brizhik, L.; Chetverikov, A. P.; Cruzeiro, Leonor; Ebeling, W.; Röpke, G.
In this study, it is shown that two added, excess electrons with opposite spins in one-dimensional crystal lattices with quartic anharmonicity may form a bisolectron, which is a localized bound state of the paired electrons to a soliton-like lattice deformation. It is also shown that when the Coulomb repulsion is included, the wave function of the bisolectron has two maxima, and such a state is stable in lattices with strong enough electron (phonon/soliton)–lattice coupling. Furthermore, the energy of the bisolectron is shown to be lower than the energy of the state with two separate, independent electrons, as even with account...

12. #### Electron pairing in one-dimensional anharmonic crystal lattices

Velarde, M. G.; Brizhik, L.; Chetverikov, A. P.; Cruzeiro, Leonor; Ebeling, W.; Röpke, G.
We show that when anharmonicity is added to the electron–phonon interaction it facilitates electron pairing in a localized state. Such localized state appears as singlet state of two electrons bound with the traveling local lattice soliton distortion, which survives when Coulomb repulsion is included.

13. #### Influence of the sign of the coupling on the temperature dependence of optical properties of one-dimensional exciton models

Cruzeiro, Leonor
A new physical cause for a temperature-dependent double peak in exciton systems is put forward within a thermal equilibrium approach for the calculation of optical properties of exciton systems. Indeed, it is found that one-dimensional exciton systems with only one molecule per unit cell can have an absorption spectrum characterized by a double peak provided that the coupling between excitations in different molecules is positive. The two peaks, whose relative intensities vary with temperature, are located around the exciton band edges, being separated by an energy of approximately 4V, where V is the average coupling between nearest neighbours. For small...

14. #### Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helix

Freedman, Holly; Martel, Paulo; Cruzeiro, Leonor
Adenosine triphosphate sATPd is known to be the main energy currency of the living cell, and is used as a coenzyme to generate energy for many cellular processes through hydrolysis to adenosine diphosphate sADPd,although the mechanism of energy transfer is not well understood. It has been proposed that following hydrolysis of the ATP cofactor bound to a protein, up to two quanta of amide-I vibrational energy are excited and utilized to bring about important structural changes in the protein. To study whether, and how, amide-I vibrational excitations are capable of leading to protein structural changes, we have added components arising...

15. #### The ves hypothesis and protein misfolding

Cruzeiro, Leonor
Proteins function by changing conformation. These conformational changes, which involve the concerted motion of a large number of atoms are classical events but, in many cases, the triggers are quantum mechani- cal events such as chemical reactions. Here the initial quantum states after the chemical reaction are assumed to be vibrational excited states, something that has been designated as the VES hypothesis. While the dynamics under classical force fields fail to explain the relatively lower structural stability of the proteins associated with misfolding diseases, the application of the VES hy- pothesis to two cases can provide a new explanation for this phenomenon. This explanation relies on...

16. #### The temperature dependent amide i band of crystalline acetanilide

Cruzeiro, Leonor; Freedman, Holly
The temperature dependent anomalous peak in the amide I band of crystalline acetanilide is thought to be due to self-trapped states. On the contrary, according to the present model, the anomalous peak comes from the fraction of ACN molecules strongly hydrogen-bonded to a neighboring ACN molecule, and its intensity decreases because, on average, this fraction decreases as temperature increases. This model provides, for the first time, an integrated and theoretically consistent view of the temperature dependence of the full amide I band and a qualitative explanation of some of the features of nonlinear pump–probe experiments.

17. #### Proteins multi-funnel energy landscape and misfolding diseases

Cruzeiro, Leonor
The problem of how a given a-amino acid sequence, in cells, most of the times, assumes the native structure, is a fundamental problem in Biology, known as the protein folding problem. Here, evidence is presented that suggests that the same a-amino acid sequence can assume several, very different, structures that have the same Gibbs energy as the native structure, in the same thermodynamic conditions. These results lend support to a multi-funnel Gibbs energy landscape for proteins in which Anfinsen’s thermodynamic hypothesis alone cannot explain protein folding. How then do proteins fold? In a multi-funnel picture, transient deterministic forces are needed to...

18. #### The davydov/scott model for energy storage and transport in proteins

Cruzeiro, Leonor
The current status of the Davydov/Scott model for energy transfer in proteins is reviewed. After a brief introduction to the theoretical framework and to the basic results, the problems of finite temperature dynamics and of the full quantum and mixed quantum-classical approximations are described, as well as recent results obtained within each of these approximations. A short survey of experimental evidence in support of the Davydov/Scott model is made and absorption spectra are calculated that show the same temperature dependence as that measured in crystalline acetanilide. Future applications of the Davydov/Scott model to protein folding and function and to misfolding...

19. #### Are the native states of proteins kinetic traps?

Cruzeiro, Leonor; Lopes, P. A.
Four proteins were selected to represent each of the four different CATH classes and, for each protein, three decoys were constructed with structures totally alien to the native state. The decoys were scored against the native state with the help of the AMBER force field, using three measures: the average energy, the average fluctuation and the resistance to a heat pulse. Two sets of simulations were performed, one with explicit solvent and the other with implicit solvent. The overall conclusion is that, of these three measures, the most successful in picking out the native states was the last one, since...

20. #### Mudflat surface morphology as a structuring agent of algae and associated macroepifauna communities: a case study in the Ria Formosa

Aníbal, J.; Rocha, C.; Sprung, Martin
Although mudflats seem relatively planar, closer inspection reveals a succession of meso-topographical features, including consecutive convex and concave meso- and micro-topographical features. The objective of this study was to determine the influence of meso-scale surface sediment morphology on the dynamics of the macroalgae Ulvales (Chlorophyta) and associated macroepifauna in the Ria Formosa tidal lagoon (southern coast of Portugal). Four sites in the Ria Formosa were sampled monthly. Two were located on convex sections (mounds) of the mudflat and the other two on concave sections (depressions). Macroalgae and related macroepifauna were sampled at each station. Biomass was quantified by determination of...

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