Markov chain montecarlo method applied to rounding zeros of compositional data: first approach

As stated in Aitchison (1986), a proper study of relative variation in a compositional data set should be based on logratios, and dealing with logratios excludes dealing with zeros. Nevertheless, it is clear that zero observations might be present in real data sets, either because the corresponding part is completely absent –essential zeros– or because it is below detection limit –rounded zeros. Because the second kind of zeros is usually understood as “a trace too small to measure”, it seems reasonable to replace them by a suitable small value, and this has been the traditional approach. As stated, e.g. by Tauber (1999) and by Martín-Fernández, Barceló-Vidal, and Pawlowsky-Glahn (2000), the principal problem in compositional data analysis is related to rounded zeros. One should be careful to use a replacement strategy that does not seriously distort the general structure of the data. In particular, the covariance structure of the involved parts –and thus the metric properties– should be preserved, as otherwise further analysis on subpopulations could be misleading. Following this point of view, a non-parametric imputation method is introduced in Martín-Fernández, Barceló-Vidal, and Pawlowsky-Glahn (2000). This method is analyzed in depth by Martín-Fernández, Barceló-Vidal, and Pawlowsky-Glahn (2003) where it is shown that the theoretical drawbacks of the additive zero replacement method proposed in Aitchison (1986) can be overcome using a new multiplicative approach on the non-zero parts of a composition. The new approach has reasonable properties from a compositional point of view. In particular, it is “natural” in the sense that it recovers the “true” composition if replacement values are identical to the missing values, and it is coherent with the basic operations on the simplex. This coherence implies that the covariance structure of subcompositions with no zeros is preserved. As a generalization of the multiplicative replacement, in the same paper a substitution method for missing values on compositional data sets is introduced

CAC controlled services sharing a link with connectionless data services in an ATM network: a performance evaluation study

In the B-ISDN there is a provision for four classes of services, all of them supported by a single transport network (the ATM network). Three of these services, the connected oriented (CO) ones, permit connection access control (CAC) but the fourth, the connectionless oriented (CLO) one, does not. Therefore, when CLO service and CO services have to share the same ATM link, a conflict may arise. This is because a bandwidth allocation to obtain maximum statistical gain can damage the contracted ATM quality of service (QOS); and vice versa, in order to guarantee the contracted QOS, the statistical gain have to be sacrificed. The paper presents a performance evaluation study of the influence of the CLO service on a CO service (a circuit emulation service or a variable bit-rate service) when sharing the same link

An improved method for discovering link criticality in transport networks

Quantitatively assessing the importance or criticality of each link in a network is of practical value to operators, as that can help them to increase the network's resilience, provide more efficient services, or improve some other aspect of the service. Betweenness is a graph-theoretical measure of centrality that can be applied to communication networks to evaluate link importance. However, as we illustrate in this paper, the basic definition of betweenness centrality produces inaccurate estimations as it does not take into account some aspects relevant to networking, such as the heterogeneity in link capacity or the difference between node-pairs in their contribution to the total traffic. A new algorithm for discovering link centrality in transport networks is proposed in this paper. It requires only static or semi-static network and topology attributes, and yet produces estimations of good accuracy, as verified through extensive simulations. Its potential value is demonstrated by an example application. In the example, the simple shortest-path routing algorithm is improved in such a way that it outperforms other more advanced algorithms in terms of blocking ratio

La Papiroflèxia a l’escola: imaginació, emoció i geometria

El plegament de paper es un art, pero tambe una ciencia. I encara que hi hagi gent que continua considerant la papiroflexia exclusivament un entreteniment, tambe es una eina molt interessant i util per modelitzar aspectes relacionats amb la tecnica, amb la medecina, la computacio o les matematiques. Algunes vegades, per fer una papirola, es necessiten dies i el plegador va insistint fins obtenir la figura que desitja. Tot i que tambe es cert que de vegades per fer-ne d’altres, com les que presentarem al taller, nomes calen uns minuts

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Conformations of poly{G}-poly{C} π stacks with high hole mobility

Charge transfer properties of DNA depend strongly on the π stack conformation. In the present paper, we identify conformations of homogeneous poly-{G}-poly-{C} stacks that should exhibit high charge mobility. Two different computational approaches were applied. First, we calculated the electronic coupling squared, V2, between adjacent base pairs for all 1 ps snapshots extracted from 15 ns molecular dynamics trajectory of the duplex G15. The average value of the coupling squared 〈 V2 〉 is found to be 0.0065 eV2. Then we analyze the base-pair and step parameters of the configurations in which V2 is at least an order of magnitude larger than 〈 V2 〉. To obtain more consistent data, ∼65 000 configurations of the (G:C)2 stack were built using systematic screening of the step parameters shift, slide, and twist. We show that undertwisted structures (twist<20°) are of special interest, because the π stack conformations with strong electronic couplings are found for a wide range of slide and shift. Although effective hole transfer can also occur in configurations with twist=30° and 35°, large mutual displacements of neighboring base pairs are required for that. Overtwisted conformation (twist38°) seems to be of limited interest in the context of effective hole transfer. The results may be helpful in the search for DNA based elements for nanoelectronics

Estimation of electronic coupling in π -stacked donor-bridge-acceptor systems: correction of the two-state model

Comparison of donor-acceptor electronic couplings calculated within two-state and three-state models suggests that the two-state treatment can provide unreliable estimates of Vda because of neglecting the multistate effects. We show that in most cases accurate values of the electronic coupling in a π stack, where donor and acceptor are separated by a bridging unit, can be obtained as Ṽ da = (E2 - E1) μ12 Rda + (2 E3 - E1 - E2) 2 μ13 μ23 Rda2, where E1, E2, and E3 are adiabatic energies of the ground, charge-transfer, and bridge states, respectively, μij is the transition dipole moments between the states i and j, and Rda is the distance between the planes of donor and acceptor. In this expression based on the generalized Mulliken-Hush approach, the first term corresponds to the coupling derived within a two-state model, whereas the second term is the superexchange correction accounting for the bridge effect. The formula is extended to bridges consisting of several subunits. The influence of the donor-acceptor energy mismatch on the excess charge distribution, adiabatic dipole and transition moments, and electronic couplings is examined. A diagnostic is developed to determine whether the two-state approach can be applied. Based on numerical results, we showed that the superexchange correction considerably improves estimates of the donor-acceptor coupling derived within a two-state approach. In most cases when the two-state scheme fails, the formula gives reliable results which are in good agreement (within 5%) with the data of the three-state generalized Mulliken-Hush model

Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31 G* and extended 6-31++ G* basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack

Charge transfer in DNA: hole charge is confined to a single base pair due to solvation effects

We include solvation effects in tight-binding Hamiltonians for hole states in DNA. The corresponding linear-response parameters are derived from accurate estimates of solvation energy calculated for several hole charge distributions in DNA stacks. Two models are considered: (A) the correction to a diagonal Hamiltonian matrix element depends only on the charge localized on the corresponding site and (B) in addition to this term, the reaction field due to adjacent base pairs is accounted for. We show that both schemes give very similar results. The effects of the polar medium on the hole distribution in DNA are studied. We conclude that the effects of polar surroundings essentially suppress charge delocalization in DNA, and hole states in (GC)n sequences are localized on individual guanines

Implícits filosòfics del convencionalisme en la geometria espaciotemporal

Treball que té com a objectiu, en primer lloc, establir quina possibilitat té el convencionalisme de ser una alternativa a les concepcions realistes de la geometria relativista; en segon lloc, assenyalar les implicacions epistemològiques que en deriven; en tercer lloc, precisar quin tipus de lectura de la hipòtesi inicial hem de fer donat que hi ha un cert marge per a l’ambigüitat i això ha permès diverses propostes; i en quart i darrer lloc, en cas que hom accepti les restriccions que el convencionalisme imposa al nostre coneixement, hem de veure quines conclusions podem extreure en l’àmbit ontològic i fins a quin punt són significatives per a la discussió sobre la relació entre matemàtica i naturalesa

La transformació del paisatge litoral de la Costa Brava: Anàlisi de l'evolució (1956-2003), diagnosi de l'estat actual i prognosi de futur

En la tesi es presenta una anàlisi de l'evolució dels canvis succeïts en el paisatge costaner de la Costa Brava (22 municipis litorals) en els darrers cinquanta anys (1956-2003); un estudi de la seva estructura ecopaisatgística, actual i passada, amb una especial èmfasi en la diagnosi de les conseqüències geoambientals de l'esclat urbanístic iniciat a la dècada de 1960, i s'ha determinat quina ha estat la tendència de canvi en els darrers vint-i-cinc anys la qual s'ha utilitzat per a elaborar models explicatius de la dinàmica territorial seguida i projectar-los cap al futur tot dissenyant escenaris probables. A les Bases teòriques s'exposa en quina parcel·la del coneixement científic es situa aquesta recerca i es repassa l'evolució dels diferents corrents i enfocaments que han precedit, dins la Ciència Geogràfica, els estudis sobre transformació del paisatge. Es posa especial en els principis i metodologies que plantegen les dues escoles d'anàlisi del paisatge en que es basa aquesta tesi: la Landscape Ecology i la estructurada a l'entorn del programa internacional Land Use and Land Cover Change (LUCC). S'ha dissenyat una pauta metodològica per a l'anàlisi paisatgística d'un territori a diferents escales: des de l'àmbit regional de tota la Costa Brava (66.230 ha), on es poden detectar les tendències generals, fins l'estudi detallat a escala local, on s'ha pres com a àrea d'estudi tres municipis del centre de la Costa Brava (6.960 Ha): Palamós, Calonge i Castell-Platja d'Aro. Els principals resultats obtinguts són els següents: Una cartografia d'usos i cobertes del sòl de tres períodes temporals i la conseqüent interpretació espacial per a cada etapa: 1957 (situació preturística), 1980 (inici de les actuacions dels ajuntaments democràtics) i 2003 (actualitat). Una anàlisi quantitativa de la transformació del paisatge i de les relacions espacials associades al canvi, a partir de la cartografia d'usos i cobertes del sòl dels tres períodes mapificats (1956, 1980, 2003). Amb l'objectiu d'arribar a definir quina ha estat la dinàmica dels canvis ocorreguts al llarg dels darrers gairebé cinquanta anys. Una anàlisi de l'estructura del mosaic paisatgístic de cadascun dels talls temporals per mitjà de l'aplicació dels principals índexs de l'Ecologia del Paisatge. S'ha analitzat la geometria de la conversió dels usos del sòl i s'han posat de manifest les repercussions ecològiques i paisatgístiques d'aquests canvis. Per una banda, a partir del càlcul i interpretació dels índexos esmentats s'ha analitzat l'evolució de la morfologia i la distribució territorial dels quatre principals usos i cobertes del sòl de la Costa Brava. Per l'altra, per a la Costa Brava centre s'ha analitzat l'estat dels dos sistemes naturals del litoral amb més pressió antròpica: la franja estrictament costanera i les masses forestals. Respecte als tres municipis de la Costa Brava centre s'han tingut en compte en l'anàlisi de l'evolució del paisatge a escala local, les actuacions desenvolupades en l'àmbit urbanístic municipal i les seves conseqüències paisatgístiques i ambientals. A partir de la informació ja processada, s'han detectat les tendències de canvi a partir de models de canvi d'usos i cobertes del sòl. S'han incorporat també els factors biofísics i antròpics, socials i econòmics, condicionants i responsables d'una determinada utilització del territori en cadascun dels tres períodes. Mitjançant l'anàlisi multivariable s'ha intentat descobrir el conjunt de factors que influencien en la taxa i el patró espacial de canvi d'usos i les seves conseqüències territorials. Finalment s'ha aplicat un model de simulació, basat en els automatismes cel·lulars de Markov, per tal de projectar les tendències de canvi i plantejar escenaris futurs, una eina bàsica per a la planificació futura del territori i per al control de les problemàtiques ambientals. Aquestes mesures serveixen per a definir, per a la Costa Brava centre, un patró espacial dels canvis d'usos del sòl a nivell local, i, per al conjunt de la Costa Brava, per a predir, mitjançant models de simulació quantitativa, els possibles desenvolupaments i per estimar els impactes.