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

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

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

The role of dynamical polarization of the ligand-to-metal charge transfer excitations in the ab initio determination of effective exchange parameters

The role of the bridging ligand on the effective Heisenberg coupling parameters is analyzed in detail. This analysis strongly suggests that the ligand-to-metal charge transfer excitations are responsible for a large part of the final value of the magnetic coupling constant. This permits us to suggest a variant of the difference dedicated configuration interaction (DDCI) method, presently one of the most accurate and reliable for the evaluation of magnetic effective interactions. This method treats the bridging ligand orbitals mediating the interaction at the same level than the magnetic orbitals and preserves the high quality of the DDCI results while being much less computationally demanding. The numerical accuracy of the new approach is illustrated on various systems with one or two magnetic electrons per magnetic center. The fact that accurate results can be obtained using a rather reduced configuration interaction space opens the possibility to study more complex systems with many magnetic centers and/or many electrons per center.

A Thermokinetic approach to radiative heat transfer at the nanoscale

Radiative heat exchange at the nanoscale presents a challenge for several areas due to its scope and nature. Here, we provide a thermokinetic description of microscale radiative energy transfer including phonon-photon coupling manifested through a non-Debye relaxation behavior. We show that a lognormal-like distribution of modes of relaxation accounts for this non-Debye relaxation behavior leading to the thermal conductance. We also discuss the validity of the fluctuation-dissipation theorem. The general expression for the thermal conductance we obtain fits existing experimental results with remarkable accuracy. Accordingly, our approach offers an overall explanation of radiative energy transfer through micrometric gaps regardless of geometrical configurations and distances.

First person experience of body transfer in virtual reality

Altering the normal association between touch and its visual correlate can result in the illusory perception of a fake limb as part of our own body. Thus, when touch is seen to be applied to a rubber hand while felt synchronously on the corresponding hidden real hand, an illusion of ownership of the rubber hand usually occurs. The illusion has also been demonstrated using visuomotor correlation between the movements of the hidden real hand and the seen fake hand. This type of paradigm has been used with respect to the whole body generating out-of-the-body and body substitution illusions. However, such studies have only ever manipulated a single factor and although they used a form of virtual reality have not exploited the power of immersive virtual reality (IVR) to produce radical transformations in body ownership.

Numerical simulation of combined heat transfer phenomena (conduction, convection, and radiation). Application to he optimisation of thermal systems

Thermal systems interchanging heat and mass by conduction, convection, radiation (solar and thermal ) occur in many engineering applications like energy storage by solar collectors, window glazing in buildings, refrigeration of plastic moulds, air handling units etc. Often these thermal systems are composed of various elements for example a building with wall, windows, rooms, etc. It would be of particular interest to have a modular thermal system which is formed by connecting different modules for the elements, flexibility to use and change models for individual elements, add or remove elements without changing the entire code. A numerical approach to handle the heat transfer and fluid flow in such systems helps in saving the full scale experiment time, cost and also aids optimisation of parameters of the system. In subsequent sections are presented a short summary of the work done until now on the orientation of the thesis in the field of numerical methods for heat transfer and fluid flow applications, the work in process and the future work.

Coupling and monotonicity of queueing processes

The main purpose of this work is to give a survey of main monotonicity properties of queueing processes based on the coupling method. The literature on this topic is quite extensive, and we do not consider all aspects of this topic. Our more concrete goal is to select the most interesting basic monotonicity results and give simple and elegant proofs. Also we give a few new (or revised) proofs of a few important monotonicity properties for the queue-size and workload processes both in single-server and multi- server systems. The paper is organized as follows. In Section 1, the basic notions and results on coupling method are given. Section 2 contains known coupling results for renewal processes with focus on construction of synchronized renewal instants for a superposition of independent renewal processes. In Section 3, we present basic monotonicity results for the queue-size and workload processes. We consider both discrete-and continuous-time queueing systems with single and multi servers. Less known results on monotonicity of queueing processes with dependent service times and interarrival times are also presented. Section 4 is devoted to monotonicity of general Jackson-type queueing networks with Markovian routing. This section is based on the notable paper [17]. Finally, Section 5 contains elements of stability analysis of regenerative queues and networks, where coupling and monotonicity results play a crucial role to establish minimal suficient stability conditions. Besides, we present some new monotonicity results for tandem networks.

Transferència d’electrò i protó als intermediaris de reacció de les hemo-catalases

Projecte de recerca elaborat a partir d’una estada a l’University of Pennsylvania, EUA, entre els mesos d’agosta a desembre del 2006. Les hemo-catalases són enzims que protegeixen les cèl•lules dels efectes tòxics del peròxid d'hidrogen. Aquesta reacció té lloc en dues etapes, via l'intermediari Compost I (Cpd I). Tanmateix, el Compost I pot seguir una reacció secundària, a través de l'intermediari Compost II. Hi ha dos tipus d'hemo-catalases: les hemo-b (com la d'Helicobacter pylori, HPC) i les hemo-d catalases (com la de Penicillium vitale, PVC). Experimentalment s'observa que les hemo-b catalases formen Cpd II més fàcilment que les hemo-d. La formació del Cpd II consta de dos processos: la reducció del catió radical porfirínic i la protonació del grup oxoferril. Durant l'estada, es va estudiar el procès de transferència electrònica a la porfirina utilitzant una metodologia desenvolupada recentment. Els resultats mostren que per PVC la reducció és més fàcil que per HPC. Posteriorment hem realitzat una sèrie de optimitzacions de geometria CPMD QM/MM al llarg del camí per la transferència de protó (PT) de la histidina distal a l'oxoferril. Mentre que per HPC aquesta PT és espontània, per PVC l'isòmer hidroxoferrílic és menys estable que el catió imidazoli.

Screening of highly modular sugar-based ligand libraries in the enantioselective C-C coupling reactions

Projecte de recerca elaborat a partir d’una estada a la University of Nottingham, Gran Bretanya, entre març i abril del 2007. Aquest treball s’ha centrat en l’aplicació de compostos derivats de la D-(+)-glucosa, de la D-(+)-fructosa i la D-galactosa com a lligands de catalitzadors homogenis quirals en dos reaccions asimètriques: addició 1,2 a aldehids catalitzada per níquel i addició 1,4 conjugada catalitzada per coure.(veure figura adjunta al final del document). En primer lloc, s’ha estudiat l’aplicació dels compostos L1-L6 a les reaccions d’addició 1,2 a aldehids catalitzades per níquel. S’ha observat que la selectivitat del procés depèn principalment del grup funcional unit a l’esquelet del lligand, de les propietats estèriques del substituent en la funció oxazolina i de l’estructura del substrat. S’ha obtingut fins a un 59% d’excés enantiomèric utilitzant el precursor de catalitzador que conté el lligand L3a. En segon lloc, aquest treball descriu l’aplicació de les tres famílies de compostos (L1-L11) com a lligands en la reacció d’addició 1,4 catalitzada per coure de compostos organometàl•lics a diferents enones amb diferents propietats estèriques. L’ús de les llibreries de compostos fosfit-oxazolina (L1-L5) i fosfit-fosforamidit (L6) han proporcionat bones enantioselectivitats (fins a 80%) en l’addició de reactius de trialquilalumini a diferents enones. En canvi, la llibreria de compostos monofosfit (L7-L11) ha mostrat bones activitats però enantioselectivitats fins a 57%.

The Global Diffusion of Regulatory Agencies: Channels of Transfer and Stages of Diffusion

The autonomous regulatory agency has recently become the ‘appropriate model’ of governance across countries and sectors. The dynamics of this process is captured in our data set, which covers the creation of agencies in 48 countries and 16 sectors since the 1920s. Adopting a diffusion approach to explain this broad process of institutional change, we explore the role of countries and sectors as sources of institutional transfer at different stages of the diffusion process. We demonstrate how the restructuring of national bureaucracies unfolds via four different channels of institutional transfer. Our results challenge theoretical approaches that overemphasize the national dimension in global diffusion and are insensitive to the stages of the diffusion process. Further advance in study of diffusion depends, we assert, on the ability to apply both cross-sectoral and cross-national analysis to the same research design and to incorporate channels of transfer with different causal mechanisms for different stages of the diffusion process.

La ironía en el transfer intercultural : aproximación pragmática en la traducción al castellano de relatos satíricos de Mijaíl Zoschenko y Mijaíl Bulgákov

El presente estudio está dedicado a analizar la traducción de la ironía en una obra de ficción literaria, más concretamente en los relatos satíricos de Mijaíl Zoschenko y Mijaíl Bulgákov en su versión castellana. Metodológicamente, el estudio presenta un enfoque pragmático, y se inscribe en las aportaciones pragmáticas de la segunda mitad del siglo XX, que permiten analizar el texto literario como un acto de comunicación y un discurso dialógico, inscribiéndolo en un contexto extralingúístico relevante. Abordaremos el análisis de lo "no dicho": el subtexto irónico que subyace como un significado implícito no-deducible de los medios lingüísticos en sí mismos, y donde cobran una gran importancia los factores comunicativos: la situación, la intención del hablante, el principio cooperativo (según Paul Grice) y toda una serie de presupuestos que pueden o no compartir los interlocutores. Partiendo del supuesto de la existencia de diferentes tipos textuales en toda traducción, la ficción literaria se abordará como un tipo de texto que presenta características particupares. En este sentido, el relato satírico de la época soviética se contempla como un género específico que implica, a su vez, una estrategia específica de traducción. Como es sabido, en los textos humorísticos predomina el efecto perlocutivo. Así pues, dependerá del tradutor que el texto transferido a otra cultura, y a menudo a otra época, consiga el mismo efecto humorístico, o similar, al que tuvo el original en su contexto histórico-cultural.

Radical cystectomy and unrinary diversion : is there a role for bowel in the fuuture?

Bladder transitional cell carcinoma (TCC) is the most frequent malignancy of the urinary tract, and its incidence is rising. The gold standard treatment of invasive TCC is radical cystectomy with configuration of urinary diversion with bowel; the need for bowel has been universally considered the prime cause of complications. Since 1960’s urologists, scientists and industry have been trying, unsuccessfully, to obviate the use of bowel with alternative materials. We provide an analysis of problems deriving from using bowel as bladder substitute, a comprehensive review of literature on previous artificial models, an analysis of benefits deriving from the ideal prosthesis.

La Baixa morbiditat perioperatòria de la prostatectomia radical laparoscòpica justifica efectuar-la en pacients majors de 70 anys

Donat l’increment en l’esperança de vida, valorem el tractament radical del càncer de pròstata en pacients & 70 anys. L’objectiu és analitzar la incidència, severitat i maneig de la morbiditat perioperatòria de la prostatectomia radical (PR) en funció de la tècnica quirúrgica. De 500 PR revisem, retrospectivament, 70 pacients & 70 anys (40 Retropúbiques i 30 Laparoscòpiques). S’empra la classificació de Clavien modificada per analitzar les complicacions. La proporció de complicacions és en PRR 57,5% i en PRL 33%. Les complicacions en la PRL són de menor gravetat. Els beneficis atribuïts a la laparoscòpia es mantenen en pacients d’edat avançada.

Internal and External Determinants of Radical and incremental Innovation in SMEs: the case of Catalonia

There is a major concern in economic literature about innovation, which is the interaction between internal and external factors.. In this paper those activities are hypothesized as being determined by some territorial characteristics like labour skills, technological infrastructure, educational facilities, agglomeration economies and industrial structure. This assumption allows understanding why those innovative activities are not spread across space and are located into specific areas. We use a detailed survey containing microdata for 497 SMEs located in Catalonia.