Treino cognitivo e intervenção psicoeducativa para indivíduos hipertensos: efeitos na cognição

OBJETIVOS: Avaliar a possibilidade de aliar o treino cognitivo à intervenção psicoeducativa de oito sessões sobre hipertensão visando melhor manejo desta condição crônica em idosos. MÉTODOS: Participaram 64 idosos que se declararam como hipertensos, divididos em grupo experimental (GE, n=35) e grupo controle (GC, n=29). O grupo controle recebeu treino após o pós teste. O protocolo incluiu dados sócio-demográficos e clínicos, o Mini-Exame do Estado Mental (MEEM), Escala de Depressão Geriátrica (EDG), Teste Comportamental de Memória de Rivermead (RBMT), Fluência Verbal categoria animais (FV) e Short Cognitive Test (SKT). RESULTADOS: Pôde-se observar que o GE apresentou melhor desempenho cognitivo, quando comparado ao GC, após a intervenção. CONCLUSÕES: Podem ocorrer ganhos cognitivos associados a uma intervenção psicoeducativa para idosos hipertensos.

Associação entre índice glicêmico e carga glicêmica dietéticos e síndrome metabólica em idosos

OBJETIVO: Investigar a associação entre índice glicêmico (IG) e/ou carga glicêmica (CG) da dieta e síndrome metabólica (SM). MÉTODOS: Trata-se de estudo documental e do tipo caso-controle, com uma amostra de 229 idosos. Calcularam-se o IG e a CG, classificando-os em adequado (baixo) e inadequado (moderado e alto). Calculou-se ainda a prevalência de consumo dos alimentos, consumidos por pelo menos metade dos avaliados. A análise estatística dos dados foi efetuada por meio do teste c² e teste t de Student. Adotou-se p < 0,05 como nível de significância. RESULTADOS: Dos indivíduos estudados (n = 229), 74,2% pertenciam ao sexo feminino. A média de idade do grupo foi de 70,1 (6,4) anos. A média diária de IG do grupo caso foi de 62,3 (6,5), e do grupo controle de 62,1 (6,1), com p = 0,864. As médias diárias de CG não foram estatisticamente diferentes (p = 0,212), sendo a do grupo caso de 99,8 (33,8) e do grupo controle de 108,9 (45,7). Os alimentos consumidos tanto pelos casos como pelos controles, com maior contribuição ao IG, foram: pão, arroz, banana e açúcar refinado. CONCLUSÃO: No grupo avaliado, não houve associação entre índice glicêmico e carga glicêmica dietéticos e síndrome metabólica. O padrão identificado, no entanto, coloca portadores e não portadores em situação de risco à saúde, merecendo ações educativas.

Chewing time and chewing strokes in different dentofacial deformities

PURPOSE: To verify whether the number of chewing strokes and the chewing time are influenced by dentofacial deformities in habitual free mastication. METHODS: Participants were 15 patients with diagnosis of class II dentofacial deformity (GII), 15 with class III (GIII), and 15 healthy control individuals with no deformity (CG). Free habitual mastication of a cornstarch cookie was analyzed, considering the number of chewing strokes and the time needed to complete two mastications. Strokes were counted by considering the opening and closing movements of the mandible. The time needed to consume each bite was determined using a digital chronometer, started after the placement of the food in the oral cavity and stopped when each portion was swallowed. RESULTS: There were no differences between groups regarding both the number of strokes and the chewing time. However, with regards to the number of strokes, CG and GII presented a significant concordance between the first and the second chewing situation, which was not observed in GIII. The analysis of time showed significant concordance between the first and second chewing situation in CG, reasonable concordance in GII, and discordance in GIII. CONCLUSION: Dentofacial deformities do not influence the number of chewing strokes or the chewing time. However, class III individuals do not show uniformity regarding these aspects.

Shape resonance spectrum of cytosine-guanine pairs.

Single and double strand breaks in DNA can be caused by low-energy electrons, the most abundant secondary products of the interaction of ionizing radiation to the biological matter. Attachment of these electrons to biomolecules lead to the formation of transient negative ions (TNIs) [1], often referred to as resonances, a process that may lead to significant vibrational excitation and dissociation. In the present study, we employ the parallel version [2] of the Schwinger Multichannel Method implemented with pseudopotentials [3] to obtain the shape resonance spectrum of cytosine-guanine (CG) pairs, with special attention to π* transient anion states. Recent experimental studies pointed out a quasi-continuum vibrational excitation spectrum for electron collisions against formic acid dimers [4], suggesting that electron attachment into π* valence orbitals could induce proton transfer in these dimers. In addition, our previous studies on the shape resonance spectra of the hydrogen-bonded complexes comprising formic acid and formamide units indicated interesting electron delocalization (localization) effects arising from the presence (absence) of inversion symmetry centers in the complexes [5]. In the present work, we extend the studies on hydrogen-bonded complexes to the CG pair, where localization of ¼¤ anions would be expected, based on the previous results. References [1]. B. Boudaïffa, P. Cloutier, D. Hunting, M. A. Huels, L. Sanche, Science 287, 1658 (2000). [2]. J. S. dos Santos, R. F. da Costa , M. T. do N. Varella, J. Chem. Phys. 136, 084307 (2012). [3]. M. H. F. Bettega, L. G. Ferreira, M. A. P. Lima, Phys. Rev. A 47, 1111 (1993). [4]. M. Allan, Phys. Rev. Lett. 98, 123201 (2007). [5]. T. C. Freitas, S. dA. Sanchez, M. T. do N. Varella, M. H. F. Bettega, Phys. Rev. A 84, 062714 (2011).

Avaliação hemodinâmica de duas vias de reposição volêmica em um modelo de hemorragia da veia cava caudal em porcos

Introdução: A reposição volêmica em pacientes traumatizados tem sido controvérsa. O A.T.L.S. recomenda a infusão de um grande volume de fluidos na fase inicial de tratamento, enquanto outros autores recomendam a administração somente quando do controle da hemorragia. O acesso venoso femoral é contra indicado em pacientes com trauma abdominal por temor de aumento de hemorragia. A solução hipertônica de NaCl a 7,5% (SH) possui benefícios consideráveis de logística e de recuperação hemodinâmica com pequenos volumes de infusão, semelhante as vantagens das soluções padrões isotônicas na fase pré-hospitalar. Objetivos: Criar um modelo de choque hemorrágico induzido por trauma venoso. Avaliar a hemodinâmica e o volume de hemorragia abdominal nos animais submetidos a choque hemorrágico e tratados com SH via acesso femoral e jugular. Métodos: Em 18 porcos da raça landrace, divididos em 3 grupos de 6 animais (Controle, Jugular e Femoral), foi induzido um choque hipovolêmico não controlado pela ruptura da veia cava caudal. Os animais do grupo controle (GC) foram observados por 40 minutos quanto ao seu padrão hemodinâmico de Pressão de Artéria Pulmonar (PAP), Pressão Artérial Média (PAM), Débito Cardíaco (DC) e Fluxo de Veia Porta (FVP), porém sem reposição volêmica. Os animais dos grupos Femoral (GC) e Jugular (GJ) foram tratados com 4 ml/Kg de solução hipertônica de NaCl a 7,5% (SH) aos 20 minutos de experimento. Ao final do experimento, o volume de hemorragia abdominal foi mensurado.Resultados: O grupo controle (GC) apresentou queda dos valores hemodinâmicos aos 10 minutos e estes permaneceram estáveis até o final do experimento. Os animais dos grupos tratamento (GF e GJ) apresentaram melhora da hemodinâmica aos 30 minutos, sem aumento da hemorragia abdominal. Conclusão: A solução hipertônica de NaCl (SH) permitiu a melhora parcial da hemodinâmica no modelo de choque hipovolêmico, sem aumento da hemorragia, independentemente do acesso utilizada para a infusão.

Strength training combined with plyometric jumps in adults: sex differences in fat-bone axis adaptations

[EN] Leptin and osteocalcin play a role in the regulation of the fat-bone axis and may be altered by exercise. To determine whether osteocalcin reduces fat mass in humans fed ad libitum and if there is a sex dimorphism in the serum osteocalcin and leptin responses to strength training, we studied 43 male (age 23.9 2.4 yr, mean +/- SD) and 23 female physical education students (age 23.2 +/- 2.7 yr). Subjects were randomly assigned to two groups: training (TG) and control (CG). TG followed a strength combined with plyometric jumps training program during 9 wk, whereas the CG did not train. Physical fitness, body composition (dual-energy X-ray absorptiometry), and serum concentrations of hormones were determined pre- and posttraining. In the whole group of subjects (pretraining), the serum concentration of osteocalcin was positively correlated (r = 0.29-0.42, P < 0.05) with whole body and regional bone mineral content, lean mass, dynamic strength, and serum-free testosterone concentration (r = 0.32). However, osteocalcin was negatively correlated with leptin concentration (r = -0.37), fat mass (r = -0.31), and the percent body fat (r = -0.44). Both sexes experienced similar relative improvements in performance, lean mass (+4-5%), and whole body (+0.78%) and lumbar spine bone mineral content (+1.2-2%) with training. Serum osteocalcin concentration was increased after training by 45 and 27% in men and women, respectively (P < 0.05). Fat mass was not altered by training. Vastus lateralis type II MHC composition at the start of the training program predicted 25% of the osteocalcin increase after training. Serum leptin concentration was reduced with training in women. In summary, while the relative effects of strength training plus plyometric jumps in performance, muscle hypertrophy, and osteogenesis are similar in men and women, serum leptin concentration is reduced only in women. The osteocalcin response to strength training is, in part, modulated by the muscle phenotype (MHC isoform composition). Despite the increase in osteocalcin, fat mass was not reduced.

Iliopsoas and gluteal muscles are asymmetric in tennis players but not in soccer players

[EN] PURPOSE: To determine the volume and degree of asymmetry of iliopsoas (IL) and gluteal muscles (GL) in tennis and soccer players. METHODS: IL and GL volumes were determined using magnetic resonance imaging (MRI) in male professional tennis (TP) and soccer players (SP), and in non-active control subjects (CG) (n = 8, 15 and 6, respectively). RESULTS: The dominant and non-dominant IL were hypertrophied in TP (24 and 36%, respectively, P<0.05) and SP (32 and 35%, respectively, P<0.05). In TP the asymmetric hypertrophy of IL (13% greater volume in the non-dominant than in the dominant IL, P<0.01) reversed the side-to-side relationship observed in CG (4% greater volume in the dominant than in the contralateral IL, P<0.01), whilst soccer players had similar volumes in both sides (P = 0.87). The degree of side-to-side asymmetry decreased linearly from the first lumbar disc to the pubic symphysis in TP (r = -0.97, P<0.001), SP (r = -0.85, P<0.01) and CG (r = -0.76, P<0.05). The slope of the relationship was lower in SP due to a greater hypertrophy of the proximal segments of the dominant IL. Soccer and CG had similar GL volumes in both sides (P = 0.11 and P = 0.19, for the dominant and contralateral GL, respectively). GL was asymmetrically hypertrophied in TP. The non-dominant GL volume was 20% greater in TP than in CG (P<0.05), whilst TP and CG had similar dominant GL volumes (P = 0.14). CONCLUSIONS: Tennis elicits an asymmetric hypertrophy of IL and reverses the normal dominant-to-non-dominant balance observed in non-active controls, while soccer is associated to a symmetric hypertrophy of IL. Gluteal muscles are asymmetrically hypertrophied in TP, while SP display a similar size to that observed in controls. It remains to be determined whether the different patterns of IL and GL hypertrophy may influence the risk of injury.

Identifikation transkriptioneller Alterationen menschlicher Tumoren und Entwicklung eines neuen auf RNA-Transfer basierenden Verfahrens zur Bestimmung der Genfunktion

Zielvorgaben der vorliegenden Arbeit war die Identifikation neuer selektiv in Tumoren aktivierter Gene sowie die Entwicklung eines methodischen Prozesses, um die molekularen Effekte der fehlerhaften Aktivierung solcher Gene zu untersuchen. Für die erste Fragestellung haben wir zwei komplementäre Methoden entwickelt. Zum einen haben wir nach neuen Mitglieder der Cancer/Germline (CG) Familie von Genen gesucht, die bereits attraktive Zielstrukturen laufender Phase I/IIa Studien sind. Zu diesem Zweck wurde ein bioinformatischer Data Mining Ansatz generiert. Dieser führte zur erfolgreichen in silico Klonierung neuer CG Gene. Zur Identifikation von in Tumorzellen überexprimierten Genen nutzten wir einen cDNA Mikroarray mit 1152 ausgewählten Genen mit direkter oder indirekter tumorimmunologischer oder tumorbiologischer Relevanz. Die komparative transkriptionelle Untersuchung von humanen Tumor- und Normalgeweben mit diesem Array führte zur Wiederentdeckung bereits bekannter, aber auch zur Aufdeckung bisher nicht beschriebener tumor-assoziierter Transkriptionsveränderungen. Der zweite große Schwerpunkt dieser Arbeit war die Technologieentwicklung eines versatilen Prozesses zur Untersuchung von molekularen Effekten eines aberrant in Zellen exprimierten Gens. Zur Simulation dieser Situation stellten wir in vitro transkribierte RNA dieses Gens her und elektroporierten diese in Zielzellen. Transkriptionsanalysen solcher Transfektanden mit Affymetrix Oligonukleotid Mikroarray deckten auf gesamt-genomischer Ebene ganze Kaskaden konsekutiver, transkriptioneller Alterationen auf.

Modeling and simulations of some anisotropic soft-matter systems: from biaxial to chiral materials

We have modeled various soft-matter systems with molecular dynamics (MD) simulations. The first topic concerns liquid crystal (LC) biaxial nematic (Nb) phases, that can be possibly used in fast displays. We have investigated the phase organization of biaxial Gay-Berne (GB) mesogens, considering the effects of the orientation, strength and position of a molecular dipole. We have observed that for systems with a central dipole, nematic biaxial phases disappear when increasing dipole strength, while for systems characterized by an offset dipole, the Nb phase is stabilized at very low temperatures. In a second project, in view of their increasing importance as nanomaterials in LC phases, we are developing a DNA coarse-grained (CG) model, in which sugar and phosphate groups are represented with Lennard-Jones spheres, while bases with GB ellipsoids. We have obtained shape, position and orientation parameters for each bead, to best reproduce the atomistic structure of a B-DNA helix. Starting from atomistic simulations results, we have completed a first parametrization of the force field terms, accounting for bonded (bonds, angles and dihedrals) and non-bonded interactions (H-bond and stacking). We are currently validating the model, by investigating stability and melting temperature of various sequences. Finally, in a third project, we aim to explain the mechanism of enantiomeric discrimination due to the presence of a chiral helix of poly(gamma-benzyl L-glutamate) (PBLG), in solution of dimethylformamide (DMF), interacting with chiral or pro-chiral molecules (in our case heptyl butyrate, HEP), after tuning properly an atomistic force field (AMBER). We have observed that DMF and HEP molecules solvate uniformly the PBLG helix, but the pro-chiral solute is on average found closer to the helix with respect to the DMF. The solvent presents a faster isotropic diffusion, twice as HEP, also indicating a stronger interaction of the solute with the helix.

Coarse-graining methods and polymer dynamics

This thesis studies molecular dynamics simulations on two levels of resolution: the detailed level of atomistic simulations, where the motion of explicit atoms in a many-particle system is considered, and the coarse-grained level, where the motion of superatoms composed of up to 10 atoms is modeled. While atomistic models are capable of describing material specific effects on small scales, the time and length scales they can cover are limited due to their computational costs. Polymer systems are typically characterized by effects on a broad range of length and time scales. Therefore it is often impossible to atomistically simulate processes, which determine macroscopic properties in polymer systems. Coarse-grained (CG) simulations extend the range of accessible time and length scales by three to four orders of magnitude. However, no standardized coarse-graining procedure has been established yet. Following the ideas of structure-based coarse-graining, a coarse-grained model for polystyrene is presented. Structure-based methods parameterize CG models to reproduce static properties of atomistic melts such as radial distribution functions between superatoms or other probability distributions for coarse-grained degrees of freedom. Two enhancements of the coarse-graining methodology are suggested. Correlations between local degrees of freedom are implicitly taken into account by additional potentials acting between neighboring superatoms in the polymer chain. This improves the reproduction of local chain conformations and allows the study of different tacticities of polystyrene. It also gives better control of the chain stiffness, which agrees perfectly with the atomistic model, and leads to a reproduction of experimental results for overall chain dimensions, such as the characteristic ratio, for all different tacticities. The second new aspect is the computationally cheap development of nonbonded CG potentials based on the sampling of pairs of oligomers in vacuum. Static properties of polymer melts are obtained as predictions of the CG model in contrast to other structure-based CG models, which are iteratively refined to reproduce reference melt structures. The dynamics of simulations at the two levels of resolution are compared. The time scales of dynamical processes in atomistic and coarse-grained simulations can be connected by a time scaling factor, which depends on several specific system properties as molecular weight, density, temperature, and other components in mixtures. In this thesis the influence of molecular weight in systems of oligomers and the situation in two-component mixtures is studied. For a system of small additives in a melt of long polymer chains the temperature dependence of the additive diffusion is predicted and compared to experiments.

Optimierung der Phenprocoumon-Dosierung durch intensivierte medizinisch-pharmazeutische Betreuung

Ein sorgfältiges INR-Monitoring ist wichtig für eine sichere und effektive Vitamin-K-antagonistische Therapie (VKA). Einer von vielen Faktoren, welcher die Einhaltung des INR-ZSB beeinflusst, ist die Compliance. Im Rahmen der vorliegenden Arbeit wurde erstmals die Effektivität einer intensiven medizinisch-pharmazeutischen Betreuung von Patienten mit Phenprocoumon-Therapie, unter besonderer Berücksichtung der Compliance, untersucht. 71 Patienten mit VKA-Therapie (Interventionsgruppe (IG) und Kontrollgruppe (KG)) wurden in die prospektive Studie eingeschlossen und über 6 Monate beobachtet. Patienten der IG erfuhren eine intensive medizinisch-pharmazeutische Betreuung im Thrombosedienst. Die Patienten der Kontrollgruppe wurden vom Hausarzt betreut. Zusätzlich fand eine Compliance-Messung mittels OtCM-Blistern (Objective-therapy-compliance-measurement-system) statt. Während die Compliance der Kontrollgruppe retrospektiv am Ende des Beobachtungszeitraums ausgewertet wurde, erfuhren die Patienten der Interventionsgruppe ein „real-time“ Monitoring der Phenprocoumon-Entnahme aus den Blistern. Nach per Protokoll-Analyse konnten die Daten von 58 Patienten ausgewertet werden. Patienten der IG zeigten eine signifikant bessere INR-Einhaltung im ZSB (Time in Therapeutic Range (TTR) 74%) im Vergleich zur Kontrollgruppe (TTR 53%; p= 0,001). Die verschiedenen gemessenen Compliance-Raten (Dosing-, Taking-, Timing Compliance und Drug Holidays) waren in der IG höher als in der KG. Patienten mit einer höheren TTR waren tendenziell besser compliant. Spezialisierte medizinisch-pharmazeutische Betreuung hat einen positiven Effekt auf das Outcome der VKA-Therapie.rnrn

Coarse-grained peptide models: conformational sampling, peptide association and dynamical properties for peptides

In dieser Arbeit wird ein vergröbertes (engl. coarse-grained, CG) Simulationsmodell für Peptide in wässriger Lösung entwickelt. In einem CG Verfahren reduziert man die Anzahl der Freiheitsgrade des Systems, so dass manrngrössere Systeme auf längeren Zeitskalen untersuchen kann. Die Wechselwirkungspotentiale des CG Modells sind so aufgebaut, dass die Peptid Konformationen eines höher aufgelösten (atomistischen) Modells reproduziert werden.rnIn dieser Arbeit wird der Einfluss unterschiedlicher bindender Wechsel-rnwirkungspotentiale in der CG Simulation untersucht, insbesondere daraufhin,rnin wie weit das Konformationsgleichgewicht der atomistischen Simulation reproduziert werden kann. Im CG Verfahren verliert man per Konstruktionrnmikroskopische strukturelle Details des Peptids, zum Beispiel, Korrelationen zwischen Freiheitsgraden entlang der Peptidkette. In der Dissertationrnwird gezeigt, dass diese “verlorenen” Eigenschaften in einem Rückabbildungsverfahren wiederhergestellt werden können, in dem die atomistischen Freiheitsgrade wieder in die CG-Strukturen eingefügt werden. Dies gelingt, solange die Konformationen des CG Modells grundsätzlich gut mit der atomistischen Ebene übereinstimmen. Die erwähnten Korrelationen spielen einerngrosse Rolle bei der Bildung von Sekundärstrukturen und sind somit vonrnentscheidender Bedeutung für ein realistisches Ensemble von Peptidkonformationen. Es wird gezeigt, dass für eine gute Übereinstimmung zwischen CG und atomistischen Kettenkonformationen spezielle bindende Wechselwirkungen wie zum Beispiel 1-5 Bindungs- und 1,3,5-Winkelpotentiale erforderlich sind. Die intramolekularen Parameter (d.h. Bindungen, Winkel, Torsionen), die für kurze Oligopeptide parametrisiert wurden, sind übertragbarrnauf längere Peptidsequenzen. Allerdings können diese gebundenen Wechselwirkungen nur in Kombination mit solchen nichtbindenden Wechselwirkungspotentialen kombiniert werden, die bei der Parametrisierung verwendet werden, sind also zum Beispiel nicht ohne weiteres mit einem andere Wasser-Modell kombinierbar. Da die Energielandschaft in CG-Simulationen glatter ist als im atomistischen Modell, gibt es eine Beschleunigung in der Dynamik. Diese Beschleunigung ist unterschiedlich für verschiedene dynamische Prozesse, zum Beispiel für verschiedene Arten von Bewegungen (Rotation und Translation). Dies ist ein wichtiger Aspekt bei der Untersuchung der Kinetik von Strukturbildungsprozessen, zum Beispiel Peptid Aggregation.rn

Simulations of amphiphilic peptides at the air-water interface

Amphiphile Peptide, Pro-Glu-(Phe-Glu)n-Pro, Pro-Asp-(Phe-Asp)n-Pro, und Phe-Glu-(Phe-Glu)n-Phe, können so aus n alternierenden Sequenzen von hydrophoben und hydrophilen Aminosäuren konstruiert werden, dass sie sich in Monolagen an der Luft-Wasser Grenzfläche anordnen. In biologischen Systemen können Strukturen an der organisch-wässrigen Grenzfläche als Matrix für die Kristallisation von Hydroxyapatit dienen, ein Vorgang der für die Behandlung von Osteoporose verwendet werden kann. In der vorliegenden Arbeit wurden Computersimulationenrneingesetzt, um die Strukturen und die zugrunde liegenden Wechselwirkungen welche die Aggregation der Peptide auf mikroskopischer Ebene steuern, zu untersuchen. Atomistische Molekulardynamik-Simulationen von einzelnen Peptidsträngen zeigen, dass sie sich leicht an der Luft-Wasser Grenzfläche anordnen und die Fähigkeit haben, sich in β-Schleifen zu falten, selbst für relativ kurze Peptidlängen (n = 2). Seltene Ereignisse wie diese (i.e. Konformationsänderungen) erfordern den Einsatz fortgeschrittener Sampling-Techniken. Hier wurde “Replica Exchange” Molekulardynamik verwendet um den Einfluss der Peptidsequenzen zu untersuchen. Die Simulationsergebnisse zeigten, dass Peptide mit kürzeren azidischen Seitenketten (Asp vs. Glu) gestrecktere Konformationen aufwiesen als die mit längeren Seitenketten, die in der Lage waren die Prolin-Termini zu erreichen. Darüber hinaus zeigte sich, dass die Prolin-Termini (Pro vs. Phe) notwendig sind, um eine 2D-Ordnung innerhalb derrnAggregate zu erhalten. Das Peptid Pro-Asp-(Phe-Asp)n-Pro, das beide dieser Eigenschaften enthält, zeigt das geordnetste Verhalten, eine geringe Verdrehung der Hauptkette, und ist in der Lage die gebildeten Aggregate durch Wasserstoffbrücken zwischen den sauren Seitenketten zu stabilisieren. Somit ist dieses Peptid am besten zur Aggregation geeignet. Dies wurde auch durch die Beurteilung der Stabilität von experimentnah-aufgesetzten Peptidaggregaten, sowie der Neigung einzelner Peptide zur Selbstorganisation von anfänglich ungeordneten Konfigurationen unterstützt. Da atomistische Simulationen nur auf kleine Systemgrößen und relativ kurze Zeitskalen begrenzt sind, wird ein vergröbertes Modell entwickelt damit die Selbstorganisation auf einem größeren Maßstab studiert werden kann. Da die Selbstorganisation an der Grenzfläche vonrnInteresse ist, wurden existierenden Vergröberungsmethoden erweitert, um nicht-gebundene Potentiale für inhomogene Systeme zu bestimmen. Die entwickelte Methode ist analog zur iterativen Boltzmann Inversion, bildet aber das Update für das Interaktionspotential basierend auf der radialen Verteilungsfunktion in einer Slab-Geometrie und den Breiten des Slabs und der Grenzfläche. Somit kann ein Kompromiss zwischen der lokalen Flüssigketsstruktur und den thermodynamischen Eigenschaften der Grenzfläche erreicht werden. Die neue Methode wurde für einen Wasser- und einen Methanol-Slab im Vakuum demonstriert, sowie für ein einzelnes Benzolmolekül an der Vakuum-Wasser Grenzfläche, eine Anwendung die von besonderer Bedeutung in der Biologie ist, in der oft das thermodynamische/Grenzflächenpolymerisations-Verhalten zusätzlich der strukturellen Eigenschaften des Systems erhalten werden müssen. Daraufrnbasierend wurde ein vergröbertes Modell über einen Fragment-Ansatz parametrisiert und die Affinität des Peptids zur Vakuum-Wasser Grenzfläche getestet. Obwohl die einzelnen Fragmente sowohl die Struktur als auch die Wahrscheinlichkeitsverteilungen an der Grenzfläche reproduzierten, diffundierte das Peptid als Ganzes von der Grenzfläche weg. Jedoch führte eine Reparametrisierung der nicht-gebundenen Wechselwirkungen für eines der Fragmente der Hauptkette in einem Trimer dazu, dass das Peptid an der Grenzfläche blieb. Dies deutet darauf hin, dass die Kettenkonnektivität eine wichtige Rolle im Verhalten des Petpids an der Grenzfläche spielt.

Statistical methods for the analysis of DNA sequences: application to dinucleotide distribution in the human genome

Questa tesi si inserisce nell'ambito delle analisi statistiche e dei metodi stocastici applicati all'analisi delle sequenze di DNA. Nello specifico il nostro lavoro è incentrato sullo studio del dinucleotide CG (CpG) all'interno del genoma umano, che si trova raggruppato in zone specifiche denominate CpG islands. Queste sono legate alla metilazione del DNA, un processo che riveste un ruolo fondamentale nella regolazione genica. La prima parte dello studio è dedicata a una caratterizzazione globale del contenuto e della distribuzione dei 16 diversi dinucleotidi all'interno del genoma umano: in particolare viene studiata la distribuzione delle distanze tra occorrenze successive dello stesso dinucleotide lungo la sequenza. I risultati vengono confrontati con diversi modelli nulli: sequenze random generate con catene di Markov di ordine zero (basate sulle frequenze relative dei nucleotidi) e uno (basate sulle probabilità di transizione tra diversi nucleotidi) e la distribuzione geometrica per le distanze. Da questa analisi le proprietà caratteristiche del dinucleotide CpG emergono chiaramente, sia dal confronto con gli altri dinucleotidi che con i modelli random. A seguito di questa prima parte abbiamo scelto di concentrare le successive analisi in zone di interesse biologico, studiando l’abbondanza e la distribuzione di CpG al loro interno (CpG islands, promotori e Lamina Associated Domains). Nei primi due casi si osserva un forte arricchimento nel contenuto di CpG, e la distribuzione delle distanze è spostata verso valori inferiori, indicando che questo dinucleotide è clusterizzato. All’interno delle LADs si trovano mediamente meno CpG e questi presentano distanze maggiori. Infine abbiamo adottato una rappresentazione a random walk del DNA, costruita in base al posizionamento dei dinucleotidi: il walk ottenuto presenta caratteristiche drasticamente diverse all’interno e all’esterno di zone annotate come CpG island. Riteniamo pertanto che metodi basati su questo approccio potrebbero essere sfruttati per migliorare l’individuazione di queste aree di interesse nel genoma umano e di altri organismi.

Contributions to exact approaches in combinatorial optimization

The focus of this thesis is to contribute to the development of new, exact solution approaches to different combinatorial optimization problems. In particular, we derive dedicated algorithms for a special class of Traveling Tournament Problems (TTPs), the Dial-A-Ride Problem (DARP), and the Vehicle Routing Problem with Time Windows and Temporal Synchronized Pickup and Delivery (VRPTWTSPD). Furthermore, we extend the concept of using dual-optimal inequalities for stabilized Column Generation (CG) and detail its application to improved CG algorithms for the cutting stock problem, the bin packing problem, the vertex coloring problem, and the bin packing problem with conflicts. In all approaches, we make use of some knowledge about the structure of the problem at hand to individualize and enhance existing algorithms. Specifically, we utilize knowledge about the input data (TTP), problem-specific constraints (DARP and VRPTWTSPD), and the dual solution space (stabilized CG). Extensive computational results proving the usefulness of the proposed methods are reported.