<p>\abstract</p><p>Transcription and translation describe the flow of genetic information from DNA to mRNA to protein. Recent studies show that at a single cell level, these processes are stochastic, which results in the variation of the number of mRNA and proteins even under identical environmental conditions. Because the number of mRNA and protein in each single cell are actually very small, these variations can be crucial for cellular function in diverse contexts, such as development, stress response, immunological and nervous system function. Most studies examine the origin and effects of stochastic gene expression using computer simulations. My goal is to develop a theoretical framework to study activity-dependent gene expression using simplified models that capture essential features. </p><p>I have examined the dynamics of stochastic gene regulation in three contexts. First, I examine how fluctuations in promoter accessibility lead to "bursty" transcription, during which genes are turned "on" or "off" stochastically. I describe a mathematical formalism to represent bursty gene expression in a coarse-grained manner as a Markov process and derive a master equation for the time evolution of the probability distribution of the number of mRNA molecules. This allows us to examine how transcript number responds to time varying stimuli. This model forms a basic building block for understanding the signal transmission and noise of the transcription process to time varying inputs as would be sensed by cells in dynamic environments. In addition to synthesis, gene expression is subject to additional modes of regulation. One such mechanism that controls transcript numbers is by microRNAs (miRNAs), which pair with target mRNAs to repress protein production following transcription. Although hundreds of miRNAs have been identified in mammalian genomes, the function of miRNA-based repression in the context of gene regulation networks still remains unclear. I explore the functional roles of feedback regulation by miRNAs and show that protein fluctuations strongly depend on the mode of miRNA-mediated repression. I discuss the functional implications of protein fluctuations arising from miRNA-mediated repression on gene regulatory networks. Finally, I examine the impact of fluctuations on alternative splicing, which is a major source for proteomic complexity in higher eukaryotes. Although the proteins regulating alternative splicing have been extensively studied, little is known about how noise arising from the stochastic nature of alternative splicing contributes to the entire gene expression process. I explore the functional roles and noise properties of alternative splicing, focusing on the case of exon skipping and intron retention. I show that while the overall counts of the mRNAs of the two isoforms are independent and Poisson distributed, diffusion and binding of the splicing factors contributes to the variance in the abundance of the isoforms. </p><p>Noise in gene expression may be of particular relevance in the nervous system. Environmental stimuli drive the rapid remodeling of neural circuitry in part by inducing the activation of genes to make proteins that modify neuronal excitability and connectivity, ultimately influencing higher order brain function. Finally, I examine the implications of our studies for activity dependent gene expression in the nervous system.</p> / Dissertation

Orientador: Prof. Dr.Fernando Luis Semião da Silva / Tese (doutorado) - Universidade Federal do ABC, Programa de Pós-Graduação em Física, 2015. / A presente tese de doutorado tem como principal objetivo empregar luz quantizada para o controle e medida em sistemas complexos como em um conjunto de cromóforos, e em um condensado de Bose-Einstein. Em especial, desenvolvemos formalismos de pulsos e equações mestras aplicáveis a esses sistemas e utilizamos teoria de estimativa quântica para determinar quantidades atômicas relevantes de maneira indireta (medindo propriedades da luz). Também empregamos técnicas variadas para obtenção de equações mestras para estudar diferentes problemas envolvendo interação de luz quântica com matéria. Em um caso, obtivemos uma equação mestra microscópica para o estudo de dois sistemas de dois níveis acoplados no espaço livre, e mostramos como a equação mestra microscópica desse sistema se distingue de equações fenomenológicas para o mesmo. Por fim, também discutimos a obtenção de uma equação mestra para o estudo de transferência de emaranhamento entre o campo eletromagnético quantizado e complexos Fenna-Matthews-Olson localizados em cavidades óticas distintas. / The main aim of the present Ph.D. thesis is to employ quantized light to control and measurement of complex systems such as a set of chromophores and a Bose- Einstein condensate in a double well. Specifically, we develop a formalism for pulses and master equations that can be applied to those systems and use quantum estimation theory to get information on relevant parameters in atomic system in a indirect way (measuring light properties). We also employ varied techniques for the obtention of master equations to study different problems involving the interaction of quantum light and matter. We obtained a microscopic master equation for the study of two coupled two-level systems in the free space, and we showed how the microscopic master equation of this system distinguish from the phenomenological ones. Finally, we also discuss the obtention of a master equation for the study of the transference of entanglement between the quantized electromagnetic field and the Fenna-Matthews-Olson complex localized in distinct optical cavities.

Das Verhalten adhärenter Zellen hängt stark von den chemischen, topographischen und mechanischen Eigenschaften ihrer Umgebung ab. Experimentelle Untersuchungen der letzten Jahre haben gezeigt, dass adhärente Zellen aktiv die elastischen Eigenschaften ihrer Umgebung erkunden, indem sie an dieser ziehen. Der resultierende Kraftaufbau hängt von den elastischen Eigenschaften der Umgebung ab und wird an den Adhäsionskontakten in entsprechende biochemische Signale umgewandelt, die zelluläre Programme wie Wachstum, Differenzierung, programmierten Zelltod und Zellbewegung mitbestimmen. Im Allgemeinen sind Kräfte wichtige Einflussgrößen in biologischen Systemen. Weitere Beispiele dafür sind Hör- und Tastsinn, Wundheilung sowie die rollende Adhäsion von weißen Blutkörperchen auf den Wänden der Blutgefäße. In der Habilitationsschrift von Ulrich Schwarz werden mehrere theoretische Projekte vorgestellt, die die Rolle von Kräften und Elastizität in der Zelladhäsion untersuchen.<br /> (1) Es wurde eine neue Methode entwickelt, um die Kräfte auszurechnen, die Zellen an den Kontaktpunkten auf mikro-strukturierte elastische Substrate ausüben. Das Hauptergebnis ist, dass Zell-Matrix-Kontakte als Mechanosensoren funktionieren, an denen interne Kräfte in Proteinaggregation umgewandelt werden.<br /> (2) Eine Ein-Schritt-Master-Gleichung, die die stochastische Dynamik von Adhäsionsclustern als Funktion von Clustergröße, Rückbindungsrate und Kraft beschreibt, wurde sowohl analytisch als auch numerisch gelöst. Zudem wurde dieses Modell auf Zell-Matrix-Kontakte, dynamische Kraftspektroskopie sowie die rollende Adhäsion angewandt.<br /> (3) Im Rahmen der linearen Elastizitätstheorie und mit Hilfe des Konzepts der Kraftdipole wurde ein Modell formuliert und gelöst, das die Positionierung und Orientierung von Zellen in weicher Umgebung vorhersagt. Diese Vorhersagen sind in guter Übereinstimmung mit zahlreichen experimentellen Beobachtungen für Fibroblasten auf elastischen Substraten und in Kollagen-Gelen. / The behaviour of an adhering cell is strongly influenced by the chemical, topographical and mechanical properties of the surface it attaches to. During recent years, it has been found experimentally that adhering cells actively sense the elastic properties of their environment by pulling on it through numerous sites of adhesion. The resulting build-up of force at sites of adhesion depends on the elastic properties of the environment and is converted into corresponding biochemical signals, which can trigger cellular programmes like growth, differentiation, apoptosis, and migration. In general, force is an important regulator of biological systems, for example in hearing and touch, in wound healing, and in rolling adhesion of leukocytes on vessel walls. In the habilitation thesis by Ulrich Schwarz, several theoretical projects are presented which address the role of forces and elasticity in cell adhesion.<br /> (1) A new method has been developed for calculating cellular forces exerted at sites of focal adhesion on micro-patterned elastic substrates. The main result is that cell-matrix contacts function as mechanosensors, converting internal force into protein aggregation.<br /> (2) A one-step master equation for the stochastic dynamics of adhesion clusters as a function of cluster size, rebinding rate and force has been solved both analytically and numerically. Moreover this model has been applied to the regulation of cell-matrix contacts, to dynamic force spectroscopy, and to rolling adhesion.<br /> (3) Using linear elasticity theory and the concept of force dipoles, a model has been introduced and solved which predicts the positioning and orientation of mechanically active cells in soft material, in good agreement with experimental observations for fibroblasts on elastic substrates and in collagen gels.

Questa tesi di dottorato studia l’interazione della cooperatività con il rumore in sistemi realistici, focalizzandosi principalmente sulla superradianza. Gli effetti cooperativi emergono dall’interazione collettiva di un insieme di elementi con un campo esterno. Esempi degni di nota sono la superconduttività, dove le coppie di Cooper elettroniche interagiscono con le vibrazioni reticolari, le eccitazioni di plasma, che sorgono dall'interazione collettiva degli elettroni in un metallo con il campo coulombiano, e la superradianza, ovvero quel processo di emissione spontanea cooperativa che sorge da un aggregato di emettitori identici. Gli effetti cooperativi sono tipicamente robusti al disordine e al rumore, cosa che li rende interessanti per delle applicazioni a dispositivi quantistici che possano operare a temperatura ambiente. In questo lavoro, inizialmente, introduciamo un formalismo di “master equations” che descrive l’accoppiamento collettivo di un aggregato di emettitori/assorbitori con il campo elettromagnetico, valido quando le dimensioni dell'aggregato sono sia maggiori che minori della lunghezza d’onda emessa/assorbita. Inoltre, il formalismo è valido per accoppiamento sia debole che forte con il campo elettromagnetico e, cosa più importante, permette di descrivere correttamente la superradianza in diversi regimi. In tale formalismo, studiamo l’interazione tra superradianza e rumore termico sia per nanotubi molecolari (di dimensioni minori della lunghezza d’onda associata alla transizione) che sono presenti nei complessi antenna fotosintetici dei Green Sulfur Bacteria, sia pure per superreticoli di quantum dots di nuova generazione, aventi dimensioni maggiori della lunghezza d’onda emessa. In entrambi i casi si dimostra che la coerenza può permanere in presenza di rumore termico alle temperature a cui questi sistemi sono stati analizzati sperimentalmente (temperatura ambiente per i nanotubi molecolari, e 6 K per i superreticoli di quantum dots). Nello specifico, nei nanotubi molecolari mostriamo che la macroscopica delocalizzazione coerente delle eccitazioni a temperatura ambiente, che copre centinaia di molecole, può essere considerata un effetto emergente che origina dall’effetto combinato della specifica disposizione geometrica delle molecole e della presenza di accoppiamenti tra subunità del cilindro, incrementati dagli effetti cooperativi. Questi risultati aprono la strada a nuovi modi per ingegnerizzare dei “quantum wires” robusti al rumore grazie alla cooperatività. Inoltre, la presente analisi di sistemi allo stato solido basati su superreticoli di “quantum dots” di perovskite (CsPbBr3) fornisce una base teorica in grado di comprendere recenti osservazioni di emissione superradiante. Sulla base della nostra teoria, suggeriamo che futuri esperimenti dove si utilizzino quantum dots più piccoli, potrebbe aumentare significativamente la robustezza del sistema al rumore termico, aprendo la strada verso la superradianza a temperatura ambiente in sistemi allo stato solido. Si considerano anche i complessi antenna dei Purple Bacteria, dove è ben risaputo che gli effetti cooperativi incrementano il trasferimento e l’accumulo di eccitazioni generate dalla luce assorbita. Mostriamo come queste proprietà possono essere sfruttate per creare un laser ispirato a sistemi biologici e basato su aggregati molecolari, dove la luce solare, benché debole, sarebbe utilizzata come sorgente di pompaggio. Il trasferimento efficiente di energia dentro questo sistema, all’atto pratico, focalizzerebbe l’eccitazione assorbita in direzione di un dimero molecolare, composto da una coppia di molecole interagenti, opportunamente scelte. L’orientazione dei momenti di dipolo di transizione in ciascun dimero è tale da concentrare tutta l’intensità del dipolo nel livello a più alta energia, lasciando lo stato eccitonico inferiore otticamente inattivo. Un dimero molecolare in tale configurazione, che è ideale per ottenere inversione di popolazione, è chiamato “H-dimer”. Tale H-dimer, nell’archittettura qui proposta per un laser ispirato a sistemi biologici, è posto al centro di un aggregato molecolare ispirato a sistemi biologici. Gli H-dimers, eccitati dagli aggregati molecolari circostanti, raggiungono inversione di popolazione e, dunque, possono emettere luce laser quando tali aggregati sono posti in una cavità ottica. Convertire l’energia incoerente fornita dal Sole in un fascio laser coerente supererebbe diverse limitazioni pratiche inerenti all’utilzzo della luce solare come sorgente di energia pulita. Per esempio, i fasci laser sono molto efficienti nell’avviare reazioni chimiche che convertono la luce solare in energia chimica. Inoltre, dal momento che i complessi fotosintetici batterici tendono ad operare nella regione spettrale del vicino infrarosso, la nostra proposta si presta in modo naturale a realizzare laser a infrarossi a corta lunghezza d’onda, i cui fasci viaggerebbero per lunghe distanze senza quasi perdere energia, quindi distribuendo in modo efficiente l’energia solare raccolta. Nella ricerca di un meccanismo comune alla cooperatività e alla sua robustezza, abbiamo confrontato il modello delle coppie di Cooper della superconduttività con la superradianza in singola eccitazione, mostrando molte somiglianze tra i due fenomeni: in particolare, i sistemi superradianti presentano una “gap” immaginaria nel piano complesso (ovvero, una segregazione tra i tempi di vita degli autostati del sistema) che, in modo simile alla gap superconduttiva, rende questi sistemi robusti al rumore statico. Più in generale, mostriamo che ogni interazione a lungo raggio tra i costituenti di un sistema induce effetti collettivi, manifestati da delle gap nello spettro eccitonico. Perciò, la nostra analisi successiva considera l’effetto delle interazioni a lungo raggio sul trasporto eccitonico lungo catene disordinate. Dimostriamo che la presenza di uno stato collettivo ben separato dagli altri stati influenza tutto lo spettro del sistema, generando dei regimi molto controintuitivi dove il trasporto è incrementato dal disordine o è indipendente da esso, e tali regimi si estendono su molti ordini di grandezza nell’intensità del disordine. Dimostriamo anche che una catena fortemente accoppiata a un modo del campo elettromagnetico in una cavità ottica è equivalente a una catena con interazione a lungo raggio, mostrandosi dunque molto promettente per esperimenti e applicazioni future. Nello specifico, mostriamo che catene molecolari realistiche, ioni intrappolati realizzati allo stato dell’arte e atomi di Rydberg sono tutti in grado di raggiungere l’intensità di interazione a lungo raggio tale per cui il trasporto sarebbe incrementato dal disordine o indipendente da esso, puntando alla realizzazione di un trasporto di energia senza dissipazione in “quantum wires” disordinati. / This Ph.D. thesis studies the interplay of cooperativity and noise in realistic systems, largely focusing on superradiance. Cooperative effects emerge from the collective interaction of an ensemble of elements to an external field. Notable examples are superconductivity, where the electron Cooper pairs interact with the lattice vibrations, plasmon excitations, arising from the collective interaction of electrons in a metal with the Coulomb field, and superradiance, that is a cooperative spontaneous emission process stemming from an aggregate of identical emitters. Cooperative effects are typically robust to disorder and noise, making them interesting for applications to quantum devices operating at room temperature. In this work, we first present a general master equation formalism that describes the collective coupling of an aggregate of emitters/absorbers to the electromagnetic field, valid both when the size of the aggregate is larger or smaller than the emitted/absorbed wavelength. Also, the formalism is valid both for weak and strong coupling of the emitters to the electromagnetic field and, most importantly, it allows to correctly describe superradiance in different regimes. Within such formalism, the interplay of superradiance and thermal noise is studied both for molecular nanotubes (of size smaller than the transition wavelength) that are present in the antenna complexes of photosynthetic Green Sulfur Bacteria, and also for novel solid state quantum dot superlattices, having size larger than the emitted wavelength. In both cases it is shown that coherence can persist in presence of thermal noise at the temperatures where these systems have been experimentally analyzed (room temperature for molecular nanotubes, and 6 K for quantum dot superlattices). Specifically, in natural molecular nanotubes we show that the macroscopic coherent delocalization of the excitation at room temperature, covering hundreds of molecules, can be considered an emergent effect originating from the combined effect of the specific geometric disposition of the molecules and the presence of cooperatively enhanced couplings between cylinder subunits. These results open the path to new ways of engineering quantum wires robust to noise thanks to cooperativity. Moreover, our analysis of solid state systems based on perovskite (CsPbBr3) quantum dot superlattices provides a theoretical framework able to explain recent observations of superradiant emission. Based on our theory, we suggest that further experiments, using smaller quantum dots, could significantly increase the robustness of the system to thermal noise, paving the way towards room-temperature superradiance in solid-state systems. We also considered the antenna complexes of Purple Bacteria, where cooperative effects are well known to boost the transfer and storage of photo-absorbed excitations. We show how these properties can be exploited to create a bio-inspired molecular aggregate laser medium, where natural sunlight, although weak, would be used as a pumping source. The efficient energy transfer within this system would effectively focus the absorbed excitation on a suitably chosen molecular dimer, composed by a pair of interacting molecules. The orientation of the molecule transition dipole moment in each dimer is such to concentrate all the dipole strength in the highest energy level, leaving the lower excitonic state dark. A molecular dimer in such configuration, which is ideal to achieve population inversion, is called H-dimer. Such an H-dimer in our proposed architecture for a bio-inspired laser medium, is placed at the center of the bio-inspired molecular aggregates. The H-dimers, pumped by the surrounding molecular aggregates, reach population inversion and, therefore, can lase when such aggregates are placed in an optical cavity. Turning the incoherent energy supply provided by the Sun into a coherent laser beam would overcome several of the practical limitations inherent in using sunlight as a source of clean energy. For example, laser beams are highly effective at driving chemical reactions which convert sunlight into chemical energy. Further, since bacterial photosynthetic complexes tend to operate in the near-infrared spectral region, our proposal naturally lends itself for realising short-wavelength infrared lasers which would allow their beams to travel nearly losslessly over large distances, thus efficiently distributing the collected sunlight energy. In search of a common mechanism to cooperativity and its robustness, we have compared the Cooper pair model of superconductivity and single-excitation superradiance, showing many similarities between the two: in particular, superradiant systems present an imaginary gap in the complex plane (that is, a segregation between the lifetimes of the system eigenstates) that, similarly to the superconducting gap, makes these systems robust to static disorder. More in general, we show that any long-range interaction between the constituents of a system generates collective behaviours, manifested by gaps in the excitonic spectrum. Therefore, our further analysis considers the effect of long-range interactions on excitation transport along disordered chains. We show that the presence of a gapped, collective state affects the whole spectrum of the system, generating quite counter-intuitive disorder-enhanced and disorder-independent transport regimes, that extend over many orders of magnitude of the disorder strength. We also prove that a chain strongly coupled to a cavity mode is equivalent to a long-range interacting chain, thus being very promising for future experiments and applications. Specifically, we show that realistic molecular chains, state-of-the-art trapped ions and Rydberg atoms are all able to reach the needed long-range interaction strength that would show disorder-enhanced or disorder-independent transport, aiming to the realization of dissipationless transport of energy in disordered quantum wires.