[pt] Uma propriedade notável dos sistemas biológicos é a formação de estruturas espaciais. Estas podem surgir por auto-organização, como consequência das próprias interações entre os indivíduos. Para estudar estas estruturas e como elas emergem, têm sido muito úteis modelos simples para a dinâmica da densidade espacial de uma população, que levam em conta apenas certos processos elementares (como reprodução, competição e dispersão). Em particular, a equação de FKPP (Fisher-Kolmogorov- Petrovski-Piskunov), que inclui simplesmente o crescimento logístico mais a difusão normal, é um modelo clássico para a dinâmica de uma população de uma única espécie. Dentro do quadro minimalista da equação de FKPP e suas variantes, a competição à distância (ou, não local) é a principal responsável por produzir oscilações espaciais na densidade da população. Entretanto, a não localidade pode ocorrer também nos demais processos. Assim, um primeiro objetivo desta tese é investigar como as diferentes escalas espaciais presentes podem interferir entre si, afetando a formação de padrões. Para isso, consideramos uma generalização da equação de FKPP em que todos os termos são não locais, em um ambiente homogêneo com condições de contorno periódicas. Enquanto a competição é o principal processo por trás da formação de padrões, mostramos que os outros dois podem agir de forma construtiva ou destrutiva. Por exemplo, a difusão, que comumente homogeniza, pode favorecer a formação de padrões dependendo do formato e alcance das funções de influência de cada processo. Em um segundo estudo, motivado por resultados experimentais, procuramos entender como a variabilidade da difusividade pode impactar a organização espacial da população dentro e fora de um refúgio (região de alta qualidade imersa em um ambiente hostil). Para tanto, consideramos uma outra generalização da equação de FKPP, com não localidade apenas no processo de competição intra-espécie, e modificada para levar em conta a presença do refúgio. Além da dependência espacial da taxa de crescimento, que é a principal característica distintiva de um refúgio em um ambiente hostil, também consideramos o fato de que a mobilidade pode ser heterogênea no espaço ou depender da densidade populacional. Focamos em dois casos em que a difusividade responde à densidade de indivíduos, diminuindo ou aumentando com a densidade populacional. Para comparação, também abordamos a difusividade dependente do espaço, com valores diferentes dentro e fora do refúgio. Observamos que o limiar da formação de padrões, no espaço de parâmetros, é bastante robusto diante destas heterogeneidades. Por outro lado, a dependência com a densidade pode produzir uma realimentação que está ausente em meios homogêneos, e que afeta a forma dos padrões. Em todos os casos, os resultados foram obtidos mediante a integração numérica das equações integro-diferenciais e realizando considerações analíticas. / [en] A remarkable property of biological systems is the formation of spatial structures. These can arise by self-organization, as a consequence of the interactions between individuals. To study these structures and how they emerge, simple models for the dynamics of the spatial density of a population, which take into account only certain elementary processes (such as reproduction, competition and dispersion) have been very useful. In particular, the FKPP (Fisher-Kolmogorov-Petrovski-Piskunov) equation, which simply includes logistic growth plus normal diffusion, is a classic model for the dynamics of a population of a single species. Within the minimalist framework of the FKPP equation and its variants, distance (or, non-local) competition is primarily responsible for producing spatial oscillations in population density. However, non-locality can also be present in other processes. Then, a first objective of this thesis is to investigate how the different spatial scales which are present in each process can interfere between them, affecting the formation of patterns in a homogeneous environment with periodic boundary conditions. For this purpose, we consider a generalization of the FKPP equation in which all terms are nonlocal. While competition is the main process behind pattern formation, we show that the other two can act constructively or destructively. For example, diffusion, which commonly homogenizes, can favor the formation of patterns depending on the format and range of the influence functions of each process. In a second study, motivated by experimental results, we seek to understand how the variability of the diffusivity can impact the spatial organization of the population inside and outside a refuge (a high-quality region immersed in a hostile environment). Therefore, we consider another generalization of the FKPP equation, with non-locality only in the intra-species competition process, modified to take into account the presence of the refuge. In addition to the spatial dependence of the growth rate, which is the main distinguishing feature of a refuge in a hostile environment, we also consider the fact that mobility can be spatially heterogeneous or depend on population density. We focus on two cases in which diffusivity responds to the density of individuals, decreasing or increasing with population density. For comparison, we also address spacedependent diffusivity, with different values inside and outside the refuge. We observed that the threshold of pattern formation in parameter space is quite robust under the presence of these heterogeneities. On the other hand, density dependence can produce a feedback that is absent in homogeneous media, and that affects the shape of the patterns. In all cases, the results were obtained by numerical simulations of the integro-differential equations and by analytical considerations.

A new method, probability distribution of diffusivities (time scaled square displacements between succeeding video frames), was developed to analyze single molecule tracking (SMT) experiments. This method was then applied to SMT experiments on ultrathin liquid tetrakis(2-ethylhexoxy)silane (TEHOS) films on Si wafer with 100 nm thermally grown oxide, and on thin semectic liquid crystal films. Spatial maps of diffusivities from SMT experiments on 220 nm thick semectic liquid crystal films reveal structure related dynamics. The SMT experiments on ultrathin TEHOS films were complemented by fluorescence correlation spectroscopy (FCS). The observed strongly heterogeneous single molecule dynamics within those films can be explained by a three-layer model consisting of (i) dye molecules adsorbed to the substrate, (ii) slowly diffusing molecules in the laterally heterogeneous near-surface region of 1 - 2 molecular diameters, and (iii) freely diffusing dye molecules in the upper region of the film. FCS and SMT experiments reveal a strong influence of substrate heterogeneity on SM dynamics. Thereby chemisorption to substrate surface silanols plays an important role. Vertical mean first passage times (mfpt) in those films are below 1 µs. This appears as fast component in FCS autocorrelation curves, which further contain a contribution from lateral diffusion and from adsorption events. Therefore, the FCS curves are approximated by a tri-component function, which contains an exponential term related to the mfpt, the correlation function for translational diffusion and a stretched exponential term for the broad distribution of adsorption events. Lateral diffusion coefficients obtained by FCS on 10 nm thick TEHOS films, thereby, are effective diffusion coefficients from dye transients in the focal area. They strongly depend on the substrate heterogeneity. Variation of the frame times for the acquisition of SMT experiments in steps of 20 ms from 20 ms to 200 ms revealed a strong dependence of the corresponding probability distributions of diffusivities on time, in particular in the range between 20 ms and 100 ms. This points to average dwell times of the dye molecules in at least one type of the heterogeneous regions (e.g. on and above silanol clusters) in the range of few tens of milliseconds. Furthermore, time series of SM spectra from Nile Red in 25 nm thick poly-n-alkyl-methacrylate (PnAMA) films were studied. In analogy to translational diffusion, spectral diffusion (shifts in energetic positions of SM spectra) can be studied by probability distributions of spectral diffusivities, i.e. time scaled square energetic displacements. Simulations were run and analyzed to study contributions from noise and fitting uncertainty to spectral diffusion. Furthermore the effect of spectral jumps during acquisition of a SM spectrum was investigated. Probability distributions of spectral diffusivites of Nile Red probing vitreous PnAMA films reveal a two-level system. In contrast, such probability distributions obtained from Nile Red within a 25 nm thick poly-n-butylmethacrylate film around glass transition and in the melt state, display larger spectral jumps. Moreover, for longer alkyl side chains a solvent shift to higher energies is observed, which supports the idea of nanophase separation within those polymers.

A new method, probability distribution of diffusivities (time scaled square displacements between succeeding video frames), was developed to analyze single molecule tracking (SMT) experiments. This method was then applied to SMT experiments on ultrathin liquid tetrakis(2-ethylhexoxy)silane (TEHOS) films on Si wafer with 100 nm thermally grown oxide, and on thin semectic liquid crystal films. Spatial maps of diffusivities from SMT experiments on 220 nm thick semectic liquid crystal films reveal structure related dynamics. The SMT experiments on ultrathin TEHOS films were complemented by fluorescence correlation spectroscopy (FCS). The observed strongly heterogeneous single molecule dynamics within those films can be explained by a three-layer model consisting of (i) dye molecules adsorbed to the substrate, (ii) slowly diffusing molecules in the laterally heterogeneous near-surface region of 1 - 2 molecular diameters, and (iii) freely diffusing dye molecules in the upper region of the film. FCS and SMT experiments reveal a strong influence of substrate heterogeneity on SM dynamics. Thereby chemisorption to substrate surface silanols plays an important role. Vertical mean first passage times (mfpt) in those films are below 1 µs. This appears as fast component in FCS autocorrelation curves, which further contain a contribution from lateral diffusion and from adsorption events. Therefore, the FCS curves are approximated by a tri-component function, which contains an exponential term related to the mfpt, the correlation function for translational diffusion and a stretched exponential term for the broad distribution of adsorption events. Lateral diffusion coefficients obtained by FCS on 10 nm thick TEHOS films, thereby, are effective diffusion coefficients from dye transients in the focal area. They strongly depend on the substrate heterogeneity. Variation of the frame times for the acquisition of SMT experiments in steps of 20 ms from 20 ms to 200 ms revealed a strong dependence of the corresponding probability distributions of diffusivities on time, in particular in the range between 20 ms and 100 ms. This points to average dwell times of the dye molecules in at least one type of the heterogeneous regions (e.g. on and above silanol clusters) in the range of few tens of milliseconds. Furthermore, time series of SM spectra from Nile Red in 25 nm thick poly-n-alkyl-methacrylate (PnAMA) films were studied. In analogy to translational diffusion, spectral diffusion (shifts in energetic positions of SM spectra) can be studied by probability distributions of spectral diffusivities, i.e. time scaled square energetic displacements. Simulations were run and analyzed to study contributions from noise and fitting uncertainty to spectral diffusion. Furthermore the effect of spectral jumps during acquisition of a SM spectrum was investigated. Probability distributions of spectral diffusivites of Nile Red probing vitreous PnAMA films reveal a two-level system. In contrast, such probability distributions obtained from Nile Red within a 25 nm thick poly-n-butylmethacrylate film around glass transition and in the melt state, display larger spectral jumps. Moreover, for longer alkyl side chains a solvent shift to higher energies is observed, which supports the idea of nanophase separation within those polymers.