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The current design methods used to determine fire progression and temperature-time development in fire compartments today are being questioned to not give accurate results in large and complex enclosures (larger than 500 m2). The established design methods proposed by Eurocode and used by fire safety engineers today are primarily the standard temperature-time curve and the parametric temperature-time curves. The parametric temperature-time curves are based on the heat and mass balance equations and both methods assume homogenous temperatures and uniform burning. These assumptions are being questioned for use in large enclosures such as open-plan compartments and compartments with multiple floors connected which are typically modern and common building types in today’s society. Today there are no established design methods developed to determine fire progression in large enclosures, but the Improved Travelling Fire Method (iTFM) and the New MT model II are new, alternative design methods which are prospects to become established engineering tools in the future. The iTFM is developed at the University of Edinburgh for travelling fires in large size compartments and the New MT model II is developed by RISE, Research Institutes of Sweden, for large tunnel fires. These two new design methods have been investigated and compared to established methods in a case study. Also localised fires from Eurocode with proposed interpretations by Ulf Wickström has been investigated and compared to the standard temperature-time curve and the parametric temperature-time curves. The new interpretation suggests that the given heat flux boundary conditions in Eurocode are interpreted as adiabatic surface temperatures based on given emissivities and convection heat transfer coefficients according to Eurocode. Through a case study the different methods were compared throughout reference buildings with constant material properties and fire loads, but with varying floor area and height. The result focused on if the new methods have more bearing on reality than the standard fire curve and the parametric temperature-time curves methods when determining fire progression and temperature-time development. Desired benefits with the new methods are to better predict and describe fire development in large enclosures. The referenceIIIbuildings were considered as occupancy class 2 (Vk2) and Br2 buildings with a load bearing fire resistance capacity demand of 30 minutes. This report is an early stage in the process of developing new fire models to improve the fire designing process when working with large compartments. The aim with the new, alternative methods and localised fires with proposed interpretation is to enable them to become engineering tools used by fire safety engineers in the future to create a more efficient and adapted design process. The results differ significantly depending on used method and reference building. The maximum temperatures conducted by the iTFM are in general higher than the standard fire curve and the parametric temperature-time curves. When applying the method to the reference building with high ceiling height and low spread rate the resulting temperatures were lower than the standard fire curve. The fire progression of the New MT model II is highly dependent on opening factor and time until temperature increase starts. In comparison to the parametric fire curves with the same opening factors the New MT model II resulted in considerably faster temperature development and higher temperatures. Localised fires with the new proposed interpretations resulted in adiabatic surface temperatures which were compared to the standard temperature-time curve after 30 minutes of fire and the maximum temperature of the parametric temperature-time curves. The comparison resulted in slightly lower temperatures for the localised fires with the new proposed interpretations compared to the standard temperature-time curve and similar temperatures compared to the parametric temperature-time curves in the case study. The results of the iTFM and the New MT model II differs significantly depending on physical parameters used in the calculation processes. The models are customizable and vary depending on fire scenarios and compartments and could possibly be future alternative methods when designing for fires in large compartments. Further studies and development together with real fire tests would provide the models with better accuracy and continuity. Localised fires with proposed new interpretations are a future prospect to become a future standard method for determination of maximum temperature of member surfaces in fire safety design.

Nanodiamonds (NDs) are an interesting platform in biological applications and disease treatment. Because of their photoluminescence properties and modifiable surface, they have been investigated as potential carriers for drugs and nucleic acids as well as fluorescent probes. In order to design NDs meeting specifically desired parameters, which would succeed in clinical trials and in medicinal therapy, understanding the mechanism of uptake and intracellular fate of NDs is crucial. The diploma thesis is focused on mechanistic investigation of ND-based nanoparticles delivering nucleic acids to human cells. First, NDs coated with a novel cationic co-polymer were prepared. NDs were then complexed with siRNA in order to transfect siRNA inside U-2 OS cells. NDs proved to be biocompatible and effective transfection particles as observed by qPCR and colorimetric cytotoxicity and cell viability tests. To examine ND uptake by cells, we inhibited endocytosis by specific inhibitors. Obtained results implicated that ND uptake was clathrin- and caveolin dependent. Nonetheless, more than half of NDs was internalized by cells in a different fashion. Some NDs colocalized with early endosomes, lysosomes and caveolin-derived endosomes after internalization. Other NDs resided either in unknown cell structures or escaped from...

Ectotherms are living creatures whose body temperature varies with the environment in which they live. Their physiology and metabolism have to rapidly respond to environmental changes in order to stay viable at across their tolerable thermal range (Lithgow et al. 1994). In nematodes such as Caenorhabditis elegans, temperature is an important factor that defines the fertility of the worm. A feature that delimits an ectotherm’s thermal range is the maximum temperature at which its germ line can produce gametes. How germ cells withstand high environmental stressors such as limiting temperatures is not well understood, especially when considering the thermodynamical principles that dominate the biochemical processes of the cytoplasm (Hyman and Brangwynne 2011). Previous studies in C. elegans have shown that the thermodynamic effects of temperature on the cell cycle rate in nematodes follows an Arrhenius relationship and defines the thermal range where worms can be fertile. At the limits of this relationship a breakdown of the Arrhenius trend is observed (Begasse et al. 2015a). It was hypothesized that some type of discontinuous phase transition occurred in the embryonic cells of C. elegans (Begasse et al 2015). However, it remains unknown if there is the physiological link between a drop off in fertility and the embryonic breakdown of the Arrhenius trend. This work finds the link between a temperature driven phase separation of P granules and fertility. P granules are important for germ line development and the fertility of C. elegans (Kawasaki et al. 1998b). Here it is shown that P granules mix with the cytoplasm upon a temperature quench of 27ºC to T=18ºC and de-mix from the cytoplasm forming droplets upon a temperature downshift of temperature from 18ºC to 27ºC. P granules also show a reversible behavior mixing and de-mixing with changes in temperature in vivo, having a strong dependence of these liquid-like compartments with entropy. These results were further confirmed using a minimally reconstituted, in vitro P granule system and showed that PGL-3, a constitutive component of P granules, can phase separate and form liquid compartments in a similar way as happens in vivo. Additionally, here it is shown that P granule phase separation does not require the chemical activity of other cytoplasmic factors to drive the phase separation of compartments in vivo and in vitro, instead their formation is strongly driven to mix and de-mix with changes in temperature. Furthermore, a binary phase diagram was constructed in order to compare the response of P granules in vivo and in vitro, showing that P granules form and function as a temperature driven liquid phaseseparation. Altogether, this indicates that P granules in vivo and PGL-3 liquid-like compartments in vitro, share the same temperature of mixing and de-mixing which coincides with the fertile temperature range over which Caenorhabditis elegans can reproduce. This suggests that P granule phase separation could define the thermal range of the worm.:Table of Contents 1. Abstract 2. Introduction 2 . 1 . CYTOPLASMIC ORGANIZAT ION 2 . 2 . CYTOPLASMIC PHASE SEPARATIONS 2 . 3 . P GRANULES RESEMBLE L IQUID- L IKE PROPERTI ES 2 . 4 . PHASE CHANGES AND THE CELL CYCLE 3. Aim 4. Methods 4 . 1 . STRAINS 4 . 2 . TEMPERATURE CONTROL 4.2.1. HEATING/COOLING SETUP DEVELOPMENT AND MICROSCOPE STAGE 4.2.2. CONFOCAL SAMPLE HOLDER AND HEATING/COOLING DEVICE 4.2.3. SAMPLE PREPARATION 4.2.4. TEMPERATURE OF THE MICROSCOPE OBJECTIVE 4 . 3 . IN VI VO ASSAYS 4 . 4 . IN VI TRO ASSAY 5. Results 5 . 1 . TEMPERATURE AND P GRANULE PHASE SEPARATION 5 . 2 . P GRANULES ARE TEMPERATURE SENSITIVE COMPARTMENTS 5 . 3 . P GRANULES MIX WITH THE CYTOPLASM AT 27ºC 5 . 4 . P GRANULES DO NOT NEED THE INFLUENCE OF PPTR- 1 TO FORM DROPLETS 5 . 5 . P GRANULES REVERSIBLY MIX AND DE-MIX IN VIVO 5 . 6 . PGL- 3 GRANULES PHASE SEPARATE IN V ITRO AT PHYSIOLOGICAL CONDITIONS 5 . 7 . P GRANULE PHASE SEPARATION IS REVERSIBLE IN VI VO AND IN VI TRO 5 . 8 . AN IN V ITRO PHASE DIAGRAM TO COMPARE THE THERMAL L IMITS OF P GRANULES IN V IVO 6. Discussion 6 . 1 . P GRANULES MIX AND DE-MIX IN A REVERSIBLE MANNER 6 . 2 . CONCENTRATION AND THE SPATIAL CONTROL OF P GRANULES 6 . 3 . THE ROLE OF OTHER CHEMICAL REGULATORS 6 . 4 . ECOLOGICAL RELEVANCE OF P GRANULE PHASE SEPARATION 7. Concluding Remarks 8. Bibliography

Nanodiamonds (NDs) are an interesting platform in biological applications and disease treatment. Because of their photoluminescence properties and modifiable surface, they have been investigated as potential carriers for drugs and nucleic acids as well as fluorescent probes. In order to design NDs meeting specifically desired parameters, which would succeed in clinical trials and in medicinal therapy, understanding the mechanism of uptake and intracellular fate of NDs is crucial. The diploma thesis is focused on mechanistic investigation of ND-based nanoparticles delivering nucleic acids to human cells. First, NDs coated with a novel cationic co-polymer were prepared. NDs were then complexed with siRNA in order to transfect siRNA inside U-2 OS cells. NDs proved to be biocompatible and effective transfection particles as observed by qPCR and colorimetric cytotoxicity and cell viability tests. To examine ND uptake by cells, we inhibited endocytosis by specific inhibitors. Obtained results implicated that ND uptake was clathrin- and caveolin dependent. Nonetheless, more than half of NDs was internalized by cells in a different fashion. Some NDs colocalized with early endosomes, lysosomes and caveolin-derived endosomes after internalization. Other NDs resided either in unknown cell structures or escaped from...

The reproductive success of the Purple Martin is dependent upon many factors. This study measured reproductive success of the Purple Martin (Progne subis subis) based on parental age and type of housing used. Reproductive parental ages consist of adults (experienced breeders) and subadults (first time breeders). Housing types included in this study were aluminum housing, wooden housing, plastic gourds, natural gourds, SuperGourds, and mailbox housing. The reproductive success was defined as the percentage of the original clutch that fledged. Study sites were located in Alabama, Indiana, North Carolina, Oklahoma, Tennessee, and Virginia. Pairs mating nonassortatively by age group had lower reproductive success than adults and subadults that were paired assortatively. Purple Martins were the most reproductively successful in SuperGourds and the least reproductively successful in wooden housing. This study provides evidence that may be basis for further research, help support the conservation of the Purple Martin, and aid reproductive success on its breeding grounds.

Liquid-liquid phase separation (LLPS) has been proposed as the underlying physical principle leading to the formation of membrane-less organelles in eukaryotic cells, following advancements, in the last two decades, in experimental observations owing to progress in confocal microscopy. These organelles can act as compartments in sequestering molecules and tuning rates of biochemical reactions, among a repertoire of functions they serve. Biochemical reactions are constantly in progress in living cells and are driven out of equilibrium due to fuel consumption in the form of ATP or GTP molecules. Free diffusion of reactive molecules through these compartments leads to their spatiotemporal sequestration and automatically implies an interplay between phase separation and chemical reactions. In this work, we are specifically interested to understand how the two processes closely affect each other and applying the understanding to tune better bottom-up design principles for synthetic life, which involves coupling compartmentalization and chemical reactions. The first part of this work is devoted to studying the interplay between phase separation and chemical reactions. To this end, we developed the theory of mass action kinetics of equilibrium and out-of-equilibrium processes occurring at phase equilibrium in a multicomponent mixture. Phase equilibrium is imposed at all times, thus restricting the chemical kinetics to the binodal manifold. We learn more about circumstances in which reaction rates can differ in coexisting phases. Next, we decouple the phase-forming components (scaffolds) and the dilute reactive components (clients), which means that the reactive dilute components respond to the heterogeneous profile in the system set by the scaffold but do not affect it. This allows us to investigate to what extent compartments can affect chemical reactions in terms of their yield at steady state for a bimolecular reaction or initial reaction rate for a nucleation process compared to the absence of compartments. We use the effective droplet model and mass reaction kinetics at phase equilibrium to address the above questions. We can understand better how the properties of reactions can be optimally tuned by compartment size. Following the theoretical developments in the first part of this work, we proceed to use the theoretical model of mass action kinetics at phase equilibrium to study emergent properties of parasitic behavior in a system composed of multiple fuel-driven reaction cycles, which lead to the formation of so-called 'building blocks' which can phase separate. This study also helps us probe the buffering capacity of phase separation. It further provides insights into how the lifetime of reactive 'building blocks' can be tuned via phase separation. Synthetic cells are generally realized by localizing minimalistic reactions in micron-scale water-filled environments, thus mimicking compartmentalization. Here we apply our model to understand how the localization of an autocatalytic process (PEN-DNA reaction) inside proteinosomes affect the reaction rates compared to the reactions in a homogeneous buffer solution. To summarize, we developed theoretical approaches to study the interplay of chemical reactions with compartmentalization and apply such approaches to systems chemistry and synthetic biology experimental studies to unravel how reactions can be controlled through compartmentalization.:1 Introduction 1 1.1 Phase Separation - A brief overview of the development of the field . . . . . . 1 1.2 Thermodynamics of phase separation in a multi-component mixture . . . . . 4 1.2.1 Mean field free energy . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.2.2 Other possible free energy considerations: Beyond mean-field . . . . . 7 1.2.3 Exchange chemical potential, chemical activity and osmotic pressure . 8 1.2.4 Thermodynamic instability leads to phase separation . . . . . . . . . 9 1.2.5 Phase equilibrium conditions . . . . . . . . . . . . . . . . . . . . . . . 10 1.2.6 Relaxation dynamics to phase equilibrium . . . . . . . . . . . . . . . . 13 1.3 Thermodynamics of chemical reactions in homogeneous mixtures . . . . . . . 14 1.3.1 Chemical equilibrium conditions . . . . . . . . . . . . . . . . . . . . . 14 1.3.2 Relaxation to chemical equilibrium . . . . . . . . . . . . . . . . . . . . 16 1.4 Thermodynamic equilibrium . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 1.5 Scope of the thesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2 Chemical reaction kinetics at phase equilibrium 21 2.1 Kinetics of chemical reactions relaxing to thermodynamic equilibrium . . . . 21 2.1.1 Volume fraction field and phase volume kinetics . . . . . . . . . . . . 22 2.1.2 Diffusive exchange rates between phases . . . . . . . . . . . . . . . . . 22 2.1.3 Reaction rates at phase equilibrium . . . . . . . . . . . . . . . . . . . 23 2.1.4 Properties of chemical reactions at phase equilibrium . . . . . . . . . 24 2.2 Unimolecular chemical reactions in coexisting phases . . . . . . . . . . . . . . 25 2.3 Bimolecular chemical reactions in coexisting phases . . . . . . . . . . . . . . . 27 2.4 Chemical reactions maintained away from chemical equilibrium . . . . . . . . 28 2.4.1 Tie-line selecting curve . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.5 Summary and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 3 Chemical reactions of dilute clients in phase-separated compartments 33 3.1 Thermodynamics of a multicomponent mixture of scaffold and clients . . . . 34 3.1.1 Phase equilibrium conditions: Dilute client limit . . . . . . . . . . . . 35 3.1.2 Relaxation dynamics to phase equilibrium: Dilute client limit . . . . . 38 3.1.3 Chemical equilibrium conditions: Dilute client limit . . . . . . . . . . 40 3.1.4 Relaxation dynamics to chemical equilibrium: Dilute client limit . . . 41 3.2 Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 3.2.1 Two-state transitions controlled by a drop . . . . . . . . . . . . . . . . 43 3.2.2 Bimolecular reaction controlled by a drop . . . . . . . . . . . . . . . . 45 3.2.3 Nucleation reaction controlled by a drop . . . . . . . . . . . . . . . . . 47 3.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 4 Fuel-driven chemical reactions in the dilute phase at phase equilibrium 50 4.1 Chemical reaction network and its properties . . . . . . . . . . . . . . . . . . 51 4.1.1 Observations from individual reaction cycles . . . . . . . . . . . . . . 52 4.1.2 Observations from combined reaction cycles . . . . . . . . . . . . . . . 53 4.2 Kinetic equations at phase equilibrium . . . . . . . . . . . . . . . . . . . . . . 55 4.3 Construction of the ternary phase diagram . . . . . . . . . . . . . . . . . . . . 57 4.4 Mechanism of co-phase separation . . . . . . . . . . . . . . . . . . . . . . . . 58 4.4.1 Composition of droplets . . . . . . . . . . . . . . . . . . . . . . . . . . 60 4.5 Co-phase separation with periodic fueling . . . . . . . . . . . . . . . . . . . . 61 4.6 Effects of activation rate constants on host-parasite identity . . . . . . . . . . 63 4.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 5 Study of enzymatic kinetics in compartmentalized systems 65 5.1 Autocatalytic reactions and their properties . . . . . . . . . . . . . . . . . . . 66 5.2 PEN DNA mass action kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . 67 5.3 Proteinosomes affect the PEN DNA reactions . . . . . . . . . . . . . . . . . . 70 5.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 6 Conclusion and Outlook 72 A Free energy calculations for block charged polymers using RPA 76 B Numerical Methods 79 C Linear first order corrections to scaffold equilibrium volume fractions 83 D Dynamic equations in dilute limit 86 E Spatial solutions 88 F Fitting routine and extracted rate coefficients 90 G Experimental methods 95 H Calibration constants and reaction rate coefficients of PEN DNA study 98 List of figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Confocal Raman Microscopy, a non-invasive, non-destructive and label-free technique, was employed to study the uptake and localization of nanoparticles (NPs) in the Hepatocarcinoma human cell line HepG2 at the level of single cells. Cells were exposed to carbon nanotubes (CNTs) the surface of which was engineered with polyelectrolytes and lipid layers, aluminium oxide and cerium dioxide nanoparticles. Raman spectra deconvolution was applied to obtain the spatial distributions of NPs together with lipids/proteins in cells. The colocalization of the NPs with different intracellular environments, lipid bodies, protein and DNA, was inferred. Lipid coated CNTs associated preferentially with lipid rich regions, whereas polyelectrolyte coated CNTs were excluded from lipid rich regions. Al2O3 NPs were found in the cytoplasm. CeO2 NPs were readily taken up and have been observed all over the cell. Raman z-scans proved the intracellular distribution of the respective NPs.

Made available in DSpace on 2014-10-09T12:35:41Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:03:56Z (GMT). No. of bitstreams: 0 / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP