Modelling the folding pathway of DNA nanostructures

DNA origami is a robust technique for bottom-up nano-fabrication. It encodes a target shape into uniquely addressable interactions between a set of short 'staple' strands and a long 'scaffold' strand. The mechanisms of self-assembly, particularly regarding kinetics, need to be better understood. Origami design usually relies on optimising the thermodynamic stability of the target structure, and thermal annealing remains the most fool-proof assembly protocol. This work focuses on studying the folding pathway of three types of origami through simulations: a reconfigurable T-junction origami, several traditional origami, and origami with coated scaffolds. The T-junction origami is intended as an economically feasible method of changing the uniqueness of interactions. My contribution to this work is to characterise the basic structural motif through oxDNA, a nucleotide-resolution model of DNA. The thesis then focuses on extending a domain-level model of DNA origami to study several experimental origami designs. We reveal design-dependent free energy barriers using biased simulations and relate this to the observed hysteresis in experiments. We also highlight the role of specific design elements in determining the folding pathway. A novel method of lowering the temperature of error-free assembly using coated scaffolds is then presented, with simulations indicating the existence of an activation barrier. By exposing particular regions of the scaffold, we can lower assembly time and temperature

Noncuring Graphene Thermal Interface Materials for Advanced Electronics

As transistors continue to decrease in size and packing densities increase, thermal management becomes a critical bottleneck for development of the next generation of compact and flexible electronics. The increase in computer usage and ever-growing dependence on cloud systems require better methods for dissipating heat away from electronic components. The important ingredients of thermal management are the thermal interface materials. The discovery of excellent heat conduction properties of graphene and few-layer graphene stimulated research on practical applications of graphene fillers in thermal interface materials. The initial studies of graphene fillers in thermal interface materials were focused almost exclusively on curing epoxy-based composites. However, many thermal management applications require specifically noncuring thermal paste type materials. This dissertation reports on the synthesis and thermal conductivity measurements of noncuring thermal paste based on mineral oil with the mixture of graphene and few-layer graphene flakes as the fillers. The relatively simple composition has been selected in order to systematically compare the performance and understand the mechanisms governing heat conduction. It was found that graphene thermal paste exhibits a distinctive thermal percolation threshold with the thermal conductivity revealing a sublinear dependence on the filler loading. This behavior contrasts with the thermal conductivity of curing graphene thermal interface materials, based on epoxy, where super-linear dependence on the filler loading is observed. The performance of graphene thermal paste was benchmarked against top-of-the-line commercial thermal pastes. The obtained results show that noncuring graphene thermal interface materials outperforms the best commercial pastes in terms of thermal conductivity, at substantially lower filler concentration. The results of this dissertation research shed light on the thermal percolation mechanism in noncuring polymeric matrices laden with quasi-two-dimensional fillers. Considering recent progress in graphene production via liquid phase exfoliation and oxide reduction, it is possible that the undertaken approach will open a pathway for large-scale industrial application of graphene in thermal management of electronics

From Social Simulation to Integrative System Design

As the recent financial crisis showed, today there is a strong need to gain "ecological perspective" of all relevant interactions in socio-economic-techno-environmental systems. For this, we suggested to set-up a network of Centers for integrative systems design, which shall be able to run all potentially relevant scenarios, identify causality chains, explore feedback and cascading effects for a number of model variants, and determine the reliability of their implications (given the validity of the underlying models). They will be able to detect possible negative side effect of policy decisions, before they occur. The Centers belonging to this network of Integrative Systems Design Centers would be focused on a particular field, but they would be part of an attempt to eventually cover all relevant areas of society and economy and integrate them within a "Living Earth Simulator". The results of all research activities of such Centers would be turned into informative input for political Decision Arenas. For example, Crisis Observatories (for financial instabilities, shortages of resources, environmental change, conflict, spreading of diseases, etc.) would be connected with such Decision Arenas for the purpose of visualization, in order to make complex interdependencies understandable to scientists, decision-makers, and the general public.Comment: 34 pages, Visioneer White Paper, see http://www.visioneer.ethz.c

Experimental Investigations Of Fluid Dynamic And Thermal Performance Of Nanofluids

Thesis (Ph.D.) University of Alaska Fairbanks, 2007The goal of this research was to investigate the fluid dynamic and thermal performance of various nanofluids. Nanofluids are dispersions of metallic nanometer size particles (<100 nm) into the base fluids. The choice of base fluid is an ethylene or propylene glycol and water mixture in cold regions. Initially the rheological characterization of copper oxide (CuO) nanofluids in water and in propylene glycol was performed. Results revealed that higher concentrations of CuO nanoparticles (5 to 15%) in water exhibited time-independent pseudoplastic and shear-thinning behavior. Lower concentrations (1 to 6%) of CuO nanofluids in propylene glycol revealed that these nanofluids behaved as Newtonian fluids. Both nanofluids showed that viscosity decreased exponentially with increase in temperature. Subsequent correlations for viscosities as a function of volume concentration and temperature were developed. Effects of different thermophysical properties on the Prandtl number of CuO, silicon dioxide (SiO2) and aluminum oxide (A12O 3) nanofluids were investigated. Results showed that the Prandtl number increased with increasing volume concentrations, which in turn increased the heat transfer coefficients of the nanofluids. Various nanofluids were compared for their heat transfer rates based on the Mouromtseff number, which is a Figure of Merit for heat transfer fluids. From this analysis, the optimal concentrations of nanoparticles in base fluids were found for CuO-water nanofluids. Experiments were performed to investigate the convective heat transfer enhancement and pressure loss of CuO, SiO2 and A12O 3 nanofluids in the turbulent regime. The increases in heat transfer coefficient by nanofluids for various volume concentrations compared to the base fluid were determined. Pressure loss was observed to increase with nanoparticle volume concentration. It was observed that an increase in particle diameter increased the heat transfer coefficient. Calculations showed that application of nanofluids in heat exchangers in buildings could result in volumetric flow reduction, reduction in the mass flow rate and size, and pumping power savings. Experiments on a diesel electric generator with nanofluids showed a reduction of cogeneration efficiency due to the decrease in specific heat compared to the base fluids. However, it was found that the efficiency of the waste heat recovery heat exchanger increased for nanofluids

RESPONSIBILITY AND SUSTAINABILITY IN THE OUTDOOR CLOTHING INDUSTRY based on the website communication of the brands in 2009 and 2021

Tämä pitkittäistutkimus on laadullinen tapaustutkimus ulkoiluvaatealan vastuullisuudesta ja kestävästä kehityksestä. Tutkimuksessa verrataan kahdentoista ulkoiluvaateyrityksen verkkosivustoilla vuosina 2009 ja 2021 keräämääni aineistoa. Tutkimuksen ensimmäinen osa tehtiin vuosina 2007-2009. Tutkin ulkoiluvaatemerkkien vastuullisten toimien viestintää niiden verkkosivustoilla. Sen jälkeen käytin verkkosisällön analyysia aineiston tulkintaan. Aineistoa analysoitiin sekä deduktiivisesti että induktiivisesti. Käytin Sustainable Apparel Coalitionin Higg Index -työkalua teemojen koodaamiseen ja poimin teemoja myös induktiivisesti aineistosta. Kestävää kehitystä ja vastuullisuutta on tutkittu laajasti, mutta en löytänyt tutkimusta vastuullisuuden kokonaisvaltaisesta tarkastelusta ulkoiluvaatealalla. Keskityin teoreettisessa taustatyössäni vastuullisuuden kahteen näkökulmaan, ympäristö- ja sosiaaliseen vastuullisuuteen. Tärkeimmät aiheet olivat kaikki toimitusketjun vaiheet, mukaan lukien materiaalit, eläinten hyvinvointi ja työntekijöiden oikeuksien periaatteet. Suurin osa vaatetusalan nykyisestä tutkimuksesta keskittyy pikamuotiin, ei erityisesti ulkoiluvaatteisiin. Ulkoiluvaatteiden tekninen luonne asettaa kuitenkin erilaisia vaatimuksia toimitusketjulle. Lisäksi ulkoiluvaateala on yhteydessä luontoon, ja siksi sen odotetaan olevan vastuullinen ja ympäristöystävällinen. Tässä tutkimuksessa tutkittiin näiden 12 yrityksen julkista viestintää vastuullisuudesta niiden verkkosivustoilla vuosina 2009 ja 2021. Näin ollen niiden verkkosivustoilla olevat tiedot eivät välttämättä vastaa sitä, mitä ne ovat tehneet tosielämässä. Toisaalta yritykset ovat voineet tehdä jotain muuta, mitä ne eivät vielä mainitse julkisesti.Tämän tutkimuksen tavoitteena oli ymmärtää, miten viestittyjä vastuullisuustoimia parannettiin kahdentoista vuoden aikana. Päätutkimuskysymyksenä oli: Miten valittujen ulkoiluvaateyritysten verkkosivujen viestintä on muuttunut kestävän kehityksen ja vastuullisuuden osalta vuosien 2009 ja 2021 välillä? Tutkimuksen ensimmäisen vaiheen johtopäätöksenä esitin: Ulkoilualan yritykset eivät voisi selviytyä liiketoiminnassa ilman ympäristövastuun tiedostamista, koska kuluttajien ympäristötietoisuus alkoi lisääntyä jo vuonna 2009. Totesin vuonna 2009, että ”ulkoiluala on herännyt ottamaan vastuuta ja alkanut työskentelemään kestävän kehityksen puolesta”. Tutkimuksessa pyrittiin selvittämään, mitä oli tapahtunut viime vuosikymmenen aikana. Monet jo vuonna 2009 todetut vastuullisuustoimet ovat edelleen ajankohtaisia. Tämän tutkimuksen tuloksena oli, että ympäristöhaasteet olivat muuttuneet entistä monimutkaisemmiksi, ja uusia on tullut esiin. Viime vuosikymmenen nousevia aiheita olivat muun muassa ilmastonmuutos, PFC-yhdisteet, mikromuovit ja eläin ten hyvinvointi. Viime vuosikymmenen aikana ovat nousseet esiin ja saaneet enemmän huomiota sosiaalisen vastuun kysymykset, kuten pakkotyö, elämiseen riittävä palkka sekä terveys ja turvallisuus. Vastuullinen toimitusketjun hallinta edellyttää usein yhteistyötä tuotemerkkien, toimialajärjestöjen, voittoa tavoittelemattomien järjestöjen, standardointiorganisaatioiden ja kansalaisjärjestöjen välillä. Brändien osallistuminen vastuullisuusjärjestöihin ja kolmannen osapuolen auditointeihin on lisääntynyt. Lopuksi totean, että viime vuosikymmenen aikana vastuullisuudesta ja kestävästä kehityksestä on tullut erottamaton osa ulkoiluvaatetusalaa.This research study is a longitudinal qualitative case study on the responsibility and sustainability in the outdoor clothing industry. The study compared the data I collected from the websites of 12 selected outdoor clothing companies between 2009 and 2021. The first part of this study was performed between 2007 and 2009. I studied the responsible actions of the outdoor brands on their websites and then used online content analysis to interpret the data. The data were analyzed both deductively and inductively. I also used the Sustainable Apparel Coalition’s Higg Index tool for coding themes, as well as picking themes inductively from the data. A broad body of existing research has addressed specific sustainability issues, but I was unable to find a study providing a holistic view of responsibility in the outdoor industry. I concentrated my theoretical background on two aspects of responsibility, environmental and social responsibility. The major topics were the phases of the supply chain, including materials, animal welfare, and principles of workers’ rights. Most of the existing research in the clothing field has concentrated on fast fashion, not specifically on outdoor clothing. However, the technical nature of outdoor clothing requires different standards for the supply chain. Additionally, the outdoor clothing industry is related to nature and therefore expected to be sustainable. This study investigated the 12 companies’ public communication about responsibility on their websites in 2009 and 2021. This information does not necessarily correlate with what the companies have done in real life or whether they took further action beyond their public communications. Rather, the objective of this study was to understand how communicated responsibility actions were improved in 12 years. The main research question was as follows: How has selected outdoor clothing companies’ websites’ communication changed regarding sustainability and responsibility between 2009 and 2021? As a final remark on the study’s first phase, I suggested that outdoor brands could not survive in the business without acknowledging environmental responsibility as consumers’ environmental awareness was increasing, even in 2009. I concluded that “the outdoor industry has awakened to take responsibility and started to work for sustainable development.” Further, this study aimed to determine what progress has happened over the past decade, and it concluded that many factors stated in 2009 are still accurate. The study found that the environmental challenges have become more complex, and new topics have emerged. Some of the emerging topics of the past decade are climate change, PFCs, microplastics, and animal welfare. Furthermore, social responsibility issues, such as forced labor, a living wage, and health and safety, have garnered attention. Responsible supply chain management often requires collaboration between brands, industry associations, non-profits, standards, and non-governmental organizations. Thus, the brands’ involvement in responsibility organizations and third-party auditioning has increased. I conclude that the past decade has rendered responsibility and sustainability inseparable parts of the outdoor clothing business

Unleashing infinite momentum bandgap using resonant material systems

The realization of photonic time crystals is a major opportunity but also comes with significant challenges. The most pressing one, potentially, is the requirement for a substantial modulation strength in the material properties to create a noticeable momentum bandgap. Reaching that noticeable bandgap in optics is highly demanding with current, and possibly also future, material platforms since their modulation strength is small by tendency. Here we demonstrate that by introducing temporal variations in a resonant material, the momentum bandgap can be drastically expanded, potentially approaching infinity with modulation strengths in reach with known low-loss materials and realistic laser pump powers. The resonance can emerge from an intrinsic material resonance or a suitably spatially structured material supporting a structural resonance. Our concept is validated for resonant bulk media and optical metasurfaces and paves the way toward the first experimental realizations of photonic time crystals

Quantum Technologies with 2D-materials

In the recent years, the continuous advancements in oxide thin films epitaxial growth and characterization techniques led to the possibility of design and control complex oxide heterointerfaces and characterize their crystal and electronic structure with atomic precision. These advancements brought to light a wealth of properties for oxide heterointerfaces and opened to new opportunities for oxide electronics and spintronics. Now the research on oxide interfaces is expanding outside the pure material science realm, entering the field of application-oriented devices. In this thesis, the innovative and intriguing functionalities arising in an oxide system where Rashba spin-orbit coupling, magnetism, superconductivity and high-mobility are combined in the same two dimensional electron gas (2DEG) have been reported. The focus of my work has two main aspects: on one side, to study the interplay between the several ground states in the 2DEG at the LaAlO3/EuTiO3/SrTiO3 interface; on the other, to realize nanodevices which will make these phenomena functional for new quantum electronics with advantages like scalability, easy top-down processing and possibility to manipulate the 2DEG system with unprecedented control

DNA Based Artificial Light-Harvesting Antenna

abstract: Scientists around the world have been striving to develop artificial light-harvesting antenna model systems for energy and other light-driven biochemical applications. Among the various approaches to achieve this goal, one of the most promising is the assembly of structurally well-defined artificial light-harvesting antennas based on the principles of structural DNA nanotechnology. DNA has recently emerged as an extremely efficient material to organize molecules such as fluorophores and proteins on the nanoscale. It is desirable to develop a hybrid smart material by combining artificial antenna systems based on DNA with natural reaction center components, so that the material can be engineered to convert light energy to chemical energy via formation of a charge-separated state. Presented here are a series of studies toward this goal. First, self-assembled seven-helix DNA bundles (7HB) with cyclic arrays of three distinct chromophores were developed. The spectral properties and energy transfer mechanisms in the artificial light-harvesting antenna were studied extensively using steady-state and time-resolved methods. Next, engineered cysteine residues in the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides were each covalently conjugated to fluorophores in order to explore the spectral requirements for energy transfer between an artificial light harvesting system and the reaction center. Finally, a structurally well-defined and spectrally tunable artificial light-harvesting system was constructed, where multiple organic dyes were conjugated to 3-arm DNA nanostructure. A reaction center protein isolated from the purple photosynthetic bacterium Rhodobacter sphaeroides was linked to one end of the 3-arm junction to serve as the final acceptor, which converts the photonic energy absorbed by the chromophores into chemical energy by charge separation. This type of model system is required to understand how parameters such as geometry, spectral characteristics of the dyes, and conformational flexibility affect energy transfer, and can be used to inform the development of more complex model light-harvesting systems.Dissertation/ThesisDoctoral Dissertation Chemistry 201