350 research outputs found

    Large-scale universality in Quantum Reaction-Diffusion from Keldysh field theory

    Full text link
    We consider the quantum reaction-diffusion dynamics in dd spatial dimensions of a Fermi gas subject to binary annihilation reactions A+AA+A \to \emptyset. These systems display collective nonequilibrium long-time behavior, which is signalled by an algebraic decay of the particle density. Building on the Keldysh formalism, we devise a field theoretical approach for the reaction-limited regime, where annihilation reactions are scarce. By means of a perturbative expansion of the dissipative interaction, we derive a description in terms of a large-scale universal kinetic equation. Our approach shows how the time-dependent generalized Gibbs ensemble assumption, which is often employed for treating low-dimensional nonequilibrium systems, emerges from systematic diagrammatics. It also allows to exactly compute -- for arbitrary spatial dimension -- the decay exponent of the particle density. The latter is based on the large-scale description of the quantum dynamics and it differs from the mean-field prediction even in dimension larger than one. We moreover consider spatially inhomogeneous setups involving an external potential. In confined systems the density decay is accelerated towards the mean-field algebraic behavior, while for deconfined scenarios the power-law decay is replaced by a slower non-algebraic decay.Comment: 6+8 pages, 3+2 figures for main text and Supplemental Material respectivel

    50 years of correlations with Michael Fisher and the renormalization group

    Full text link
    This paper will be published in ``50 years of the renormalization group", dedicated to the memory of Michael E. Fisher, edited by Amnon Aharony, Ora Entin-Wohlman, David Huse, and Leo Radzihovsky, World Scientific. I start with a review of my personal and scientific interactions with Michael E. Fisher, who was my post-doc mentor in 1972-1974. I then describe several recent renormalization group studies, which started during those years, and still raise some open issues. These include the magnets with dipole-dipole interactions, the puzzle of the bicritical points and the random field Ising model.Comment: Added Fig. 4 ad foototes. Pls identify people in Fig

    Compact fermion to qubit mappings for quantum simulation

    Get PDF
    Fermions are one of two types of particles that make up matter in the universe, characterised by many-body wavefunctions that are antisymmetric under particle exchange. Electrons, which underpin many physical systems of interest, are included in this group, so the ability to accurately simulate fermionic physics would be a great asset to research. However, the antisymmetric nature of these particles means that classical simulation of systems of multiple fermions is, in general, infeasible due to sign problems. This infeasibility extends even to simplified systems such as the Fermi-Hubbard model on a 2D grid. Simulation of fermions on a quantum device would avoid this problem entirely. A requisite step in simulating fermions on a quantum computer is mapping a many-body fermionic system onto qubits through a fermionic encoding. Significant properties of fermionic encodings include their qubit to fermionic mode ratio and the weight of their encoded fermionic interaction operators. Both affect the runtime of quantum simulation algorithms so it is ideal to minimise these quantities. This thesis presents the novel ``compact'' encoding which outperforms all previous local encodings in these metrics. The construction of the encoding is shown for a number of interaction graph structures and its general properties are explored. Special attention is given to a remarkable feature where low weight undetectable noise on the encoding corresponds to a natural noise process on fermionic systems, indicating that it may have utility in simulation even on imperfect, noisy quantum devices. An interesting feature of the compact encoding and others is an apparent link to topological error correcting codes like the toric code. Inspection of the compact encoding for a cubic lattice reveals a link to an apparently novel 3D topological code with some unusual properties. This size of its codespace and code distance are calculated and the exact form of its logical operators and syndromes are shown. Excitations with fermionic character exist in this code, consistent with the other codes linked with fermionic encodings, pointing to a possible unifying picture for local fermionic encodings. \end{abstract} \begin{impactstatement} Quantum computers have the potential for a wide reaching impact. The development of a fault tolerant quantum computer would allow hitherto infeasible problems to be tackled computationally. A significant application, which has been a primary motivator for the field since its inception, is the simulation of other quantum systems. Systems containing many fermions are of particular interest. Not only because they are fundamentally difficult to simulate with normal computers but because they include systems of electrons, the particles which underpin almost all of chemistry. Simulating these systems on a quantum computer is not a simple task however, as there must be a procedure to map the physics of many indistinguishable fermions onto the physics of stationary qubits, two fundamentally different systems. This procedure is called a \textit{fermionic encoding} and the main subject of this thesis is an example of this. The content of this thesis could benefit researchers in a number of fields. It adds to the rich zoo of fermionic encodings and may provide inspiration for further results in the field, it also highlights a possible link between the seemingly disparate local fermionic encodings which may pave the way to a more unified general theory of representing fermions on qubits. The encoding presented in this work has favourable properties for simulation on noisy devices so it may benefit research groups working on near term quantum hardware by providing the means to perform interesting fermionic simulation experiments. The content of the last chapter may also be of interest to the error correction community as it provides an example of an apparently unclassified topological code, this may lead to the development of new classes of code. This research may also yield benefits outside of academia. The quantum simulation of electronic systems would lead to greater understanding of chemical reactions such as Nitrogen fixing and materials such as superconductors and batteries. This understanding could lead to improvements in efficiency or the development of new substances which would be invaluable to industries including agriculture, transportation and battery production

    On robustness in biology: from sensing to functioning

    Get PDF
    Living systems are subject to various types of spatial and temporal noise at all scales and stages. Nevertheless, evolving under the pressure of natural selection, biology has mastered the ability of dealing with stochasticity. This is particularly crucial because these systems encounter numerous situations which require taking robust and proper actions in the presence of noise. Due to the complexity and variability of these situations, it is impossible to have a prescribed plan for an organism that keeps it alive and fully functional. Therefore, they have to be active, rather than passive, by following three essential steps: I) gathering information about their fluctuating environment, II) processing the information and making decisions via circuits that are inevitably noisy, and finally, III) taking the appropriate action robustly with organizations crossing multiple scales. Although various aspects of this general scheme have been subject of many studies, there are still many questions that remain unanswered: How can a dynamic environmental signal be sensed collectively by cell populations? and how does the topology of interactions affect the quality of this sensing? When processing information via the regulatory network, what are the drawbacks of multifunctional circuits? and how does the reliability of the decisions decrease as the multifunctionality increases? Finally, when the right decision is made and a tissue is growing with feedbacks crossing different scales, what are the crucial features that remain preserved from one subject to another? How can one use these features to understand the mechanisms behind these processes? This thesis addresses the main challenges for answering these questions and many more using methods from dynamical systems, network science, and stochastic processes. Using stochastic models, we investigate the fundamental limits arising from temporal noise on collective signal sensing and context-dependent information processing. Furthermore, by combining stochastic models and cross-scale data analyses, we study pattern formation during complex tissue growth.Lebende Systeme sind in allen Größenordnungen und Stadien verschiedenen Arten von räumlichem und zeitlichem Rauschen ausgesetzt. Dennoch hat die Biologie, die sich unter dem Druck der natürlichen Selektion entwickelt hat, die Fähigkeit gemeistert, mit stochastischen Fluktuationen umzugehen. Dies ist besonders wichtig, da Organismen auf zahlreiche Situationen stoßen, die es erfordern, in Gegenwart von Rauschen robuste und angemessene Maßnahmen zu ergreifen. Aufgrund der Komplexität und Variabilität dieser Situationen ist es unmöglich, einen vorgeschriebenen Plan für einen Organismus zu haben, der ihn überlebens- und funktionsfähig hält. Daher können Organismen sich nicht passiv verhalten, sondern befolgen aktiv drei wesentliche Schritte: I) Das Sammeln von Informationen über ihre dynamische Umgebung, II) Das Verarbeiten von Informationen und das Treffen von Entscheidungen über Regelnetzwerke, die unvermeidlich mit Rauschen behaftet sind, und schließlich, III) das robuste Funktionieren durch organisierte Maßnahmen, welche mehrere Größenordnungen überbrücken. Obwohl verschiedene Aspekte dieses allgemeinen Schemas Gegenstand vieler Studien waren, bleiben noch viele Fragen unbeantwortet: Wie kann ein dynamisches externes Signal kollektiv von Zellpopulationen wahrgenommen werden? Wie beeinflusst die Topologie der Interaktionen die Qualität dieser Wahrnehmung? Was sind die Nachteile multifunktionaler Schaltkreise bei der Verarbeitung von Informationen über das Regelnetzwerk? Wie nimmt die Zuverlässigkeit der Entscheidungen mit zunehmender Multifunktionalität ab? Und abschließend, wenn die richtige Entscheidung getroffen wurde und ein Gewebe wächst und dabei Rückkopplungen auf verschiedenen Größenordnungen erfährt, was sind die entscheidenden Merkmale, die von einem Versuchsobjekt zum anderen erhalten bleiben? Wie kann man diese Merkmale nutzen, um die Prozesse zu verstehen? Diese Arbeit befasst sich mit den wichtigsten Herausforderungen zur Beantwortung dieser und vieler weiterer Fragen mit Methoden aus dynamischen Systemen, Netzwerkforschung und stochastischen Prozessen

    Hydrogel-based logic circuits for planar microfluidics and lab-on-a-chip automation

    Get PDF
    The transport of vital nutrient supply in fluids as well as the exchange of specific chemical signals from cell to cell has been optimized over billion years of natural evolution. This model from nature is a driving factor in the field of microfluidics, which investigates the manipulation of the smallest amounts of fluid with the aim of applying these effects in fluidic microsystems for technical solutions. Currently, microfluidic systems are receiving attention, especially in diagnostics, \textit{e.g.} as SARS-CoV-2 antigen tests, or in the field of high-throughput analysis, \textit{e.g.} for cancer research. Either simple-to-use or large-scale integrated microfluidic systems that perform biological and chemical laboratory investigations on a so called Lab-on-a-Chip (LoC) provide fast analysis, high functionality, outstanding reproducibility at low cost per sample, and small demand of reagents due to system miniaturization. Despite the great progress of different LoC technology platforms in the last 30 years, there is still a lack of standardized microfluidic components, as well as a high-performance, fully integrated on-chip automation. Quite promising for the microfluidic system design is the similarity of the Kirchhoff's laws from electronics to predict pressure and flow rate in microchannel structures. One specific LoC platform technology approach controls fluids by active polymers which respond to specific physical and chemical signals in the fluid. Analogue to (micro-)electronics, these active polymer materials can be realized by various photolithographic and micro patterning methods to generate functional elements at high scalability. The so called chemofluidic circuits have a high-functional potential and provide “real” on-chip automation, but are complex in system design. In this work, an advanced circuit concept for the planar microfluidic chip architecture, originating from the early era of the semiconductor-based resistor-transistor-logic (RTL) will be presented. Beginning with the state of the art of microfluidic technologies, materials, and methods of this work will be further described. Then the preferred fabrication technology is evaluated and various microfluidic components are discussed in function and design. The most important component to be characterized is the hydrogel-based chemical volume phase transition transistor (CVPT) which is the key to approach microfluidic logic gate operations. This circuit concept (CVPT-RTL) is robust and simple in design, feasible with common materials and manufacturing techniques. Finally, application scenarios for the CVPT-RTL concept are presented and further development recommendations are proposed.:1 The transistor: invention of the 20th century 2 Introduction to fluidic microsystems and the theoretical basics 2.1 Fluidic systems at the microscale 2.2 Overview of microfluidic chip fabrication 2.2.1 Common substrate materials for fluidic microsystems 2.2.2 Structuring polymer substrates for microfluidics 2.2.3 Polymer chip bonding technologies 2.3 Fundamentals and microfluidic transport processes 2.3.1 Fluid dynamics in miniaturized systems 2.3.2 Hagen-Poiseuille law: the fluidic resistance 2.3.3 Electronic and microfluidic circuit model analogy 2.3.4 Limits of the electro-fluidic analogy 2.4 Active components for microfluidic control 2.4.1 Fluid transport by integrated micropumps 2.4.2 Controlling fluids by on-chip microvalves 2.4.3 Hydrogel-based microvalve archetypes 2.5 LoC technologies: lost in translation? 2.6 Microfluidic platforms providing logic operations 2.6.1 Hybrids: MEMS-based logic concepts 2.6.2 Intrinsic logic operators for microfluidic circuits 2.7 Research objective: microfluidic hydrogel-based logic circuits 3 Stimuli-responsive polymers for microfluidics 3.1 Introduction to hydrogels 3.1.1 Application variety of hydrogels 3.1.2 Hydrogel microstructuring methods 3.2 Theory: stimuli-responsive hydrogels 3.3 PNIPAAm: a multi-responsive hydrogel 4 Design, production and characterization methods of hydrogel-based microfluidic systems 4.1 The semi-automated computer aided design approach for microfluidic systems 4.2 The applied design process 4.3 Fabrication of microfluidic chips 4.3.1 Photoresist master fabrication 4.3.2 Soft lithography for PDMS chip production 4.3.3 Assembling PDMS chips by plasma bonding 4.4 Integration of functional hydrogels in microfluidic chips 4.4.1 Preparation of a monomer solution for hydrogel synthesis 4.4.2 Integration methods 4.5 Effects on hydrogel photopolymerization and the role of integration method 4.5.1 Photopolymerization from monomer solutions: managing the diffusion of free radicals 4.5.2 Hydrogel adhesion and UV light intensity distribution in the polymerization chamber 4.5.3 Hydrogel shrinkage behavior of different adhesion types 4.6 Comparison of the integration methods 4.7 Characterization setups for hydrogel actuators and microfluidic measurements . 71 4.7.1 Optical characterization method to describe swelling behavior 4.7.2 Setup of a microfluidic test stand 4.8 Conclusion: design, production and characterization methods 5 VLSI technology for hydrogel-based microfluidics 5.1 Overview of photolithography methods 5.2 Standard UV photolithography system for microfluidic structures 5.3 Self-made UV lithography system suitable for the mVLSI 5.3.1 Lithography setup for the DFR and SU-8 master exposure 5.3.2 Comparison of mask-based UV induced crosslinking for DFR and SU-8 5.4 Mask-based UV photopolymerization for mVLSI hydrogel patterning 5.4.1 Lithography setup for the photopolymerization of hydrogels 5.4.2 Hydrogel photopolymerization: experiments and results 5.4.3 Troubleshooting: photopolymerization of hydrogels 5.5 Conclusion: mVLSI technologies for hydrogel-based LoCs 6 Components for chemofluidic circuit design 6.1 Passive components in microfluidics 6.1.1 Microfluidic resistor 6.1.2 Planar-passive microfluidic signal mixer 6.1.3 Phase separation: laminar flow signal splitter 6.1.4 Hydrogel-based microfluidic one-directional valves 6.2 Hydrogel-based active components 6.2.1 Reversible hydrogel-based valves 6.2.2 Hydrogel-based variable resistors 6.2.3 CVPT: the microfluidic transistor 6.3 Conclusion: components for chemofluidic circuits 7 Hydrogel-based logic circuits in planar microfluidics 7.1 Development of a planar CVPT logic concept 7.1.1 Challenges of planar microfluidics 7.1.2 Preparatory work and conceptional basis 7.2 The microfluidic CVPT-RTL concept 7.3 The CVPT-RTL NAND gate 7.3.1 Circuit optimization stabilizing the NAND operating mode 7.3.2 Role of laminar flow for the CVPT-RTL concept 7.3.3 Hydrogel-based components for improved switching reliability 7.4 One design fits all: the NOR, AND and OR gate 7.5 Control measures for cascaded systems 7.6 Application scenarios for the CVPT-RTL concept 7.6.1 Use case: automated cell growth system 7.6.2 Use case: chemofluidic converter 7.7 Conclusion: Hydrogel-based logic circuits 8 Summary and outlook 8.1 Scientific achievements 8.2 Summarized recommendations from this work Supplementary information SI.1 Swelling degree of BIS-pNIPAAm gels SI.2 Simulated ray tracing of UV lithography setup by WinLens® SI.3 Determination of the resolution using the intercept theorem SI.4 Microfluidic master mold test structures SI.4.1 Polymer and glass mask comparison SI.4.2 Resolution Siemens star in DFR SI.4.3 Resolution Siemens star in SU-8 SI.4.4 Integration test array 300 μm for DFR and SU-8 SI.4.5 Integration test array 100 μm for SU-8 SI.4.6 Microfluidic structure for different technology parameters SI.5 Microfluidic test setups SI.6 Supplementary information: microfluidic components SI.6.1 Compensation methods for flow stabilization in microfluidic chips SI.6.2 Planar-passive microfluidic signal mixer SI.6.3 Laminar flow signal splitter SI.6.4 Variable fluidic resistors: flow rate characteristics SI.6.5 CVPT flow rate characteristics for high Rout Standard operation proceduresDer Transport von lebenswichtigen Nährstoffen in Flüssigkeiten sowie der Austausch spezifischer chemischer Signale von Zelle zu Zelle wurde in Milliarden Jahren natürlicher Evolution optimiert. Dieses Vorbild aus der Natur ist ein treibender Faktor im Fachgebiet der Mikrofluidik, welches die Manipulation kleinster Flüssigkeitsmengen erforscht um diese Effekte in fluidischen Mikrosystemen für technische Lösungen zu nutzen. Derzeit finden mikrofluidische Systeme vor allem in der Diagnostik, z.B. wie SARS-CoV-2-Antigentests, oder im Bereich der Hochdurchsatzanalyse, z.B. in der Krebsforschung, besondere Beachtung. Entweder einfach zu bedienende oder hochintegrierte mikrofluidische Systeme, die biologische und chemische Laboruntersuchungen auf einem sogenannten Lab-on-a-Chip (LoC) durchführen, bieten schnelle Analysen, hohe Funktionalität, hervorragende Reproduzierbarkeit bei niedrigen Kosten pro Probe und einen geringen Bedarf an Reagenzien durch die Miniaturisierung des Systems. Trotz des großen Fortschritts verschiedener LoC-Technologieplattformen in den letzten 30 Jahren mangelt es noch an standardisierten mikrofluidischen Komponenten sowie an einer leistungsstarken, vollintegrierten On-Chip-Automatisierung. Vielversprechend für das Design mikrofluidischer Systeme ist die Ähnlichkeit der Kirchhoff'schen Gesetze aus der Elektronik zur Vorhersage von Druck und Flussrate in Mikrokanalstrukturen. Ein spezifischer Ansatz der LoC-Plattformtechnologie steuert Flüssigkeiten durch aktive Polymere, die auf spezifische physikalische und chemische Signale in der Flüssigkeit reagieren. Analog zur (Mikro-)Elektronik können diese aktiven Polymermaterialien durch verschiedene fotolithografische und mikrostrukturelle Methoden realisiert werden, um funktionelle Elemente mit hoher Skalierbarkeit zu erzeugen.\\ Die sogenannten chemofluidischen Schaltungen haben ein hohes funktionales Potenzial und ermöglichen eine 'wirkliche' on-chip Automatisierung, sind jedoch komplex im Systemdesign. In dieser Arbeit wird ein fortgeschrittenes Schaltungskonzept für eine planare mikrofluidische Chiparchitektur vorgestellt, das aus der frühen Ära der halbleiterbasierten Resistor-Transistor-Logik (RTL) hervorgeht. Beginnend mit dem Stand der Technik der mikrofluidischen Technologien, werden Materialien und Methoden dieser Arbeit näher beschrieben. Daraufhin wird die bevorzugte Herstellungstechnologie bewertet und verschiedene mikrofluidische Komponenten werden in Funktion und Design diskutiert. Die wichtigste Komponente, die es zu charakterisieren gilt, ist der auf Hydrogel basierende chemische Volumen-Phasenübergangstransistor (CVPT), der den Schlüssel zur Realisierung mikrofluidische Logikgatteroperationen darstellt. Dieses Schaltungskonzept (CVPT-RTL) ist robust und einfach im Design und kann mit gängigen Materialien und Fertigungstechniken realisiert werden. Zuletzt werden Anwendungsszenarien für das CVPT-RTL-Konzept vorgestellt und Empfehlungen für die fortlaufende Entwicklung angestellt.:1 The transistor: invention of the 20th century 2 Introduction to fluidic microsystems and the theoretical basics 2.1 Fluidic systems at the microscale 2.2 Overview of microfluidic chip fabrication 2.2.1 Common substrate materials for fluidic microsystems 2.2.2 Structuring polymer substrates for microfluidics 2.2.3 Polymer chip bonding technologies 2.3 Fundamentals and microfluidic transport processes 2.3.1 Fluid dynamics in miniaturized systems 2.3.2 Hagen-Poiseuille law: the fluidic resistance 2.3.3 Electronic and microfluidic circuit model analogy 2.3.4 Limits of the electro-fluidic analogy 2.4 Active components for microfluidic control 2.4.1 Fluid transport by integrated micropumps 2.4.2 Controlling fluids by on-chip microvalves 2.4.3 Hydrogel-based microvalve archetypes 2.5 LoC technologies: lost in translation? 2.6 Microfluidic platforms providing logic operations 2.6.1 Hybrids: MEMS-based logic concepts 2.6.2 Intrinsic logic operators for microfluidic circuits 2.7 Research objective: microfluidic hydrogel-based logic circuits 3 Stimuli-responsive polymers for microfluidics 3.1 Introduction to hydrogels 3.1.1 Application variety of hydrogels 3.1.2 Hydrogel microstructuring methods 3.2 Theory: stimuli-responsive hydrogels 3.3 PNIPAAm: a multi-responsive hydrogel 4 Design, production and characterization methods of hydrogel-based microfluidic systems 4.1 The semi-automated computer aided design approach for microfluidic systems 4.2 The applied design process 4.3 Fabrication of microfluidic chips 4.3.1 Photoresist master fabrication 4.3.2 Soft lithography for PDMS chip production 4.3.3 Assembling PDMS chips by plasma bonding 4.4 Integration of functional hydrogels in microfluidic chips 4.4.1 Preparation of a monomer solution for hydrogel synthesis 4.4.2 Integration methods 4.5 Effects on hydrogel photopolymerization and the role of integration method 4.5.1 Photopolymerization from monomer solutions: managing the diffusion of free radicals 4.5.2 Hydrogel adhesion and UV light intensity distribution in the polymerization chamber 4.5.3 Hydrogel shrinkage behavior of different adhesion types 4.6 Comparison of the integration methods 4.7 Characterization setups for hydrogel actuators and microfluidic measurements . 71 4.7.1 Optical characterization method to describe swelling behavior 4.7.2 Setup of a microfluidic test stand 4.8 Conclusion: design, production and characterization methods 5 VLSI technology for hydrogel-based microfluidics 5.1 Overview of photolithography methods 5.2 Standard UV photolithography system for microfluidic structures 5.3 Self-made UV lithography system suitable for the mVLSI 5.3.1 Lithography setup for the DFR and SU-8 master exposure 5.3.2 Comparison of mask-based UV induced crosslinking for DFR and SU-8 5.4 Mask-based UV photopolymerization for mVLSI hydrogel patterning 5.4.1 Lithography setup for the photopolymerization of hydrogels 5.4.2 Hydrogel photopolymerization: experiments and results 5.4.3 Troubleshooting: photopolymerization of hydrogels 5.5 Conclusion: mVLSI technologies for hydrogel-based LoCs 6 Components for chemofluidic circuit design 6.1 Passive components in microfluidics 6.1.1 Microfluidic resistor 6.1.2 Planar-passive microfluidic signal mixer 6.1.3 Phase separation: laminar flow signal splitter 6.1.4 Hydrogel-based microfluidic one-directional valves 6.2 Hydrogel-based active components 6.2.1 Reversible hydrogel-based valves 6.2.2 Hydrogel-based variable resistors 6.2.3 CVPT: the microfluidic transistor 6.3 Conclusion: components for chemofluidic circuits 7 Hydrogel-based logic circuits in planar microfluidics 7.1 Development of a planar CVPT logic concept 7.1.1 Challenges of planar microfluidics 7.1.2 Preparatory work and conceptional basis 7.2 The microfluidic CVPT-RTL concept 7.3 The CVPT-RTL NAND gate 7.3.1 Circuit optimization stabilizing the NAND operating mode 7.3.2 Role of laminar flow for the CVPT-RTL concept 7.3.3 Hydrogel-based components for improved switching reliability 7.4 One design fits all: the NOR, AND and OR gate 7.5 Control measures for cascaded systems 7.6 Application scenarios for the CVPT-RTL concept 7.6.1 Use case: automated cell growth system 7.6.2 Use case: chemofluidic converter 7.7 Conclusion: Hydrogel-based logic circuits 8 Summary and outlook 8.1 Scientific achievements 8.2 Summarized recommendations from this work Supplementary information SI.1 Swelling degree of BIS-pNIPAAm gels SI.2 Simulated ray tracing of UV lithography setup by WinLens® SI.3 Determination of the resolution using the intercept theorem SI.4 Microfluidic master mold test structures SI.4.1 Polymer and glass mask comparison SI.4.2 Resolution Siemens star in DFR SI.4.3 Resolution Siemens star in SU-8 SI.4.4 Integration test array 300 μm for DFR and SU-8 SI.4.5 Integration test array 100 μm for SU-8 SI.4.6 Microfluidic structure for different technology parameters SI.5 Microfluidic test setups SI.6 Supplementary information: microfluidic components SI.6.1 Compensation methods for flow stabilization in microfluidic chips SI.6.2 Planar-passive microfluidic signal mixer SI.6.3 Laminar flow signal splitter SI.6.4 Variable fluidic resistors: flow rate characteristics SI.6.5 CVPT flow rate characteristics for high Rout Standard operation procedure

    Advances in Molecular Simulation

    Get PDF
    Molecular simulations are commonly used in physics, chemistry, biology, material science, engineering, and even medicine. This book provides a wide range of molecular simulation methods and their applications in various fields. It reflects the power of molecular simulation as an effective research tool. We hope that the presented results can provide an impetus for further fruitful studies

    Towards the implementation of distributed systems in synthetic biology

    Get PDF
    The design and construction of engineered biological systems has made great strides over the last few decades and a growing part of this is the application of mathematical and computational techniques to problems in synthetic biology. The use of distributed systems, in which an overall function is divided across multiple populations of cells, has the potential to increase the complexity of the systems we can build and overcome metabolic limitations. However, constructing biological distributed systems comes with its own set of challenges. In this thesis I present new tools for the design and control of distributed systems in synthetic biology. The first part of this thesis focuses on biological computers. I develop novel design algorithms for distributed digital and analogue computers composed of spatial patterns of communicating bacterial colonies. I prove mathematically that we can program arbitrary digital functions and develop an algorithm for the automated design of optimal spatial circuits. Furthermore, I show that bacterial neural networks can be built using our system and develop efficient design tools to do so. I verify these results using computational simulations. This work shows that we can build distributed biological computers using communicating bacterial colonies and different design tools can be used to program digital and analogue functions. The second part of this thesis utilises a technique from artificial intelligence, reinforcement learning, in first the control and then the understanding of biological systems. First, I show the potential utility of reinforcement learning to control and optimise interacting communities of microbes that produce a biomolecule. Second, I apply reinforcement learning to the design of optimal characterisation experiments within synthetic biology. This work shows that methods utilising reinforcement learning show promise for complex distributed bioprocessing in industry and the design of optimal experiments throughout biology

    Exact Open Quantum System Dynamics – Investigating Environmentally Induced Entanglement

    Get PDF
    When calculating the dynamics of a quantum system, including the effect of its environment is highly relevant since virtually any real quantum system is exposed to environmental influences. It has turned out that the widely used perturbative approaches to treat such so-called open quantum systems have severe limitations. Furthermore, due to current experiments which have implemented strong system-environment interactions the non-perturbative regime is far from being academical. Therefore determining the exact dynamics of an open quantum system is of fundamental relevance. The hierarchy of pure states (HOPS) formalism poses such an exact approach. Its novel and detailed derivation, as well as several numerical aspects constitute the main methodical part of this work. Motivated by fundamental issues but also due to practical relevance for real world devices exploiting quantum effects, the entanglement dynamics of two qubits in contact with a common environment is investigated extensively. The HOPS formalism is based on the exact stochastic description of open quantum system dynamics in terms of the non-Markovian quantum state diffusion (NMQSD) theory. The distinguishing and numerically beneficial features of the HOPS approach are the stochastic nature, the implicit treatment of the environmental dynamics and, related to this, the enhanced statistical convergence (importance sampling), as well as the fact that only pure states have to be propagated. In order to claim that the HOPS approach is exact, we develop schemes to ensure that the numerical errors can be made arbitrarily small. This includes the sampling of Gaussian stochastic processes, the multi-exponential representation of the bath correlation function and the truncation of the hierarchy. Moreover, we incorporated thermal effects on the reduced dynamics by a stochastic Hermitian contribution to the system Hamiltonian. In particular, for strong system-environment couplings this is very beneficial for the HOPS. To confirm the accuracy assertion we utilize the seemingly simple, however, non-trivial spin-boson model to show agreement between the HOPS and other methods. The comparison shows the HOPS method’s versatile applicability over a broad range of model parameters including weak and strong coupling to the environment, as well as zero and high temperatures. With the gained knowledge that the HOPS method is versatile and accurately applicable, we investigate the specific case of two qubits while focusing on their entanglement dynamics. It is well known that entanglement, the relevant property when exploiting quantum effects in fields like quantum computation, communication and metrology, is fragile when exposed to environmental noise. On the other hand, a common environment can also mediate an effective interaction between the two parties featuring entanglement generation. In this work we elucidate the interplay between these competing effects, focusing on several different aspects. For the perturbative (weak coupling) regime we enlighten the difficulties inherent to the frequently used rotating wave approximation (RWA), an approximation often applied to ensure positivity of the reduced state for all times. We show that these difficulties are best overcome when simply omitting the RWA. The seemingly unphysical dynamics can still be used to approximate the exact entanglement dynamics very well. Furthermore, the influence of the renormalizing counter term is investigated. It is expected that under certain conditions (adiabatic regime) the generation of entanglement is suppressed by the presence of the counter term. It is shown, however, that for a deep sub-Ohmic environment this expectation fails. Leaving the weak coupling regime, we show that the generation of entanglement due to the influence of the common environment is a general property of the open two-spin system. Even for non-zero temperatures it is demonstrated that entanglement can still be generated and may last for arbitrary long times. Finally, we determine the maximum of the steady state entanglement as a function of the coupling strength and show how the known delocalization-to-localization phase transition is reflected in the long time entanglement dynamics. All these results require an exact treatment of the open quantum system dynamics and, thus, contribute to the fundamental understanding of the entanglement dynamics of open quantum systems.Bei der Bestimmung der Dynamik eines Quantensystems ist die Berücksichtigung seiner Umgebung von großem Interessen, da faktisch jedes reale Quantensystem von seiner Umgebung beeinflusst wird. Es zeigt sich, dass die viel verwendeten störungstheoretischen Ansätze starken Einschränkungen unterliegen. Außerdem, da es in aktuellen Experimenten gelungen ist starke Wechselwirkung zwischen dem System und seiner Umgebung zu realisieren, gewinnt das nicht-störungstheoretischen Regime stets an Relevanz. Dementsprechend ist die Berechnung der exakten Dynamik offener Quantensysteme von grundlegender Bedeutung. Einen solchen exakten nummerischen Zugang stellt der hierarchy of pure states (HOPS) Formalismus dar. Dessen neuartige und detaillierte Herleitung, sowie diverse nummerische Aspekte werden im methodischen Teil dieser Arbeit dargelegt. In vielerlei Hinsicht relevant folgt als Anwendung eine umfangreiche Untersuchung der Verschränkungsdynamik zweier Qubits unter dem Einfluss einer gemeinsamen Umgebung. Vor allem im Hinblick auf die experimentell realisierbare starke Kopplung mit der Umgebung ist dieses Analyse von Interesse. Der HOPS Formalismus basiert auf der stochastischen Beschreibung der Dynamik offener Quantensysteme im Rahmen der non-Markovian quantum state diffusion (NMQSD) Theorie. Der stochastische Charakter der Methode, die implizite Berücksichtigung der Umgebungsdynamik, sowie das damit verbundene Importance Sampling, als auch die Tatsache dass lediglich reine Zustände propagiert werden müssen unterscheidet diese Methode maßgeblich von anderen Ansätzen und birgt numerische Vorteile. Um zu behaupten, dass die HOPS Methode exakte Ergebnisse liefert, müssen auftretenden nummerischen Fehler beliebig klein gemacht werden können. Ein grundlegender Teil der hier vorgestellten methodischen Arbeit liegt in der Entwicklung diverser Schemata, die genau das erreichen. Dazu zählen die numerische Realisierung von Gauss’schen stochastischen Prozessen, die Darstellung der Badkorrelationsfunktion als Summe von Exponentialfunktionen sowie das Abschneiden der Hierarchie. Außerdem wird gezeigt, dass sich der temperaturabhängige Einfluss der Umgebung durch einen stochastischen Hermiteschen Beitrag zum System-Hamiltonoperator berücksichtigen lässt. Vor allem bei starker Kopplung ist diese Variante besonders geeignet für den HOPS Zugang. Um die Genauigkeitsbehauptung der HOPS Methode zu überprüfen wird die Übereinstimmung mit anderen Methode gezeigt, wobei das vermeintlich einfachste, jedoch nicht triviale spin-boson-Modell als Testsystem verwendet wird. Diese Untersuchung belegt, dass die HOPS Methode für eine Vielzahl an Szenarien geeignet ist. Das beinhaltet schwache und starke Kopplung an die Umgebung, sowie Temperatur null als auch hohe Temperaturen. Mit dem gewonnenen Wissen, dass die HOPS Methode vielseitig einsetzbar ist und genaue Ergebnisse liefert wird anschließend der spezielle Fall zweier Qubits untersucht. Im Hinblick auf die Ausnutzung von Quanteneffekten in Bereichen wie Rechentechnik, Kommunikation oder Messtechnik liegt der primäre Fokus auf der Dynamik der Verschränkung zwischen den Qubits. Es ist bekannt, dass durch von außen induziertes Rauschen die Verschränkung im Laufe der Zeit abnimmt. Andererseits weiß man auch, dass eine gemeinsame Umgebung zu einer effektiven Wechselwirkung zwischen den Qubits führt, welche Verschränkung aufbauen kann. In dieser Arbeit wird das Wechselspiel zwischen diesen beiden gegensätzlichen Effekten untersucht, wobei die folgenden Aspekte beleuchtet werden. Für den Fall schwacher Kopplung, wo eine störungstheoretische Behandlung in Frage kommt, werden die Probleme der rotating wave approximation (RWA) analysiert. Diese Näherung wird häufig verwendet um die Positivität des reduzierten Zustands zu allen Zeiten zu gewährleisten. Es wird gezeigt, dass sich diese Probleme am besten vermeiden lassen, wenn die RWA einfach weggelassen wird. Die auf den ersten Blick nicht-physikalische Dynamik ist sehr gut geeignet um die exakte Verschränkungsdynamik näherungsweise wiederzugeben. Des Weiteren wird der Einfluss der Renormalisierung des sogenannten counter terms untersucht. Unter bestimmten Voraussetzungen (adiabatisches Regime) ist zu erwarten, dass der Verschränkungsaufbau durch den counter term verhindert wird. Es zeigt sich, dass für eine sehr sub-Ohm’sche Umgebung (deep sub-Ohmic regime) diese Erwartung nicht zutrifft. Weiterhin wird der Fall starker Kopplung zwischen dem zwei-Qubit-System und der Umgebung betrachtet. Die Berechnungen zeigen das generelle Bild, dass sich zwei nicht wechselwirkende Qubits durch den Einfluss einer gemeinsamen Umgebung verschränken. Selbst bei Temperaturen größer als null kann Verschränkung aufgebaut werden und auch für beliebig lange Zeiten erhalten bleiben. In einem letzten Punkt wird das Maximum der stationären Verschränkung (Langzeit-Limes) in Abhängigkeit von der Kopplungsstärke bestimmt. Dabei wird gezeigt, dass sich der bekannte Phasenübergang von Delokalisierzung zu Lokalisierung auch in der Langzeitdynamik der Verschränkung widerspiegelt. All diese Erkenntnisse erfordern eine exakte Behandlung der offenen Systemdynamik und erweitern somit das fundamentalen Verständnis der Verschränkungsdynamik offener Quantensysteme

    Avian genomics: insight into bitter taste receptors

    Get PDF
    Dissertação de mestrado em BioinformáticaThe detection of bitter taste is of major importance for animal survival since it provides an earlier evaluation of which food resources are safer, avoiding the ingestion of toxic compounds and regulating the feeding behavior. The taste receptor protein type 2 (T2R) family of G protein-coupled receptors (GPCRs) is responsible for bitter taste perception and its study is relevant to better understand the evolution of the sense of taste. Additionally, birds are a group of animals which are considered good models to evolutionary studies due to their abundance, high diversity of species and global widespread across varied ecological conditions. Phylogenetic reconstructions and selection analysis present a great approach to understand the evolutionary history and diversification of avian T2Rs. Additionally, comparative methodologies can assess the selective pressures acting on these genes. This work aims to assess the evolutionary genomics of the animal taste receptor gene type 2 (Tas2r) gene family in 245 bird species, distributed across 14 orders and, through a set of bioinformatics and genomic tools, to clarify their genomic representation, selective pressures and phylogenetic relationships. The results herein obtained reveal an acceleration of Tas2rs in the order Passeriformes. In addition, it was previously reported that diet has an influence on the Tas2r repertoire. Therefore, we studied the effect of additional ecological traits such as habitat and migration. Our results indicate that Tas2r show conservation on water birds and a stronger evolutionary pressure on non-migratory birds.A deteção de sabor amargo é muito importante para a sobrevivência animal uma vez que permite avaliar que fontes de alimento são seguras consumir, prevenindo assim a ingestão de xenobióticos. Para além disso, estes receptores também regulam o comportamento alimentar dos animais. Os recetores de sabor tipo 2 (T2R), uma família de receptores acoplados às proteínas G (GPCRs), são responsáveis pela deteção de sabor amargo e o seu estudo é relevante para clarificar a evolução do sentido do paladar. Adicionalmente, as aves são um grupo de animais considerados como sendo bons modelos de evolução devido à sua abundância, grande diversidade de espécies e distribuição global em diferentes condições ecológicas. As reconstruções filogenéticas e análises de seleção, apresentam uma abordagem interessante para entender a história evolutiva e a diversificação de T2Rs em aves. Adicionalmente, metodologias comparativas podem avaliar as pressões seletivas que atuam nestes genes. Este estudo tem o objetivo de analisar a genómica evolutiva da família de genes dos receptores de sabor tipo 2 de animais (Tas2r) em 245 espécies de aves em 14 ordens. Através de um conjunto de ferramentas bioinformáticas e genómicas, pretende-se também esclarecer a sua representação genómica, pressões seletivas e relações filogenéticas. Os resultados obtidos revelam uma aceleração da pressão seletiva na ordem Passeriformes. Para além disso, foi anteriormente reportado que a dieta influencia o repertório de T2R. Assim, analisou-se o efeito de traços ecológicos adicionais como migração e habitat. Os nossos resultados indicam que Tas2r apresenta conservação em aves aquáticas e uma maior pressão evolutiva em aves não migratórias.This research was partially supported by the Strategic Funding UIDB/04423/2020 and UIDP/04423/2020 through national funds provided by the Fundação para a Ciência e a Tecnologia (FCT) and the European Regional Development Fund (ERDF) in the framework of the program PT2020, by the European Structural and Investment Funds (ESIF) through the Competitiveness and Internationalization Operational Program - COMPETE 2020 and by National Funds through the FCT under the project PTDC/AAG-GLO/6887/2014 (POCI-01-0124-FEDER-016845) and PTDC/CTA-AMB/31774/2017 (POCI-01-0145-FEDER/031774/2017)
    corecore