As ligações entre a termodinâmica e a mecânica quântica mostram-se interessantes tópicos de pesquisa desde os anos 50 e tem atraído cada vez mais atenção nos últimos anos, tanto por suas possíveis aplicações tecnológicas, quanto pelo aspecto teórico - como, por exemplo, as relações de sistemas quânticos com a segunda lei da termodinâmica. Para sistemas quânticos mesoscópicos, restritos apenas a um número relativamente pequeno de estados energéticos, torna-se necessária uma generalização da termodinâmica usual. Neste trabalho mostramos como construir uma máquina de Stirling no contexto de íons aprisionados. Para isso, faz-se necessária a engenharia de frequências dependentes do tempo do modo vibracional do íon, além da engenharia de reservatórios térmicos com temperaturas controladas. Após a construção da máquina de Stirling e do cálculo do trabalho e da eficiência associados apresentamos um protocolo para a medida da função de distribuição do trabalho que recorre às medidas dos níveis de energia eletrônicos do íon para, a partir dessas, extrair-se informação sobre o seu estado vibracional. / The connections between quantum mechanics and thermodynamics have been an interesting research topic since the 1950´s and began attracting more and more attention recently, not only for the technological applications, but also from a theoretical point of view - as, for instance, when dealing with the relations between quantum systems and the second law of thermodynamics. For mesoscopic (or even macroscopic) quantum systems, restricted to relatively few energy states, a generalization of the usual thermodynamics becomes necessary. In the present work we show how to engeneer a Stirling engine in an ionic trap. To achieve this we have to engeneer an ionic vibrational mode with a time dependent frequency, and simutaneously engeneer a thermal reservoir with controled temperatures. After the construction of the Stirling machine and the calculation of the associated work and efficiency, we show a protocol that allows the measurement of the work distribution function which call on the measurement of the electronic energy levels of the ion and, from them, extract information about the vibrational state of the trap.

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

As ligações entre a termodinâmica e a mecânica quântica mostram-se interessantes tópicos de pesquisa desde os anos 50 e tem atraído cada vez mais atenção nos últimos anos, tanto por suas possíveis aplicações tecnológicas, quanto pelo aspecto teórico - como, por exemplo, as relações de sistemas quânticos com a segunda lei da termodinâmica. Para sistemas quânticos mesoscópicos, restritos apenas a um número relativamente pequeno de estados energéticos, torna-se necessária uma generalização da termodinâmica usual. Neste trabalho mostramos como construir uma máquina de Stirling no contexto de íons aprisionados. Para isso, faz-se necessária a engenharia de frequências dependentes do tempo do modo vibracional do íon, além da engenharia de reservatórios térmicos com temperaturas controladas. Após a construção da máquina de Stirling e do cálculo do trabalho e da eficiência associados apresentamos um protocolo para a medida da função de distribuição do trabalho que recorre às medidas dos níveis de energia eletrônicos do íon para, a partir dessas, extrair-se informação sobre o seu estado vibracional. / The connections between quantum mechanics and thermodynamics have been an interesting research topic since the 1950´s and began attracting more and more attention recently, not only for the technological applications, but also from a theoretical point of view - as, for instance, when dealing with the relations between quantum systems and the second law of thermodynamics. For mesoscopic (or even macroscopic) quantum systems, restricted to relatively few energy states, a generalization of the usual thermodynamics becomes necessary. In the present work we show how to engeneer a Stirling engine in an ionic trap. To achieve this we have to engeneer an ionic vibrational mode with a time dependent frequency, and simutaneously engeneer a thermal reservoir with controled temperatures. After the construction of the Stirling machine and the calculation of the associated work and efficiency, we show a protocol that allows the measurement of the work distribution function which call on the measurement of the electronic energy levels of the ion and, from them, extract information about the vibrational state of the trap.

Indiana University-Purdue University Indianapolis (IUPUI) / Open quantum systems have become a rapidly developing sector for research. Such systems present novel physical phenomena, such as topological chirality, enhanced sensitivity, and unidirectional invisibility resulting from both their non-equilibrium dynamics and the presence of exceptional points. We begin by introducing the core features of open systems governed by non-Hermitian Hamiltonians, providing the PT -dimer as an illustrative example. Proceeding, we introduce the Lindblad master equation which provides a working description of decoherence in quantum systems, and investigate its properties through the Decohering Dimer and periodic potentials. We then detail our preferred experimental apparatus governed by the Lindbladian. Finally, we introduce the Liouvillian, its relation to non-Hermitian Hamiltonians and Lindbladians, and through it investigate multiple properties of open quantum systems.

Multifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular Dynamics (MD) computations to investigate the structural conversion of RfaH-CTD from its all-a to all-b form. I used various structural and statistical mechanics tools to identify important residues involved in controlling the conformational changes. In the full-length RfaH, the interdomain interactions were found to present the major barrier in the structural conversion of RfaH-CTD from all-a to all-b form. I mapped the energy landscape for the conformational changes by calculating the potential of mean force using the Adaptive Biasing Force and Jarzynski Equality methods. Similarly, the interdomain salt-bridges in the eVP40 protomer were found to play a critical role in domain association and plasma membrane (PM) assembly. This molecular dynamic simulation study is supported by virus like particle budding assays investigated by using live cell imaging that highlighted the important role of these saltbridges. I also investigated the plasma membrane association of the eVP40 dimer in various PM compositions and found that the eVP40 dimer readily associates with the PM containing POPS and PIP2 lipids. Also, the CTD helices were observed to be important in stabilizing the dimer-membrane complex. Coarse-grained MD simulations of the eVP40 hexamer and PM system revealed that the hexamer enhances the PIP2 lipid clustering at the lower leaflet of the PM. These results provide insight on the critical steps in the Ebola virus life cycle.

[pt] A Igualdade de Jarzynski (IJ) é um tipo especial de Teorema de Flutuação, de trabalho, que caracteriza sistemas termodinâmicos microscópicos fora do equilíbrio. A IJ pode ser usada como uma calibração de experimentos e simulações, o que nos permite estudar comportamentos não triviais da dinâmica desses sistemas. Um desses comportamentos é a troca de entropia e informação que o sistema realiza junto a um banho térmico de contato. Neste ensejo, modelamos via uma dinâmica não-Markoviana, i.e., uma dinâmica com memória, que leva a fluxos reversos de informação do reservatório para o sistema. / [en] The Jarzynski Equality (JE) is a special kind of Fluctuation Theorem, of work, which characterizes non-equilibrium small thermodynamics systems. The JE can be used as gauge of experiments and simulations allowing us to study the non-trivial behaviours of these systems dynamics. One of these behaviours is the entropy and information flow the system makes in contact with a thermal bath. In this framework, we modelled through a non-Markovian dynamic, i.e., with a memory effect, leading to reverse flows of information from the reservoir to the system.

<p>Open quantum systems have become a rapidly developing sector for research. Such systems present novel physical phenomena, such as topological chirality, enhanced sensitivity, and unidirectional invisibility resulting from both their non-equilibrium dynamics and the presence of exceptional points.</p> <p><br></p> <p>We begin by introducing the core features of open systems governed by non-Hermitian Hamiltonians, providing the PT -dimer as an illustrative example. Proceeding, we introduce the Lindblad master equation which provides a working description of decoherence in quantum systems, and investigate its properties through the Decohering Dimer and periodic potentials. We then detail our preferred experimental apparatus governed by the Lindbladian. Finally, we introduce the Liouvillian, its relation to non-Hermitian Hamiltonians and Lindbladians, and through it investigate multiple properties of open quantum systems.</p>