Nonequilibrium Phenomena in Confined Systems

Confined systems exhibit a large variety of nonequilibrium phenomena. In this special issue, we have collected a limited number of papers that were presented during the XXV Sitges Conference on Statistical Mechanics, devoted to "Nonequilibrium phenomena in confined systems". The conference took place in Barcelona from the 6th until the 10th of June 2016 (http://www.ffn.ub.es/~sitges25/), was organized by G. Franzese, I. Latella, D. Reguera, and J.M. Rubi, and gathered more than 60 international scientists in the areas of physics, chemistry, and biology working on confined systems in topics like: Diffusion and entropic transport in confined systems; Ion and polymer translocation; Phase transitions and chemical reactions in confined media; Forces induced by fluctuations in confined systems and Casimir effect; Confined active matter; Macromolecular crowding; and Energy conversion in confinement

Toy trains, loaded dice and the origin of life: dimerization on mineral surfaces under periodic drive with Gaussian inputs

In a major extension of previous work, we model the putative hydrothermal rock pore setting for the origin of life on Earth as a series of coupled continuous flow units (the toy train). Perfusing through this train are reactants that set up thermochemical and pH oscillations, and an activated nucleotide that produces monomer and dimer monophosphates. The dynamical equations that model this system are thermally self-consistent. In an innovative step that breaks some new ground, we build stochasticity of the inputs into the model. The computational results infer various constraints and conditions on, and insights into, chemical evolution and the origin of life and its physical setting: long, interconnected porous structures with longitudinal non-uniformity would have been favourable, and the ubiquitous pH dependences of biology may have been established in the prebiotic era. We demonstrate the important role of Gaussian fluctuations of the inputs in driving polymerization, evolution and diversification. In particular, we find that the probability distribution of the resulting output fluctuations is left-skewed and right-weighted (the loaded dice), which could favour chemical evolution towards a living RNA world. We tentatively name this distribution ‘Goldilocks’. These results also vindicate the general approach of constructing and running a simple model to learn important new information about a complex system

Deep geothermal exploration by means of electromagnetic methods: New insights from the Larderello geothermal field (Italy)

The main target of this research is the improvement of the knowledge on the deep structures of the Larderello-Travale geothermal field (Tuscany, Italy), with a focus on the Lago Boracifero sector, particularly on the heat source of the system, the tectonics and its relation with the hydrothermal circulation. In the frame of the PhD program and of the IMAGE project (Integrated Methods for Advanced Geothermal Exploration; EU FP7), we acquired new magnetotelluric (MT) and Time Domain EM (TDEM) data in a key sector of the field (Lago Boracifero). These data integrate the MT datasets previously acquired in the frame of exploration and scientific projects. This study is based also on a integrated modelling, which included and organized in Petrel (Schlumberger) environment, a large quantity of geological and geophysical data. We also propose an integrated approach to improve the reliability of the 2D MT inversion models, by using external information from the integrated model of the field as well as an innovative probabilistic analysis of the MT data. We present our attempt to treat the 1D magnetotelluric inverse problem with a probabilistic approach, by adopting the Particle Swarm Optimization (PSO), a heuristic method based on the concept of the adaptive behaviour to solve complex problems. The user-friendly software “GlobalEM” was implemented for the analysis and probabilistic optimization of MT data. The results from theoretical and measured MT data are promising, also for the possibility to implement different schemes of constrained optimization as well as joint optimization (e.g. MT and TDEM). The analysis of the a-posteriori distribution of the results can be of help to understand the reliability of the model. The 2D MT inversion models and the integrated study of the Larderello-Travale geothermal field improved the knowledge about the deep structures of the system, with a relevant impact on the conceptual geothermal model. In Micaschist and Gneiss complexes we observed a generally high electrical resistivity response locally interrupted by low resistivity anomalies that are well correlated with the most productive sectors of the field. A still partial melted igneous intrusion beneath the Lago Boracifero sector was detected based on the interpretation of the low resistivity anomalies located at a mid-crustal level (> 6 km). New insights on the tectonics are proposed in this research. The fundamental role of a large tectonic structure, i.e. the Cornia Fault, located along the homonymous river, was highlighted. In our opinion, this fault played an important role in the geothermal evolution of the Lago Boracifero sector, favouring both the hydrothermal circulation and the emplacement of magma bodies. In our opinion, the system can be ascribed to a “young convective and intrusive” field feed by a complex composite batholite

Micro-Scale Complex Flows Enables Robust DNA Replication, Enhanced Transport and Tunable Fluid-Particle Interactions

The ability of convective flows in micro-scale confinement to direct chemical processes along accelerated kinetic pathways has been recognized for some time. However, practical applications have been slow to emerge because optimal results are often counterintuitively achieved in flows that appear to possess undesirably high disorder. Here we investigate the nature of these thermal instability driven Rayleigh-Bénard convective flows by altering the Rayleigh number and geometry of the cylindrical enclosure and thus identifying the chaotic flow regime. We then assess the ability of these flows to replicate DNA through polymerase chain reaction (PCR) across a broad ensemble of geometric states. The resulting parametric map reveals an unexpectedly wide chaotic regime where reaction rates remain constant over 2 orders of magnitude of the Rayleigh number, enabling robust convective PCR. With the new optimal design rules, we engineer a rugged, ultra-portable (300 g), inexpensive (<$20) bioanalysis platform for rapid nucleic acid-based diagnostics. The isothermal convective isothermal PCR format enables low power operation (5 V USB source). Time-resolved fluorescence detection and quantification is achieved using a smart-phone camera and integrated image analysis app. These advancements make it possible to provide gold standard nucleic acid-based diagnostics to remote field sites using consumer class quad-copter drones. The surprising interplay between reactions and micro-scale convective flows led us to consider adaptations beyond PCR. Specifically, we demonstrate that such flows, naturally established over a broad range of hydrothermally relevant pore sizes, function as highly efficient conveyors to continually shuttle molecular precursors from the bulk fluid to targeted locations on the solid boundaries, enabling greatly accelerated chemical synthesis. Insights from this study has the potential to provide a breakthrough in our understanding of the fundamental biochemical processes underlying the origin of life. The phenomenon of particle resuspension plays a vital role in numerous fields and thus an accurate description and formulation of van der Waals (vdW) interactions between the particle and substrate is of utmost importance. An approach based on Lifshitz continuum theory has been developed to calculate the principal many body interactions between arbitrary geometries at all separation distances to a high degree of accuracy. The new formulation can now provide realistic interactions for various particle-substrate systems which can then be coupled with computational fluid dynamics (CFD) models to improve the predictive capabilities of particle resuspension dynamics. Finally, We analyze trajectories of micro sized particles subject to all relevant hydrodynamic forces and torques by coupling discrete element modeling with CFD. The results provide us with important design rules to construct membraneless microfluidic filtration channels where pressure driven transverse flows and curvature induced dean flows can be simultaneously harnessed to assist size based particle separation with high throughput

RGD-bases metal organic frameworks for selective delivery of therapeutics to tumor vasculature

Dissertação de mestrado integrado. Mestrado Integrado em Bioengenharia. Faculdade de Engenharia. Universidade do Porto. 201