Gap equation with pairing correlations beyond mean field and its equivalence to a Hugenholtz-Pines condition for fermion pairs

The equation for the gap parameter represents the main equation of the pairing theory of superconductivity. Although it is formally defined through a single-particle property, physically it reflects the pairing correlations between opposite-spin fermions. Here, we exploit this physical connection and cast the gap equation in an alternative form which explicitly highlights these two-particle correlations, by showing that it is equivalent to a Hugenholtz-Pines condition for fermion pairs. At a formal level, a direct connection is established in this way between the treatment of the condensate fraction in condensate systems of fermions and bosons. At a practical level, the use of this alternative form of the gap equation is expected to make easier the inclusion of pairing fluctuations beyond mean field. As a proof-of-concept of the new method, we apply the modified form of the gap equation to the long-pending problem about the inclusion of the Gorkov-Melik-Barkhudarov correction across the whole BCS-BEC crossover, from the BCS limit of strongly overlapping Cooper pairs to the BEC limit of dilute composite bosons, and for all temperatures in the superfluid phase. Our numerical calculations yield excellent agreement with the recently determined experimental values of the gap parameter for an ultra-cold Fermi gas in the intermediate regime between BCS and BEC, as well as with the available quantum Monte Carlo data in the same regime.Comment: 24 pages, 13 figure

Entanglement between pairing and screening in the Gorkov-Melik-Barkhudarov correction to the critical temperature throughout the BCS-BEC crossover

The theoretical description of the critical temperature Tc of a Fermi superfluid dates back to the work by Gor'kov and Melik-Barkhudarov (GMB), who addressed it for a weakly-coupled (dilute) superfluid in the BCS (weak-coupling) limit of the BCS-BEC crossover. The point made by GMB was that particle-particle (pairing) excitations, which are responsible for superfluidity to occur below Tc, and particle-hole excitations, which give rise to screening also in a normal system, get effectively disentangled from each other in the BCS limit, thus yielding a reduction by a factor 2.2 of the value of Tc obtained when neglecting screening effects. Subsequent work on this topic, aimed at extending the original GMB argument away from the BCS limit with diagrammatic methods, has kept this disentangling between pairing and screening throughout the BCS-BEC crossover, without realising that the conditions for it to be valid are soon violated away from the BCS limit. Here, we reconsider this problem from a more general perspective and argue that pairing and screening are intrinsically entangled with each other along the whole BCS-BEC crossover but for the BCS limit considered by GMB. We perform a detailed numerical calculation of the GMB diagrammatic contribution extended to the whole BCS-BEC crossover, where the full wave-vector and frequency dependence occurring in the repeated in-medium two-particle scattering is duly taken into account. Our numerical calculations are tested against analytic results available in both the BCS and BEC limits, and the contribution of the GMB diagrammatic term to the scattering length of composite bosons in the BEC limit is highlighted. We calculate Tc throughout the BCS-BEC crossover and find that it agrees quite well with Quantum Monte Carlo calculations and experimental data available in the unitarity regime.Comment: 21 pages, 11 figure

Spatial emergence of off-diagonal long-range order throughout the BCS-BEC crossover

In a superfluid system, off-diagonal long-range order is expected to be exhibited in the appropriate reduced density matrices when the relevant particles (either bosons or fermion pairs) are considered to recede sufficiently far apart from each other. This concept is usually exploited to identify the value of the condensate density, without explicit concern, however, as to the spatial range over which this asymptotic condition can effectively be achieved. Here, based on a diagrammatic approach that includes beyond-mean-field pairing fluctuations in the broken-symmetry phase at the level of the t-matrix also with the inclusion of the Gorkov-Melik-Barkhudarov (GMB) correction, we present a systematic study of the two-particle reduced density matrix for a superfluid fermionic system undergoing the BCS-BEC crossover, when the entities to recede far apart from each other evolve with continuity from largely overlapping Cooper pairs in the BCS limit to dilute composite bosons in the BEC limit. By this approach, we not only provide the coupling and temperature dependence of the condensate density at the level of our diagrammatic approach, which includes the GMB correction, but we also obtain the evolution of the spatial dependence of the two-particle reduced density matrix, from a power law at low temperature to an exponential dependence at high temperature in the superfluid phase, when the interparticle coupling spans the BCS-BEC crossover. Our results put limitations on the minimum spatial extent of a finite-size system for which superfluid correlations can effectively be established

Critical current throughout the BCS-BEC crossover with the inclusion of pairing fluctuations

The present work aims at providing a systematic analysis of the current density versus momentum characteristics for a fermionic superfluid throughout the BCS-BEC crossover, even in the fully homogeneous case. At low temperatures, where pairing fluctuations are not strong enough to invalidate a quasiparticle approach, a sharp threshold for the inception of a back-flow current is found, which sets the onset of dissipation and identifies the critical momentum according to Landau. This momentum is seen to smoothly evolve from the BCS to the BEC regimes, whereby a single expression for the single-particle current density that includes pairing fluctuations enables us to incorporate on equal footing two quite distinct dissipative mechanisms, namely, pair breaking and phonon excitations in the two sides of the BCS-BEC crossover, respectively. At finite temperature, where thermal fluctuations broaden the excitation spectrum and make the dissipative (kinetic and thermal) mechanisms intertwined with each other, an alternative criterion due to Bardeen is instead employed to signal the loss of superfluid behavior. In this way, detailed comparison with available experimental data in linear and annular geometries is significantly improved with respect to previous approaches, thereby demonstrating the crucial role played by quantum fluctuations in renormalizing the single-particle excitation spectrum

Active human full-length CDKL5 produced in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125

Background: A significant fraction of the human proteome is still inaccessible to in vitro studies since the recombinant production of several proteins failed in conventional cell factories. Eukaryotic protein kinases are difficult-to-express in heterologous hosts due to folding issues both related to their catalytic and regulatory domains. Human CDKL5 belongs to this category. It is a serine/threonine protein kinase whose mutations are involved in CDKL5 Deficiency Disorder (CDD), a severe neurodevelopmental pathology still lacking a therapeutic intervention. The lack of successful CDKL5 manufacture hampered the exploitation of the otherwise highly promising enzyme replacement therapy. As almost two-thirds of the enzyme sequence is predicted to be intrinsically disordered, the recombinant product is either subjected to a massive proteolytic attack by host-encoded proteases or tends to form aggregates. Therefore, the use of an unconventional expression system can constitute a valid alternative to solve these issues. Results: Using a multiparametric approach we managed to optimize the transcription of the CDKL5 gene and the synthesis of the recombinant protein in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 applying a bicistronic expression strategy, whose generalization for recombinant expression in the cold has been here confirmed with the use of a fluorescent reporter. The recombinant protein largely accumulated as a full-length product in the soluble cell lysate. We also demonstrated for the first time that full-length CDKL5 produced in Antarctic bacteria is catalytically active by using two independent assays, making feasible its recovery in native conditions from bacterial lysates as an active product, a result unmet in other bacteria so far. Finally, the setup of an in cellulo kinase assay allowed us to measure the impact of several CDD missense mutations on the kinase activity, providing new information towards a better understanding of CDD pathophysiology. Conclusions: Collectively, our data indicate that P. haloplanktis TAC125 can be a valuable platform for both the preparation of soluble active human CDKL5 and the study of structural–functional relationships in wild type and mutant CDKL5 forms. Furthermore, this paper further confirms the more general potentialities of exploitation of Antarctic bacteria to produce “intractable” proteins, especially those containing large intrinsically disordered regions

Querying regular graph patterns

Artículo de publicación ISIGraph data appears in a variety of application domains, and many uses of it, such as querying, matching, and transforming data, naturally result in incompletely specified graph data, that is, graph patterns. While queries need to be posed against such data, techniques for querying patterns are generally lacking, and properties of such queries are not well understood. Our goal is to study the basics of querying graph patterns. The key features of patterns we consider here are node and label variables and edges specified by regular expressions. We provide a classification of patterns, and study standard graph queries on graph patterns. We give precise characterizations of both data and combined complexity for each class of patterns. If complexity is high, we do further analysis of features that lead to intractability, as well as lower-complexity restrictions. Since our patterns are based on regular expressions, query answering for them can be captured by a new automata model. These automata have two modes of acceptance: one captures queries returning nodes, and the other queries returning paths. We study properties of such automata, and the key computational tasks associated with them. Finally, we provide additional restrictions for tractability, and show that some intractable cases can be naturally cast as instances of constraint satisfaction problems.Partial support for this work was provided by Fondecyt grant 1110171, EPSRC grant G049165, and FET-Open Project FoX, grant agreement 233599

Development of high-copy number plasmids in Pseudoalteromonas haloplanktis TAC125

Abstract: The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) is considered an interesting alternative host for the recombinant protein production, that can be explored when the conventional bacterial expression systems fail. Indeed, the manufacture of all the difficult-to-express proteins produced so far in this bacterial platform gave back soluble and active products. Despite these promising results, the low yield of recombinant protein production achieved is hampering the wider and industrial exploitation of this psychrophilic cell factory. All the expression plasmids developed so far in PhTAC125 are based on the origin of replication of the endogenous pMtBL plasmid and are maintained at a very low copy number. In this work, we set up an experimental strategy to select mutated OriR sequences endowed with the ability to establish recombinant plasmids at higher multiplicity per cell. The solution to this major production bottleneck was achieved by the construction of a library of psychrophilic vectors, each containing a randomly mutated version of pMtBL OriR, and its screening by fluorescence-activated cell sorting (FACS). The selected clones allowed the identification of mutated OriR sequences effective in enhancing the plasmid copy number of approximately two orders of magnitude, and the production of the recombinant green fluorescent protein was increased up to twenty times approximately. Moreover, the molecular characterization of the different mutant OriR sequences allowed us to suggest some preliminary clues on the pMtBL replication mechanism that deserve to be further investigated in the future. Key points: • Setup of an electroporation procedure for Pseudoalteromonas haloplanktis TAC125. • Two order of magnitude improvement of OriR-derived psychrophilic expression systems. • Almost twenty times enhancement in Green fluorescent protein production

Case and Activity Identification for Mining Process Models from Middleware

Process monitoring aims to provide transparency over operational aspects of a business process. In practice, it is a challenge that traces of business process executions span across a number of diverse systems. It is cumbersome manual engineering work to identify which attributes in unstructured event data can serve as case and activity identifiers for extracting and monitoring the business process. Approaches from literature assume that these identifiers are known a priori and data is readily available in formats like eXtensible Event Stream (XES). However, in practice this is hardly the case, specifically when event data from different sources are pooled together in event stores. In this paper, we address this research gap by inferring potential case and activity identifiers in a provenance agnostic way. More specifically, we propose a semi-automatic technique for discovering event relations that are semantically relevant for business process monitoring. The results are evaluated in an industry case study with an international telecommunication provider

Introducing Preference-Based Argumentation to Inconsistent Ontological Knowledge Bases

International audienceHandling inconsistency is an inherent part of decision making in traditional agri-food chains – due to the various concerns involved. In order to explain the source of inconsistency and represent the existing conflicts in the ontological knowledge base, argumentation theory can be used. However, the current state of art methodology does not allow to take into account the level of significance of the knowledge expressed by the various ontological knowledge sources. We propose to use preferences in order to model those differences between formulas and evaluate our proposal practically by implementing it within the INRA platform and showing a use case using this formalism in a bread making decision support system

Synthetic gauge fields in synthetic dimensions: interactions and chiral edge modes

Synthetic ladders realized with one-dimensional alkaline-earth(-like) fermionic gases and subject to a gauge field represent a promising environment for the investigation of quantum Hall physics with ultracold atoms. Using density-matrix renormalization group calculations, we study how the quantum Hall-like chiral edge currents are affected by repulsive atom-atom interactions. We relate the properties of such currents to the asymmetry of the spin resolved momentum distribution function, a quantity which is easily addressable in state-of-art experiments. We show that repulsive interactions significantly enhance the chiral currents. Our numerical simulations are performed for atoms with two and three internal spin states