Jump-diffusion unravelling of a non Markovian generalized Lindblad master equation

The "correlated-projection technique" has been successfully applied to derive a large class of highly non Markovian dynamics, the so called non Markovian generalized Lindblad type equations or Lindblad rate equations. In this article, general unravellings are presented for these equations, described in terms of jump-diffusion stochastic differential equations for wave functions. We show also that the proposed unravelling can be interpreted in terms of measurements continuous in time, but with some conceptual restrictions. The main point in the measurement interpretation is that the structure itself of the underlying mathematical theory poses restrictions on what can be considered as observable and what is not; such restrictions can be seen as the effect of some kind of superselection rule. Finally, we develop a concrete example and we discuss possible effects on the heterodyne spectrum of a two-level system due to a structured thermal-like bath with memory.Comment: 23 page

Distributed Symmetry Breaking in Hypergraphs

Fundamental local symmetry breaking problems such as Maximal Independent Set (MIS) and coloring have been recognized as important by the community, and studied extensively in (standard) graphs. In particular, fast (i.e., logarithmic run time) randomized algorithms are well-established for MIS and $\Delta +1$-coloring in both the LOCAL and CONGEST distributed computing models. On the other hand, comparatively much less is known on the complexity of distributed symmetry breaking in {\em hypergraphs}. In particular, a key question is whether a fast (randomized) algorithm for MIS exists for hypergraphs. In this paper, we study the distributed complexity of symmetry breaking in hypergraphs by presenting distributed randomized algorithms for a variety of fundamental problems under a natural distributed computing model for hypergraphs. We first show that MIS in hypergraphs (of arbitrary dimension) can be solved in $O(\log^2 n)$ rounds ($n$ is the number of nodes of the hypergraph) in the LOCAL model. We then present a key result of this paper --- an $O(\Delta^{\epsilon}\text{polylog}(n))$-round hypergraph MIS algorithm in the CONGEST model where $\Delta$ is the maximum node degree of the hypergraph and $\epsilon > 0$ is any arbitrarily small constant. To demonstrate the usefulness of hypergraph MIS, we present applications of our hypergraph algorithm to solving problems in (standard) graphs. In particular, the hypergraph MIS yields fast distributed algorithms for the {\em balanced minimal dominating set} problem (left open in Harris et al. [ICALP 2013]) and the {\em minimal connected dominating set problem}. We also present distributed algorithms for coloring, maximal matching, and maximal clique in hypergraphs.Comment: Changes from the previous version: More references adde

Crossing Boundaries: Tapestry Within the Context of the 21st Century

International audienceGraphical model processing is a central problem in artificial intelligence. The optimization of the combined cost of a network of local cost functions federates a variety of famous problems including CSP, SAT and Max-SAT but also optimization in stochastic variants such as Markov Random Fields and Bayesian networks. Exact solving methods for these problems typically include branch and bound and local inference-based bounds.In this paper we are interested in understanding when and how dynamic programming based optimization can be used to efficiently enforce soft local consistencies on Global Cost Functions, defined as parameterized families of cost functions of unbounded arity. Enforcing local consistencies in cost function networks is performed by applying so-called Equivalence Preserving Transformations (EPTs) to the cost functions. These EPTs may transform global cost functions and make them intractable to optimize.We identify as tractable projection-safe those global cost functions whose optimization is and remains tractable after applying the EPTs used for enforcing arc consistency. We also provide new classes of cost functions that are tractable projection-safe thanks to dynamic programming.We show that dynamic programming can either be directly used inside filtering algorithms, defining polynomially DAG-filterable cost functions, or emulated by arc consistency filtering on a Berge-acyclic network of bounded-arity cost functions, defining Berge-acyclic network-decomposable cost functions. We give examples of such cost functions and we provide a systematic way to define decompositions from existing decomposable global constraints.These two approaches to enforcing consistency in global cost functions are then embedded in a solver for extensive experiments that confirm the feasibility and efficiency of our proposal

A self-organized model for cell-differentiation based on variations of molecular decay rates

Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation characteristic to living systems. At any point in time only small subsets of these networks are active. Any active subset of the GRN leads to the expression of particular sets of molecules (expression modes). The subsets of active networks change over time, leading to the observed complex dynamics of expression patterns. Understanding of this dynamics becomes increasingly important in systems biology and medicine. While the importance of transcription rates and catalytic interactions has been widely recognized in modeling genetic regulatory systems, the understanding of the role of degradation of biochemical agents (mRNA, protein) in regulatory dynamics remains limited. Recent experimental data suggests that there exists a functional relation between mRNA and protein decay rates and expression modes. In this paper we propose a model for the dynamics of successions of sequences of active subnetworks of the GRN. The model is able to reproduce key characteristics of molecular dynamics, including homeostasis, multi-stability, periodic dynamics, alternating activity, differentiability, and self-organized critical dynamics. Moreover the model allows to naturally understand the mechanism behind the relation between decay rates and expression modes. The model explains recent experimental observations that decay-rates (or turnovers) vary between differentiated tissue-classes at a general systemic level and highlights the role of intracellular decay rate control mechanisms in cell differentiation.Comment: 16 pages, 5 figure

A simple proof of Kotake-Narasimhan theorem in some classes of ultradifferentiable functions

[EN] We give a simple proof of a general theorem of Kotake-Narasimhan for elliptic operators in the setting of ultradifferentiable functions in the sense of Braun, Meise and Taylor. We follow the ideas of Komatsu. Based on an example of Metivier, we also show that the ellipticity is a necessary condition for the theorem to be true.C. Boiti and D. Jornet were partially supported by the INdAM-GNAMPA Projects 2014 and 2015. D. Jornet was partially supported by MINECO, Project MTM2013-43540-PBoiti, C.; Jornet Casanova, D. (2017). A simple proof of Kotake-Narasimhan theorem in some classes of ultradifferentiable functions. Journal of Pseudo-Differential Operators and Applications. 8(2):297-317. https://doi.org/10.1007/s11868-016-0163-yS29731782Boiti, C., Jornet, D.: The problem of iterates in some classes of ultradifferentiable functions. Oper. Theory Adv. Appl. Birkhauser Basel 245, 21–33 (2015)Boiti, C., Jornet, D.: A characterization of the wave front set defined by the iterates of an operator with constant coefficients. arXiv:1412.4954Boiti, C., Jornet, D., Juan-Huguet, J.: Wave front set with respect to the iterates of an operator with constant coefficients. Abstr. Appl. Anal. 2014, 1–17 Article ID 438716 (2014). doi: 10.1155/2014/438716Bolley, P., Camus, J., Mattera, C.: Analyticité microlocale et itérés d’operateurs hypoelliptiques. Séminaire Goulaouic-Schwartz, 1978–1979, Exp No. 13, École Polytech, PalaiseauBonet, J., Meise, R., Melikhov, S.N.: A comparison of two different ways of define classes of ultradifferentiable functions. Bull. Belg. Math. Soc. Simon Stevin 14, 425–444 (2007)Braun, R.W., Meise, R., Taylor, B.A.: Ultradifferentiable functions and Fourier analysis. Result. Math. 17, 206–237 (1990)Fernández, C., Galbis, A.: Superposition in classes of ultradifferentiable functions. Publ. Res. I Math. Sci. 42(2), 399–419 (2006)Jornet Casanova, D.: Operadores Pseudodiferenciales en Clases no Casianalíticas de Tipo Beurling. Universitat Politècnica de València (2004). doi: 10.4995/Thesis/10251/54953Juan-Huguet, J.: Iterates and hypoellipticity of partial differential operators on non-quasianalytic classes. Integr. Equ. Oper. Theory 68, 263–286 (2010)Juan-Huguet, J.: A Paley–Wiener type theorem for generalized non-quasianalytic classes. Stud. Math. 208(1), 31–46 (2012)Komatsu, H.: A characterization of real analytic functions. Proc. Jpn Acad. 36, 90–93 (1960)Komatsu, H.: On interior regularities of the solutions of principally elliptic systems of linear partial differential equations. J. Fac. Sci. Univ. Tokyo Sect. 1, 9, 141–164 (1961)Komatsu, H.: A proof of Kotaké and Narasimhan’s theorem. Proc. Jpn Acad. 38(9), 615–618 (1962)Kotake, T., Narasimhan, M.S.: Regularity theorems for fractional powers of a linear elliptic operator. Bull. Soc. Math. Fr. 90, 449–471 (1962)Kumano-Go, H.: Pseudo-Differential Operators. The MIT Press, Cambridge, London (1982)Langenbruch, M.: P-Funktionale und Randwerte zu hypoelliptischen Differentialoperatoren. Math. Ann. 239(1), 55–74 (1979)Langenbruch, M.: Fortsetzung von Randwerten zu hypoelliptischen Differentialoperatoren und partielle Differentialgleichungen. J. Reine Angew. Math. 311/312, 57–79 (1979)Langenbruch, M.: On the functional dimension of solution spaces of hypoelliptic partial differential operators. Math. Ann. 272, 217–229 (1985)Langenbruch, M.: Bases in solution sheaves of systems of partial differential equations. J. Reine Angew. Math. 373, 1–36 (1987)Lions, J.L., Magenes, E.: Problèmes aux limites non homogènes et applications, vol. 3. Dunod, Paris (1970)Métivier, G.: Propriété des itérés et ellipticité. Commun. Part. Differ. Eq. 3(9), 827–876 (1978)Nelson, E.: Analytic vectors. Ann. Math. 70, 572–615 (1959)Newberger, E., Zielezny, Z.: The growth of hypoelliptic polynomials and Gevrey classes. Proc. Am. Math. Soc. 39(3), 547–552 (1973)Oldrich, J.: Sulla regolarità delle soluzioni delle equazioni lineari ellittiche nelle classi di Beurling. (Italian) Boll. Un. Mat. Ital. (4) 2, 183–195 (1969)Petzsche, H.-J., Vogt, D.: Almost analytic extension of ultradifferentiable functions and the boundary values of holomorphic functions. Math. Ann. 267(1), 17–35 (1984

Cytosine-to-Uracil Deamination by SssI DNA Methyltransferase

The prokaryotic DNA(cytosine-5)methyltransferase M.SssI shares the specificity of eukaryotic DNA methyltransferases (CG) and is an important model and experimental tool in the study of eukaryotic DNA methylation. Previously, M.SssI was shown to be able to catalyze deamination of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing from the reaction. To test whether this side-activity of the enzyme can be used to distinguish between unmethylated and C5-methylated cytosines in CG dinucleotides, we re-investigated, using a sensitive genetic reversion assay, the cytosine deaminase activity of M.SssI. Confirming previous results we showed that M.SssI can deaminate cytosine to uracil in a slow reaction in the absence of SAM and that the rate of this reaction can be increased by the SAM analogue 5’-amino-5’-deoxyadenosine. We could not detect M.SssI-catalyzed deamination of C5-methylcytosine (m5C). We found conditions where the rate of M.SssI mediated C-to-U deamination was at least 100-fold higher than the rate of m5C-to-T conversion. Although this difference in reactivities suggests that the enzyme could be used to identify C5-methylated cytosines in the epigenetically important CG dinucleotides, the rate of M.SssI mediated cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction. Amino acid replacements in the presumed SAM binding pocket of M.SssI (F17S and G19D) resulted in greatly reduced methyltransferase activity. The G19D variant showed cytosine deaminase activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase activity was also detectable in an E. coli ung+ host proficient in uracil excision repair

Uniform regularity for the Navier-Stokes equation with Navier boundary condition

We prove that there exists an interval of time which is uniform in the vanishing viscosity limit and for which the Navier-Stokes equation with Navier boundary condition has a strong solution. This solution is uniformly bounded in a conormal Sobolev space and has only one normal derivative bounded in $L^\infty$. This allows to get the vanishing viscosity limit to the incompressible Euler system from a strong compactness argument

A characterization of the wave front set defined by the iterates of an operator with constant coefficients

[EN] We characterize the wave front set WF*P (u) with respect to the iterates of a linear partial differential operator with constant coefficients of a classical distribution u is an element of D '(Omega), Omega an open subset in R-n. We use recent Paley-Wiener theorems for generalized ultradifferentiable classes in the sense of Braun, Meise and Taylor. We also give several examples and applications to the regularity of operators with variable coefficients and constant strength. Finally, we construct a distribution with prescribed wave front set of this type.The authors were partially supported by FAR2011 (Universita di Ferrara), "Fondi per le necessita di base della ricerca" 2012 and 2013 (Universita di Ferrara) and the INDAM-GNAMPA Project 2014 "Equazioni Differenziali a Derivate Parziali di Evoluzione e Stocastiche" The research of the second author was partially supported by MINECO of Spain, Project MTM2013-43540-P.Boiti, C.; Jornet Casanova, D. (2017). A characterization of the wave front set defined by the iterates of an operator with constant coefficients. Revista de la Real Academia de Ciencias Exactas Físicas y Naturales Serie A Matemáticas. 111(3):891-919. https://doi.org/10.1007/s13398-016-0329-8S8919191113Albanese, A.A., Jornet, D., Oliaro, A.: Quasianalytic wave front sets for solutions of linear partial differential operators. Integr. Equ. Oper. Theory 66, 153–181 (2010)Boiti, C., Jornet, D.: The problem of iterates in some classes of ultradifferentiable functions. In: “Operator Theory: Advances and Applications”. Birkhauser, Basel. 245, 21–32 (2015)Boiti, C., Jornet, D., Juan-Huguet, J.,: Wave front set with respect to the iterates of an operator with constant coefficients. Abstr. Appl. Anal., 1–17 (2014). doi: 10.1155/2014/438716 (Article ID 438716)Bolley, P., Camus, J., Mattera, C.: Analyticité microlocale et itérés d’operateurs hypoelliptiques. In: Séminaire Goulaouic–Schwartz, 1978–79, Exp N.13. École Polytech., PalaiseauBonet, J., Fernández, C., Meise, R.: Characterization of the $$\omega$$ ω -hypoelliptic convolution operators on ultradistributions. Ann. Acad. Sci. Fenn. Math. 25, 261–284 (2000)Bonet, J., Meise, R., Melikhov, S.N.: A comparison of two different ways to define classes of ultradifferentiable functions. Bull. Belg. Math. Soc. Simon Stevin 14, 425–444 (2007)Braun, R.W., Meise, R., Taylor, B.A.: Ultradifferentiable functions and Fourier analysis. Result. Math. 17, 206–237 (1990)Fernández, C., Galbis, A., Jornet, D.: $$\omega$$ ω -hypoelliptic differential operators of constant strength. J. Math. Anal. Appl. 297, 561–576 (2004)Fernández, C., Galbis, A., Jornet, D.: Pseudodifferential operators of Beurling type and the wave front set. J. Math. Anal. Appl. 340, 1153–1170 (2008)Hörmander, L.: On interior regularity of the solutions of partial differential equations. Comm. Pure Appl. Math. XI, 197–218 (1958)Hörmander, L.: Uniqueness theorems and wave front sets for solutions of linear partial differential equations with analytic coefficients. Comm. Pure Appl. Math. 24, 671–704 (1971)Hörmander, L.: The Analysis of Linear Partial Differential Operators I. Springer, Berlin (1990)Hörmander, L.: The Analysis of Linear Partial Differential Operators II. Springer, Berlin (1983)Juan-Huguet, J.: Iterates and hypoellipticity of partial differential operators on non-quasianalytic classes. Integr. Equ. Oper. Theory 68, 263–286 (2010)Juan-Huguet, J.: A Paley–Wiener type theorem for generalized non-quasianalytic classes. Studia Math. 208(1), 31–46 (2012)Komatsu, H.: A characterization of real analytic functions. Proc. Jpn. Acad. 36, 90–93 (1960)Kotake, T., Narasimhan, M.S.: Regularity theorems for fractional powers of a linear elliptic operator. Bull. Soc. Math. France 90, 449–471 (1962)Langenbruch, M.: P-Funktionale und Randwerte zu hypoelliptischen Differentialoperatoren. Math. Ann. 239(1), 55–74 (1979)Langenbruch, M.: Fortsetzung von Randwerten zu hypoelliptischen Differentialoperatoren und partielle Differentialgleichungen. J. Reine Angew. Math. 311/312, 57–79 (1979)Langenbruch, M.: On the functional dimension of solution spaces of hypoelliptic partial differential operators. Math. Ann. 272, 217–229 (1985)Langenbruch, M.: Bases in solution sheaves of systems of partial differential equations. J. Reine Angew. Math. 373, 1–36 (1987)Métivier, G.: Propriété des itérés et ellipticité. Comm. Partial Differ. Equ. 3(9), 827–876 (1978)Newberger, E., Zielezny, Z.: The growth of hypoelliptic polynomials and Gevrey classes. Proc. Amer. Math. Soc. 39(3), 547–552 (1973)Rodino, L.: On the problem of the hypoellipticity of the linear partial differential equations. In: Buttazzo, G. (ed.) Developments in Partial Differential Equations and Applications to Mathematical Physics. Plenum Press, New York (1992)Rodino, L.: Linear partial differential operators in Gevrey spaces. World Scientific, Singapore (1993)Zanghirati, L.: Iterates of a class of hypoelliptic operators and generalized Gevrey classes. Boll. U.M.I. Suppl. 1, 177–195 (1980

Highly Sensitive Fluorescence Probe Based on Functional SBA-15 for Selective Detection of Hg2+

An inorganic–organic hybrid fluorescence chemosensor (DA/SBA-15) was prepared by covalent immobilization of a dansylamide derivative into the channels of mesoporous silica material SBA-15 via (3-aminopropyl)triethoxysilane (APTES) groups. The primary hexagonally ordered mesoporous structure of SBA-15 was preserved after the grafting procedure. Fluorescence characterization shows that the obtained inorganic–organic hybrid composite is highly selective and sensitive to Hg2+ detection, suggesting the possibility for real-time qualitative or quantitative detection of Hg2+ and the convenience for potential application in toxicology and environmental science