• Perturbative and non-perturbative renormalization results of the chromomagnetic operator on the lattice

      Constantinou, M; Costa, M; Frezzotti, R; Lubicz, V; Martinelli, G; Meloni, D; Panagopoulos, H; Simula, S (2014-01-01)
      © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence. The Chromomagnetic operator (CMO) mixes with a large number of operators under renormal-ization. We identify which operators can mix with the CMO, at the quantum level. Even in dimensional regularization (DR), which has the simplest mixing pattern, the CMO mixes with a total of 9 other operators, forming a basis of dimension-five, Lorentz scalar operators with the same flavor content as the CMO. Among them, there are also gauge noninvariant operators; these are BRST invariant and vanish by the equations of motion, as required by renormalization theory. On the other hand using a lattice regularization further operators with d ≤ 5 will mix; choosing the lattice action in a manner as to preserve certain discrete symmetries, a minimul set of 3 additional operators (all with d < 5) will appear. In order to compute all relevant mixing coefficients, we calculate the quark-antiquark (2-pt) and the quark-antiquark-gluon (3-pt) Green's functions of the CMO at nonzero quark masses. These calculations were performed in the continuum (dimensional regularization) and on the lattice using the maximally twisted mass fermion action and the Symanzik improved gluon action. In parallel, non-perturbative measurements of the K - π matrix element are being performed in simulations with 4 dynamical (Nf = 2 + 1 + 1) twisted mass fermions and the Iwasaki improved gluon action.
    • Perturbative renormalization of staggered fermion operators with stout improvement: Application to the magnetic susceptibility of QCD

      Bali, GS; Bruckmann, F; Constantinou, M; Costa, M; Endrödi, G; Katz, SD; Panagopoulos, H; Schäfer, A (2013-01-01)
      We calculate the fermion propagator and the quark-antiquark Green's functions for a complete set of ultralocal fermion bilinears, Γ [Γ: scalar (S), pseudoscalar (P), vector (V), axial (A) and tensor (T)], using perturbation theory up to one-loop and to lowest order in the lattice spacing. We employ the staggered action for fermions and the Symanzik Improved action for gluons. From our calculations we determine the renormalization functions for the quark field and for all ultralocal taste-singlet bilinear operators. The novel aspect of our calculations is that the gluon links which appear both in the fermion action and in the definition of the bilinears have been improved by applying a stout smearing procedure up to two times, iteratively. Compared to most other improved formulations of staggered fermions, the above action, as well as the HISQ action, lead to smaller taste violating effects [1, 2, 3]. The renormalization functions are presented in the RI′ scheme; the dependence on all stout parameters, as well as on the coupling constant, the number of colors, the lattice spacing, the gauge fixing parameter and the renormalization scale, is shown explicitly. We apply our results to a nonperturbative study of the magnetic susceptibility of QCD at zero and finite temperature. In particular, we evaluate the "tensor coefficient", t, which is relevant to the anomalous magnetic moment of the muon.
    • Perturbative Renormalization of Wilson line operators

      Constantinou, M; Panagopoulos, H (2018-03-26)
      © The Authors, published by EDP Sciences, 2018. We present results for the renormalization of gauge invariant nonlocal fermion operators which contain a Wilson line, to one loop level in lattice perturbation theory. Our calculations have been performed for Wilson/clover fermions and a wide class of Symanzik improved gluon actions. The extended nature of such 'long-link' operators results in a nontrivial renormalization, including contributions which diverge linearly as well as logarithmically with the lattice spacing, along with additional finite factors. We present nonperturbative prescriptions to extract the linearly divergent contributions.
    • Perturbative subtraction of lattice artifacts in the computation of renormalization constants

      Constantinou, M; Costa, M; Göckeler, M; Horsley, R; Panagopoulos, H; Perlt, H; Rakow, PEL; Schierholz, G; Schiller, A (2012-01-01)
      The determination of renormalization factors is of crucial importance. They relate the observ- ables obtained on finite, discrete lattices to their measured counterparts in the continuum in a suitable renormalization scheme. Therefore, they have to be computed as precisely as possible. A widely used approach is the nonperturbative Rome-Southampton method. It requires, however, a careful treatment of lattice artifacts. They are always present because simulations are done at lattice spacings a and momenta p with ap not necessarily small. In this paper we try to suppress these artifacts by subtraction of one-loop contributions in lattice perturbation theory. We compare results obtained from a complete one-loop subtraction with those calculated for a subtraction of O(a2).
    • Progress in computing parton distribution functions from the quasi-PDF approach

      Alexandrou, C; Cichy, K; Constantinou, M; Hadjiyiannakou, K; Jansen, K; Panagopoulos, H; Scapellato, A; Steffens, F (2018-03-26)
      © The Authors, published by EDP Sciences, 2018. We discuss the current developments by the European Twisted Mass Collaboration in extracting parton distribution functions from the quasi-PDF approach. We concentrate on the non-perturbative renormalization prescription recently developed by us, using the RI′ scheme. We show results for the renormalization functions of matrix elements needed for the computation of quasi-PDFs, including the conversion to the MS scheme, and for renormalized matrix elements. We discuss the systematic effects present in the Z-factors and the possible ways of addressing them in the future.
    • Protein disorder in the human diseasome: Unfoldomics of human genetic diseases

      Midic, U; Oldfield, CJ; Keith, AK; Obradovic, Z; Uversky, VN (2009-07-07)
      Background: Intrinsically disordered proteins lack stable structure under physiological conditions, yet carry out many crucial biological functions, especially functions associated with regulation, recognition, signaling and control. Recently, human genetic diseases and related genes were organized into a bipartite graph (Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases. Methods and findings: We analyzed the abundance of intrinsic disorder in these diseasome network proteins by means of several prediction algorithms, and we analyzed the functional repertoires of these proteins based on prior studies relating disorder to function. Our analyses revealed that (i) Intrinsic disorder is common in proteins associated with many human genetic diseases; (ii) Different disease classes vary in the IDP contents of their associated proteins; (iii) Molecular recognition features, which are relatively short loosely structured protein regions within mostly disordered sequences and which gain structure upon binding to partners, are common in the diseasome, and their abundance correlates with the intrinsic disorder level; (iv) Some disease classes have a significant fraction of genes affected by alternative splicing, and the alternatively spliced regions in the corresponding proteins are predicted to be highly disordered; and (v) Correlations were found among the various diseasome graph-related properties and intrinsic disorder. Conclusion: These observations provide the basis for the construction of the human-genetic-disease-associated unfoldome. © 2009 Midic et al; licensee BioMed Central Ltd.
    • Provably efficient algorithms for joint placement and allocation of virtual network functions

      Sang, Y; Ji, B; Gupta, GR; Du, X; Ye, L; Du, Xiaojiang|0000-0003-4235-9671 (2017-10-02)
      © 2017 IEEE. Network Function Virtualization (NFV) has the potential to significantly reduce the capital and operating expenses, shorten product release cycle, and improve service agility. In this paper, we focus on minimizing the total number of Virtual Network Function (VNF) instances to provide a specific service (possibly at different locations) to all the flows in a network. Certain network security and analytics applications may allow fractional processing of a flow at different nodes (corresponding to datacenters), giving an opportunity for greater optimization of resources. Through a reduction from the set cover problem, we show that this problem is NP-hard and cannot even be approximated within a factor of (1 - o(1))lnm (where m is the number of flows) unless P=NP. Then, we design two simple greedy algorithms and prove that they achieve an approximation ratio of (1 - o(1))ln m + 2, which is asymptotically optimal. For special cases where each node hosts multiple VNF instances (which is typically true in practice), we also show that our greedy algorithms have a constant approximation ratio. Further, for tree topologies we develop an optimal greedy algorithm by exploiting the inherent topological structure. Finally, we conduct extensive numerical experiments to evaluate the performance of our proposed algorithms in various scenarios.
    • Recent progress in hadron structure from Lattice QCD

      Constantinou, M (2015-01-01)
      We review recent progress in hadron structure using lattice QCD simulations, with main focus in the evaluation of nucleon quantities such as the axial and tensor charges, and the spin content of the nucleon, using simulations at pion masses close to the physical value. We highlight developments on the evaluation of the gluon moment, a new direct approach to compute quark parton distributions functions on the lattice, as well as, the neutron electric dipole moment. A discussion of the systematic uncertainties and the computation of the disconnected contributions using dynamical simulations is also included.
    • Recent results for the proton spin decomposition from lattice QCD

      Alexandrou, C; Constantinou, M; Hadjiyiannakou, K; Kallidonis, C; Koutsou, G; Jansen, K; Panagopoulos, H; Steffens, F; Vaquero, A; Wiese, C (2016-01-01)
      The exact decomposition of the proton spin has been a much debated topic, on the experimental as well as the theoretical side. In this talk we would like to report on recent non-perturbative results and ongoing efforts to explore the proton spin from lattice QCD. We present results for the relevant generalized form factors from gauge field ensembles that feature a physical value of the pion mass. These generalized form factors can be used to determine the total spin and angular momentum carried by the quarks. In addition we present first results for our ongoing effort to compute the angular momentum of the gluons in the proton.
    • Renormalization of flavor singlet and nonsinglet fermion bilinear operators

      Constantinou, M; Hadjiantonis, M; Panagopoulos, H (2014-01-01)
      © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence. We compute the difference in the renormalization of flavor singlet and nonsinglet fermion bilinear operators, to two loops in perturbation theory. Our results are applicable to a rather wide class of lattice actions with Symanzik improved gluons, stout links and clover fermions, including the Twisted Mass and SLiNC actions. A more detailed presentation of our results, along with relevant references, will appear in our forthcoming publication [1].
    • Results on the disconnected contributions for hadron structure

      Alexandrou, C; Constantinou, M; Drach, V; Hadjiyiannakou, K; Jansen, K; Koutsou, G; Vaquero, A (2014-01-01)
      © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence. We present results on the disconnected contributions to three point functions entering in studies of hadron structure. We use Nf = 2+1+1 twisted mass fermions and give a detailed description on the results of the nucleon sigma-terms, isoscalar axial charge and first moments of bare parton distributions for a range of pions masses. In addition we give the s-terms and the computations are performed using QUDA code implemented on GPUS.
    • Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions

      Ren, S; Uversky, VN; Chen, Z; Dunker, AK; Obradovic, Z (2008-09-16)
      Background: Protein interactions are essential for most cellular functions. Interactions mediated by domains that appear in a large number of proteins are of particular interest since they are expected to have an impact on diversities of cellular processes such as signal transduction and immune response. Many well represented domains recognize and bind to primary sequences less than 10 amino acids in length called Short Linear Motifs (SLiMs). Results: In this study, we systematically studied the evolutionary conservation of SLiMs recognized by SH2, SH3 and Ser/Thr Kinase domains in both ordered and disordered protein regions. Disordered protein regions are protein sequences that lack a fixed three-dimensional structure under putatively native conditions. We find that, in all these domains examined, SLiMs are more conserved in disordered regions. This trend is more evident in those protein functional groups that are frequently reported to interact with specific domains. Conclusion: The correlation between SLiM conservation with disorder prediction demonstrates that functional SLiMs recognized by each domain occur more often in disordered as compared to structured regions of proteins. © 2008 Ren et al; licensee BioMed Central Ltd.
    • Sigma terms and strangeness content of the nucleon with N f = 2+1+1 twisted mass fermions

      Alexandroua, C; Constantinou, M; Dinter, S; Drach, V; Hadjiyiannakou, K; Jansen, K; Koutsou, G; Strelchenko, A; Vaquero, A (2012-01-01)
      We investigate excited state contaminations in a direct computation of the nucleon s-terms. This is an important source of systematic effects that needs to be controlled besides the light quark mass dependence and lattice artefacts. We use maximally twisted mass fermions with dynamical light (u,d), strange and charm degrees of freedom. Employing an efficient stochastic evaluation of the disconnected contribution available for twisted mass fermions, we show that the effect of excited states is large in particular for the strange s-terms, where it can be as big as O(and 40%). This leads to the unfortunate conclusion that even with a source-sink separation of -1.5 fm and a good statistical accuracy it is not clear, whether excited state effects are under control for this quantity.
    • The chromomagnetic operator on the lattice

      Constantinou, M; Costa, M; Frezzotti, R; Lubicz, V; Martinelli, G; Meloni, D; Panagopoulos, H; Simula, S (2013-01-01)
      We study matrix elements of the "chromomagnetic" operator on the lattice. This operator is contained in the strangeness-changing effective Hamiltonian which describes electroweak effects in the Standard Model and beyond. Having dimension 5, the chromomagnetic operator is characterized by a rich pattern of mixing with other operators of equal and lower dimensionality, including also non gauge invariant quantities; it is thus quite a challenge to extract from lattice simulations a clear signal for the hadronic matrix elements of this operator. We compute all relevant mixing coefficients to one loop in lattice perturbation theory; this necessitates calculating both 2-point (quark- Antiquark) and 3-point (gluon-quark- Antiquark) Green's functions at nonzero quark masses. We use the twisted mass lattice formulation, with Symanzik improved gluon action. For a comprehensive presentation of our results, along with detailed explanations and a more complete list of references, we refer to our forthcoming publication [1].
    • The electric dipole moment of the neutron from N<inf>f</inf> = 2+1+1 twisted mass fermions

      Alexandrou, C; Athenodorou, A; Constantinou, M; Hadjiyiannakou, K; Jansen, K; Koutsou, G; Ottnad, K; Petschlies, M (2015-01-01)
      We extract the neutron electric dipole moment (nEDM) dn on configurations produced with Nf = 2+1+1 twisted mass fermions with lattice spacing of a ≃ 0.082fm and a light quark mass that correpsonds to Mπ ≃ 373 MeV. We do so by evaluating the CP-odd form factor F3 for small values of the CP-violation parameter θ in the limit of zero momentum transfer. This limit is extracted using the usual parametrization but in addition position space methods. The topological charge is computed via cooling and gradient flow using the Wilson, Symanzik treelevel improved and Iwasaki actions for smoothing. We obtain consistent results for all choices of smoothing procedures and methods to extract F3 at zero momentum transfer. For the ensemble analyzed we find a value of nEDM of dn/θ = 0.045(6)(1)e · fm.
    • The quark contents of the nucleon and their implication for dark matter search

      Alexandrou, C; Constantinou, M; Drach, V; Hadjiyiannakou, K; Jansen, K; Koutsou, G; Strelchenko, A; Vaquero, A (2013-01-01)
      We present results concerning the light and strange quark contents of the nucleon using Nf = 2+1+1 flavours of maximally twisted mass fermions. The corresponding σ- Terms are casting light on the origin of the nucleon mass and their values are important to interpret experimental data from direct dark matter searches. We discuss our strategy to estimate systematic uncertainties arising in our computations. Our preliminary results for the σ- Terms read σπN = 37(2:6)(24:7)MeV and σs = 28(8)(10)MeV. We present our recent final analysis of the yN parameter and found yN = 0:135(46) including systematics[1].
    • The salmon genome (and other issues in bioinformatics)

      Milchert, LEF; Liberles, DA; Elofsson, A; Liberles, David A|0000-0003-3487-8826 (2002-10-07)
      A report on the fourth annual conference of the Society for Bioinformatics in the Nordic Countries (SOCBIN), Bioinformatics 2002, Bergen, Norway, 4-7 April 2002.
    • The unfoldomics decade: An update on intrinsically disordered proteins

      Dunker, AK; Oldfield, CJ; Meng, J; Romero, P; Yang, JY; Chen, JW; Vacic, V; Obradovic, Z; Uversky, VN (2008-09-16)
      Background; Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90-95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins. Results: Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships. Conclusion: Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets. © 2008 Dunker et al; licensee BioMed Central Ltd.
    • Thermodynamic properties of QCD in external magnetic fields

      Bali, GS; Bruckmann, F; Constantinou, M; Costa, M; Endrodi, G; Fodor, Z; Katz, SD; Krieg, S; Panagopoulos, H; Schäfer, A; Szabó, KK (2012-12-01)
      We consider the effect of strong external electromagnetic fields on thermodynamic observables in QCD, through lattice simulations with 1+1+1 flavors of staggered quarks at physical quark masses. Continuum extrapolated results are presented for the light quark condensates and for their tensor polarizations, as functions of the temperature and the magnetic field. We find the light condensates to undergo inverse magnetic catalysis in the transition region, in a manner that the transition temperature decreases with growing magnetic field. We also compare the results to other approaches and lattice simulations. Furthermore, we relate the tensor polarization to the spin part of the magnetic susceptibility of the QCD vacuum, and show that this contribution is diamagnetic. © Copyright owned by the author(s).
    • Unfoldomics of human diseases: Linking protein intrinsic disorder with diseases

      Uversky, VN; Oldfield, CJ; Midic, U; Xie, H; Xue, B; Vucetic, S; Iakoucheva, LM; Obradovic, Z; Keith, AK (2009-07-07)
      Background: Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack stable tertiary and/or secondary structure yet fulfills key biological functions. The recent recognition of IDPs and IDRs is leading to an entire field aimed at their systematic structural characterization and at determination of their mechanisms of action. Bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. These activities complement the functions of structured proteins. IDPs and IDRs were shown to participate in both one-to-many and many-to-one signaling. Alternative splicing and posttranslational modifications are frequently used to tune the IDP functionality. Several individual IDPs were shown to be associated with human diseases, such as cancer, cardiovascular disease, amyloidoses, diabetes, neurodegenerative diseases, and others. This raises questions regarding the involvement of IDPs and IDRs in various diseases. Results: IDPs and IDRs were shown to be highly abundant in proteins associated with various human maladies. As the number of IDPs related to various diseases was found to be very large, the concepts of the disease-related unfoldome and unfoldomics were introduced. Novel bioinformatics tools were proposed to populate and characterize the disease-associated unfoldome. Structural characterization of the members of the disease-related unfoldome requires specialized experimental approaches. IDPs possess a number of unique structural and functional features that determine their broad involvement into the pathogenesis of various diseases. Conclusion: Proteins associated with various human diseases are enriched in intrinsic disorder. These disease-associated IDPs and IDRs are real, abundant, diversified, vital, and dynamic. These proteins and regions comprise the disease-related unfoldome, which covers a significant part of the human proteome. Profound association between intrinsic disorder and various human diseases is determined by a set of unique structural and functional characteristics of IDPs and IDRs. Unfoldomics of human diseases utilizes unrivaled bioinformatics and experimental techniques, paves the road for better understanding of human diseases, their pathogenesis and molecular mechanisms, and helps develop new strategies for the analysis of disease-related proteins. © 2009 Uversky et al; licensee BioMed Central Ltd.