John von Neumann Institute for Computing

We present two classes of improved estimators for mutual information M(X,Y), from samples of random points distributed according to some joint probability density mu(x,y). In contrast to conventional estimators based on binnings, they are based on entropy estimates from k -nearest neighbor distances. This means that they are data efficient (with k=1 we resolve structures down to the smallest possible scales), adaptive (the resolution is higher where data are more numerous), and have minimal bias. Indeed, the bias of the underlying entropy estimates is mainly due to nonuniformity of the density at the smallest resolved scale, giving typically systematic errors which scale as functions of k/N for N points. Numerically, we find that both families become exact for independent distributions, i.e. the estimator M(X,Y) vanishes (up to statistical fluctuations) if mu(x,y)=mu(x)mu(y). This holds for all tested marginal distributions and for all dimensions of x and y. In addition, we give estimators for redundancies between more than two random variables. We compare our algorithms in detail with existing algorithms. Finally, we demonstrate the usefulness of our estimators for assessing the actual independence of components obtained from independent component analysis (ICA), for improving ICA, and for estimating the reliability of blind source separation.

BACKGROUND: Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. RESULTS: TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004) are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. CONCLUSIONS: TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

We study the synchronization between left and right hemisphere rat electroencephalographic (EEG) channels by using various synchronization measures, namely nonlinear interdependences, phase synchronizations, mutual information, cross correlation, and the coherence function. In passing we show a close relation between two recently proposed phase synchronization measures and we extend the definition of one of them. In three typical examples we observe that except mutual information, all these measures give a useful quantification that is hard to be guessed beforehand from the raw data. Despite their differences, results are qualitatively the same. Therefore, we claim that the applied measures are valuable for the study of synchronization in real data. Moreover, in the particular case of EEG signals their use as complementary variables could be of clinical relevance.

We review lattice results related to pion, kaon, [Formula: see text]- and [Formula: see text]-meson physics with the aim of making them easily accessible to the particle-physics community. More specifically, we report on the determination of the light-quark masses, the form factor [Formula: see text], arising in semileptonic [Formula: see text] transition at zero momentum transfer, as well as the decay-constant ratio [Formula: see text] of decay constants and its consequences for the CKM matrix elements [Formula: see text] and [Formula: see text]. Furthermore, we describe the results obtained on the lattice for some of the low-energy constants of [Formula: see text] and [Formula: see text] Chiral Perturbation Theory and review the determination of the [Formula: see text] parameter of neutral kaon mixing. The inclusion of heavy-quark quantities significantly expands the FLAG scope with respect to the previous review. Therefore, we focus here on [Formula: see text]- and [Formula: see text]-meson decay constants, form factors, and mixing parameters, since these are most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. In addition we review the status of lattice determinations of the strong coupling constant [Formula: see text].

Abstract We review lattice results related to pion, kaon, D -meson, B -meson, and nucleon physics with the aim of making them easily accessible to the nuclear and particle physics communities. More specifically, we report on the determination of the light-quark masses, the form factor $$f_+(0)$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mo>+</mml:mo></mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mn>0</mml:mn><mml:mo>)</mml:mo></mml:mrow></mml:mrow></mml:math> arising in the semileptonic $$K \rightarrow \pi $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>K</mml:mi><mml:mo>→</mml:mo><mml:mi>π</mml:mi></mml:mrow></mml:math> transition at zero momentum transfer, as well as the decay constant ratio $$f_K/f_\pi $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>f</mml:mi><mml:mi>K</mml:mi></mml:msub><mml:mo>/</mml:mo><mml:msub><mml:mi>f</mml:mi><mml:mi>π</mml:mi></mml:msub></mml:mrow></mml:math> and its consequences for the CKM matrix elements $$V_{us}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi>us</mml:mi></mml:mrow></mml:msub></mml:math> and $$V_{ud}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>V</mml:mi><mml:mrow><mml:mi>ud</mml:mi></mml:mrow></mml:msub></mml:math> . Furthermore, we describe the results obtained on the lattice for some of the low-energy constants of $$SU(2)_L\times SU(2)_R$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>S</mml:mi><mml:mi>U</mml:mi><mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mn>2</mml:mn><mml:mo>)</mml:mo></mml:mrow><mml:mi>L</mml:mi></mml:msub><mml:mo>×</mml:mo><mml:mi>S</mml:mi><mml:mi>U</mml:mi><mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mn>2</mml:mn><mml:mo>)</mml:mo></mml:mrow><mml:mi>R</mml:mi></mml:msub></mml:mrow></mml:math> and $$SU(3)_L\times SU(3)_R$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>S</mml:mi><mml:mi>U</mml:mi><mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mn>3</mml:mn><mml:mo>)</mml:mo></mml:mrow><mml:mi>L</mml:mi></mml:msub><mml:mo>×</mml:mo><mml:mi>S</mml:mi><mml:mi>U</mml:mi><mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mn>3</mml:mn><mml:mo>)</mml:mo></mml:mrow><mml:mi>R</mml:mi></mml:msub></mml:mrow></mml:math> Chiral Perturbation Theory. We review the determination of the $$B_K$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>B</mml:mi><mml:mi>K</mml:mi></mml:msub></mml:math> parameter of neutral kaon mixing as well as the additional four B parameters that arise in theories of physics beyond the Standard Model. For the heavy-quark sector, we provide results for $$m_c$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>m</mml:mi><mml:mi>c</mml:mi></mml:msub></mml:math> and $$m_b$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>m</mml:mi><mml:mi>b</mml:mi></mml:msub></mml:math> as well as those for D - and B -meson decay constants, form factors, and mixing parameters. These are the heavy-quark quantities most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. We review the status of lattice determinations of the strong coupling constant $$\alpha _s$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msub><mml:mi>α</mml:mi><mml:mi>s</mml:mi></mml:msub></mml:math> . Finally, in this review we have added a new section reviewing results for nucleon matrix elements of the axial, scalar and tensor bilinears, both isovector and flavor diagonal.

More than 99% of the mass of the visible universe is made up of protons and neutrons. Both particles are much heavier than their quark and gluon constituents, and the Standard Model of particle physics should explain this difference. We present a full ab initio calculation of the masses of protons, neutrons, and other light hadrons, using lattice quantum chromodynamics. Pion masses down to 190 mega-electron volts are used to extrapolate to the physical point, with lattice sizes of approximately four times the inverse pion mass. Three lattice spacings are used for a continuum extrapolation. Our results completely agree with experimental observations and represent a quantitative confirmation of this aspect of the Standard Model with fully controlled uncertainties.

Abstract We review lattice results related to pion, kaon, D -meson, B -meson, and nucleon physics with the aim of making them easily accessible to the nuclear and particle physics communities. More specifically, we report on the determination of the light-quark masses, the form factor $$f_+(0)$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>f</mml:mi> <mml:mo>+</mml:mo> </mml:msub> <mml:mrow> <mml:mo>(</mml:mo> <mml:mn>0</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> </mml:mrow> </mml:math> arising in the semileptonic $$K \rightarrow \pi $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>K</mml:mi> <mml:mo>→</mml:mo> <mml:mi>π</mml:mi> </mml:mrow> </mml:math> transition at zero momentum transfer, as well as the decay constant ratio $$f_K/f_\pi $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>f</mml:mi> <mml:mi>K</mml:mi> </mml:msub> <mml:mo>/</mml:mo> <mml:msub> <mml:mi>f</mml:mi> <mml:mi>π</mml:mi> </mml:msub> </mml:mrow> </mml:math> and its consequences for the CKM matrix elements $$V_{us}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>V</mml:mi> <mml:mrow> <mml:mi>us</mml:mi> </mml:mrow> </mml:msub> </mml:math> and $$V_{ud}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>V</mml:mi> <mml:mrow> <mml:mi>ud</mml:mi> </mml:mrow> </mml:msub> </mml:math> . Furthermore, we describe the results obtained on the lattice for some of the low-energy constants of $$SU(2)_L\times SU(2)_R$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>S</mml:mi> <mml:mi>U</mml:mi> <mml:msub> <mml:mrow> <mml:mo>(</mml:mo> <mml:mn>2</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> <mml:mi>L</mml:mi> </mml:msub> <mml:mo>×</mml:mo> <mml:mi>S</mml:mi> <mml:mi>U</mml:mi> <mml:msub> <mml:mrow> <mml:mo>(</mml:mo> <mml:mn>2</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> <mml:mi>R</mml:mi> </mml:msub> </mml:mrow> </mml:math> and $$SU(3)_L\times SU(3)_R$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>S</mml:mi> <mml:mi>U</mml:mi> <mml:msub> <mml:mrow> <mml:mo>(</mml:mo> <mml:mn>3</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> <mml:mi>L</mml:mi> </mml:msub> <mml:mo>×</mml:mo> <mml:mi>S</mml:mi> <mml:mi>U</mml:mi> <mml:msub> <mml:mrow> <mml:mo>(</mml:mo> <mml:mn>3</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> <mml:mi>R</mml:mi> </mml:msub> </mml:mrow> </mml:math> Chiral Perturbation Theory. We review the determination of the $$B_K$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>B</mml:mi> <mml:mi>K</mml:mi> </mml:msub> </mml:math> parameter of neutral kaon mixing as well as the additional four B parameters that arise in theories of physics beyond the Standard Model. For the heavy-quark sector, we provide results for $$m_c$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>m</mml:mi> <mml:mi>c</mml:mi> </mml:msub> </mml:math> and $$m_b$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>m</mml:mi> <mml:mi>b</mml:mi> </mml:msub> </mml:math> as well as those for the decay constants, form factors, and mixing parameters of charmed and bottom mesons and baryons. These are the heavy-quark quantities most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. We review the status of lattice determinations of the strong coupling constant $$\alpha _s$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>α</mml:mi> <mml:mi>s</mml:mi> </mml:msub> </mml:math> . We consider nucleon matrix elements, and review the determinations of the axial, scalar and tensor bilinears, both isovector and flavor diagonal. Finally, in this review we have added a new section reviewing determinations of scale-setting quantities.

-meson-decay constants, form factors, and mixing parameters. These are the heavy-quark quantities most relevant for the determination of CKM matrix elements and the global CKM unitarity-triangle fit. Finally, we review the status of lattice determinations of the strong coupling constant [Formula: see text].

Abstract: Lattice gauge theories, which originated from particle physics in the context of Quantum Chromodynamics (QCD), provide an important intellectual stimulus to further develop quantum information technologies. While one long-term goal is the reliable quantum simulation of currently intractable aspects of QCD itself, lattice gauge theories also play an important role in condensed matter physics and in quantum information science. In this way, lattice gauge theories provide both motivation and a framework for interdisciplinary research towards the development of special purpose digital and analog quantum simulators, and ultimately of scalable universal quantum computers. In this manuscript, recent results and new tools from a quantum science approach to study lattice gauge theories are reviewed. Two new complementary approaches are discussed: first, tensor network methods are presented – a classical simulation approach – applied to the study of lattice gauge theories together with some results on Abelian and non-Abelian lattice gauge theories. Then, recent proposals for the implementation of lattice gauge theory quantum simulators in different quantum hardware are reported, e.g., trapped ions, Rydberg atoms, and superconducting circuits. Finally, the first proof-of-principle trapped ions experimental quantum simulations of the Schwinger model are reviewed. Graphical abstract:

Abstract Lattice gauge theories, which originated from particle physics in the context of Quantum Chromodynamics (QCD), provide an important intellectual stimulus to further develop quantum information technologies. While one long-term goal is the reliable quantum simulation of currently intractable aspects of QCD itself, lattice gauge theories also play an important role in condensed matter physics and in quantum information science. In this way, lattice gauge theories provide both motivation and a framework for interdisciplinary research towards the development of special purpose digital and analog quantum simulators, and ultimately of scalable universal quantum computers. In this manuscript, recent results and new tools from a quantum science approach to study lattice gauge theories are reviewed. Two new complementary approaches are discussed: first, tensor network methods are presented – a classical simulation approach – applied to the study of lattice gauge theories together with some results on Abelian and non-Abelian lattice gauge theories. Then, recent proposals for the implementation of lattice gauge theory quantum simulators in different quantum hardware are reported, e.g., trapped ions, Rydberg atoms, and superconducting circuits. Finally, the first proof-of-principle trapped ions experimental quantum simulations of the Schwinger model are reviewed. Graphical abstract

We propose a simple method to measure synchronization and time-delay patterns between signals. It is based on the relative timings of events in the time series, defined, e.g., as local maxima. The degree of synchronization is obtained from the number of quasisimultaneous appearances of events, and the delay is calculated from the precedence of events in one signal with respect to the other. Moreover, we can easily visualize the time evolution of the delay and synchronization level with an excellent resolution. We apply the algorithm to short rat electroencephalogram (EEG) signals, some of them containing spikes. We also apply it to an intracranial human EEG recording containing an epileptic seizure, and we propose that the method might be useful for the detection of epileptic foci. It can be easily extended to other types of data and it is very simple and fast, thus being suitable for on-line implementations.

We present a measure for characterizing statistical relationships between two time sequences. In contrast to commonly used measures like cross-correlations, coherence and mutual information, the proposed measure is non-symmetric and provides information about the direction of interdependence. It is closely related to recent attempts to detect generalized synchronization. However, we do not assume a strict functional relationship between the two time sequences and try to define the measure so as to be robust against noise, and to detect also weak interdependences. We apply our measure to intracranially recorded electroencephalograms of patients suffering from severe epilepsies.

We present a lattice QCD calculation of the double-virtual neutral pion transition form factor, with the goal to cover the kinematic range relevant to hadronic light-by-light scattering in the muon $g\ensuremath{-}2$. Several improvements have been made compared to our previous work. First, we take into account the effects of the strange quark by using the ${N}_{f}=2+1$ coordinated lattice simulation gauge ensembles. Second, we have implemented the on-shell $\mathcal{O}(a)$ improvement of the vector current to reduce the discretization effects associated with Wilson quarks. Finally, in order to have access to a wider range of photon virtualities, we have computed the transition form factor in a moving frame as well as in the pion rest frame. After extrapolating the form factor to the continuum and to physical quark masses, we compare our results with phenomenology. We extract the normalization of the form factor with a precision of 3.5% and confirm within our uncertainty previous somewhat conflicting estimates for a low-energy constant that appears in chiral perturbation theory for the decay ${\ensuremath{\pi}}^{0}\ensuremath{\rightarrow}\ensuremath{\gamma}\ensuremath{\gamma}$ at the next-to-leading order. With additional input from experiment and theory, we reproduce recent estimates for the decay width $\mathrm{\ensuremath{\Gamma}}({\ensuremath{\pi}}^{0}\ensuremath{\rightarrow}\ensuremath{\gamma}\ensuremath{\gamma})$. We also study the asymptotic large-${Q}^{2}$ behavior of the transition form factor in the double-virtual case. Finally, we provide as our main result a more precise model-independent lattice estimate of the pion-pole contribution to hadronic light-by-light scattering in the muon $g\ensuremath{-}2$: ${a}_{\ensuremath{\mu}}^{\text{HLbL};{\ensuremath{\pi}}^{0}}=(59.7\ifmmode\pm\else\textpm\fi{}3.6)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}11}$. Using in addition the normalization of the form factor obtained by the PrimEx experiment, we get the lattice and data-driven estimate ${a}_{\ensuremath{\mu}}^{\text{HLbL};{\ensuremath{\pi}}^{0}}=(62.3\ifmmode\pm\else\textpm\fi{}2.3)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}11}$.

We numerically investigate the transition of the static quark-antiquark string into a static-light meson-antimeson system. Improving noise reduction techniques, we are able to resolve the signature of string breaking dynamics for ${n}_{f}=2$ lattice QCD at zero temperature. This result can be related to properties of quarkonium systems. We also study short-distance interactions between two static-light mesons.

We describe a new set of gauge configurations generated within the CLS effort. These ensembles have N f = 2 + 1 flavors of non-perturbatively improved Wilson fermions in the sea with the Lüscher-Weisz action used for the gluons. Open boundary conditions in time are used to address the problem of topological freezing at small lattice spacings and twisted-mass reweighting for improved stability of the simulations. We give the bare parameters at which the ensembles have been generated and how these parameters have been chosen. Details of the algorithmic setup and its performance are presented as well as measurements of the pion and kaon masses alongside the scale parameter t 0.

We propose a modification of the hybrid Monte Carlo algorithm that allows for a larger step-size of the integration scheme at constant acceptance rate. The key ingredient is that the pseudo-fermion action is split into two parts. We test our proposal at the example of the two-dimensional lattice Schwinger model with two degenerate flavours of Wilson-fermions.

We present a comprehensive study of the lowest moments of nucleon generalized parton distributions in ${N}_{f}=2+1$ lattice QCD using domain-wall valence quarks and improved staggered sea quarks. Our investigation includes helicity dependent and independent generalized parton distributions for pion masses as low as 350 MeV and volumes as large as $(3.5\text{ }\text{ }\mathrm{fm}{)}^{3}$, for a lattice spacing of 0.124 fm. We use perturbative renormalization at one-loop level with an improvement based on the nonperturbative renormalization factor for the axial vector current, and only connected diagrams are included in the isosinglet channel.

Biodegradation of synthetic polymers, in particular polyethylene terephthalate (PET), is of great importance, since environmental pollution with PET and other plastics has become a severe global problem. Here, we report on the polyester degrading ability of a novel carboxylic ester hydrolase identified in the genome of the marine hydrocarbonoclastic bacterium Pseudomonas aestusnigri VGXO14T. The enzyme, designated PE-H, belongs to the type IIa family of PET hydrolytic enzymes as indicated by amino acid sequence homology. It was produced in Escherichia coli, purified and its crystal structure was solved at 1.09 Å resolution representing the first structure of a type IIa PET hydrolytic enzyme. The structure shows a typical α/β-hydrolase fold and high structural homology to known polyester hydrolases. PET hydrolysis was detected at 30°C with amorphous PET film (PETa), but not with PET film from a commercial PET bottle (PETb). A rational mutagenesis study to improve the PET degrading potential of PE-H yielded variant PE-H (Y250S) which showed improved activity, ultimately also allowing the hydrolysis of PETb. The crystal structure of this variant solved at 1.35 Å resolution allowed to rationalize the improvement of enzymatic activity. A PET oligomer binding model was proposed by molecular docking simulations. Our results indicate a significant potential of the marine bacterium P. aestusnigri for PET degradation.

We present results of lattice QCD simulations with mass-degenerate up and down and mass-split strange and charm (N f = 2 + 1 + 1) dynamical quarks using Wilson twisted mass fermions at maximal twist. The tuning of the strange and charm quark masses is performed at two values of the lattice spacing a ≈ 0:078 fm and a ≈ 0:086 fm with lattice sizes ranging from L ≈ 1:9 fm to L ≈ 2:8 fm. We measure with high statistical precision the light pseudoscalar mass m PS and decay constant f PS in a range 270 ≲ m PS ≲ 510 MeV and determine the low energy parameters f 0 and $ {\bar{l}_{3,4}} $ of SU(2) chiral perturbation theory. We use the two values of the lattice spacing, several lattice sizes as well as different values of the light, strange and charm quark masses to explore the systematic effects. A first study of discretisation effects in light-quark observables and a comparison to N f = 2 results are performed.

We test recent claims that causal (driver-response) relationships can be deduced from interdependencies between simultaneously measured time series. We apply two recently proposed interdependence measures that should give results similar to cross predictabilities used by previous authors. The systems that we study are asymmetrically coupled simple models (Lorenz, Roessler, and Hénon models), the couplings being such that they lead to generalized synchronization. If the data were perfect (noise-free, infinitely long), we should be able to detect, at least in some cases, which of the coupled systems is the driver and which the response. This might no longer be true if the time series has finite length. Instead, estimated interdependencies depend strongly on which of the systems has a higher effective dimension at the typical neighborhood sizes used to estimate them, and causal relationships are more difficult to detect. We also show that slightly different variants of the interdependence measure can have quite different sensitivities.