nils-herrmann/clean_scirepeval huggingface dataset:
Predicting binding free energies in solution

Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational or reaction free energy differences or activation free energies in any solvent.
Food web assembly rules

In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species.
Social Networking by Proxy: A Case Study of Catster, Dogster and Hamsterster

The proliferation of online social networks in the last decadehas not stopped short of pets, and many di erent onlineplatforms now exist catering to owners of various pets suchas cats and dogs. These online pet social networks providea unique opportunity to study an online social network inwhich a single user manages multiple user pro les, i.e. onefor each pet they own. These types of multi-pro le net-works allow us to investigate two questions: (1) What isthe relationship between the pet-level and human-level net-work, and (2) what is the relationship between friendshiplinks and family ties? Concretely, we study the online petsocial networks Catster, Dogster and Hamsterster, the rsttwo of which are the two largest online pet networks in ex-istence. We show how the networks on the two levels inter-act, and perform experiments to nd out whether knowledgeabout friendships on a pro le-level alone can be used to pre-dict which users are behind which pro le. In order to doso, we introduce the concept of multi-pro le social network,extend a previously de ned spectral test of diagonality tomulti-pro le networks, de ne two new homophily measuresfor multi-pro le social networks, perform a two-level socialnetwork analysis, and present an algorithm for predictingwhether two pro les were created by the same user. Asa result, we are able to predict with very high precisionwhether two pro les were created by a same user. Our workis thus relevant for the analysis of other online communitiesin which users may use multiple pro les.
DEEP IMAGING OF M51: A NEW VIEW OF THE WHIRLPOOL’S EXTENDED TIDAL DEBRIS

We present deep, wide-field imaging of the M51 system using CWRU’s Burrell Schmidt Telescope at KPNO to study the faint tidal features that constrain its interaction history. Our images trace M51's tidal morphology down to a limiting surface brightness of μB,lim ∼ 30 mag arcsec−2 and provide accurate colors ( &sgr; B - V < 0.1 ?> ) down to μB ∼ 28. We identify two new tidal streams in the system (the south and northeast plumes) with surface brightnesses of μB = 29 and luminosities of ∼106L⊙,B. While the northeast plume may be a faint outer extension of the tidal “crown” north of NGC 5195 (M51b), the south plume has no analog in any existing M51 simulation and may represent a distinct tidal stream or disrupted dwarf galaxy. We also trace the extremely diffuse northwest plume out to a total extent of 20′ (43 kpc) from NGC 5194 (M51a) and show it to be physically distinct from the overlapping bright tidal streams from M51b. The northwest plume’s morphology and red color ( B - V = 0.8 ?> ) instead argue that it originated from tidal stripping of M51a’s extreme outer disk. Finally, we confirm the strong segregation of gas and stars in the southeast tail and do not detect any diffuse stellar component in the H i portion of the tail. Extant simulations of M51 have difficulty matching both the wealth of tidal structure in the system and the lack of stars in the H i tail, motivating new modeling campaigns to study the dynamical evolution of this classic interacting system.
Color Confinement and Screening in the θ Vacuum of QCD.

QCD perturbation theory ignores the compact nature of the SU(3) gauge group that gives rise to the periodic θ vacuum of the theory. We propose to modify the gluon propagator to reconcile perturbation theory with the anomalous Ward identities for the topological current in the θ vacuum. As a result, the gluon couples to the Veneziano ghost describing the tunneling transitions between different Chern-Simons sectors of the vacuum; we call the emerging gluon dressed by ghost loops a "glost." We evaluate the glost propagator and find that it has the form G(p)=(p(2)+χ(top)/p(2))(-1) where χ(top) is the Yang-Mills topological susceptibility related to the η' mass by the Witten-Veneziano relation; this propagator describes the confinement of gluons at distances ∼χ(top)(-1/4)≃1  fm. The same functional form of the propagator was originally proposed by Gribov as a solution to the gauge copies problem that plagues perturbation theory. The resulting running coupling coincides with the perturbative one at p(2)≫√[χ(top)], but in the infrared region either freezes (in pure Yang-Mills theory) or vanishes ( QCD with light quarks), in accord with experimental evidence. Our scenario makes explicit the connection between confinement and topology of the QCD vacuum; we discuss the implications for spin physics, high energy scattering, and the physics of quark-gluon plasma.
Linear mode stability of the Kerr-Newman black hole and its quasinormal modes.

We provide strong evidence that, up to 99.999% of extremality, Kerr-Newman black holes (KNBHs) are linear mode stable within Einstein-Maxwell theory. We derive and solve, numerically, a coupled system of two partial differential equations for two gauge invariant fields that describe the most general linear perturbations of a KNBH. We determine the quasinormal mode (QNM) spectrum of the KNBH as a function of its three parameters and find no unstable modes. In addition, we find that the lowest radial overtone QNMs that are connected continuously to the gravitational ℓ=m=2 Schwarzschild QNM dominate the spectrum for all values of the parameter space (m is the azimuthal number of the wave function and ℓ measures the number of nodes along the polar direction). Furthermore, the (lowest radial overtone) QNMs with ℓ=m approach Reω=mΩH(ext) and Imω=0 at extremality; this is a universal property for any field of arbitrary spin |s|≤2 propagating on a KNBH background (ω is the wave frequency and ΩH(ext) the black hole angular velocity at extremality). We compare our results with available perturbative results in the small charge or small rotation regimes and find good agreement.
Plasmon signature in Dirac-Weyl liquids

We consider theoretically as a function of temperature the plasmon mode arising in three-dimensional Dirac liquids, i.e., systems with linear chiral relativistic single-particle dispersion, within the random phase approximation. We find that whereas no plasmon mode exists in the intrinsic (undoped) system at zero temperature, there is a well-defined finite-temperature plasmon with superlinear temperature dependence, rendering the plasmon dispersion widely tunable with temperature. The plasmon dispersion contains a logarithmic correction due to the ultraviolet-logarithmic renormalization of the electron charge, manifesting a fundamental many-body interaction effect as in quantum electrodynamics. The plasmon dispersion of the extrinsic (doped) system displays a minimum at finite temperature before it crosses over to the superlinear intrinsic behavior at higher temperature, implying that the high-temperature plasmon is a universal feature of Dirac liquids irrespective of doping. This striking characteristic temperature dependence of intrinsic Dirac plasmons along with the logarithmic renormalization is a unique manifestation of the three-dimensional relativistic Dirac nature of quasiparticle excitations and serves as an experimentally observable signature of three-dimensional Dirac materials.
Decay of solutions to the Maxwell equation on the Schwarzschild background

A new Morawetz or integrated local energy decay estimate for Maxwell test fields on the exterior of a Schwarzschild black hole spacetime is proved. The proof makes use of a new superenergy tensor H ab ?> defined in terms of the Maxwell field and its first derivatives. The superenergy tensor, although not conserved, yields a conserved higher order energy current H ab ( ∂ t ) b ?> . The tensor H ab ?> vanishes for the static Coulomb field, and the Morawetz estimate proved here therefore yields integrated decay for the Maxwell field to the Coulomb solution on the Schwarzschild exterior.
Theory of resonant tunneling in bilayer-graphene/hexagonal-boron-nitride heterostructures

A theory is developed for calculating vertical tunneling current between two sheets of bilayer graphene separated by a thin, insulating layer of hexagonal boron nitride, neglecting many-body effects. Results are presented using physical parameters that enable comparison of the theory with recently reported experimental results. Observed resonant tunneling and negative differential resistance in the current–voltage characteristics are explained in terms of the electrostatically-induced band gap, gate voltage modulation, density of states near the band edge, and resonances with the upper sub-band. These observations are compared to ones from similar heterostructures formed with monolayer graphene.
Microscopic Advances with Large-Scale Learning: Stochastic Optimization for Cryo-EM

Determining the 3D structures of biological molecules is a key problem for both biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising technique for structure estimation which relies heavily on computational methods to reconstruct 3D structures from 2D images. This paper introduces the challenging Cryo-EM density estimation problem as a novel application for stochastic optimization techniques. Structure discovery is formulated as MAP estimation in a probabilistic latent-variable model, resulting in an optimization problem to which an array of seven stochastic optimization methods are applied. The methods are tested on both real and synthetic data, with some methods recovering reasonable structures in less than one epoch from a random initialization. Complex quasi-Newton methods are found to converge more slowly than simple gradient-based methods, but all stochastic methods are found to converge to similar optima. This method represents a major improvement over existing methods as it is significantly faster and is able to converge from a random initialization.
Multiplexed Readout Demonstration of a TES-Based Detector Array in a Resistance-Locked Loop

TES-based bolometer and microcalorimeter arrays with thousands of pixels are under development for several space-based and ground-based applications. A linear detector response and low levels of crosstalk facilitate the calibration of the instruments. In an effort to improve the properties of TES-based detectors, fixing the TES resistance in a resistance-locked loop (RLL) under optical loading has recently been proposed. Earlier theoretical work on this mode of operation has shown that the detector speed, linearity, and dynamic range should improve with respect to voltage-biased operation. This paper presents an experimental demonstration of multiplexed readout in this mode of operation in a TES-based detector array with noise equivalent power (NEP) values of 3.5 · 10-19 W/√Hz. The measured noise and dynamic properties of the detector in the RLL will be compared with the earlier modeling work. Furthermore, the practical implementation routes for future FDM systems for the readout of bolometer and microcalorimeter arrays will be discussed.
Complex structures for an S-matrix of Klein–Gordon theory on AdS spacetimes

While the standard construction of the S-matrix fails on anti-de Sitter (AdS) spacetime, a generalized S-matrix makes sense, based on the hypercylinder geometry induced by the boundary of AdS. In contrast to quantum field theory in Minkowski spacetime, there is not yet a standard way to resolve the quantization ambiguities arising in its construction. These ambiguities are conveniently encoded in the choice of a complex structure. We explore in this paper the space of complex structures for real scalar Klein–Gordon theory based on a number of criteria. These are: invariance under AdS isometries, induction of a positive definite inner product, compatibility with the standard S-matrix picture and recovery of standard structures in Minkowski spacetime under a limit of vanishing curvature. While there is no complex structure that satisfies all demands, we emphasize two interesting candidates that satisfy most: in one case we have to give up part of the isometry invariance, and in the other case the induced inner product is indefinite.
Community detection from location-tagged networks

Many real world systems or web services can be represented as a network such as social networks and transportation networks. In the past decade, many algorithms have been developed to detect the communities in a network. However, the impact of locations on community has not been fully investigated by the research literature. In this paper, we propose a method to determine if a location-based community detection method is suitable for a given network and provide a new community detection algorithm that pushes the location information into the community detection. We test our proposed method on both synthetic data and real world network datasets. The results show that the communities detected by our method distribute in a smaller area compared with the traditional methods and have the similar or higher tightness on network connections.
Rotational State Microwave Mixing for Laser Cooling of Complex Diatomic Molecules.

We demonstrate the mixing of rotational states in the ground electronic state using microwave radiation to enhance optical cycling in the molecule yttrium (II) monoxide (YO). This mixing technique is used in conjunction with a frequency modulated and chirped continuous wave laser to slow longitudinally a cryogenic buffer-gas beam of YO. We generate a flux of YO below 10 m/s, directly loadable into a three-dimensional magneto-optical trap. This technique opens the door for laser cooling of diatomic molecules with more complex loss channels due to intermediate states.
Black hole complementarity in gravity's rainbow

To see how the gravity's rainbow works for black hole complementary, we evaluate the required energy for duplication of information in the context of black hole complementarity by calculating the critical value of the rainbow parameter in the certain class of the rainbow Schwarzschild black hole. The resultant energy can be written as the well-defined limit for the vanishing rainbow parameter which characterizes the deformation of the relativistic dispersion relation in the freely falling frame. It shows that the duplication of information in quantum mechanics could not be allowed below a certain critical value of the rainbow parameter; however, it might be possible above the critical value of the rainbow parameter, so that the consistent formulation in our model requires additional constraints or any other resolutions for the latter case.
Modularity enhances the rate of evolution in a rugged fitness landscape

Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. Approximately 25% of the observed rate of fitness increase of the virus could be ascribed to a modular viral landscape.
ON THE STABILITY OF A GALACTIC DISK IN MODIFIED GRAVITY

We find the dispersion relation for tightly wound spiral density waves in the surface of rotating, self-gravitating disks in the framework of Modified Gravity (MOG). Also, the Toomre-like stability criterion for differentially rotating disks has been derived for both fluid and stellar disks. More specifically, the stability criterion can be expressed in terms of a matter density threshold over which the instability occurs. In other words the local stability criterion can be written as &Sgr; 0 < &Sgr; crit ( v s , κ , &agr; , &mgr; 0 ) ?> , where &Sgr; crit ?> is a function of vs (sound speed), κ (epicycle frequency) and α and &mgr; 0 ?> are the free parameters of the theory. In the case of a stellar disk the radial velocity dispersion &sgr; r ?> appears in &Sgr; crit ?> instead of vs. We find the exact form of the function &Sgr; crit ?> for both stellar and fluid self-gravitating disks. Also, we use a sub-sample of THINGS catalog of spiral galaxies in order to compare the local stability criteria. In this perspective, we have compared MOG with Newtonian gravity and investigated the possible and detectable differences between these theories.
Robust Reconstruction of Complex Networks from Sparse Data

Reconstructing complex networks from measurable data is a fundamental problem for understanding and controlling collective dynamics of complex networked systems. However, a significant challenge arises when we attempt to decode structural information hidden in limited amounts of data accompanied by noise and in the presence of inaccessible nodes. Here, we develop a general framework for robust reconstruction of complex networks from sparse and noisy data. Specifically, we decompose the task of reconstructing the whole network into recovering local structures centered at each node. Thus, the natural sparsity of complex networks ensures a conversion from the local structure reconstruction into a sparse signal reconstruction problem that can be addressed by using the lasso, a convex optimization method. We apply our method to evolutionary games, transportation, and communication processes taking place in a variety of model and real complex networks, finding that universal high reconstruction accuracy can be achieved from sparse data in spite of noise in time series and missing data of partial nodes. Our approach opens new routes to the network reconstruction problem and has potential applications in a wide range of fields.
Personal Data: Thinking Inside the Box

We are in a 'personal data gold rush' driven by advertising being the primary revenue source for most online companies. These companies accumulate extensive personal data about individuals with minimal concern for us, the subjects of this process. This can cause many harms: privacy infringement, personal and professional embarrassment, restricted access to labour markets, restricted access to best value pricing, and many others. There is a critical need to provide technologies that enable alternative practices, so that individuals can participate in the collection, management and consumption of their personal data. In this paper we discuss the Databox, a personal networked device (and associated services) that collates and mediates access to personal data, allowing us to recover control of our online lives. We hope the Databox is a first step to re-balancing power between us, the data subjects, and the corporations that collect and use our data.
Creation of a neutrino laboratory for search for sterile neutrino at SM-3 reactor

In connection with the question of possible existence of sterile neutrino the laboratory on the basis of SM-3 reactor was created to search for oscillations of reactor antineutrino. A prototype of a neutrino detector with scintillator volume of 400 l can be moved at the distance of 6-11 m from the reactor core. The measurements of background conditions have been made. It is shown that the main experimental problem is associated with cosmic radiation background. Test measurements of dependence of a reactor antineutrino flux on the distance from a reactor core have been made. The prospects of search for oscillations of reactor antineutrino at short distances are discussed.
Entailment among Probabilistic Implications

We study a natural variant of the implicational fragment of propositional logic. Its formulas are pairs of conjunctions of positive literals, related together by an implicational-like connective, the semantics of this sort of implication is defined in terms of a threshold on a conditional probability of the consequent, given the antecedent: we are dealing with what the data analysis community calls confidence of partial implications or association rules. Existing studies of redundancy among these partial implications have characterized so far only entailment from one premise and entailment from two premises. By exploiting a previously noted alternative view of this entailment in terms of linear programming duality, we characterize exactly the cases of entailment from arbitrary numbers of premises. As a result, we obtain decision algorithms of better complexity, additionally, for each potential case of entailment, we identify a critical confidence threshold and show that it is, actually, intrinsic to each set of premises and antecedent of the conclusion.
A CONNECTION BETWEEN OBSCURATION AND STAR FORMATION IN LUMINOUS QUASARS

We present a measurement of the star formation properties of a uniform sample of mid-IR-selected, optically unobscured, and obscured quasars (QSO1s and QSO2s) in the Boötes survey region. We use a spectral energy distribution analysis for photometric data spanning optical to far-IR wavelengths to separate the active galactic nucleus (AGN) and host galaxy components. We find that when compared to a matched sample of QSO1s, the QSO2s have roughly twice the far-IR detection fractions, far-IR fluxes, and infrared star formation luminosities ( L IR SF ?> ). Correspondingly, we show that the AGN obscured fraction rises from 0.3 to 0.7 between (4–40) × 10 11 L ⊙ ?> . We also find evidence associating X-ray absorption with the presence of far-IR-emitting dust. Overall, these results are consistent with galaxy evolution models in which quasar obscuration is associated with dust-enshrouded starburst galaxies.