nils-herrmann/clean_scirepeval huggingface dataset:
The Force Field for Amino Acid Based Ionic Liquids: Polar Residues

Ionic liquids (ILs) constitute one of the most active fields of research nowadays. Many organic and inorganic molecules can be converted into ions via relatively simple procedures. These ions can be combined into ILs. Amino acid based ILs (AAILs) represent a specific interest due to solubilization of biological species, participation in enzymatic catalysis, and capturing toxic gases. We develop a new force field (FF) for the seven selected AAILs comprising 1-ethyl-3-methylimidazolium cation and amino acid anions with polar residues. The anions were obtained via deprotonation of carboxyl group. We account for peculiar interactions between the anion and the cation by fitting electrostatic potential for an ion pair, in contrast to isolated ions. The van der Waals interactions were transferred from the CHARMM36 FF with minor modifications, as suggested by hybrid density functional theory. Compatibility between our parameters and CHARMM36 parameters is preserved. The developed interaction model fosters computational investigation of ionic liquids.
Z-Score-Based Modularity for Community Detection in Networks

Identifying community structure in networks is an issue of particular interest in network science. The modularity introduced by Newman and Girvan is the most popular quality function for community detection in networks. In this study, we identify a problem in the concept of modularity and suggest a solution to overcome this problem. Specifically, we obtain a new quality function for community detection. We refer to the function as Z-modularity because it measures the Z-score of a given partition with respect to the fraction of the number of edges within communities. Our theoretical analysis shows that Z-modularity mitigates the resolution limit of the original modularity in certain cases. Computational experiments using both artificial networks and well-known real-world networks demonstrate the validity and reliability of the proposed quality function.
Paradoxes of cosmological physics in the beginning of the 21-st century

In the history of cosmology physical paradoxes played important role for development of contemporary world models. Within the modern standard cosmological model there are both observational and conceptual cosmological paradoxes which stimulate to search their solution. Confrontation of theoretical predictions of the standard cosmological model with the latest astrophysical observational data is considered. A review of conceptual problems of the Friedmann space expending models, which are in the bases of modern cosmological model, is discussed. The main paradoxes, which are discussed in modern literature, are the Newtonian character of the exact Friedmann equation, the violation of the energy conservation within any comoving local volume, violation of the limiting recession velocity of galaxies for the observed high redshift objects. Possible observational tests of the nature of the cosmological redshift are discussed
Momentum entanglement in relativistic quantum mechanics

I present a new group-theoretical approach to the interaction mechanism of elementary particle physics. Within an irreducible unitary two-particle representation of the Poincare group, the commutation relations of the Poincare group require that the two-particle states be momentum entangled. As in gauge theories, momentum entanglement defines a correlation between two particles that can be described as an interaction provided by the exchange of virtual (gauge) quanta. The coupling constant of this interaction is uniquely determined by the structure of the irreducible two-particle state space. For two massive spin one-half particles, the coupling constant matches the empirical value of the electromagnetic coupling constant.
From Self-Assembly to Controlled-Assembly, From Optical Manipulation to AFM Manipulation

Moving nanoparticles/atoms to study the nearfield interaction between them is one of the many approaches to explore the optical and electrical properties of these assemblies. Traditional approach included the self assembly by spinning or drying nanoparticles in aqua on the substrate is well practiced. Lithography technique is another popular approach to deposit limited nano/micro patterns on substrates. Later optical and mechanical manipulations were used to have more control over moving individual elements of nano and microstructures and even atoms. Optical tweezers, optical trapping and AFM manipulation are examples of these precise approaches.
Calibrating an Ice Sheet Model Using High-Dimensional Binary Spatial Data

Rapid retreat of ice in the Amundsen Sea sector of West Antarctica may cause drastic sea level rise, posing significant risks to populations in low-lying coastal regions. Calibration of computer models representing the behavior of the West Antarctic Ice Sheet is key for informative projections of future sea level rise. However, both the relevant observations and the model output are high-dimensional binary spatial data; existing computer model calibration methods are unable to handle such data. Here we present a novel calibration method for computer models whose output is in the form of binary spatial data. To mitigate the computational and inferential challenges posed by our approach, we apply a generalized principal component based dimension reduction method. To demonstrate the utility of our method, we calibrate the PSU3D-ICE model by comparing the output from a 499-member perturbed-parameter ensemble with observations from the Amundsen Sea sector of the ice sheet. Our methods help rigorously characterize the parameter uncertainty even in the presence of systematic data-model discrepancies and dependence in the errors. Our method also helps inform environmental risk analyses by contributing to improved projections of sea level rise from the ice sheets.
How to bend galaxy disc profiles: the role of halo spin

The radial density profiles of stellar galaxy discs can be well approximated as an exponential. Compared to this canonical form, however, the profiles in the majority of disc galaxies show downward or upward breaks at large radii. Currently, there is no coherent explanation in a galaxy formation context of the radial profile per se, along with the two types of profile breaks. Using a set of controlled hydrodynamic simulations of disc galaxy formation, we find a correlation between the host halo's initial angular momentum and the resulting radial profile of the stellar disc: galaxies that live in haloes with a low spin parameter {\lambda} <~ 0.03 show an up-bending break in their disc density profiles, while galaxies in haloes of higher angular momentum show a down-bending break. We find that the case of pure exponential profiles ({\lambda} ~ 0.035) coincides with the peak of the spin parameter distribution from cosmological simulations. Our simulations not only imply an explanation of the observed behaviours, but also suggest that the physical origin of this effect is related to the amount of radial redistribution of stellar mass, which is anti-correlated with {\lambda}.
Natural Supersymmetry without Light Higgsinos

In this study, we present a mechanism that allows a large Higgsino mass without large fine-tuning. The Higgs is a pseudo-Nambu-Goldstone boson (PNGB) of the global symmetry breaking pattern SO(5)→SO(4). Because of the PNGB nature of the light Higgs, the SO(5) invariant Higgsino mass does not directly contribute to the Higgs mass. Large couplings in the Higgs sector that spontaneously breaks SO(5) minimize the tuning, and are also motivated by the requirements of generating a sufficiently large Higgs quartic coupling and of maintaining a natural approximate global SO(5) symmetry. When these conditions are imposed, theories of this type predict heavy Higgsinos. This construction differs from composite Higgs models in that no new particles are introduced to form complete SO(5) multiplets involving the top quark—the stop is the only top partner. Compatibility with Higgs coupling measurements requires cancellations among contributions to the Higgs mass-squared parameter at the 10% level. An important implication of this construction is that the compressed region of stop and sbottom searches can still be natural.
Green Valley Galaxies

The "green valley" is a wide region separating the blue and the red peaks in the ultraviolet-optical color magnitude diagram, first revealed using GALEX UV photometry. The term was coined by Christopher Martin in 2005. Green valley highlights the discriminating power of UV to very low relative levels of ongoing star formation, to which the optical colors, including u-r, are insensitive. It corresponds to massive galaxies below the star-forming "main" sequence, and therefore represents a critical tool for the study of the quenching of star formation and its possible resurgence in otherwise quiescent galaxies. This article reviews the results pertaining to morphology, structure, environment, dust content and gas properties of green valley galaxies in the local universe. Their relationship to AGN is also discussed. Attention is given to biases emerging from defining the "green valley" using optical colors. We review various evolutionary scenarios and we present evidence for a new, quasi-static view of the green valley, in which the majority of galaxies currently in the green valley were only partially quenched in the distant past and now participate in a slow cosmic decline of star formation, which also drives down the activity on the main sequence, presumably as a result of the dwindling accretion/cooling onto galaxy disks.
The stellar kinematics of corotating spiral arms in Gaia mock observations

We have observed an N-body/Smoothed Particle Hydrodynamics simulation of a Milky Way like barred spiral galaxy. We present a simple method that samples N-body model particles into mock Gaia stellar observations and takes into account stellar populations, dust extinction and Gaia's science performance estimates. We examine the kinematics around a nearby spiral arm at a similar position to the Perseus arm at three lines of sight in the disc plane; (l,b)=(90,0), (120,0) and (150,0) degrees. We find that the structure of the peculiar kinematics around the co-rotating spiral arm, which is found in Kawata et al. (2014b), is still visible in the observational data expected to be produced by Gaia despite the dust extinction and expected observational errors of Gaia. These observable kinematic signatures will enable testing whether the Perseus arm of the Milky Way is similar to the co-rotating spiral arms commonly seen in N-body simulations.
Semiclassical limit for the many-body localization transition

We introduce a semi-classical limit for many-body localization in the absence of global symmetries. Microscopically, this limit is realized by disordered Floquet circuits composed of Clifford gates. In $d=1$, the resulting dynamics are always many-body localized with a complete set of strictly local integrals of motion. In $d\geq 2$, the system realizes both localized and delocalized phases separated by a continuous transition in which ergodic puddles percolate. We argue that the phases are stable to deformations away from the semi-classical limit and estimate the resulting phase boundary. The Clifford circuit model is a distinct tractable limit from that of free fermions and suggests bounds on the critical exponents for the generic transition.
From Veneziano to Riemann: A String Theory Statement of the Riemann Hypothesis

We discuss a precise relation between the Veneziano amplitude of string theory, rewritten in terms of ratios of the Riemann zeta function, and two elementary criteria for the Riemann hypothesis formulated in terms of integrals of the logarithm and the argument of the zeta function. We also discuss how the integral criterion based on the argument of the Riemann zeta function relates to the Li criterion for the Riemann hypothesis. We provide a new generalization of this integral criterion. Finally, we comment on the physical interpretation of our recasting of the Riemann hypothesis in terms of the Veneziano amplitude.
Electromagnetic and neutral-weak response functions of 4 He and 12 C

Ab initio calculations of the quasi-elastic electromagnetic and neutral-weak response functions of 4He and 12C are carried out for the first time. They are based on a realistic approach to nuclear dynamics, in which the strong interactions are described by two- and three-nucleon potentials and the electroweak interactions with external fields include one- and two-body terms. The Green's function Monte Carlo method is used to calculate directly the Laplace transforms of the response functions, and maximum-entropy techniques are employed to invert the resulting imaginary-time correlation functions with associated statistical errors. The theoretical results, confirmed by experiment in the electromagnetic case, show that two-body currents generate excess transverse strength from threshold to the quasi-elastic to the dip region and beyond. These findings challenge the conventional picture of quasi-elastic inclusive scattering as being largely dominated by single-nucleon knockout processes.
Neutrino-Nucleus Interactions and the Short-Range Structure of Nuclei

Improvements in theoretical modeling of Short Range structures and phenomena, and comparisons with data, will require sustained collaboration between nuclear theorists and neutrino experimentalists. The extensive history of studying this area of nuclear physics in electron- and hadron-scattering experiments, coupled with the transformative capabilities of LArTPCs to identify neutrinos, will provide a ripe opportunity for new discoveries that will further our understanding of the nucleus.
The Parametrized Post-Newtonian-Vainshteinian formalism

Light degrees of freedom that modify gravity on cosmological scales must be ``screened" on solar system scales in order to be compatible with data. The Vainshtein mechanism achieves this through a breakdown of classical perturbation theory, as large interactions involving new degrees of freedom become important below the so-called Vainshtein radius. We begin to develop an extension of the Parameterized Post-Newtonian (PPN) formalism that is able to handle Vainshteinian corrections. We argue that theories with a unique Vainshtein scale must be expanded using two small parameters. In this Parameterized Post-Newtonian-Vainshteinian (PPNV) expansion, the primary expansion parameter that controls the PPN order is, as usual, the velocity v. The secondary expansion parameter, α, controls the strength of the Vainshteinian correction and is a theory-specific combination of the Schwarzschild radius and the Vainshtein radius of the source that is independent of its mass. We present the general framework and apply it to Cubic Galileon theory both inside and outside the Vainshtein radius. The PPNV framework can be used to determine the compatibility of such theories with solar system and other strong-field data.
Andreev reflection in edge states of time-reversal-invariant Landau levels

We describe the conductance of a normal-superconducting junction in systems with Landau levels that preserve time-reversal symmetry. Those Landau levels have been observed in strained honeycomb lattices. The current is carried along the edges in both the normal and superconducting regions. When the Landau levels in the normal region are half filled, the Andreev reflection is maximal and the conductance plateaus have a peak as a function of the filling factor. The height of those peaks is quantized at $4{e}^{2}/h$. The interface of the junction has Andreev edge states, which form a coherent superposition of electrons and holes that can carry a net valley current. We identify unique experimental signatures for superconductivity in time-reversal-invariant Landau levels.
The role of periodic orbits and bubbles of chaos during the transition to turbulence

Starting with turbulence that explores a wide region in phase space, we discover several relative periodic orbits (RPOs) embedded within a subregion of the chaotic turbulent saddle. We also extract directly from simulation, several travelling waves (TWs). These TWs together with the RPOs are unstable states and are believed to provide the skeleton of the chaotic saddle. Earlier studies have shown that such invariant solutions can help to explain wall bounded shear flows, and a finite subset of them are expected to dominate the dynamics (Faisst & Eckhardt 2003; Pringle & Kerswell 2007; Hof et al. 2004). The introduction of symmetries is typically necessary to facilitate this approach. Applying only the shift-reflect symmetry, the geometry is less constrained than previous studies in pipe flow. A 'long-period' RPO is identified that is only very weakly repelling. Turbulent trajectories are found to frequently approach and frequently shadow this orbit. In addition the orbit characterises a resulting 'bubble' of chaos, itself a saddle, deep within the turbulent sea (Kreilos et al. 2014). We explicitly analyse the merger of the two saddles and show how it results in a considerable increase of the total lifetime. Both exits and entries to the bubble are observed, as the stable manifolds of the inner and outer saddles intertwine. We observe that the typical lifetime of the turbulence is influenced by switches between the inner and outer saddles, and is thereby dependent on whether or not it 'shadows' or 'visits' the vicinity of the long-period RPO (Cvitanovic et al. 2014). These observations, along with comparisons of flow structures, show that RPOs play a significant role in structuring the dynamics of turbulence.
Stable localized moving patterns in the 2-D Gray-Scott model

I show stable, localized, single and multi-spot patterns of three classes { stationary, moving, and rotating { that exist within a limited range of parameter values in the two-dimensional Gray-Scott reaction-diusion model with = Du=Dv = 2. These patterns exist in domains of any size, and appear to derive their stability from a constructive reinforcement eect of the standing waves that surround any feature. There are several common elements { including a spot that behaves as a quasiparticle, a U-shaped stripe, and a ring or annulus, or a portion thereof { which combine to form a great variety of stable structures. These patterns interact with each other in a variety of ways. There are similarities to other reaction-diusion systems and to physical experiments; I oer several suggestions for further research.
Leptonic B- and D-Meson Decay Constants with 2+1 Flavors of Asqtad Fermions

We present the status of our updated D- and B-meson decay-constant analysis, based on the MILC Nf =2+1 asqtad gauge ensembles. Heavy quarks are incorporated using the Wilson clover action with the Fermilab interpretation. This analysis includes ensembles at five lattice spacings from α ≈ 0.045 to 0.15 fm, and light sea-quark masses down to 1/20th of the strange-quark mass. Projected error budgets for ratios of decay constants, in particular between bottom- and charm-meson decay constants, are presented.
Transition to turbulence in ferrofluids

It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed bifurcation analysis and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A striking finding is that, as the magnetic field is increased, the onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence can be greatly facilitated by using ferrofluids, opening up a new avenue to probe into the fundamentals of turbulence and the challenging problem of turbulence control.
Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows.

We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids.
Shortfall Deviation Risk: An alternative to risk measurement

We present the Shortfall Deviation Risk (SDR), a risk measure that represents the expected loss that occurs with certain probability penalized by the dispersion of results that are worse than such an expectation. SDR combines Expected Shortfall (ES) and Shortfall Deviation (SD), which we also introduce, contemplating two fundamental pillars of the risk concept, the probability of adverse events and the variability of an expectation, and considers extreme results. We demonstrate that SD is a generalized deviation measure, whereas SDR is a coherent risk measure. We achieve the dual representation of SDR, and we discuss issues such as its representation by a weighted ES, acceptance sets, convexity, continuity and the relationship with stochastic dominance. Illustrations with real and simulated data allow us to conclude that SDR offers greater protection in risk measurement compared with VaR and ES, especially in times of significant turbulence in riskier scenarios.
Decoherence and spin echo in biological systems.

The spin-echo approach is extended to include biocomplexes for which the interaction with dynamical noise, produced by the protein environment, is strong. Significant restoration of the free induction decay signal due to homogeneous (decoherence) and inhomogeneous (dephasing) broadening is demonstrated analytically and numerically for both an individual dimer of interacting chlorophylls and for an ensemble of dimers. Our approach does not require the use of small interaction constants between the electron states and the protein fluctuations. It is based on an exact and closed system of ordinary differential equations that can be easily solved for a wide range of parameters that are relevant for bioapplications.