nils-herrmann/clean_scirepeval huggingface dataset:
Quantum Path Interference through Incoherent Motions in Multilevel Quantum Systems

Quantum path interferences or resonances in multilevel dissipative quantum systems play an important and intriguing role in the transport processes of nanoscale systems. Many previous minimalistic models used to describe the quantum path interference driven by incoherent fields are based on the approximations including the second order perturbation for the weak coupling limit, the ad-hoc choices of two-time correlation functions and $\it{etc}$. On the other hand, the similar model to study the non-adiabatic molecular electronic excitation have been extensively developed and many efficient quantum molecular dynamics simulation schemes, such as the Ehrenfest scheme, have been proposed. 
In this paper, I aim to propose an unified model, extend the Ehrenfest scheme to study the interactions of system-light and system-phonon simultaneously and gain insight into and principles of the roles of quantum path interferences in the realistic molecular systems. I discuss how to derive the time-dependent stochastic Schr$\ddot{o}$dinger equation from the Ehrenfest scheme as a foundation to discuss the detailed balance for the weak coupling limit and therefore the quantum correction in the Ehrenfest scheme. Different from the master equation technique, the Ehrenfest scheme doesn't need any specific assumptions about spectral densities and two time correlation functions. With simple open two-level and three-level quantum systems, I show the effect of the quantum path interference on the steady state populations. Currently I only focus on the role of the phonon thermal reservoir. The electromagnetic field (solar light) will be modeled as a thermal reservoir and discussed in detail in the future paper.
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the 19th century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the 20th century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity.
Simpsonian 'Evolution by Jumps' in an Adaptive Radiation of Anolis Lizards

In his highly influential view of evolution, G. G. Simpson hypothesized that clades of species evolve in adaptive zones, defined as collections of niches occupied by species with similar traits and patterns of habitat use. Simpson hypothesized that species enter new adaptive zones in one of three ways: extinction of competitor species, dispersal to a new geographic region, or the evolution of a key trait that allows species to exploit resources in a new way. However, direct tests of Simpson's hypotheses for the entry into new adaptive zones remain elusive. Here we evaluate the fit of a Simpsonian model of jumps between adaptive zones to phylogenetic comparative data. We use a novel statistical approach to show that anoles, a well-studied adaptive radiation of Caribbean lizards, have evolved by a series of evolutionary jumps in trait evolution. Furthermore, as Simpson predicted, trait axes strongly tied to habitat specialization show jumps that correspond with the evolution of key traits and/or dispersal between islands in the Greater Antilles. We conclude that jumps are commonly associated with major adaptive shifts in the evolutionary radiation of anoles.
Modeling self-sustained activity cascades in socio-technical networks

The ability to understand and eventually predict the emergence of information and activation cascades in social networks is core to complex socio-technical systems research. However, the complexity of social interactions makes this a challenging enterprise. Previous works on cascade models assume that the emergence of this collective phenomenon is related to the activity observed in the local neighborhood of individuals, but do not consider what determines the willingness to spread information in a time-varying process. Here we present a mechanistic model that accounts for the temporal evolution of the individual state in a simplified setup. We model the activity of the individuals as a complex network of interacting integrate-and-fire oscillators. The model reproduces the statistical characteristics of the cascades in real systems, and provides a framework to study the time evolution of cascades in a state-dependent activity scenario.
Competition-induced criticality in a model of meme popularity

Heavy-tailed distributions of meme popularity occur naturally in a model of meme diffusion on social networks. Competition between multiple memes for the limited resource of user attention is identified as the mechanism that poises the system at criticality. The popularity growth of each meme is described by a critical branching process, and asymptotic analysis predicts power-law distributions of popularity with very heavy tails (exponent α<2, unlike preferential-attachment models), similar to those seen in empirical data.
Note on a proposed proof of the Riemann Hypothesis by Jin Gyu Lee

This is a reformulation and refutation of a proposed proof of the Riemann hypothesis published in 2013  and in 2014 . Proceeding by contradiction, the author wants to prove that if zeta(s)=0 where 1/2<Re s<1, then zeta(2s)=0, which is known to be impossible. We show that both versions of the proof are incomplete.
Relativity violations and beta decay

In some quantum theories of gravity, deviations from the laws of relativity could be comparatively large while escaping detection to date. In the neutrino sector, precision experiments with beta decay yield new and improved constraints on these countershaded relativity violations. Existing data are used to extract bounds of $3\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}8}\text{ }\text{ }\mathrm{GeV}$ on the magnitudes of two of the four possible coefficients, and estimates are provided of future attainable sensitivities in a variety of experiments.
Interacting Epidemics and Coinfection on Contact Networks

The spread of certain diseases can be promoted, in some cases substantially, by prior infection with another disease. One example is that of HIV, whose immunosuppressant effects significantly increase the chances of infection with other pathogens. Such coinfection processes, when combined with nontrivial structure in the contact networks over which diseases spread, can lead to complex patterns of epidemiological behavior. Here we consider a mathematical model of two diseases spreading through a single population, where infection with one disease is dependent on prior infection with the other. We solve exactly for the sizes of the outbreaks of both diseases in the limit of large population size, along with the complete phase diagram of the system. Among other things, we use our model to demonstrate how diseases can be controlled not only by reducing the rate of their spread, but also by reducing the spread of other infections upon which they depend.
What is a leader of opinion formation in bounded confidence models?

Taking a decision in democratic social groups is based on the opinion of the majority or on the consensus. So, the study of opinion dynamics is of great interest in analyzing social phenomena. Among the different models of opinion dynamics, bounded confidence models have been studied in different contexts and shown interesting dynamics [1-3]. In [E. Kurmyshev, H.A. Ju\'arez, and R.A. Gonz\'alez-Silva,  A 390, 16 (2011)] we proposed a new bounded confidence model and studied the self-formation of opinion in heterogeneous societies composed by agents of two psychological types, concord (C-) and partial antagonism (PA-) agents. In this work we study the influence of "leaders" on the clustering of opinions. Mixed C/PA-societies along with the pure C- and PA-society are studied. The influence of the leader's connectivity in the network, his toughness or tolerance and his opinion on the opinion dynamics is studied as a function of the initial opinion uncertainty (tolerance) of the population. Numerical results obtained with leaders at low, high and average tolerance show complex bifurcation patterns of the group opinion; a decrease or even the total lost of control of the leader over the society is observed in different intervals of tolerance of agents in the case of C/PA-societies. We found that in the C-society a leader showing high opinion tolerance has more control over the population. In the PA-society a leader changes the bifurcation pattern of group opinion in a drastic and unexpected way, contrary to the common sense, and generates stronger polarization in the opposite opinion groups; the connectivity of the leader is an important factor that usually improves the adhesion of agents to the leader's opinion. A low tolerance (authoritarian) leader has greater control over a PA-society than that of a high tolerance (democratic) one; the opposite result is obtained in the C-society.
Nature of the epidemic threshold for the susceptible-infected-susceptible dynamics in networks.

We develop an analytical approach to the susceptible-infected-susceptible epidemic model that allows us to unravel the true origin of the absence of an epidemic threshold in heterogeneous networks. We find that a delicate balance between the number of high degree nodes in the network and the topological distance between them dictates the existence or absence of such a threshold. In particular, small-world random networks with a degree distribution decaying slower than an exponential have a vanishing epidemic threshold in the thermodynamic limit.
Two-nucleon systems in a finite volume: Quantization conditions

The quantization condition for interacting energy eigenvalues of the two-nucleon system in a finite cubic volume is derived in connection to the nucleon-nucleon scattering amplitudes. This condition is derived using an auxiliary (dimer) field formalism that is generalized to arbitrary partial waves in the context of nonrelativistic effective field theory. The quantization condition presented gives access to the scattering parameters of the two-nucleon systems with arbitrary parity, spin, isospin, angular momentum and center-of-mass motion, from a lattice QCD calculation of the energy eigenvalues. In particular, as it includes all noncentral interactions, such as the two-nucleon tensor force, it makes explicit the dependence of the mixing parameters of nucleon-nucleon systems calculated from lattice QCD when there is a physical mixing among different partial waves, e.g. $S\mathrm{\text{\ensuremath{-}}}D$ partial wave mixing in the deuteron channel. We provide explicit relations among scattering parameters and their corresponding point group symmetry class eigenenergies with orbital angular momentum $l\ensuremath{\le}3$, and for center-of-mass boost vectors of the form $\frac{2\ensuremath{\pi}}{L}(2{n}_{1},2{n}_{2},2{n}_{3})$, $\frac{2\ensuremath{\pi}}{L}(2{n}_{1},2{n}_{2},2{n}_{3}+1)$ and $\frac{2\ensuremath{\pi}}{L}(2{n}_{1}+1,2{n}_{2}+1,2{n}_{3})$. $L$ denotes the special extent of the cubic volume and ${n}_{1}$, ${n}_{2}$, ${n}_{3}$ are integers. Our results are valid below inelastic thresholds up to exponential volume corrections that are governed by the pion mass.
Review of asymmetric dark matter

Asymmetric dark matter models are based on the hypothesis that the present-day abundance of dark matter has the same origin as the abundance of ordinary or visible matter: an asymmetry in the number densities of particles and antiparticles. They are largely motivated by the observed similarity in the mass densities of dark and visible matter, with the former observed to be about five times the latter. This review discusses the construction of asymmetric dark matter models, summarizes cosmological and astrophysical implications and bounds, and touches on direct detection prospects and collider signatures.
Stability of the Self-accelerating Universe in Massive Gravity

We study linear perturbations around time dependent spherically symmetric solutions in the Lambda_3 massive gravity theory, which self-accelerate in the vacuum. We find that the dynamics of the scalar perturbations depend on the coordinate choice for the background solutions. For particular choices of coordinates there is a symmetry enhancement, leaving no propagating scalar degrees of freedom at linear order in perturbations. In contrast, any other coordinate choice propagates a single scalar mode. We find that the Hamiltonian of this scalar mode is unbounded from below for all self-accelerating solutions, signalling an instability.
THE RADIAL VELOCITY DETECTION OF EARTH-MASS PLANETS IN THE PRESENCE OF ACTIVITY NOISE: THE CASE OF α CENTAURI Bb

We present an analysis of the publicly available HARPS radial velocity (RV) measurements for α Cen B, a star hosting an Earth-mass planet candidate in a 3.24 day orbit. The goal is to devise robust ways of extracting low-amplitude RV signals of low-mass planets in the presence of activity noise. Two approaches were used to remove the stellar activity signal which dominates the RV variations: (1) Fourier component analysis (pre-whitening), and (2) local trend filtering (LTF) of the activity using short time windows of the data. The Fourier procedure results in a signal at P = 3.236 days and K = 0.42 m s−1, which is consistent with the presence of an Earth-mass planet, but the false alarm probability for this signal is rather high at a few percent. The LTF results in no significant detection of the planet signal, although it is possible to detect a marginal planet signal with this method using a different choice of time windows and fitting functions. However, even in this case the significance of the 3.24 day signal depends on the details of how a time window containing only 10% of the data is filtered. Both methods should have detected the presence of α Cen Bb at a higher significance than is actually seen. We also investigated the influence of random noise with a standard deviation comparable to the HARPS data and sampled in the same way. The distribution of the noise peaks in the period range 2.8–3.3 days has a maximum of ≈3.2 days and amplitudes approximately one-half of the K-amplitude for the planet. The presence of the activity signal may boost the velocity amplitude of these signals to values comparable to the planet. It may be premature to attribute the 3.24 day RV variations to an Earth-mass planet. A better understanding of the noise characteristics in the RV data as well as more measurements with better sampling will be needed to confirm this exoplanet.
Community detection and graph partitioning

Many methods have been proposed for community detection in networks. Some of the most promising are methods based on statistical inference, which rest on solid mathematical foundations and return excellent results in practice. In this paper we show that two of the most widely used inference methods can be mapped directly onto versions of the standard minimum-cut graph partitioning problem, which allows us to apply any of the many well-understood partitioning algorithms to the solution of community detection problems. We illustrate the approach by adapting the Laplacian spectral partitioning method to perform community inference, testing the resulting algorithm on a range of examples, including computer-generated and real-world networks. Both the quality of the results and the running time rival the best previous methods.
Robust Logistic Regression using Shift Parameters

Annotation errors can significantly hurt classifier performance, yet datasets are only growing noisier with the increased use of Amazon Mechanical Turk and techniques like distant supervision that automatically generate labels. In this paper, we present a robust extension of logistic regression that incorporates the possibility of mislabelling directly into the objective. This model can be trained through nearly the same means as logistic regression, and retains its efficiency on highdimensional datasets. We conduct experiments on named entity recognition data and find that our approach can provide a significant improvement over the standard model when annotation errors are present.
Risk Measure Estimation On Fiegarch Processes

We consider the Fractionally Integrated Exponential Generalized Autoregressive Conditional Heteroskedasticity process, denoted by FIEGARCH(p,d,q), introduced by Bollerslev and Mikkelsen (1996). We present a simulated study regarding the estimation of the risk measure $VaR_p$ on FIEGARCH processes. We consider the distribution function of the portfolio log-returns (univariate case) and the multivariate distribution function of the risk-factor changes (multivariate case). We also compare the performance of the risk measures $VaR_p$, $ES_p$ and MaxLoss for a portfolio composed by stocks of four Brazilian companies.
Two Field Matter Bounce Cosmology

We re-examine the non-singular Matter Bounce scenario first developed in [20], which starts with a matter-dominated period of contraction and transitions into an Ekpyrotic phase of contraction. We consider both matter fields, the first of which plays the role of regular matter, and the second of which is responsible for the non-singular bounce. Since the dominant matter field is massive, the induced curvature fluctuations are initially not scale-invariant, whereas the fluctuations of the second scalar field (which are initially entropy fluctuations) are scale-invariant. We study the transfer of the initial entropy perturbations into curvature fluctuations in the matter-dominated phase of contraction and show that the latter become nearly scale invariant on large scales but are blue tilted on small scales. We study the evolution of both curvature and entropy fluctuations through the bounce, and show that both have a scale-invariant spectrum which is blue-tilted on small scales. However, we find that the entropy fluctuations have an amplitude that is much smaller than that of the curvature perturbations, due to gravitational amplification of curvature perturbations during the bounce phase.
Resurrecting power law inflation in the light of Planck results

It is well known that a canonical scalar field with an exponential potential can drive power law inflation (PLI). However, the tensor-to-scalar ratio in such models turns out to be larger than the stringent limit set by recent Planck results. We propose a new model of power law inflation for which the scalar spectra index, the tensor-to-scalar ratio and the non-gaussianity parameter fNLequil are in excellent agreement with Planck results. Inflation, in this model, is driven by a non-canonical scalar field with an inverse power law potential. The Lagrangian for our model is structurally similar to that of a canonical scalar field and has a power law form for the kinetic term. A simple extension of our model resolves the graceful exit problem which usually afflicts models of power law inflation.
Investigating Deletion in Wikipedia

Several hundred Wikipedia articles are deleted every day because they lack sufficient significance to be included in the encyclopedia. We collect a dataset of deleted articles and analyze them to determine whether or not the deletions were justified. We find evidence to support the hypothesis that many deletions are carried out correctly, but also find that a large number were done very quickly. Based on our conclusions, we make some recommendations to reduce the number of non-significant pages and simultaneously improve retention of new editors.
The second laws of quantum thermodynamics

In ordinary thermodynamics, transitions are governed by a single quantity–the free energy. Its monotonicity is a formulation of the second law. Here, we find that the second law for microscopic or highly correlated systems takes on a very different form than it does at the macroscopic scale, imposing not just one constraint on state transformations, but many. We find a family of quantum free energies which generalize the standard free energy, and can never increase. The ordinary second law corresponds to the nonincreasing of one of these free energies, with the remainder imposing additional constraints on thermodynamic transitions. In the thermodynamic limit, these additional second laws become equivalent to the standard one. We also prove a strengthened version of the zeroth law of thermodynamics, allowing a definition of temperature. The second law of thermodynamics places constraints on state transformations. It applies to systems composed of many particles, however, we are seeing that one can formulate laws of thermodynamics when only a small number of particles are interacting with a heat bath. Is there a second law of thermodynamics in this regime? Here, we find that for processes which are approximately cyclic, the second law for microscopic systems takes on a different form compared to the macroscopic scale, imposing not just one constraint on state transformations, but an entire family of constraints. We find a family of free energies which generalize the traditional one, and show that they can never increase. The ordinary second law relates to one of these, with the remainder imposing additional constraints on thermodynamic transitions. We find three regimes which determine which family of second laws govern state transitions, depending on how cyclic the process is. In one regime one can cause an apparent violation of the usual second law, through a process of embezzling work from a large system which remains arbitrarily close to its original state. These second laws are relevant for small systems, and also apply to individual macroscopic systems interacting via long-range interactions. By making precise the definition of thermal operations, the laws of thermodynamics are unified in this framework, with the first law defining the class of operations, the zeroth law emerging as an equivalence relation between thermal states, and the remaining laws being monotonicity of our generalized free energies.
AN INTRODUCTION TO THE EINSTEIN TOOLKIT

We give an introduction to the Einstein Toolkit, a mature, open-source computational infrastructure for numerical relativity based on the Cactus Framework, for the target group of new users. This toolkit is composed of several different modules, is developed by researchers from different institutions throughout the world and is in active continuous development. Documentation for the toolkit and its several modules is often scattered across different locations, a difficulty new users may at times have to struggle with. Scientific papers exist describing the toolkit and its methods in detail, but they might be overwhelming at first. With these lecture notes we hope to provide an initial overview for new users. We cover how to obtain, compile and run the toolkit, and give an overview of some of the tools and modules provided with it.