Author Correction: SciPy 1.0: fundamental algorithms for scientific computing in Python.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

SciPy 1.0: fundamental algorithms for scientific computing in Python.

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

VGsim: Scalable viral genealogy simulator for global pandemic.

Accurate simulation of complex biological processes is an essential component of developing and validating new technologies and inference approaches. As an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been sequenced from most regions in the world. More than 5.5 million viral sequences are publicly available as of November 2021. Many studies estimate viral genealogies from these sequences, as these can provide valuable information about the spread of the pandemic across time and space. Additionally such data are a rich source of information about molecular evolutionary processes including natural selection, for example allowing the identification of new variants with transmissibility and immunity evasion advantages. To our knowledge, there is no framework that is both efficient and flexible enough to simulate the pandemic to approximate world-scale scenarios and generate viral genealogies of millions of samples. Here, we introduce a new fast simulator VGsim which addresses the problem of simulation genealogies under epidemiological models. The simulation process is split into two phases. During the forward run the algorithm generates a chain of population-level events reflecting the dynamics of the pandemic using an hierarchical version of the Gillespie algorithm. During the backward run a coalescent-like approach generates a tree genealogy of samples conditioning on the population-level events chain generated during the forward run. Our software can model complex population structure, epistasis and immunity escape.

Impact of the Injection Protocol on an Impurity's Stationary State.

We examine stationary-state properties of an impurity particle injected into a one-dimensional quantum gas. We show that the value of the impurity's end velocity lies between zero and the speed of sound in the gas and is determined by the injection protocol. This way, the impurity's constant motion is a dynamically emergent phenomenon whose description goes beyond accounting for the kinematic constraints of the Landau approach to superfluidity. We provide exact analytic results in the thermodynamic limit and perform finite-size numerical simulations to demonstrate that the predicted phenomena are within the reach of the ultracold gas experiments.

Finite-size analysis in neural network classification of critical phenomena.

We analyze the problem of supervised learning of ferromagnetic phase transitions from the statistical physics perspective. We consider two systems in two universality classes, the two-dimensional Ising model and two-dimensional Baxter-Wu model, and perform careful finite-size analysis of the results of the supervised learning of the phases of each model. We find that the variance of the neural network (NN) output function (VOF) as a function of temperature has a peak in the critical region. Qualitatively, the VOF is related to the classification rate of the NN. We find that the width of the VOF peak displays the finite-size scaling governed by the correlation length exponent ν of the universality class of the model. We check this conclusion using several NN architectures-a fully connected NN, a convolutional NN, and several members of the ResNet family-and discuss the accuracy of the extracted critical exponents ν.

Thermodynamics of the 3D Hubbard model on approaching the Néel transition.

We study the thermodynamic properties of the 3D Hubbard model for temperatures down to the Néel temperature by using cluster dynamical mean-field theory. In particular, we calculate the energy, entropy, density, double occupancy, and nearest-neighbor spin correlations as a function of chemical potential, temperature, and repulsion strength. To make contact with cold-gas experiments, we also compute properties of the system subject to an external trap in the local density approximation. We find that an entropy per particle S/N ≈ 0.65(6) at U/t = 8 is sufficient to achieve a Néel state in the center of the trap, substantially higher than the entropy required in a homogeneous system. Precursors to antiferromagnetism can clearly be observed in nearest-neighbor spin correlators.

Critical and geometric properties of magnetic polymers across the globule-coil transition.

We study a lattice model of a single magnetic polymer chain, where Ising spins are located on the sites of a lattice self-avoiding walk in d=2. We consider the regime where both conformations and magnetic degrees of freedom are dynamic, thus the Ising model is defined on a dynamic lattice and conformations generate an annealed disorder. Using Monte Carlo simulations, we characterize the globule-coil and ferromaget-to-paramagnet transitions, which occur simultaneously at a critical value of the spin-spin coupling. We argue that the transition is continuous-in contrast to d=3 where it is first order. Our results suggest that at the transition the metric exponent takes the θ-polymer value ν=4/7 but the crossover exponent ϕ≈0.7, which differs from the expected value for a θ polymer.

VGsim: scalable viral genealogy simulator for global pandemic.

Accurate simulation of complex biological processes is an essential component of developing and validating new technologies and inference approaches. As an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been sequenced from most regions in the world. More than 5.5 million viral sequences are publicly available as of November 2021. Many studies estimate viral genealogies from these sequences, as these can provide valuable information about the spread of the pandemic across time and space. Additionally such data are a rich source of information about molecular evolutionary processes including natural selection, for example allowing the identification of new variants with transmissibility and immunity evasion advantages. To our knowledge, there is no framework that is both efficient and flexible enough to simulate the pandemic to approximate world-scale scenarios and generate viral genealogies of millions of samples. Here, we introduce a new fast simulator VGsim which addresses the problem of simulation genealogies under epidemiological models. The simulation process is split into two phases. During the forward run the algorithm generates a chain of population-level events reflecting the dynamics of the pandemic using an hierarchical version of the Gillespie algorithm. During the backward run a coalescent-like approach generates a tree genealogy of samples conditioning on the population-level events chain generated during the forward run. Our software can model complex population structure, epistasis and immunity escape. The code is freely available at https://github.com/Genomics-HSE/VGsim.

Luttinger liquid of trimers in Fermi gases with unequal masses.

We investigate one dimensional attractive Fermi gases in spin-dependent optical lattices. We show that three-body bound states--"trimers"--exist as soon as the two tunneling rates are different. We calculate the binding energy and the effective mass of a single trimer. We then show numerically that for finite and commensurate densities n(up) = n(down)/2 an energy gap appears, implying that the gas is a one-component Luttinger liquid of trimers with suppressed superfluid correlations. The boundaries of this novel phase are given. We discuss experimental situations to test our predictions.

Multiparticle composites in density-imbalanced quantum fluids.

We consider two-component one-dimensional quantum gases with a density imbalance. While generically such fluids are two-component Luttinger liquids, we show that if the ratio of the densities is a rational number, p/q, and mass asymmetry between components is sufficiently strong, one of the two eigenmodes acquires a gap. The gapped phase corresponds to (algebraic) ordering of (p+q)-particle composites. In particular, for attractive mixtures, this implies that the superconducting correlations are destroyed. We illustrate our predictions by numerical simulations of the fermionic Hubbard model with hopping asymmetry.

Acceptance rate is a thermodynamic function in local Monte Carlo algorithms.

We study properties of Markov chain Monte Carlo simulations of classical spin models with local updates. We derive analytic expressions for the mean value of the acceptance rate of single-spin-flip algorithms for the one-dimensional Ising model. We find that for the Metropolis algorithm the average acceptance rate is a linear function of energy. We further provide numerical results for the energy dependence of the average acceptance rate for the three- and four-state Potts model, and the XY model in one and two spatial dimensions. In all cases, the acceptance rate is an almost linear function of the energy in the critical region. The variance of the acceptance rate is studied as a function of the specific heat. While the specific heat develops a singularity in the vicinity of a phase transition, the variance of the acceptance rate stays finite.

Exact treatment of exciton-polaron formation by diagrammatic Monte Carlo simulations.

We develop an approximation-free diagrammatic Monte Carlo technique to study fermionic particles interacting with each other simultaneously through both an attractive Coulomb potential and bosonic excitations of the underlying medium. Exemplarily we apply the method to the long-standing exciton-polaron problem and present numerically exact results for the wave function, ground-state energy, binding energy and effective mass of this quasiparticle. Focusing on the electron-hole pair bound-state formation, we discuss various limiting cases of a generic exciton-polaron model. The frequently used instantaneous approximation to the retarded interaction due to the exchange of phonons is found to be of very limited applicability.

Critical temperature curve in BEC-BCS crossover.

The strongly correlated regime of the crossover from Bardeen-Cooper-Schrieffer pairing to Bose-Einstein condensation can be realized by diluting a system of two-component fermions with a short-range attractive interaction. We investigate this system via a novel continuous-space-time diagrammatic determinant Monte Carlo method and determine the universal curve Tc/epsilonF for the transition temperature between the normal and the superfluid states as a function of the scattering length with the maximum on the Bose-Einstein condensation side. At unitarity, we confirm that Tc/epsilonF=0.152(7).

Critical temperature and thermodynamics of attractive fermions at unitarity.

The unitarity regime of the BCS-BEC crossover can be realized by diluting a system of two-component lattice fermions with an on-site attractive interaction. We perform a systematic-error-free finite-temperature simulation of this system by diagrammatic determinant Monte Carlo method. The critical temperature in units of Fermi energy is found to be T(C)/epsilonF=0.152(7). We also report the behavior of the thermodynamic functions, and discuss the issues of thermometry of ultracold Fermi gases.

Superfluid interfaces in quantum solids.

One scenario for the nonclassical moment of inertia of solid 4He discovered by Kim and Chan [Nature (London) 427, 225 (2004)] is the superfluidity of microcrystallite interfaces. On the basis of the most simple model of a quantum crystal--the checkerboard lattice solid--we show that the superfluidity of interfaces between solid domains can exist in a wide range of parameters. At strong enough interparticle interaction, a superfluid interface becomes an insulator via a quantum phase transition. Under the conditions of particle-hole symmetry, the transition is of the standard U(1) universality class in 3D, while in 2D the onset of superfluidity is accompanied by the interface roughening, driven by fractionally charged topological excitations.