Two fitness inference schemes compared using allele frequencies from 1068 391 sequences sampled in the UK during the COVID-19 pandemic.

Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV-2 to escape antibody neutralization or to bind more strongly to the receptors that it uses to enter human cells. Here, we compared two methods that estimate the fitness effects of viral mutations using the abundant sequence data gathered over the course of the pandemic.

Random Pure Gaussian States and Hawking Radiation.

A black hole evaporates by Hawking radiation. Each mode of that radiation is thermal. If the total state is nevertheless to be pure, modes must be entangled.

Statistical genetics in and out of quasi-linkage equilibrium.

This review is about statistical genetics, an interdisciplinary topic between statistical physics and population biology. The focus is on the phase of(QLE). Our goals here are to clarify under which conditions the QLE phase can be expected to hold in population biology and how the stability of the QLE phase is lost.

Temporal epistasis inference from more than 3 500 000 SARS-CoV-2 genomic sequences.

We use direct coupling analysis (DCA) to determine epistatic interactions between loci of variability of the SARS-CoV-2 virus, segmenting genomes by month of sampling. We use full-length, high-quality genomes from the GISAID repository up to October 2021 for a total of over 3 500 000 genomes. We find that DCA terms are more stable over time than correlations but nevertheless change over time as mutations disappear from the global population or reach fixation.

Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes.

Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to deeper understanding of microbial pathogenesis. We have considered all complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes deposited in the Global Initiative on Sharing All Influenza Data (GISAID) repository until four different cutoff dates, and used direct coupling analysis together with an assumption of quasi-linkage equilibrium to infer epistatic contributions to fitness from polymorphic loci. We find eight interactions, of which three are between pairs where one locus lies in gene ORF3a, both loci holding nonsynonymous mutations.

Fröhlich-coupled qubits interacting with fermionic baths.

We consider a quantum system such as a qubit, interacting with a bath of fermions as in the Fröhlich polaron model. The interaction Hamiltonian is thus linear in the system variable and quadratic in the fermions. Using the recently developed extension of Feynman-Vernon theory to nonharmonic baths we evaluate quadratic and the quartic terms in the influence action.

Inferring genetic fitness from genomic data.

The genetic composition of a naturally developing population is considered as due to mutation, selection, genetic drift, and recombination. Selection is modeled as single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). The problem is posed to infer epistatic fitness from population-wide whole-genome data from a time series of a developing population.

Large deviations and fluctuation theorem for the quantum heat current in the spin-boson model.

We study the heat current flowing between two baths consisting of harmonic oscillators interacting with a qubit through a spin-boson coupling. An explicit expression for the generating function of the total heat flowing between the right and left baths is derived by evaluating the corresponding Feynman-Vernon path integral by performing the noninteracting blip approximation (NIBA). We recover the known expression, obtained by using the polaron transform.

Dynamic insights on transcription initiation and RNA processing during bacterial adaptation.

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σ system in was coupled to our previously described tagRNA-seq method to yield process kinetics information.

Theory of Nonequilibrium Local Search on Random Satisfaction Problems.

We study local search algorithms to solve instances of the random k-satisfiability problem, equivalent to finding (if they exist) zero-energy ground states of statistical models with disorder on random hypergraphs. It is well known that the best such algorithms are akin to nonequilibrium processes in a high-dimensional space. In particular, algorithms known as focused, and which do not obey detailed balance, outperform simulated annealing and related methods in the task of finding the solution to a complex satisfiability problem, that is to find (exactly or approximately) the minimum in a complex energy landscape.

Erratum: Characteristic functions of quantum heat with baths at different temperatures [Phys. Rev. E 97, 062117 (2018)].

This corrects the article DOI: 10.1103/PhysRevE.97.

Thermal power of heat flow through a qubit.

In this paper we consider the thermal power of a heat flow through a qubit between two baths. The baths are modeled as a set of harmonic oscillators initially at equilibrium, at two temperatures. Heat is defined as the change of energy of the cold bath, and thermal power is defined as expected heat per unit time, in the long-time limit.

DCA for genome-wide epistasis analysis: the statistical genetics perspective.

Direct coupling analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to sequences of homologous proteins, and also more recently to whole-genome population-wide sequencing data. We here argue that the use of DCA on the genome scale is contingent on fundamental issues of population genetics.

Characteristic functions of quantum heat with baths at different temperatures.

This paper is about quantum heat defined as the change in energy of a bath during a process. The presentation takes into account recent developments in classical strong-coupling thermodynamics and addresses a version of quantum heat that satisfies quantum-classical correspondence. The characteristic function and the full counting statistics of quantum heat are shown to be formally similar.

Exploring the diluted ferromagnetic p-spin model with a cavity master equation.

We introduce an alternative solution to Glauber multispin dynamics on random graphs. The solution is based on the recently introduced cavity master equation (CME), a time-closure turning the, in principle, exact dynamic cavity method into a practical method of analysis and of fast simulation. Running CME once is of comparable computational complexity as one Monte Carlo run on the same problem.

Unified picture of strong-coupling stochastic thermodynamics and time reversals.

Strong-coupling statistical thermodynamics is formulated as the Hamiltonian dynamics of an observed system interacting with another unobserved system (a bath). It is shown that the entropy production functional of stochastic thermodynamics, defined as the log ratio of forward and backward system path probabilities, is in a one-to-one relation with the log ratios of the joint initial conditions of the system and the bath. A version of strong-coupling statistical thermodynamics where the system-bath interaction vanishes at the beginning and at the end of a process is, as is also weak-coupling stochastic thermodynamics, related to the bath initially in equilibrium by itself.

Steady diffusion in a drift field: A comparison of large-deviation techniques and multiple-scale analysis.

A particle with internal unobserved states diffusing in a force field will generally display effective advection-diffusion. The drift velocity is proportional to the mobility averaged over the internal states, or effective mobility, while the effective diffusion has two terms. One is of the equilibrium type and satisfies an Einstein relation with the effective mobility while the other is quadratic in the applied force.

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.

Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus).

Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry.

We consider coupled diffusions in n-dimensional space and on a compact manifold and the resulting effective advective-diffusive motion on large scales in space. The effective drift (advection) and effective diffusion are determined as a solvability conditions in a multiscale analysis. As an example, we consider coupled diffusions in three-dimensional space and on the group manifold SO(3) of proper rotations, generalizing results obtained by H.

The bulk and the tail of minimal absent words in genome sequences.

Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words.

Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape.

The observed intercellular heterogeneity within a clonal cell population can be mapped as dynamical states clustered around an attractor point in gene expression space, owing to a balance between homeostatic forces and stochastic fluctuations. These dynamics have led to the cancer cell attractor conceptual model, with implications for both carcinogenesis and new therapeutic concepts. Immortalized and malignant EBV-carrying B-cell lines were used to explore this model and characterize the detailed structure of cell attractors.

Entropy production of a Brownian ellipsoid in the overdamped limit.

We analyze the translational and rotational motion of an ellipsoidal Brownian particle from the viewpoint of stochastic thermodynamics. The particle's Brownian motion is driven by external forces and torques and takes place in an heterogeneous thermal environment where friction coefficients and (local) temperature depend on space and time. Our analysis of the particle's stochastic thermodynamics is based on the entropy production associated with single particle trajectories.

Dynamic message-passing approach for kinetic spin models with reversible dynamics.

A method to approximately close the dynamic cavity equations for synchronous reversible dynamics on a locally treelike topology is presented. The method builds on (a) a graph expansion to eliminate loops from the normalizations of each step in the dynamics and (b) an assumption that a set of auxilary probability distributions on histories of pairs of spins mainly have dependencies that are local in time. The closure is then effectuated by projecting these probability distributions on n-step Markov processes.