Controlling wall-particle interactions with activity.

We theoretically determine the effective forces on hard disks near walls embedded inside active nematic liquid crystals. When the disks are sufficiently close to the wall and the flows are sufficiently slow, we can obtain exact expressions for the effective forces. We find these forces and the dynamics of disks near the wall depend both on the properties of the active nematic and on the anchoring conditions on the disks and the wall.

Field Theory for Mechanical Criticality in Disordered Fiber Networks.

Strain-controlled criticality governs the elasticity of jamming and fiber networks. While the upper critical dimension of jamming is believed to be d_{u}=2, non-mean-field exponents are observed in numerical studies of 2D and 3D fiber networks. The origins of this remains unclear.

Multiscale topology classifies cells in subcellular spatial transcriptomics.

Spatial transcriptomics measures in situ gene expression at millions of locations within a tissue, hitherto with some trade-off between transcriptome depth, spatial resolution and sample size. Although integration of image-based segmentation has enabled impactful work in this context, it is limited by imaging quality and tissue heterogeneity. By contrast, recent array-based technologies offer the ability to measure the entire transcriptome at subcellular resolution across large samples.

Elliptic PDE learning is provably data-efficient.

Partial differential equations (PDE) learning is an emerging field that combines physics and machine learning to recover unknown physical systems from experimental data. While deep learning models traditionally require copious amounts of training data, recent PDE learning techniques achieve spectacular results with limited data availability. Still, these results are empirical.

Non-pharmaceutical interventions for COVID-19: a systematic review on environmental control measures.

The purpose of this review was to identify the effectiveness of environmental control (EC) non-pharmaceutical interventions (NPIs) in reducing transmission of SARS-CoV-2 through conducting a systematic review. EC NPIs considered in this review are room ventilation, air filtration/cleaning, room occupancy, surface disinfection, barrier devices, [Formula: see text] monitoring and one-way-systems. Systematic searches of databases from Web of Science, Medline, EMBASE, preprint servers MedRxiv and BioRxiv were conducted in order to identify studies reported between 1 January 2020 and 1 December 2022.

Homology of homologous knotted proteins.

Quantification and classification of protein structures, such as knotted proteins, often requires noise-free and complete data. Here, we develop a mathematical pipeline that systematically analyses protein structures. We showcase this geometric framework on proteins forming open-ended trefoil knots, and we demonstrate that the mathematical tool, persistent homology, faithfully represents their structural homology.

Challenges of integrating economics into epidemiological analysis of and policy responses to emerging infectious diseases.

COVID-19 has shown that the consequences of a pandemic are wider-reaching than cases and deaths. Morbidity and mortality are important direct costs, but infectious diseases generate other direct and indirect benefits and costs as the economy responds to these shocks: some people lose, others gain and people modify their behaviours in ways that redistribute these benefits and costs. These additional effects feedback on health outcomes to create a complicated interdependent system of health and non-health outcomes.

The Wiener-Hopf technique, its generalizations and applications: constructive and approximate methods.

This paper reviews the modern state of the Wiener-Hopf factorization method and its generalizations. The main constructive results for matrix Wiener-Hopf problems are presented, approximate methods are outlined and the main areas of applications are mentioned. The aim of the paper is to offer an overview of the development of this method, and demonstrate the importance of bringing together pure and applied analysis to effectively employ the Wiener-Hopf technique.

A proof that multiple waves propagate in ensemble-averaged particulate materials.

Effective medium theory aims to describe a complex inhomogeneous material in terms of a few important macroscopic parameters. To characterize wave propagation through an inhomogeneous material, the most crucial parameter is the . For this reason, there are many published studies on how to calculate a single effective wavenumber.

Self-Organization and Flow of Low-Functionality Telechelic Star Polymers with Varying Attraction.

We combine state-of-the art synthesis, simulations, and physical experiments to explore the tunable, responsive character of telechelic star polymers as models for soft patchy particles. We focus on the simplest possible system: a star comprising three asymmetric block copolymer arms with solvophilic inner and solvophobic outer blocks. Our dilute solution studies reveal the onset of a second slow mode in the intermediate scattering functions as the temperature decreases below the θ-point of the outer block, as well as the size reduction of single stars upon further decreasing temperature.

Rule-Based Modeling Using Wildcards in the Smoldyn Simulator.

Many biological molecules exist in multiple variants, such as proteins with different posttranslational modifications, DNAs with different sequences, and phospholipids with different chain lengths. Representing these variants as distinct species, as most biochemical simulators do, leads to the problem that the number of species, and chemical reactions that interconvert them, typically increase combinatorially with the number of ways that the molecules can vary. This can be alleviated by "rule-based modeling methods," in which software generates the chemical reaction network from relatively simple "rules.

Reflection from a multi-species material and its transmitted effective wavenumber.

We formally deduce closed-form expressions for the transmitted effective wavenumber of a material comprising multiple types of inclusions or particles (multi-species), dispersed in a uniform background medium. The expressions, derived here for the first time, are valid for moderate volume fractions and without restriction on the frequency. We show that the multi-species effective wavenumber is not a straightforward extension of expressions for a single species.

Avoiding overstating the strength of forensic evidence: Shrunk likelihood ratios/Bayes factors.

When strength of forensic evidence is quantified using sample data and statistical models, a concern may be raised as to whether the output of a model overestimates the strength of evidence. This is particularly the case when the amount of sample data is small, and hence sampling variability is high. This concern is related to concern about precision.

Score based procedures for the calculation of forensic likelihood ratios - Scores should take account of both similarity and typicality.

Score based procedures for the calculation of forensic likelihood ratios are popular across different branches of forensic science. They have two stages, first a function or model which takes measured features from known-source and questioned-source pairs as input and calculates scores as output, then a subsequent model which converts scores to likelihood ratios. We demonstrate that scores which are purely measures of similarity are not appropriate for calculating forensically interpretable likelihood ratios.

What should a forensic practitioner's likelihood ratio be? II.

In the debate as to whether forensic practitioners should assess and report the precision of the strength of evidence statements that they report to the courts, I remain unconvinced by proponents of the position that only a subjectivist concept of probability is legitimate. I consider this position counterproductive for the goal of having forensic practitioners implement, and courts not only accept but demand, logically correct and scientifically valid evaluation of forensic evidence. In considering what would be the best approach for evaluating strength of evidence, I suggest that the desiderata be (1) to maximise empirically demonstrable performance; (2) to maximise objectivity in the sense of maximising transparency and replicability, and minimising the potential for cognitive bias; and (3) to constrain and make overt the forensic practitioner's subjective-judgement based decisions so that the appropriateness of those decisions can be debated before the judge in an admissibility hearing and/or before the trier of fact at trial.

Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface.

Motivation: Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features.

Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming.

Biotechnological applications of microbial pectate lyases (Pels) in plant fiber processing are promising, eco-friendly substitutes for conventional chemical degumming processes. However, to potentiate the enzymes' use for industrial applications, resolving the molecular structure to elucidate catalytic mechanisms becomes necessary. In this manuscript, we report the high resolution (1.

Receptor dimer stabilization by hierarchical plasma membrane microcompartments regulates cytokine signaling.

The interaction dynamics of signaling complexes is emerging as a key determinant that regulates the specificity of cellular responses. We present a combined experimental and computational study that quantifies the consequences of plasma membrane microcompartmentalization for the dynamics of type I interferon receptor complexes. By using long-term dual-color quantum dot (QD) tracking, we found that the lifetime of individual ligand-induced receptor heterodimers depends on the integrity of the membrane skeleton (MSK), which also proved important for efficient downstream signaling.

A comment on the PCAST report: Skip the "match"/"non-match" stage.

This letter comments on the report "Forensic science in criminal courts: Ensuring scientific validity of feature-comparison methods" recently released by the President's Council of Advisors on Science and Technology (PCAST). The report advocates a procedure for evaluation of forensic evidence that is a two-stage procedure in which the first stage is "match"/"non-match" and the second stage is empirical assessment of sensitivity (correct acceptance) and false alarm (false acceptance) rates. Almost always, quantitative data from feature-comparison methods are continuously-valued and have within-source variability.

Synchronization and liquid crystalline order in soft active fluids.

We introduce a phenomenological theory for a new class of soft active fluids with the ability to synchronize. Our theoretical framework describes the macroscopic behavior of a collection of interacting anisotropic elements with cyclic internal dynamics and a periodic phase variable. This system can (i) spontaneously undergo a transition to a state with macroscopic orientational order, with the elements aligned, a liquid crystal, (ii) attain another broken symmetry state characterized by synchronization of their phase variables, or (iii) a combination of both types of order.

Possible resonance effect of axionic dark matter in Josephson junctions.

We provide theoretical arguments that dark-matter axions from the galactic halo that pass through Earth may generate a small observable signal in resonant S/N/S Josephson junctions. The corresponding interaction process is based on the uniqueness of the gauge-invariant axion Josephson phase angle modulo 2π and is predicted to produce a small Shapiro steplike feature without externally applied microwave radiation when the Josephson frequency resonates with the axion mass. A resonance signal of so far unknown origin observed by C.

Inertial effects in the response of viscous and viscoelastic fluids.

We consider the effect of inertia on the high frequency response of a general linear viscoelastic material to local deformations. We calculate the displacement response and correlation functions for points separated by a distance r. The effects of inertia and incompressibility lead to anticorrelations in the correlation or response functions, which become more pronounced for more elastic materials.