arXiv subjects

Bjarke Frost Nielsen

Publications and source records attributed to Bjarke Frost Nielsen.

5 recordsLinked to original sources

arXiv2026

Mechanics of Pandemics

COVID-19 and previous pandemics have shown how diseases can disrupt, threaten, and transform daily life. Since pathogens and societies are continuously evolving, every pandemic is different. However, certain fundamental principles of disease transmission appear to hold true across different outbreaks. These ``mechanisms'' are grounded in natural laws or the very structure of our biology and societies. This paper compiles ten fundamental mechanisms, curated by a multidisciplinary team with backgrounds spanning public health, medicine, epidemiology, political science, mathematics, physics, and psychology. These mechanisms, although perhaps underappreciated, substantially shape how pandemics unfold and are controlled. The better we succeed in understanding these mechanisms and establishing this knowledge in our societies, the better we will be able to prepare for future pandemics and respond appropriately when they occur.

q-bio.PE↗

arXiv2025

Complex multiannual cycles of Mycoplasma pneumoniae: persistence and the role of stochasticity

The epidemiological dynamics of Mycoplasma pneumoniae is characterized by poorly understood complex multiannual cycles. The origins of these cycles have long been debated, and multiple explanations of varying complexity have been suggested. Using Bayesian methods, we fit a dynamical model to half a century of M. pneumoniae surveillance data from Denmark (1958-1995, 2010-2025) and uncover a parsimonious explanation for the persistent cycles, based on the theory of quasicycles. The period of the multiannual cycle (approx. 5 years in Denmark) is explained by susceptible replenishment due, primarily, to loss of immunity. While an excellent fit to shorter time series (a few decades), the deterministic model eventually settles into an annual cycle, unable to reproduce the persistent cycles. We find that environmental stochasticity (e.g., varying contact rates) stabilizes the multiannual cycles and so does demographic noise, at least in smaller or incompletely mixing populations. The temporary disappearance of cycles during 1979-1985 is explained as a consequence of stochastic mode-hopping. The circulation of M. pneumoniae was recently disrupted by COVID-19 non-pharmaceutical interventions (NPIs), providing a natural experiment on the effects of large perturbations. Consequently, the effects of NPIs are included in the model and medium-term predictions are explored. Our findings highlight the intrinsic sensitivity of M. pneumoniae dynamics to perturbations and interventions, underscoring the limitations for long-term prediction. More generally, our findings provide further evidence for the role of stochasticity as a driver of complex cycles across endemic and recurring pathogens.

q-bio.PE↗

arXiv2025

Applications of the Vendi score in genomic epidemiology

The Vendi score (VS), a diversity metric recently conceived in the context of machine learning, with applications in a wide range of fields, has a few distinct advantages over the metrics commonly used in ecology. It is classification-independent, incorporates abundance information, and has a tunable sensitivity to rare/abundant types. Using rich COVID-19 sequence data as a paradigm, we develop methods for applying the VS to time-resolved sequence data. We show how the VS allows for characterization of the overall diversity of circulating viruses and for discernment of emerging variants prior to formal identification. Furthermore, applying the VS to phylogenetic trees provides a convenient overview of within-clade diversity which can aid viral variant detection.

q-bio.PE↗

arXiv2020

Newton-Cartan Submanifolds and Fluid Membranes

We develop the geometric description of submanifolds in Newton--Cartan spacetime. This provides the necessary starting point for a covariant spacetime formulation of Galilean-invariant hydrodynamics on curved surfaces. We argue that this is the natural geometrical framework to study fluid membranes in thermal equilibrium and their dynamics out of equilibrium. A simple model of fluid membranes that only depends on the surface tension is presented and, extracting the resulting stresses, we show that perturbations away from equilibrium yield the standard result for the dispersion of elastic waves. We also find a generalisation of the Canham--Helfrich bending energy for lipid vesicles that takes into account the requirements of thermal equilibrium.

hep-th↗

arXiv2019

Substrate curvature governs texture orientation in thin films of smectic block copolymers

Self-assembly of ordered nanometer-scale patterns is interesting in itself, but its practical value depends on the ability to predict and control pattern formation. In this paper we demonstrate theoretically and numerically that engineering of extrinsic as well as intrinsic substrate geometry may provide such a controllable ordering mechanism for block copolymers films. We develop an effective two-dimensional model of thin films of striped-phase diblock copolymers on general curved substrates. The model is obtained as an expansion in the film thickness and thus takes the third dimension into account, which crucially allows us to predict the preferred orientations even in the absence of intrinsic curvature. We determine the minimum-energy textures on several curved surfaces and arrive at a general principle for using substrate curvature as an ordering field, namely that the stripes will tend to align along directions of maximal curvature.

cond-mat.soft↗