arXiv subjects

Simon Bauer

Publications and source records attributed to Simon Bauer.

12 recordsLinked to original sources

arXiv2025

Capillary wave formation in conserved active emulsions

The dynamics of phase-separated interfaces shape the behavior of both passive and active condensates. While surface tension in equilibrium systems minimizes interface length, non-equilibrium fluxes can destabilize flat or constantly curved interfaces, giving rise to complex interface morphologies. Starting from a minimal model that couples a conserved, phase-separating species to a self-generated chemical field, we identify the conditions under which interfacial instabilities may emerge. Specifically, we show that non-reciprocal chemotactic interactions induce two distinct types of instabilities: a stationary (non-oscillatory) instability that promotes interface deformations, and an oscillatory instability that can give rise to persistent capillary waves propagating along the boundaries of phase-separated domains. To characterize these phenomena, we develop a perturbative framework that predicts the onset, wavelength, and velocity of capillary waves, and quantitatively validate these predictions through numerical simulations. Beyond the linear regime, our simulations reveal that capillary waves undergo a secondary instability, leading to either stationary or dynamically evolving superpositions of different wave modes. Finally, we investigate whether capillary waves can facilitate directed mass transport, either along phase boundaries (conveyor belts) or through self-sustained liquid gears crawling along a solid wall. Taken together, our results establish a general framework for interfacial dynamics in active phase-separating systems and suggest new strategies for controlling mass transport in soft matter and biological condensates.

cond-mat.soft↗

arXiv2023

Evaluating the Benefits: Quantifying the Effects of TCP Options, QUIC, and CDNs on Throughput

To keep up with increasing demands on quality of experience, assessing and understanding the performance of network connections is crucial for web service providers. While different measures, like TCP options, alternative transport layer protocols like QUIC, or the hosting of services in CDNs, are expected to improve connection performance, no studies are quantifying such impacts on connections on the Internet. This paper introduces an active Internet measurement approach to assess the impacts of mentioned measures on connection performance. We conduct downloads from public web servers considering different vantage points, extract performance indicators like throughput, RTT, and retransmission rate, and survey speed-ups due to TCP option usage. Further, we compare the performance of QUIC-based downloads to TCP-based downloads considering different option configurations. Next to significant throughput improvements due to TCP option usage, in particular TCP window scaling, and QUIC, our study shows significantly increased performance for connections to domains hosted by different giant CDNs.

cs.NI↗

arXiv2023

Societal self-regulation induces complex infection dynamics and chaos

Classically, endemic infectious diseases are expected to display relatively stable, predictable infection dynamics. Accordingly, basic disease models such as the susceptible-infected-recovered-susceptible model display stable endemic states or recurrent seasonal waves. However, if the human population reacts to high infection numbers by mitigating the spread of the disease, then this delayed behavioral feedback loop can generate infection waves itself, driven by periodic mitigation and subsequent relaxation. We show that such behavioral reactions, together with a seasonal effect of comparable impact, can cause complex and unpredictable infection dynamics, including Arnold tongues, coexisting attractors, and chaos. Importantly, these arise in epidemiologically relevant parameter regions where the costs associated to infections and mitigation are jointly minimized. By comparing our model to data, we find signs that COVID-19 was mitigated in a way that favored complex infection dynamics. Our results challenge the intuition that endemic disease dynamics necessarily implies predictability and seasonal waves and show the emergence of complex infection dynamics when humans optimize their reaction to increasing infection numbers.

physics.soc-ph↗

arXiv2021

Interplay between risk perception, behaviour, and COVID-19 spread

Pharmaceutical and non-pharmaceutical interventions (NPIs) have been crucial for controlling COVID-19. They are complemented by voluntary health-protective behaviour, building a complex interplay between risk perception, behaviour, and disease spread. We studied how voluntary health-protective behaviour and vaccination willingness impact the long-term dynamics. We analysed how different levels of mandatory NPIs determine how individuals use their leeway for voluntary actions. If mandatory NPIs are too weak, COVID-19 incidence will surge, implying high morbidity and mortality before individuals react; if they are too strong, one expects a rebound wave once restrictions are lifted, challenging the transition to endemicity. Conversely, moderate mandatory NPIs give individuals time and room to adapt their level of caution, mitigating disease spread effectively. When complemented with high vaccination rates, this also offers a robust way to limit the impacts of the Omicron variant of concern. Altogether, our work highlights the importance of appropriate mandatory NPIs to maximise the impact of individual voluntary actions in pandemic control.

q-bio.PE↗

arXiv2021

The winter dilemma

With winter coming in the northern hemisphere, disadvantageous seasonality of SARS-CoV-2 requires high immunity levels in the population or increasing non-pharmaceutical interventions (NPIs), compared to summer. Otherwise intensive care units (ICUs) might fill up. However, compliance with mandatory NPIs, vaccine uptake, and individual protective measures depend on individuals' opinions and behavior. Opinions, in turn, depend on information, e.g., about vaccine safety or current infection levels. Therefore, understanding how information about the pandemic affects its spread through the modulation of voluntary protection-seeking behaviors is crucial for better preparedness this winter and for future crises.

q-bio.PE↗

arXiv2021

Mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants

The emergence of SARS-CoV-2 variants of concern endangers the long-term control of COVID-19, especially in countries with limited genomic surveillance. In this work, we explored genomic drivers of contagion in Chile. We sequenced 3443 SARS-CoV-2 genomes collected between January and July 2021, where the Gamma (P.1), Lambda (C.37), Alpha (B.1.1.7), B.1.1.348, and B.1.1 lineages were predominant. Using a Bayesian model tailored for limited genomic surveillance, we found that Lambda and Gamma variants' reproduction numbers were about 5% and 16% larger than Alpha's, respectively. We observed an overabundance of mutations in the Spike gene, strongly correlated with the variant's transmissibility. Furthermore, the variants' mutational signatures featured a breakpoint concurrent with the beginning of vaccination (mostly CoronaVac, an inactivated virus vaccine), indicating an additional putative selective pressure. Thus, our work provides a reliable method for quantifying novel variants' transmissibility under subsampling (as newly-reported Delta, B.1.617.2) and highlights the importance of continuous genomic surveillance.

q-bio.PE↗

arXiv2021

A look into the future of the COVID-19 pandemic in Europe: an expert consultation

How will the coronavirus disease 2019 (COVID-19) pandemic develop in the coming months and years? Based on an expert survey, we examine key aspects that are likely to influence COVID-19 in Europe. The future challenges and developments will strongly depend on the progress of national and global vaccination programs, the emergence and spread of variants of concern, and public responses to nonpharmaceutical interventions (NPIs). In the short term, many people are still unvaccinated, VOCs continue to emerge and spread, and mobility and population mixing is expected to increase over the summer. Therefore, policies that lift restrictions too much and too early risk another damaging wave. This challenge remains despite the reduced opportunities for transmission due to vaccination progress and reduced indoor mixing in the summer. In autumn 2021, increased indoor activity might accelerate the spread again, but a necessary reintroduction of NPIs might be too slow. The incidence may strongly rise again, possibly filling intensive care units, if vaccination levels are not high enough. A moderate, adaptive level of NPIs will thus remain necessary. These epidemiological aspects are put into perspective with the economic, social, and health-related consequences and thereby provide a holistic perspective on the future of COVID-19.

q-bio.OT↗

arXiv2021

Relaxing restrictions at the pace of vaccination increases freedom and guards against further COVID-19 waves

Mass vaccination offers a promising exit strategy for the COVID-19 pandemic. However, as vaccination progresses, demands to lift restrictions increase, despite most of the population remaining susceptible. Using our age-stratified SEIRD-ICU compartmental model and curated epidemiological and vaccination data, we quantified the rate (relative to vaccination progress) at which countries can lift non-pharmaceutical interventions without overwhelming their healthcare systems. We analyzed scenarios ranging from immediately lifting restrictions (accepting high mortality and morbidity) to reducing case numbers to a level where test-trace-and-isolate (TTI) programs efficiently compensate for local spreading events. In general, the age-dependent vaccination roll-out implies a transient decrease of more than ten years in the average age of ICU patients and deceased. The pace of vaccination determines the speed of lifting restrictions; Taking the European Union (EU) as an example case, all considered scenarios allow for steadily increasing contacts starting in May 2021 and relaxing most restrictions by autumn 2021. Throughout summer 2021, only mild contact restrictions will remain necessary. However, only high vaccine uptake can prevent further severe waves. Across EU countries, seroprevalence impacts the long-term success of vaccination campaigns more strongly than age demographics. In addition, we highlight the need for preventive measures to reduce contagion in school settings throughout the year 2021, where children might be drivers of contagion because of them remaining susceptible...

q-bio.PE↗

arXiv2020

Low case numbers enable long-term stable pandemic control without lockdowns

The traditional long-term solutions for epidemic control involve eradication or population immunity. Here, we analytically derive the existence of a third viable solution: a stable equilibrium at low case numbers, where test-trace-and-isolate policies partially compensate for local spreading events, and only moderate restrictions remain necessary. In this equilibrium, daily cases stabilize around ten new infections per million people or less. However, stability is endangered if restrictions are relaxed or case numbers grow too high. The latter destabilization marks a tipping point beyond which the spread self-accelerates. We show that a lockdown can reestablish control and that recurring lockdowns are not necessary given sustained, moderate contact reduction. We illustrate how this strategy profits from vaccination and helps mitigate variants of concern. This strategy reduces cumulative cases (and fatalities) 4x more than strategies that only avoid hospital collapse. In the long term, immunization, large-scale testing, and international coordination will further facilitate control.

q-bio.PE↗

arXiv2019

User Space Network Drivers

The rise of user space packet processing frameworks like DPDK and netmap makes low-level code more accessible to developers and researchers. Previously, driver code was hidden in the kernel and rarely modified, or even looked at, by developers working at higher layers. These barriers are gone nowadays, yet developers still treat user space drivers as black-boxes magically accelerating applications. We want to change this: every researcher building high-speed network applications should understand the intricacies of the underlying drivers, especially if they impact performance. We present ixy, a user space network driver designed for simplicity and educational purposes to show that fast packet IO is not black magic but careful engineering. ixy focuses on the bare essentials of user space packet processing: a packet forwarder including the whole NIC driver uses less than 1,000 lines of C code. This paper is partially written in tutorial style on the case study of our implementations of drivers for both the Intel 82599 family and for virtual VirtIO NICs. The former allows us to reason about driver and framework performance on a stripped-down implementation to assess individual optimizations in isolation. VirtIO support ensures that everyone can run it in a virtual machine. Our code is available as free and open source under the BSD license at https://github.com/emmericp/ixy

cs.NI↗

arXiv2017

A stencil scaling approach for accelerating matrix-free finite element implementations

We present a novel approach to fast on-the-fly low order finite element assembly for scalar elliptic partial differential equations of Darcy type with variable coefficients optimized for matrix-free implementations. Our approach introduces a new operator that is obtained by appropriately scaling the reference stiffness matrix from the constant coefficient case. Assuming sufficient regularity, an a priori analysis shows that solutions obtained by this approach are unique and have asymptotically optimal order convergence in the $H^1$- and the $L^2$-norm on hierarchical hybrid grids. For the pre-asymptotic regime, we present a local modification that guarantees uniform ellipticity of the operator. Cost considerations show that our novel approach requires roughly one third of the floating-point operations compared to a classical finite element assembly scheme employing nodal integration. Our theoretical considerations are illustrated by numerical tests that confirm the expectations with respect to accuracy and run-time. A large scale application with more than a hundred billion ($1.6\cdot10^{11}$) degrees of freedom executed on 14,310 compute cores demonstrates the efficiency of the new scaling approach.

math.NA↗

arXiv2016

A two-scale approach for efficient on-the-fly operator assembly in massively parallel high performance multigrid codes

Matrix-free finite element implementations of massively parallel geometric multigrid save memory and are often significantly faster than implementations using classical sparse matrix techniques. They are especially well suited for hierarchical hybrid grids on polyhedral domains. In the case of constant coefficients all fine grid node stencils in the interior of a coarse macro element are equal. However, for non-polyhedral domains the situation changes. Then even for the Laplace operator, the non-linear element mapping leads to fine grid stencils that can vary from grid point to grid point. This observation motivates a new two-scale approach that exploits a piecewise polynomial approximation of the fine grid operator with respect to the coarse mesh size. The low-cost evaluation of these surrogate polynomials results in an efficient stencil assembly on-the-fly for non-polyhedral domains that can be significantly more efficient than matrix-free techniques that are based on an element-wise assembly. The performance analysis and additional hardware-aware code optimizations are based on the Execution-Cache-Memory model. Several aspects such as two-scale a priori error bounds and double discretization techniques are presented. Weak and strong scaling results illustrate the benefits of the new technique when used within large scale PDE solvers.

math.NA↗