arXiv subjects

Mogens H. Jensen

Publications and source records attributed to Mogens H. Jensen.

At least 19 recordsLinked to original sources

arXiv2026

Oscillating concentrations suppress condensate coarsening

Living cells utilize condensates to spatially concentrate molecules in response to dynamic signals. For instance, nuclear condensates respond to oscillations in transcription factor levels in the nucleoplasm, including those involved in repairing multiple DNA breaks. To understand how oscillating signals affect condensates, we analyze a theoretical model using numerical simulations and analytical theory. While passive dynamics would drive all molecules into a single condensate, we find that sufficiently fast oscillations stabilize multiple droplets, allowing control of their sizes. We thus reveal a new behavior of chemically active droplets, which could be exploited in synthetic applications.

physics.bio-ph↗

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↗

arXiv2020

Spatiotemporal model of cellular mechanotransduction via Rho and YAP

How cells sense and respond to mechanical stimuli remains an open question. Recent advances have identified the translocation of Yes-associated protein (YAP) between nucleus and cytoplasm as a central mechanism for sensing mechanical forces and regulating mechanotransduction. We formulate a spatiotemporal model of the mechanotransduction signalling pathway that includes coupling of YAP with the cell force-generation machinery through the Rho family of GTPases. Considering the active and inactive forms of a single Rho protein (GTP/GDP-bound) and of YAP (non-phosphorylated/phosphorylated), we study the cross-talk between cell polarization due to active Rho and YAP activation through its nuclear localization. For fixed mechanical stimuli, our model predicts stationary nuclear-to-cytoplasmic YAP ratios consistent with experimental data at varying adhesive cell area. We further predict damped and even sustained oscillations in the YAP nuclear-to-cytoplasmic ratio by accounting for recently reported positive and negative YAP-Rho feedback. Extending the framework to time-varying mechanical stimuli that simulate cyclic stretching and compression, we show that the YAP nuclear-to-cytoplasmic ratio's time dependence follows that of the cyclic mechanical stimulus. The model presents one of the first frameworks for understanding spatiotemporal YAP mechanotransduction, providing several predictions of possible YAP localization dynamics, and suggesting new directions for experimental and theoretical studies.

physics.bio-ph↗

arXiv2020

Bifractal nature of chromosome contact maps

Modern biological techniques such as Hi-C permit to measure probabilities that different chromosomal regions are close in space. These probabilities can be visualised as matrices called contact maps. In this paper, we introduce a multifractal analysis of chromosomal contact maps. Our analysis reveals that Hi-C maps are bifractal, i.e. complex geometrical objects characterized by two distinct fractal dimensions. To rationalize this observation, we introduce a model that describes chromosomes as a hierarchical set of nested domains and we solve it exactly. The predicted multifractal spectrum is in excellent quantitative agreement with experimental data. Moreover, we show that our theory yields to a more robust estimation of the scaling exponent of the contact probability than existing methods. By applying this method to experimental data, we detect subtle conformational changes among chromosomes during differentiation of human stem cells.

q-bio.BM↗

arXiv2018

Gender Bias in Nobel Prizes

Strikingly few Nobel laureates within medicine, natural and social sciences are women. Although it is obvious that there are fewer women researchers within these fields, does this gender ratio still fully account for the low number of female Nobel laureates? We examine whether women are awarded the Nobel Prizes less often than the gender ratio suggests. Based on historical data across four scientific fields and a Bayesian hierarchical model, we quantify any possible bias. The model reveals, with exceedingly large confidence, that indeed women are strongly under-represented among Nobel laureates across all disciplines examined.

stat.AP↗

arXiv2017

Spatiotemporal expressions reflecting topological classes of repressor networks

A family of repressor networks is proposed as a simple model of gene regulatory networks. We analytically show three topological classes of the repressor networks, each of which exhibits distinctly growing complexity of spatiotemporal expressions starting from nearly homogeneous states. Further, by focusing on locally interacting cases such as chain networks, including a generalized repressilator, or feedforward(back)-loop networks, spatiotemporal expressions in the long time regime and elusive relationships between such different networks are discussed in detail.

cond-mat.stat-mech↗

arXiv2016

Measure of Node Similarity in Multilayer Networks

The weight of links in a network is often related to the similarity of the nodes. Here, we introduce a simple tunable measure for analysing the similarity of nodes across different link weights. In particular, we use the measure to analyze homophily in a group of 659 freshman students at a large university. Our analysis is based on data obtained using smartphones equipped with custom data collection software, complemented by questionnaire-based data. The network of social contacts is represented as a weighted multilayer network constructed from different channels of telecommunication as well as data on face-to-face contacts. We find that even strongly connected individuals are not more similar with respect to basic personality traits than randomly chosen pairs of individuals. In contrast, several socio-demographics variables have a significant degree of similarity. We further observe that similarity might be present in one layer of the multilayer network and simultaneously be absent in the other layers. For a variable such as gender, our measure reveals a transition from similarity between nodes connected with links of relatively low weight to dis-similarity for the nodes connected by the strongest links. We finally analyze the overlap between layers in the network for different levels of acquaintanceships.

cs.SI↗

arXiv2014

Glucagon stop-go kinetics supports a monomer-trimer fibrillation model

We investigate in vitro fibrillation kinetics of the hormone peptide glucagon at various concentrations using confocal microscopy and determine the glucagon fibril persistence length $60 μ\textrm{m}$. At all concentrations we observe that periods of individual fibril growth are interrupted by periods of stasis. The growth probability is large at high and low concentrations and is reduced for intermediate glucagon concentrations. To explain this behavior we propose a simple model, where fibrils come in two forms, one built entirely from glucagon monomers and one entirely from glucagon trimers. The opposite building blocks act as fibril growth blockers, and this generic model reproduces experimental behavior well.

physics.bio-ph↗

arXiv2014

Statistics of co-occurring keywords on Twitter

Online social media such as the micro-blogging site Twitter has become a rich source of real-time data on online human behaviors. Here we analyze the occurrence and co-occurrence frequency of keywords in user posts on Twitter. From the occurrence rate of major international brand names, we provide examples on predictions of brand-user behaviors. From the co-occurrence rates, we further analyze the user-perceived relationships between international brand names and construct the corresponding relationship networks. In general the user activity on Twitter is highly intermittent and we show that the occurrence rate of brand names forms a highly correlated time signal.

physics.soc-ph↗

arXiv2013

Excitable human dynamics driven by extrinsic events in massive communities

Using empirical data from a social media site (Twitter) and on trading volumes of financial securities, we analyze the correlated human activity in massive social organizations. The activity, typically excited by real-world events and measured by the occurrence rate of international brand names and trading volumes, is characterized by intermittent fluctuations with bursts of high activity separated by quiescent periods. These fluctuations are broadly distributed with an inverse cubic tail and have long-range temporal correlations with a $1/f$ power spectrum. We describe the activity by a stochastic point process and derive the distribution of activity levels from the corresponding stochastic differential equation. The distribution and the corresponding power spectrum are fully consistent with the empirical observations.

physics.soc-ph↗

arXiv2013

Modular networks of word correlations on Twitter

Complex networks are important tools for analyzing the information flow in many aspects of nature and human society. Using data from the microblogging service Twitter, we study networks of correlations in the appearance of words from three different categories, international brands, nouns and US major cities. We create networks where the strength of links is determined by a similarity measure based on the rate of coappearance of words. In comparison with the null model, where words are assumed to be uncorrelated, the heavy-tailed distribution of pair correlations is shown to be a consequence of modules of words representing similar entities.

physics.soc-ph↗

arXiv2013

Entrainment of noise-induced and limit cycle oscillators under weak noise

Theoretical models that describe oscillations in biological systems are often either a limit cycle oscillator, where the deterministic nonlinear dynamics gives sustained periodic oscillations, or a noise-induced oscillator, where a fixed point is linearly stable with complex eigenvalues and addition of noise gives oscillations around the fixed point with fluctuating amplitude. We investigate how each class of model behaves under the external periodic forcing, taking the well-studied van der Pol equation as an example. We find that, when the forcing is additive, the noise-induced oscillator can show only one-to-one entrainment to the external frequency, in contrast to the limit cycle oscillator which is known to entrain to any ratio. When the external forcing is multiplicative, on the other hand, the noise-induced oscillator can show entrainment to a few ratios other than one-to-one, while the limit cycle oscillator shows entrain to any ratio. The noise blurs the entrainment in general, but clear entrainment regions for limit cycles can be identified as long as the noise is not too strong.

q-bio.QM↗

arXiv2012

Switching between oscillations and homeostasis in competing negative and positive feedback motifs

We analyze a class of network motifs in which a short, two-node positive feed- back motif is inserted in a three-node negative feedback loop. We demonstrate that such networks can undergo a bifurcation to a state where a stable fixed point and a stable limit cycle coexist. At the bifurcation point the period of the oscillations diverges. Further, intrinsic noise can make the system switch between oscillatory state and the stationary state spontaneously. We find that this switching also occurs in previous models of circadian clocks that use this combination of positive and negative feedback. Our results suggest that real- life circadian systems may need specific regulation to prevent or minimize such switching events.

q-bio.MN↗

arXiv2012

Population dynamics in compressible flows

Organisms often grow, migrate and compete in liquid environments, as well as on solid surfaces. However, relatively little is known about what happens when competing species are mixed and compressed by fluid turbulence. In these lectures we review our recent work on population dynamics and population genetics in compressible velocity fields of one and two dimensions. We discuss why compressible turbulence is relevant for population dynamics in the ocean and we consider cases both where the velocity field is turbulent and when it is static. Furthermore, we investigate populations in terms of a continuos density field and when the populations are treated via discrete particles. In the last case we focus on the competition and fixation of one species compared to another

q-bio.PE↗

arXiv2012

Global and Local: Synchronization and Emergence

When a dynamical system contains several different modes of oscillations it may behave in a variety of ways: If the modes oscillate at their own individual frequencies, it exhibits quasiperiodic behavior; when the modes lock to one another it becomes synchronized, or, as a third possibility, complex chaotic behavior may emerge. With two modes present, like an internal oscillation coupled to a periodic external signal, one obtains a highly structured phase diagram that exhibits these possibilities. In essence, the details are related to the difference between rational and irrational numbers. Natural system can display fragments of this phase diagram, thereby offering insights into their dynamical mechanisms.

nlin.CD↗

arXiv2011

Inducing phase-locking and chaos in cellular oscillators by modulating the driving stimuli

Inflammatory responses in eucaryotic cells are often associated with oscillations in the nuclear-cytoplasmic translocation of the transcription factor NF-kB. In most laboratory realizations, the oscillations are triggered by a cytokine stimulus, like the tumor necrosis factor alpha, applied as a step change to a steady level. Here we use a mathematical model to show that an oscillatory external stimulus can synchronize the NF-kB oscillations into states where the ratios of the internal to external frequency are close to rational numbers. We predict a specific response diagram of the TNF-driven NF-kB system which exhibits bands of synchronization known as "Arnold tongues". Our model also suggests that when the amplitude of the external stimulus exceeds a certain threshold there is the possibility of coexistence of multiple different synchronized states and eventually chaotic dynamics of the nuclear NF-kB concentration. This could be used as a way of externally controlling immune response, DNA repair and apoptotic pathways.

physics.bio-ph↗

arXiv2011

Population genetics in compressible flows

We study competition between two biological species advected by a compressible velocity field. Individuals are treated as discrete Lagrangian particles that reproduce or die in a density-dependent fashion. In the absence of a velocity field and fitness advantage, number fluctuations lead to a coarsening dynamics typical of the stochastic Fisher equation. We then study three examples of compressible advecting fields: a shell model of turbulence, a sinusoidal velocity field and a linear velocity sink. In all cases, advection leads to a striking drop in the fixation time, as well as a large reduction in the global carrying capacity. Despite localization on convergence zones, one species goes extinct much more rapidly than in well-mixed populations. For a weak harmonic potential, one finds a bimodal distribution of fixation times. The long-lived states in this case are demixed configurations with a single boundary, whose location depends on the fitness advantage.

q-bio.PE↗

arXiv2010

Dickkopf1 - a new player in modelling the Wnt pathway

The Wnt signalling pathway transducing the stabilization of beta-catenin is essential for metazoan embryo development and is misregulated in many diseases such as cancers. In recent years models have been proposed for the Wnt signalling pathway during the segmentation process in developing embryos. Many of these include negative feedback loops build around Axin2 regulation. In this article we propose a new negative feedback model for the Wnt pathway with Dickkopf1 (Dkk1) at its core. Dkk1 is a negative regulator of Wnt signalling. In chicken and mouse embryos there is a gradient of Wnt in the presomitic mesoderm (PSM) decreasing from the posterior to the anterior end. The formation of somites and the oscillations of Wnt target genes are controlled by this gradient. Here we incorporate a Wnt gradient and show that synchronization of neighbouring cells in the PSM is important in accordance with experimental observations.

q-bio.CB↗