Mogens Jensen | University of Copenhagen (original) (raw)

Papers by Mogens Jensen

Physical Review Letters, 2001

The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrog... more The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to long-range order and to conformations displaying secondary structures. For compact polymers a transition is found between helix-rich states and low-entropy sheet-dominated states. The consequences of this transition for protein folding and, in particular, for the problem of prions are discussed.

Raul Donangelo, ∗ Mogens H. Jensen, † Ingve Simonsen, 4, ‡ and Kim Sneppen § Instituto de Fisica ... more Raul Donangelo, ∗ Mogens H. Jensen, † Ingve Simonsen, 4, ‡ and Kim Sneppen § Instituto de Fisica da UFRJ, Caixa Postal 68528, 21941-972 Rio de Janeiro, Brazil The Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen, Denmark Department of physics, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway NORDITA, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark (Dated: February 2, 2008)

Nature Communications

The control of proteins by a transcription factor with periodically varying concentration exhibit... more The control of proteins by a transcription factor with periodically varying concentration exhibits intriguing dynamical behaviour. Even though it is accepted that transcription factors vary their dynamics in response to different situations, insight into how this affects downstream genes is lacking. Here, we investigate how oscillations and chaotic dynamics in the transcription factor NF-κB can affect downstream protein production. We describe how it is possible to control the effective dynamics of the transcription factor by stimulating it with an oscillating ligand. We find that chaotic dynamics modulates gene expression and upregulates certain families of low-affinity genes, even in the presence of extrinsic and intrinsic noise. Furthermore, this leads to an increase in the production of protein complexes and the efficiency of their assembly. Finally, we show how chaotic dynamics creates a heterogeneous population of cell states, and describe how this can be beneficial in multi-toxic environments.

Physical Review E

We explore waves and entrainment in a model of coupled oscillators, inspired from the cellular os... more We explore waves and entrainment in a model of coupled oscillators, inspired from the cellular oscillators in the presomitic mesoderm (PSM) of mice. The internal clock in each cell is based on a negative feedback loop which couples to the clocks of neighboring cells through a Notch mechanism. We investigate how a morphogen gradient in the mesoderm, which affects the period of oscillating cells, gives rise to phase waves traveling from the posterior to the anterior part of the PSM. We show that the phase waves can be entrained by an external periodic variation in this morphogen and also observe that multiple oscillatory solutions can coexist in the cell population. Together, these provide a way to potentially control phase waves and thereby manipulate somite patterning in embryos, based on entrainment properties of coupled nonlinear oscillators.

Cell systems, Jan 27, 2017

Previous studies have suggested that changes in extracellular ion concentrations initiate the tra... more Previous studies have suggested that changes in extracellular ion concentrations initiate the transition from an activity state that characterizes sleep in cortical neurons to states that characterize wakefulness. However, because neuronal activity and extracellular ion concentrations are interdependent, isolating their unique roles during sleep-wake transitions is not possible in vivo. Here, we extend the Averaged-Neuron model and demonstrate that, although changes in extracellular ion concentrations occur concurrently, decreasing the conductance of calcium-dependent potassium channels initiates the transition from sleep to wakefulness. We find that sleep is governed by stable, self-sustained oscillations in neuronal firing patterns, whereas the quiet awake state and active awake state are both governed by irregular oscillations and chaotic dynamics; transitions between these separable awake states are prompted by ionic changes. Although waking is indicative of a shift from stable ...

Physical Review B

The mean-field theory of systems which are inhomogeneous in one direction, such as modulated stru... more The mean-field theory of systems which are inhomogeneous in one direction, such as modulated structures, can be formulated as an area-(volume-) preserving mapping. As a specific example we have investigated the anisotropic Ising model with nearestand nextnearest-neighbor interactions (ANNNI model) by studying the corresponding fourdimensional mapping. The mapping generates spin structures characterized by fixed points, one-dimensional orbits, two-dimensional surfaces, and chaotic trajectories. From the eigenvalues of the linearized mapping in the disordered phase the transition temperature and the critical wave vector can be calculated analytically. We have developed numerical methods to locate the various orbits and determine their physical stability away from the critical line. The orbits of the thermodynamically stable phases are embedded in regimes with positive Lyapunov exponents and they are unstable under numerical iteration. The one-dimensional trajectories describe incommensurate phases which may be stable between the commensurate phases associated with high-order limit cycles. At low temperatures and near the loworder commensurate phases there seem to be no incommensurate trajectories. As the commensurate phase of period 4 is approached, the incommensurate phase takes the form of a soliton lattice. The soliton energy, soliton-soliton interaction, and pinning energy are calculated, and the critical wave vector for a pinned soliton lattice is estimated. The transition from the modulated phase to the ferromagnetic phase is found to be of first order. Our findings are in agreement with the conclusions reached in a previous study of an approximate two-dimensional mapping representation of the model. I. INTRODUCTION Mean-field (MF) theory is an extremely powerful tool for determining the states of condensed-matter systems. Although the mean-field approximation does not apply very well to two-dimensional systems, and does not provide a sufficient description of the effect of fluctuations near phase transitions, it usually yields a correct picture of the structure of phase diagrams in three dimensions, and a useful first approximation for the location of transition lines. It is the purpose of this paper to present the mean-field theory of a three-dimensional (3D) spin system in a somewhat unorthodox way, namely, by means of a discrete nonlinear mapping. The mapping is an exact representation of the mean-field theory and must of course give results which agree with more traditional mean-field approaches. The mapping representation is particularly useful in the study of systems which are inhomogeneous along one direction, such as modulated structures with incommensurate, or even chaotic, stable or metastable phases which cannot be found by the usual techniques. The dimension of the mapping is determined by the range of the spin-spin interactions. Although we here consider a specific and rather simple modelthe anisotropic Ising model with nearestand next-nearest-neighbor interactions (the ANNNI model)the method is in no way restricted to a narrow class of models. Also, we believe that the features found here for the ANNNI model are quite general for physical systems with commensurate and incommensurate phases. The idea of presenting the mean-field theory as an area-preserving mapping was put forward in a recent article by one of the authors. ' The method was applied to a two-dimensional approximate mapping representation of the MF theory of the ANNNI model. We shall see that the conclusions reached there agree with some of our findings here, based on the exact four-dimensional representation. Recently, Pandit and Wortis applied the method to a nearest-neighbor Ising model of surface and interface structures. In their model the inhomogeneity was brought about by the introduction of the interface, and the resulting mapping was twodimensional.

PLoS biology, 2017

Early mammalian development is both highly regulative and self-organizing. It involves the interp... more Early mammalian development is both highly regulative and self-organizing. It involves the interplay of cell position, predetermined gene regulatory networks, and environmental interactions to generate the physical arrangement of the blastocyst with precise timing. However, this process occurs in the absence of maternal information and in the presence of transcriptional stochasticity. How does the preimplantation embryo ensure robust, reproducible development in this context? It utilizes a versatile toolbox that includes complex intracellular networks coupled to cell-cell communication, segregation by differential adhesion, and apoptosis. Here, we ask whether a minimal set of developmental rules based on this toolbox is sufficient for successful blastocyst development, and to what extent these rules can explain mutant and experimental phenotypes. We implemented experimentally reported mechanisms for polarity, cell-cell signaling, adhesion, and apoptosis as a set of developmental rul...

ACS synthetic biology, Jun 23, 2017

Protein synthesis in cells has been thoroughly investigated and characterized over the past 60 ye... more Protein synthesis in cells has been thoroughly investigated and characterized over the past 60 years. However, some fundamental issues remain unresolved, including the reasons for genetic code redundancy and codon bias. In this study, we changed the kinetics of the E. coli transcription and translation processes by mutating the promoter and ribosome binding domains and by using genetic code expansion. The results expose a counterintuitive phenomenon, whereby an increase in the initiation rates of transcription and translation lead to a decrease in protein expression. This effect can be rescued by introducing slow translating codons into the beginning of the gene, by shortening gene length or by reducing initiation rates. Based on the results, we developed a biophysical model, which suggests that the density of co-transcriptional translation plays a role in bacterial protein synthesis. These findings indicate how cells use codon bias to tune translation speed and protein synthesis.

Cell systems, Jan 21, 2016

Oscillations and noise drive many processes in biology, but how both affect the activity of the t... more Oscillations and noise drive many processes in biology, but how both affect the activity of the transcription factor nuclear factor κB (NF-κB) is not understood. Here, we observe that when NF-κB oscillations are entrained by periodic tumor necrosis factor (TNF) inputs in experiments, NF-κB exhibits jumps between frequency modes, a phenomenon we call "cellular mode-hopping." By comparing stochastic simulations of NF-κB oscillations to deterministic simulations conducted inside and outside the chaotic regime of parameter space, we show that noise facilitates mode-hopping in all regimes. However, when the deterministic system is driven by chaotic dynamics, hops between modes are erratic and short-lived, whereas in experiments, the system spends several periods in one entrainment mode before hopping and rarely visits more than two modes. The experimental behavior matches our simulations of noise-induced mode-hopping outside the chaotic regime. We suggest that mode-hopping is a...

PLOS ONE, 2016

The weight of links in a network is often related to the similarity of the nodes. Here, we introd... more 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.

Phys Rev E, 1994

Multidiffusion in critical dynamics of strings and membranes. Kim Sneppen and Mogens H. Jensen Ni... more Multidiffusion in critical dynamics of strings and membranes. Kim Sneppen and Mogens H. Jensen Niels Bohr Institute and NORDITA, Blegdamsvej 17, DK-2100 Copenhagen O/, Denmark. Received 29 March 1993 We study ...

Fluctuations and scaling in a model for boundary-layer-induced turbulence. Mogens H. Jensen Nordi... more Fluctuations and scaling in a model for boundary-layer-induced turbulence. Mogens H. Jensen Nordita, Blegdamsvej 17, DK-2100 Copenhagen, Denmark The James Franck Institute, The University of Chicago, Chicago, Illinois 60637. Received 28 November 1988 ...

Phys Rev a, 1984

Transition to chaos by interaction of resonances in dissipative systems. I. Circle maps. Mogens H... more Transition to chaos by interaction of resonances in dissipative systems. I. Circle maps. Mogens Hϕgh Jensen HC ϕrsted Institute, Universitetsparken 5, DK-2100 Copenhagen ϕ, Denmark. Per Bak Physics Department, Brookhaven National Laboratory, Upton, New York 11973. ...

Pnas, 2005

The NF-kB signalling system is involved in a variety of cellular processes including immune respo... more The NF-kB signalling system is involved in a variety of cellular processes including immune response, inflammation, and apoptosis. Recent experiments have found oscillations in the nuclear-cytoplasmic translocation of the NF-kB transcription factor. How the cell uses the oscillations to differentiate input conditions and send specific signals to downstream genes is an open problem. We shed light on this issue by examining the small core network driving the oscillations, which, we show, is designed to produce periodic spikes in nuclear NF-kB concentration. The oscillations can be used to regulate downstream genes in a variety of ways. In particular, we show that genes to whose operator sites NF-kB binds and dissociates fast can respond very sensitively to changes in the input signal, with effective Hill coefficients in excess of 20.

J Stat Mech Theory Exp, 2006

The waiting time needed for a stock market index to undergo a given percentage change in its valu... more The waiting time needed for a stock market index to undergo a given percentage change in its value is found to have an up-down asymmetry, which, surprisingly, is not observed for the individual stocks composing that index. To explain this, we introduce a market model consisting of randomly fluctuating stocks that occasionally synchronize their short term draw-downs. These synchronous events are parameterized by a ``fear factor'', that reflects the occurrence of dramatic external events which affect the financial market.