10 research outputs found
Growth and division of active droplets provides a model for protocells
No full textNature Physics | Article Print Share/bookmark Growth and division of active droplets provides a model for protocells David Zwicker, Rabea Seyboldt, Christoph A. Weber, Anthony A. Hyman & Frank Jülicher Affiliations Contributions Corresponding author Nature Physics 13, 408–413 (2017) doi:10.1038/nphys3984 Received 29 April 2016 Accepted 10 November 2016 Published online 12 December 2016 Article tools PDF Citation Reprints Rights & permissions Article metrics Abstract Abstract• Introduction• Division of active droplets• Chemically active droplets as a model for protocells• Methods• References• Acknowledgements• Author information• Supplementary information It has been proposed that during the early steps in the origin of life, small droplets could have formed via the segregation of molecules from complex mixtures by phase separation. These droplets could have provided chemical reaction centres. However, whether these droplets could divide and propagate is unclear. Here we examine the behaviour of droplets in systems that are maintained away from thermodynamic equilibrium by an external supply of energy. In these systems, droplets grow by the addition of droplet material generated by chemical reactions. Surprisingly, we find that chemically driven droplet growth can lead to shape instabilities that trigger the division of droplets into two smaller daughters. Therefore, chemically active droplets can exhibit cycles of growth and division that resemble the proliferation of living cells. Dividing active droplets could serve as a model for prebiotic protocells, where chemical reactions in the droplet play the role of a prebiotic metabolism
The dynamics of chemically active droplets
No full textIn unserem täglichen Leben begegnen wir Tropfen oft in physikalischen Systems, beispielsweise als Öltropfen in Salatsoße. Diese Tropfen sind meist chemisch inaktiv. In biologischen Zellen bilden Proteine und RNA zusammen Tropfen. Zellen sind chemisch aktiv, so dass die Tropfenkomponenten neu gebildet, abgebaut und modifiziert werden können.
In dieser Doktorarbeit wird das dynamische Verhalten von chemisch aktiven Tropfen mit analytischen und numerischen Methoden untersucht. Um das dynamische Verhalten von solchen aktiven Tropfen zu untersuchen, benutzen wir ein Minimalmodell mit zwei Komponenten, die zwei Phasen bilden und durch chemische Reaktionen ineinander umgewandelt werden. Die chemischen Reaktionen werden durch das Brechen von Detailed Balance aus dem Gleichgewicht gehalten, so dass die Tropfen chemisch aktiv sind. Wir konzentrieren uns auf den Fall, in dem Tropfenmaterial im Tropfen in die äußere Komponente umgewandelt wird, und in der äußeren Phase erzeugt wird.
Wir finden ein vielfältiges dynamisches Phasendiagramm mit Regionen, in denen Tropfen schrumpfen und verschwinden, Regionen, in denen Tropfen eine stabile stationäre Größe besitzen, und Regionen, in denen eine Forminstabilität zu komplexer Tropfen-Dynamik führt. In der letzten Region deformieren sich Tropfen typischenweise prolat, verformen sich zu einer Hantel, und teilen sich in zwei Tochtertropfen, die wieder anwachsen. Dies kann zu Zyklen von Wachstum und Teilung von Tropfen führen, bis die Tropfen das gesamte Volumen füllen. Während spherische Tropfen durch die chemischen Reaktionen entgegen ihrer Oberflächenspannung deformiert werden, können Tropfen- Zylinder und Platten durch chemische Reaktionen stabilisiert werden.
Generell ist die Dynamik von Tropfen ein hydrodynamisches Problem, da die Oberflächenspannung von deformierten Tropfen hydrodynamische Flüsse erzeugt. Wir finden, dass chemische Reaktionen entgegen die Oberflächenspannung Arbeit verrichten können, so dass die Tropfenteilung auch unter Berücksichtigung hydrodynamischer Flüsse möglich ist.
Diese Doktorarbeit zeigt, dass die Kombination von chemische Reaktionen und Phasenseparation unter Nichtgleichgewichtsbedingungen zu neuem dynamischen Verhalten führen kann. Die Ergebnisse zeigen die Relevanz von chemischen Reaktionen zum Verständnis von Phasenseparation in biologischen Systemen auf, und können bei der Umsetzung der diskutierten Phänomene in experimentellen Systemen helfen. Die Tropfenteilung, die in dieser Doktorarbeit diskutiert wird, erinnert an die Teilung von biologischen Zellen. Davon motiviert schlagen wir vor, dass die Teilung von chemisch aktiven Tropfen ein Mechanismus für die Replikation von Tropfen-artigen Protozellen am Ursprung des Lebens gewesen sein könnte.:1. Introduction
2. Theory of multi-component phase-separating systems with chemical reactions
3. Minimal model for chemically active droplets in two formulations
4. Shape instability of spherical droplets with chemical reactions
5. Dynamical behavior of chemically active droplets
6. Shape instability of droplets with various geometries
7. Role of hydrodynamic flows in chemically driven droplet division
8. Chemically active droplets as a model for protocells at the origin of life
9. Conclusion
AppendicesIn our everyday environment, we regularly encounter liquid-liquid phase separation in physical systems such as oil droplets in vinegar. These droplets tend to be chemically inert. In biological cells, protein and RNA may together form liquid droplets. Cells are chemically active, so that droplet components can be created, degraded and modified.
In this thesis we study the influence of nonequilibrium chemical reactions on the shape dynamics of a droplet theoretically, using analytical and numerical methods. To discuss the dynamical behavior that results from combining phase separation and chemical reactions in sustained nonequilibrium conditions, we introduce a minimal model with only two components that separate into distinct phases. These two components are converted into each other by chemical reactions. The reactions are kept out of equilibrium by breaking of detailed balance, so that the droplet becomes active. We concentrate on the case where the reaction inside the droplet degrades droplet material into the outer component, and where the reaction outside creates new droplet material.
We find that chemically active droplets have a rich dynamic phase space, with regions where droplets shrink and vanish, regions where droplets have a stable stationary size, and regions where the flux-driven instability leads to complex dynamic behavior of droplets. In the latter, droplets typically elongate into a dumbbell shape and then split into two symmetrical daughter droplets. These droplets then grow until they have the same size as the initial droplet. This can lead to cycles of growth and division, so that an initial droplet divides until droplets fill the simulation volume. We analyze the stationary spherical state of the droplet, which is created by a balance of the fluxes driven by the chemical reactions. We find that stationary droplets may have a shape instability, which is driven by the continuous fluxes across the droplet interface and which may trigger the division. We also find that while reactions may destabilize spherical droplet shapes despite the surface tension of the droplet, they can have stabilizing effects on cylindrical droplets and droplet plates.
Generally, the shape dynamics of droplets is a hydrodynamic problem because surface tension in non-spherical droplets drives hydrodynamic flows that redistribute material and deform the droplet shape. We therefore study the influence of hydrodynamic flows on the shape changes of chemically active droplets. We find that chemical reactions in active droplets can perform work against surface tension and flows, so that the droplet division is possible even in the presence of hydrodynamic flows.
The present thesis highlights how the combination of basic physical behaviors – phase separation and chemical reactions – may create novel dynamic behavior under sustained nonequilibrium conditions. The results demonstrate the importance of considering chemical reactions for understanding the dynamics of droplets in biological systems, as well as proposes a minimalist model for experimentalists that are interested in creating a system of dividing droplets. Finally, the division of chemically active droplets is reminiscent of the division of biological cells, and it motivates us to propose that chemically active droplets could have provided a simple mechanism for the self-replication of droplet-like protocells at the origin of life.:1. Introduction
2. Theory of multi-component phase-separating systems with chemical reactions
3. Minimal model for chemically active droplets in two formulations
4. Shape instability of spherical droplets with chemical reactions
5. Dynamical behavior of chemically active droplets
6. Shape instability of droplets with various geometries
7. Role of hydrodynamic flows in chemically driven droplet division
8. Chemically active droplets as a model for protocells at the origin of life
9. Conclusion
Appendice
Shear moduli of two dimensional colloidal mixtures
No full textIn this thesis a Mode Coupling Theory (MCT) equation is derived that calculates the shearmodulus for multi-component colloidal mixtures in two-dimensional systems in linear approximation.With this equation, the plateau shear modulus G∞ is calculated for two two-dimensionalsystems at the glass transition: for a binary mixture of hard spheres and for a binary mixtureof dipolar particles.The results for the shear modulus are compared with a three-dimensional system of hardspheres using data by Götze and Voigtmann. The plateau shear modulus has about the sizeG∞/(nkT) ≈ 20 and a variation of ±10 for all systems. Here n denotes the total number density.We find that for all systems (the dipolar, the two-dimensional and the three-dimensionalhard sphere system) the critical surface (φc resp. Γc) and G∞ have maxima in the region oflarge differences in the size of the particles and large concentration of the smaller particles.We disagree with the common explanation of depletion attraction for this effect but showthat the maxima in the plateau shear modulus are produced by the big particles and theforce of the small ones on them.With exception of the region of these maxima, all systems show a lowering of G∞ throughmixing. This can be compared to the effect of plasticizing for polymers.The glass transition surface shows that for all systems the liquid is stabilized, but for thehard sphere systems there exists a threshold for the size ratio of the particles. Above thatthe glass is stabilized. This threshold is lower for the two-dimensional system.For the dipolar system there exist experimental values for the system developed by Königet al. A comparison shows a good agreement of the plateau shear modulus. The transitionparameter Γc is overestimated by MCT by a factor two, as has been found for other systems.A perturbational method, where the shear moduli of the particles are calculated separatelyas would be done for a monodisperse system and then added up, shows good qualitativeand mostly even quantitative agreements with the two-component calculation, although themaximum in the region of large differences in the size of the particles and large concentrationof the smaller particles is overestimated.Overall MCT seems to yield good results for the systems studied here. Only close tothe boundaries some small-scale crystallizing is visible in the particle plots of the dipolarsystem.publishe
Numerical simulation of the induction heating of hybrid semi-finished materials into the semi-solid state
No full text
Shear moduli of two dimensional binary glasses
No full textThe shear moduli of two-component glasses in two dimensions are studied within mode coupling theory. Varying the concentration, strong mixing effects are observed along the glass transition lines for two interaction potentials. Nonoverlapping disks with size ratios between 0.3 and 0.9, and point particles interacting with (magnetic) dipoles of strength ratio between 0.1 and 0.6 are considered. Equilibrium structure factors (partially obtained from Monte Carlo simulations) and glass form factors, and perturbative calculations show that a softening of the elastic shear constant of glass upon adding another component arises from a dilution effect of the majority component. For very disparate mixtures, an anomalous elastic strenghtening results from what we interpret as clustering of the smaller particles in the voids between the larger ones. This might point to a glass–glass transition. We include simulation data on hard disk mixtures which show that the theory underestimates the moduli by around 50%, but otherwise captures the qualitative trends (within the rather large simulational error bars).publishe
Latent space of a small genetic network: Geometry of dynamics and information
No full textInternational audienceThe high-dimensional character of most biological systems presents genuine challenges for modeling and prediction. Here we propose a neural network–based approach for dimensionality reduction and analysis of biological gene expression data, using, as a case study, a well-known genetic network in the early Drosophila embryo, the gap gene patterning system. We build an autoencoder compressing the dynamics of spatial gap gene expression into a two-dimensional (2D) latent map. The resulting 2D dynamics suggests an almost linear model, with a small bare set of essential interactions. Maternally defined spatial modes control gap genes positioning, without the classically assumed intricate set of repressive gap gene interactions. This, surprisingly, predicts minimal changes of neighboring gap domains when knocking out gap genes, consistent with previous observations. Latent space geometries in maternal mutants are also consistent with the existence of such spatial modes. Finally, we show how positional information is well defined and interpretable as a polar angle in latent space. Our work illustrates how optimization of small neural networks on medium-sized biological datasets is sufficiently informative to capture essential underlying mechanisms of network function
Divergence of the third harmonic stress response to oscillatory strain approaching the glass transition
No full textThe leading nonlinear stress response in a periodically strained concentrated colloidal dispersion is studied experimentally and by theory. A thermosensitive microgel dispersion serves as well-characterized glass-forming model, where the stress response at the first higher harmonic frequency (3 omega for strain at frequency omega) is investigated in the limit of small amplitude. The intrinsic nonlinearity at the third harmonic exhibits a scaling behavior which has a maximum in an intermediate frequency window and diverges when approaching the glass transition. It captures the (in-) stability of the transient elastic structure. Elastic stresses in-phase with the third power of the strain dominate the scaling. Our results qualitatively differ from previously derived scaling behavior in dielectric spectroscopy of supercooled molecular liquids. This might indicate a dependence of the nonlinear response on the symmetry of the external driving under time reversal
Design of an Information Security Model for Research Projects in the Environmental Area
No full textEste documento presenta la propuesta de diseño conceptual para un modelo de seguridad de la información aplicado a proyectos de investigación en el ámbito medioambiental. La iniciativa surge a partir de la necesidad de responder a las particularidades operativas y normativas de estos entornos, en los que se gestionan datos sensibles, distribuidos y sujetos a riesgos específicos. El modelo propuesto se estructura conforme al ciclo PHVA (Planificar, Hacer, Verificar, Actuar). Integra lineamientos de normas internacionales como ISO/IEC 27001:2022, ISO/IEC 27002:2022, ISO/IEC 27005:2022, MAGERIT v3 y NIST SP 800-53 Rev. 5. Esta base normativa permite establecer un enfoque sistemático para la identificación, análisis y tratamiento de riesgos, alineado con los objetivos de investigación y las condiciones técnicas del entorno. El diseño contempla políticas, prácticas y controles organizados por función (preventivos, detectivos, correctivos y disuasivos), clasificados según el nivel de riesgo de los activos y su nivel de madurez tecnológica. Sumado a esto, incorpora mecanismos de segmentación, trazabilidad y documentación que favorecen su aplicación en contextos institucionales o programas de investigación científica. El resultado es un modelo conceptual integral que, al alinear marcos normativos con las particularidades del sector, constituye una guía estratégica para fortalecer la protección de activos críticos y mejorar la resiliencia operativa en proyectos de investigación medioambiental.This document presents a conceptual design proposal for an information security model applied to environmental research projects. The initiative arises from the need to address the operational and regulatory particularities of these environments, where sensitive, distributed data are managed and subject to specific risks. The proposed model is structured according to the PDCA cycle (Plan, Do, Check, Act). It integrates guidelines from international standards such as ISO/IEC 27001:2022, ISO/IEC 27002:2022, ISO/IEC 27005:2022, MAGERIT v3, and NIST SP 800-53 Rev. 5. This normative foundation enables a systematic approach to the identification, analysis, and treatment of risks, aligned with research objectives and the technical conditions of the environment. The design includes policies, practices, and controls organized by function (preventive, detective, corrective, and deterrent), classified according to the risk level of the assets and their technological maturity. In addition, it incorporates segmentation, traceability, and documentation mechanisms that support its application in institutional contexts or scientific research programs. The result is a comprehensive conceptual model that, by aligning regulatory frameworks with sector-specific characteristics, serves as a strategic guide to strengthen the protection of critical assets and enhance operational resilience in environmental research projects
