arXiv subjects

Christoph A. Weber

Publications and source records attributed to Christoph A. Weber.

At least 37 records · Page 2Linked to original sources

arXiv2022

Selection of prebiotic oligonucleotides by cyclic phase separation

The emergence of functional oligonucleotides on early Earth required a molecular selection mechanism to screen for specific sequences with prebiotic functions. Cyclic processes such as daily temperature oscillations were ubiquitous in this environment and could trigger oligonucleotide phase separation. Here, we propose sequence selection based on phase separation cycles realized through sedimentation in a system subjected to the feeding of oligonucleotides. Using theory and experiments with DNA, we show sequence-specific enrichment in the sedimented dense phase, in particular of short 22-mer DNA sequences. The underlying mechanism selects for complementarity, as it enriches sequences that tightly interact in the condensed phase through base-pairing. Our mechanism also enables initially weakly biased pools to enhance their sequence bias or to replace the most abundant sequences as the cycles progress. Our findings provide an example of a selection mechanism that may have eased screening for the first auto-catalytic self-replicating oligonucleotides.

physics.chem-ph↗

arXiv2022

Thermodynamics of Wetting, Prewetting and Surface Phase Transitions with Surface Binding

In living cells, protein-rich condensates can wet the cell membrane and surfaces of membrane-bound organelles. Interestingly, many phase-separating proteins also bind to membranes leading to a molecular layer of bound molecules. Here we investigate how binding to membranes affects wetting, prewetting and surface phase transitions. We derive a thermodynamic theory for a three-dimensional bulk in the presence of a two-dimensional, flat membrane. At phase coexistence, we find that membrane binding facilitates complete wetting and thus lowers the wetting angle. Moreover, below the saturation concentration, binding facilitates the formation of a thick layer at the membrane and thereby shifts the prewetting phase transition far below the saturation concentration. The distinction between bound and unbound molecules near the surface leads to a large variety of surface states {and complex surface phase diagrams with a rich topology of phase transitions. Our work suggests that surface phase transitions combined with molecular binding represent a versatile mechanism to control the formation of protein-rich domains at intra-cellular surfaces.

physics.bio-ph↗

arXiv2022

Energy and Matter Supply for Active Droplets

Chemically active droplets provide simple models for cell-like systems that can grow and divide. Such active droplet systems are driven away from thermodynamic equilibrium and turn over chemically, which corresponds to a simple metabolism. We consider two scenarios of non-equilibrium driving. First, droplets are driven via the system boundaries by external reservoirs that supply nutrient and remove waste (boundary-driven). Second, droplets are driven by a chemical energy provided by a fuel in the bulk (bulk-driven). For both scenarios, we discuss the conservation of energy and matter as well as the balance of entropy. We use conserved and non-conserved fields to analyze the non-equilibrium steady states of active droplets. Using an effective droplet model, we explore droplet stability and instabilities leading to droplet division. Our work reveals that droplet division occurs quite generally in active droplet systems. Our results suggest that life-like processes such as metabolism and division can emerge in simple non-equilibrium systems that combine the physics of phase separation and chemical reactions.

physics.bio-ph↗

arXiv2022

Heat Fluctuations in Chemically Active Systems

Chemically active systems such as living cells are maintained out of thermal equilibrium due to chemical events which generate heat and lead to active fluctuations. A key question is to understand on which time and length scales active fluctuations dominate thermal fluctuations. Here, we formulate a stochastic field theory with Poisson white noise to describe the heat fluctuations which are generated by stochastic chemical events and lead to active temperature fluctuations. We find that on large length and time scales, active fluctuations always dominate thermal fluctuations. However, at intermediate length and time scales, multiple crossovers exist which highlight the different characteristics of active and thermal fluctuations. Our work provides a framework to characterize fluctuations in active systems and reveals that local equilibrium holds at certain length and time scales.

cond-mat.stat-mech↗

arXiv2021

Chemical Kinetics and Mass Action in Coexisting Phases

The kinetics of chemical reactions are determined by the law of mass action, which has been successfully applied to homogeneous, dilute mixtures. At non-dilute conditions, interactions among the components can give rise to coexisting phases, which can significantly alter the kinetics of chemical reactions. Here, we derive a theory for chemical reactions in coexisting phases at phase equilibrium. We show that phase equilibrium couples the rates of chemical reactions of components with their diffusive exchanges between the phases. Strikingly, the chemical relaxation kinetics can be represented as a flow along the phase equilibrium line in the phase diagram. A key finding of our theory is that differences in reaction rates between coexisting phases stem solely from phase-dependent reaction rate coefficients. Our theory is key to interpret how concentration levels of reactive components in condensed phases control chemical reaction rates in synthetic and biological systems.

physics.bio-ph↗

arXiv2020

Flow-driven branching in a frangible porous medium

Channel formation and branching is widely seen in physical systems where movement of fluid through a porous structure causes the spatiotemporal evolution of the medium in response to the flow, in turn causing flow pathways to evolve. We provide a simple theoretical framework that embodies this feedback mechanism in a multi-phase model for flow through a fragile porous medium with a dynamic permeability. Numerical simulations of the model show the emergence of branched networks whose topology is determined by the geometry of external flow forcing. This allows us to delineate the conditions under which splitting and/or coalescing branched network formation is favored, with potential implications for both understanding and controlling branching in soft frangible media.

physics.flu-dyn↗

arXiv2019

Liquid phase separation controlled by pH

We present a minimal model to study liquid phase separation in a fixed pH ensemble. The model describes a mixture composed of macromolecules that exist in three different charge states and have a tendency to phase separate. We introduce the pH dependence of phase separation by means of a set of reactions describing the protonation and deprotonation of macromolecules, as well as the self-ionisation of water. We use conservation laws to identify the conjugate thermodynamic variables at chemical equilibrium. Using this thermodynamic conjugate variables we perform a Legendre transform which defines the corresponding free energy at fixed pH. We first study the possible phase diagram topologies at the isoelectric point of the macromolecules. We then show how the phase behavior depends on pH by moving away from the isoelectric point. We find that phase diagrams as a function of pH strongly depend on whether oppositely charged macromolecules or neutral macromolecules have a stronger tendency to phase separate. We predict the existence of reentrant behavior as a function of pH. In addition, our model also predicts that the region of phase separation is typically broader at the isoelectric point. This model could account for both, the protein separation observed in yeast cells for pH values close to the isoelectric point of many cytosolic proteins and also for the in vitro experiments of single proteins exhibiting phase separation as a function of pH.

physics.bio-ph↗

arXiv2019

How bacterial cells and colonies move on solid substrates

Many bacteria rely on active cell appendages, such as type IV pili, to move over substrates and interact with neighboring cells. Here, we study the motion of individual cells and bacterial colonies, mediated by the collective interactions of multiple pili. It was shown experimentally that the substrate motility of Neisseria gonorrhoeae cells can be described as a persistent random walk with a persistence length that exceeds the mean pili length. Moreover, the persistence length increases for a higher number of pili per cell. With the help of a simple, tractable stochastic model, we test whether a tug-of-war without directional memory can explain the persistent motion of single Neisseria gonorrhoeae cells. While the persistent motion of single cells indeed emerges naturally in the model, a tug-of-war alone is not capable of explaining the motility of microcolonies, which becomes weaker with increasing colony size. We suggest sliding friction between the microcolonies and the substrate as the missing ingredient. While such friction almost does not affect the general mechanism of single cell motility, it has a strong effect on colony motility. We validate the theoretical predictions by using a three-dimensional computational model that includes explicit details of the pili dynamics, force generation and geometry of cells.

physics.bio-ph↗

arXiv2018

Pili mediated intercellular forces shape heterogeneous bacterial microcolonies prior to multicellular differentiation

Microcolonies are aggregates of a few dozen to a few thousand cells exhibited by many bacteria. The formation of microcolonies is a crucial step towards the formation of more mature bacterial communities known as biofilms, but also marks a significant change in bacterial physiology. Within a microcolony, bacteria forgo a single cell lifestyle for a communal lifestyle hallmarked by high cell density and physical interactions between cells potentially altering their behaviour. It is thus crucial to understand how initially identical single cells start to behave differently while assembling in these tight communities. Here we show that cells in the microcolonies formed by the human pathogen Neisseria gonorrhoeae (Ng) present differential motility behaviors within an hour upon colony formation. Observation of merging microcolonies and tracking of single cells within microcolonies reveal a heterogeneous motility behavior: cells close to the surface of the microcolony exhibit a much higher motility compared to cells towards the center. Numerical simulations of a biophysical model for the microcolonies at the single cell level suggest that the emergence of differential behavior within a multicellular microcolony of otherwise identical cells is of mechanical origin. It could suggest a route toward further bacterial differentiation and ultimately mature biofilms.

physics.bio-ph↗

arXiv2018

Physics of Active Emulsions

Phase separating systems that are maintained away from thermodynamic equilibrium via molecular processes represent a class of active systems, which we call active emulsions. These systems are driven by external energy input for example provided by an external fuel reservoir. The external energy input gives rise to novel phenomena that are not present in passive systems. For instance, concentration gradients can spatially organise emulsions and cause novel droplet size distributions. Another example are active droplets that are subject to chemical reactions such that their nucleation and size can be controlled and they can spontaneously divide. In this review we discuss the physics of phase separation and emulsions and show how the concepts that governs such phenomena can be extended to capture the physics of active emulsions. This physics is relevant to the spatial organisation of the biochemistry in living cells, for the development novel applications in chemical engineering and models for the origin of life.

cond-mat.soft↗

arXiv2018

Spatial control of irreversible protein aggregation

Liquid cellular compartments spatially segregate from the cytoplasm and can regulate aberrant protein aggregation, a process linked to several medical conditions, including Alzheimer's and Parkinson's diseases. Yet the mechanisms by which these droplet-like compartments affect protein aggregation remain unknown. Here, we combine kinetic theory of protein aggregation and liquid-liquid phase separation to study the spatial control of irreversible protein aggregation in the presence of liquid compartments. We find that, even for weak interactions between the compartment constituents and the aggregating monomers, aggregates are strongly enriched inside the liquid compartment relative to the surrounding cytoplasm. We show that this enrichment is caused by a positive feedback mechanism of aggregate nucleation and growth which is mediated by a flux maintaining the phase equilibrium between the compartment and the cytoplasm. Our model predicts that the compartment volume that maximizes aggregate enrichment in the compartment is determined by the reaction orders of aggregate nucleation. The underlying mechanism of aggregate enrichment could be used to confine cytotoxic protein aggregates inside droplet-like compartments suggesting potential new avenues against aberrant protein aggregation. Our findings could also represent a common mechanism for the spatial control of irreversible chemical reactions in general.

physics.bio-ph↗

arXiv2017

Discontinuous switching of position of two coexisting phases

Here we investigate how the positions of a condensed phase can be controlled by using concentration gradients of a regulator that influences phase separation. We consider a mean field model of a ternary mixture where a concentration gradient of a regulator is imposed by an external potential. We show that novel first order phase transition exists at which the position of the condensed phase switches in a discontinuous manner. This mechanism could have implications for the spatial organization of biological cells and provides a control mechanism for droplets in microfluidic systems.

cond-mat.soft↗

arXiv2017

Droplet Ripening in Concentration Gradients

Living cells use phase separation and concentration gradients to organize chemical compartments in space. Here, we present a theoretical study of droplet dynamics in gradient systems. We derive the corresponding growth law of droplets and find that droplets exhibit a drift velocity and position dependent growth. As a consequence, the dissolution boundary moves through the system, thereby segregating droplets to one end. We show that for steep enough gradients, the ripening leads to a transient arrest of droplet growth that is induced by an narrowing of the droplet size distribution.

physics.bio-ph↗

arXiv2016

Growth and Division of Active Droplets: A Model for Protocells

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 centers. However, whether these droplets could divide and propagate is unclear. Here we examine the behavior 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.

physics.bio-ph↗

arXiv2016

Binary Mixtures of Particles with Different Diffusivities Demix

The influence of size differences, shape, mass and persistent motion on phase separation in binary mixtures has been intensively studied. Here we focus on the exclusive role of diffusivity differences in binary mixtures of equal-sized particles. We find an effective attraction between the less diffusive particles, which are essentially caged in the surrounding species with the higher diffusion constant. This effect leads to phase separation for systems above a critical size: A single close-packed cluster made up of the less diffusive species emerges. Experiments for testing of our predictions are outlined.

cond-mat.soft↗

arXiv2014

Numerical treatment of the Boltzmann equation for self-propelled particle systems

Kinetic theories constitute one of the most promising tools to decipher the characteristic spatio-temporal dynamics in systems of actively propelled particles. In this context, the Boltzmann equation plays a pivotal role, since it provides a natural translation between a particle-level description of the system's dynamics and the corresponding hydrodynamic fields. Yet, the intricate mathematical structure of the Boltzmann equation substantially limits the progress toward a full understanding of this equation by solely analytical means. Here, we propose a general framework to numerically solve the Boltzmann equation for self-propelled particle systems in two spatial dimensions and with arbitrary boundary conditions. We discuss potential applications of this numerical framework to active matter systems, and use the algorithm to give a detailed analysis to a model system of self-propelled particles with polar interactions. In accordance with previous studies, we find that spatially homogeneous isotropic and broken symmetry states populate two distinct regions in parameter space, which are separated by a narrow region of spatially inhomogeneous, density-segregated moving patterns. We find clear evidence that these three regions in parameter space are connected by first order phase transitions, and that the transition between the spatially homogeneous isotropic and polar ordered phases bears striking similarities to liquid-gas phase transitions in equilibrium systems. Within the density segregated parameter regime, we find a novel stable limit-cycle solution of the Boltzmann equation, which consists of parallel lanes of polar clusters moving in opposite directions, so as to render the overall symmetry of the system's ordered state nematic, despite purely polar interactions on the level of single particles.

cond-mat.soft↗

arXiv2014

Defect-Mediated Phase Transitions in Active Soft Matter

How do topological defects affect the degree of order in active matter? To answer this question we investigate an agent-based model of self-propelled particles, which accounts for polar alignment and short-ranged repulsive interactions. For strong alignment forces we find collectively moving polycrystalline states with fluctuating networks of grain boundaries. In the regime where repulsive forces dominate, the fluctuations generated by the active system give rise to quasi-long-range transitional order, but---unlike thermal system---without creating topological defects.

cond-mat.soft↗

arXiv2013

Understanding Collective Dynamics of Soft Active Colloids by Binary Scattering

Collective motion in actively propelled particle systems is triggered on the very local scale by nucleation of coherently moving units consisting of just a handful of particles. These units grow and merge over time, ending up in a long-range ordered, coherently-moving state. So far, there exists no bottom-up understanding of how the microscopic dynamics and interactions between the constituents are related to the system's ordering instability. In this paper, we study a class of models for propelled colloids allowing an explicit treatment of the microscopic details of the collision process. Specifically, the model equations are Newtonian equations of motion with separate force terms for particles' driving, dissipation and interaction forces. Focusing on dilute particle systems, we analyze the binary scattering behavior for these models, and determine-based on the microscopic dynamics-the corresponding collision-rule, i.e., the mapping of pre-collisional velocities and impact parameter on post-collisional velocities. By studying binary scattering we also find that the considered models for active colloids share the same principle for parallel alignment: the first incoming particle (with respect to the center of collision) is aligned to the second particle as a result of the encounter. This behavior is distinctively different to alignment in non-driven dissipative gases. Moreover, the obtained collision rule lends itself as a starting point to apply kinetic theory for propelled particle systems in order to determine the phase boundary to a long-range ordered, coherently-moving state. The microscopic origin of the collision rule offers the opportunity to quantitatively scrutinize the predictions of kinetic theory for propelled particle systems through direct comparison with multi-particle simulations.

cond-mat.soft↗