arXiv subjects

Jaime Agudo-Canalejo

Publications and source records attributed to Jaime Agudo-Canalejo.

At least 37 records · Page 2Linked to original sources

arXiv2023

Self-organization of primitive metabolic cycles due to non-reciprocal interactions

We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next species in the cycle. Through a combination of catalytic activity and chemotactic mobility, the active particles develop effective non-reciprocal interactions with particles belonging to neighbouring species in the cycle. We find that such model metabolic cycles are able to self-organize through a macroscopic instability, with a strong dependence on the number of species they incorporate. The parity of that number has a key influence: cycles containing an even number of species are able to minimize repulsion between their component particles by aggregating all even-numbered species in one cluster, and all odd-numbered species in another. Such a grouping is not possible if the cycle contains an odd number of species, which can lead to oscillatory steady states in the case of chasing interactions.

cond-mat.soft↗

arXiv2023

Collective synchronization of dissipatively-coupled noise-activated processes

A system of two enzymes mechanically coupled to each other in a viscous medium was recently studied, and conditions for obtaining synchronization and an enhanced average rate of the thermally-activated catalytic reactions of the enzymes were identified. The transition to synchronization occurred as the result of a global bifurcation in the underlying dynamical system. Here, we extend and generalize this idea to an arbitrary number of noise-activated cyclic processes, or oscillators, that are all coupled to each other via a dissipative coupling. The $N$ coupled oscillators are described by $N$ phase coordinates driven in a tilted washboard potential. At low $N$ and strong coupling, we find synchronization as well as an enhancement in the average speed of the oscillators. In the large $N$ regime, we show that the collective dynamics can be described through a mean-field theory, which predicts a great enhancement in the average speed. In fact, beyond a critical value of the coupling strength, noise activation becomes irrelevant and the dynamics switch to an effectively deterministic "running" mode. Finally, we study the stochastic thermodynamics of the coupled oscillators, in particular their performance with regards to the thermodynamic uncertainty relation.

cond-mat.stat-mech↗

arXiv2022

Catalysis-Induced Phase Separation and Autoregulation of Enzymatic Activity

We present a thermodynamically consistent model describing the dynamics of a multi-component mixture where one enzyme component catalyzes a reaction between other components. We find that the catalytic activity alone can induce phase separation for sufficiently active systems and large enzymes, without any equilibrium interactions between components. In the limit of fast reaction rates, binodal lines can be calculated using a mapping to an effective free energy. We also explain how this catalysis-induced phase separation (CIPS) can act to autoregulate the enzymatic activity, which points at the biological relevance of this phenomenon.

physics.bio-ph↗

arXiv2022

Chemotactic self-caging in active emulsions

A common feature of biological self-organization is how active agents communicate with each other or their environment via chemical signaling. Such communications, mediated by self-generated chemical gradients, have consequences for both individual motility strategies and collective migration patterns. Here, in a purely physicochemical system, we use self-propelling droplets as a model for chemically active particles that modify their environment by leaving chemical footprints, which act as chemorepulsive signals to other droplets. We analyze this communication mechanism quantitatively both on the scale of individual agent-trail collisions as well as on the collective scale where droplets actively remodel their environment while adapting their dynamics to that evolving chemical landscape. We show in experiment and simulation how these interactions cause a transient dynamical arrest in active emulsions where swimmers are caged between each other's trails of secreted chemicals. Our findings provide new insight into the collective dynamics of chemically active particles and yield principles for predicting how negative autochemotaxis shapes their navigation strategy.

cond-mat.soft↗

arXiv2021

Synchronization and enhanced catalysis of mechanically coupled enzymes

We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is driven by stochastic steps along a biased chemical free energy landscape. We find conditions under which the enzymes can synchronize their catalytic steps, and discover that the coupling can lead to a significant enhancement in their overall catalytic rate. Both effects can be understood as arising from a global bifurcation in the underlying dynamical system at sufficiently strong coupling. Our findings suggest that, despite their molecular scale, enzymes can be cooperative and improve their performance in metabolic clusters.

cond-mat.stat-mech↗

arXiv2021

Comment on "Relative Diffusivities of Bound and Unbound Protein Can Control Chemotactic Directionality''

This is a comment on a recently published paper in Langmuir: Mandal, N. S.; Sen, A. Relative Diffusivities of Bound and Unbound Protein Can Control Chemotactic Directionality. Langmuir 2021, PMID: 34647749 [arXiv:2103.13469]. In this study, Mandal and Sen claim to propose a new kinetic model to analyze the directional movement of enzyme molecules in response to a gradient of their substrate, with the supposedly new prediction that net movement occurs up the substrate gradient when the diffusivity of the substrate-bound enzyme is lower than that of the unbound enzyme, and movement down the substrate gradient when the diffusivity of the substrate-bound enzyme is higher than that of the unbound enzyme. They develop this theoretical scheme to present an alternative to our previously published theoretical framework [Agudo-Canalejo, J.; Illien, P.; Golestanian, R. Phoresis and enhanced diffusion compete in enzyme chemotaxis. Nano Lett. 2018, 18, 2711-2717; arXiv:2104.02394]. We demonstrate that despite their claim, what they present is exactly the same theory as our work, and therefore, we conclude that their claim of novelty is unsubstantiated.

physics.bio-ph↗

arXiv2021

Molecular Diffusivity of Click Reaction Components: The Diffusion Enhancement Question

Micrometer-sized objects are widely known to exhibit chemically-driven motility in systems away from equilibrium. Experimental observation of reaction-induced motility or enhancement in diffusivity at the much shorter length scale of small molecules is however still a matter of debate. Here, we investigate the molecular diffusivity of reactants, catalyst and product of a model reaction, the copper-catalyzed azide-alkyne cycloaddition click reaction, and develop new NMR diffusion approaches that allow the probing of reaction-induced diffusion enhancement in nano-sized molecular systems with higher precision than the state of the art. Following two different approaches that enable the accounting of time-dependent concentration changes during NMR experiments, we closely monitored the diffusion coefficient of reaction components during the reaction. The reaction components showed distinct changes in the diffusivity: while the two reactants underwent a time-dependent decrease in their diffusivity, the diffusion coefficient of the product gradually increased and the catalyst showed only slight diffusion enhancement within the range expected for reaction-induced sample heating. The decrease in diffusion coefficient of the alkyne, one of the two reactants of click reaction, was not reproduced during its copper coordination when the second reactant, azide, was absent. Our results do not support the catalysis-induced diffusion enhancement of the components of click reaction and, instead, point to the role of a relatively large intermediate species within the reaction cycle with diffusivity lower than both the reactants and product molecule.

physics.chem-ph↗

arXiv2021

Non-equilibrium phase separation in mixtures of catalytically active particles: size dispersity and screening effects

Biomolecular condensates in cells are often rich in catalytically-active enzymes. This is particularly true in the case of the large enzymatic complexes known as metabolons, which contain different enzymes that participate in the same catalytic pathway. One possible explanation for this self-organization is the combination of the catalytic activity of the enzymes and a chemotactic response to gradients of their substrate, which leads to a substrate-mediated effective interaction between enzymes. These interactions constitute a purely non-equilibrium effect and show exotic features such as non-reciprocity. Here, we analytically study a model describing the phase separation of a mixture of such catalytically-active particles. We show that a Michaelis-Menten-like dependence of the particles' activities manifests itself as a screening of the interactions, and that a mixture of two differently-sized active species can exhibit phase separation with transient oscillations. We also derive a rich stability phase diagram for a mixture of two species with both concentration-dependent activity and size dispersity. This work highlights the variety of possible phase separation behaviours in mixtures of chemically-active particles, which provides an alternative pathway to the passive interactions more commonly associated with phase separation in cells. Our results highlight non-equilibrium organizing principles that can be important for biologically relevant liquid-liquid phase separation.

q-bio.SC↗

arXiv2021

Dynamics of Spontaneous Wrapping of Microparticles by Floppy Lipid Membranes

Lipid membranes form the barrier between the inside and outside of cells and many of their subcompartments. As such, they bind to a wide variety of nano- and micrometer sized objects and, in the presence of strong adhesive forces, strongly deform and envelop particles. This wrapping plays a key role in many healthy and disease-related processes. So far, little work has focused on the dynamics of the wrapping process. Here, using a model system of micron-sized colloidal particles and giant unilamellar lipid vesicles with tunable adhesive forces, we measure the velocity of the particle during its wrapping process as well as the forces exerted on it by the lipid membrane. Dissipation at the contact line appears to be the main factor determining the wrapping velocity and time to wrap an object.

cond-mat.soft↗

arXiv2021

Topology protects chiral edge currents in stochastic systems

Constructing systems that exhibit time-scales much longer than those of the underlying components, as well as emergent dynamical and collective behavior, is a key goal in fields such as synthetic biology and materials self-assembly. Inspiration often comes from living systems, in which robust global behavior prevails despite the stochasticity of the underlying processes. Here, we present two-dimensional stochastic networks that consist of minimal motifs representing out-of-equilibrium cycles at the molecular scale and support chiral edge currents in configuration space. These currents arise in the topological phase due to the bulk-boundary correspondence and dominate the system dynamics in the steady-state, further proving robust to defects or blockages. We demonstrate the topological properties of these networks and their uniquely non-Hermitian features such as exceptional points and vorticity, while characterizing the edge state localization. As these emergent edge currents are associated to macroscopic timescales and length scales, simply tuning a small number of parameters enables varied dynamical phenomena including a global clock, dynamical growth and shrinkage, and synchronization. Our construction provides a novel topological formalism for stochastic systems and fresh insights into non-Hermitian physics, paving the way for the prediction of robust dynamical states in new classical and quantum platforms.

cond-mat.stat-mech↗

arXiv2021

Enhanced diffusion and chemotaxis at the nanoscale

Enzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo enhanced diffusion in the presence of their corresponding substrate, when this substrate is uniformly distributed in solution. Moreover, if the concentration of the substrate is non-uniform, enzymes and other small molecules have been reported to show chemotaxis -- biased stochastic movement in the direction of the substrate gradient -- typically towards higher concentrations of this substrate, with a few exceptions. The underlying physical mechanisms responsible for enhanced diffusion and chemotaxis at the nanoscale, however, are still not well understood. Understanding these processes is important both for fundamental biological research, e.g. in the context of spatial organization of enzymes in metabolic pathways (metabolon formation), as well as for engineering applications, such as in the design of new vehicles for targeted drug delivery. In this Account, we will review the available experimental observations of both enhanced diffusion and chemotaxis, and we will discuss critically the different theories that have been proposed to explain the two. We first focus on enhanced diffusion, beginning with an overview of the experimental results. We then discuss the two main types of mechanisms that have been proposed, namely active mechanisms relying on the catalytic step of the enzymatic reaction, and equilibrium mechanisms which consider the reversible binding and unbinding of the substrate to the enzyme. We put particular emphasis on an equilibrium model recently introduced by us, which describes how the diffusion of dumbbell-like modular enzymes can be enhanced in the presence of substrate, thanks to a binding-induced reduction of the internal fluctuations of the enzyme. We then turn to chemotaxis, [...]

physics.bio-ph↗

arXiv2021

Phoresis and Enhanced Diffusion Compete in Enzyme Chemotaxis

Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for chemotaxis, valid for enzymes and other small molecules. Our theory includes both non-specific interactions between enzyme and substrate, as well as complex formation through specific binding between the enzyme and the substrate. We find that two distinct mechanisms contribute to enzyme chemotaxis: a diffusiophoretic mechanism due to the non-specific interactions, and a new type of mechanism due to binding-induced changes in the diffusion coefficient of the enzyme. The latter chemotactic mechanism points towards lower substrate concentration if the substrate enhances enzyme diffusion, and towards higher substrate concentration if the substrate inhibits enzyme diffusion. For a typical enzyme, attractive phoresis and binding-induced enhanced diffusion will compete against each other. We find that phoresis dominates above a critical substrate concentration, whereas binding-induced enhanced diffusion dominates for low substrate concentration. Our results resolve an apparent contradiction regarding the direction of urease chemotaxis observed in experiments, and in general clarify the relation between enhanced diffusion and chemotaxis of enzymes. Finally, we show that the competition between the two distinct chemotactic mechanisms may be used to engineer nanomachines that move towards or away from regions with a specific substrate concentration.

physics.bio-ph↗

arXiv2020

Wrapping of Microparticles by Floppy Lipid Vesicles

Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the particles, an essential step in crossing the membrane for a variety of health and disease-related processes. A large body of theoretical and numerical work has focused on identifying the physical properties that underly wrapping. Using a model system of micron-sized colloidal particles and giant unilamellar lipid vesicles with tunable adhesive forces, we measure a wrapping phase diagram and make quantitative comparisons to theoretical models. Our data is consistent with a model of membrane-particle interactions accounting for the adhesive energy per unit area, membrane bending rigidity, particle size, and vesicle radius.

cond-mat.soft↗

arXiv2020

Scalar Active Mixtures: The Non-Reciprocal Cahn-Hilliard Model

Pair interactions between active particles need not follow Newton's third law. In this work we propose a continuum model of pattern formation due to non-reciprocal interaction between multiple species of scalar active matter. The classical Cahn-Hilliard model is minimally modified by supplementing the equilibrium Ginzburg-Landau dynamics with particle number conserving currents which cannot be derived from a free energy, reflecting the microscopic departure from action-reaction symmetry. The strength of the asymmetry in the interaction determines whether the steady state exhibits a macroscopic phase separation or a traveling density wave displaying global polar order. The latter structure, which is equivalent to an active self-propelled smectic phase, coarsens via annihilation of defects, whereas the former structure undergoes Ostwald ripening. The emergence of traveling density waves, which is a clear signature of broken time-reversal symmetry in this active system, is a generic feature of any multi-component mixture with microscopic non-reciprocal interactions.

cond-mat.stat-mech↗

arXiv2020

Cooperatively enhanced reactivity and 'stabilitaxis' of dissociating oligomeric proteins

Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein complexes assembled from a few proteins. By studying the generic spatial transport properties of such proteins, we investigate here whether their ability to reversibly associate and dissociate may confer them a functional advantage with respect to non-dissociating proteins. In uniform environments with position-independent association-dissociation, we find that enhanced diffusion in the monomeric state coupled to reassociation into the functional oligomeric form leads to enhanced reactivity with distant targets. In non-uniform environments with position-dependent association-dissociation, caused e.g. by spatial gradients of an inhibiting chemical, we find that dissociating proteins generically tend to accumulate in regions where they are most stable, a process that we term 'stabilitaxis'.

physics.chem-ph↗

arXiv2019

Diffusion and steady state distributions of flexible chemotactic enzymes

Many experiments in recent years have reported that, when exposed to their corresponding substrate, catalytic enzymes undergo enhanced diffusion as well as chemotaxis (biased motion in the direction of a substrate gradient). Among other possible mechanisms, in a number of recent works we have explored several passive mechanisms for enhanced diffusion and chemotaxis, in the sense that they require only binding and unbinding of the enzyme to the substrate rather than the catalytic reaction itself. These mechanisms rely on conformational changes of the enzyme due to binding, as well as on phoresis due to non-contact interactions between enzyme and substrate. Here, after reviewing and generalizing our previous findings, we extend them in two different ways. In the case of enhanced diffusion, we show that an exact result for the long-time diffusion coefficient of the enzyme can be obtained using generalized Taylor dispersion theory, which results in much simpler and transparent analytical expressions for the diffusion enhancement. In the case of chemotaxis, we show that the competition between phoresis and binding-induced changes in diffusion results in non-trivial steady state distributions for the enzyme, which can either accumulate in or be depleted from regions with a specific substrate concentration.

cond-mat.soft↗

arXiv2019

Active phase separation in mixtures of chemically interacting particles

We theoretically study mixtures of chemically-interacting particles, which produce or consume a chemical to which they are attracted or repelled, in the most general case of many coexisting species. We find a new class of active phase separation phenomena in which the nonequilibrium chemical interactions between particles, which break action-reaction symmetry, can lead to separation into phases with distinct density and stoichiometry. Due to the generic nature of our minimal model, our results shed light on the underlying fundamental principles behind nonequilibrium self-organization of cells and bacteria, catalytic enzymes, or phoretic colloids.

cond-mat.soft↗

arXiv2018

Chemical and hydrodynamic alignment of an enzyme

Motivated by the implications of the complex and dynamic modular geometry of an enzyme on its motion, we investigate the effect of combining long-range internal and external hydrodynamic interactions due to thermal fluctuations with short-range surface interactions. An asymmetric dumbbell consisting of two unequal subunits, in a nonuniform suspension of a solute with which it interacts via hydrodynamic interactions as well as non-contact surface interactions, is shown to have two alignment mechanisms due to the two types of interactions. In addition to alignment, the chemical gradient results in a drift velocity that is modified by hydrodynamic interactions between the constituents of the enzyme.

cond-mat.soft↗