publications

2026

1. Spatiotemporal Organization of Chemical Oscillators via Phase Separation

   Jonathan Bauermann, Giacomo Bartolucci, and Artemy Kolchinsky

   Phys. Rev. Lett., Apr 2026

   DOI
2. Theory for sequence selection via phase separation and oligomerization

   Ivar S. Haugerud, Giacomo Bartolucci, Dieter Braun, and 1 more author

   Proceedings of the National Academy of Sciences, Apr 2026

   Abs DOI

   An unresolved question is how specific oligonucleotide sequences such as DNA and RNA, which store genetic information and catalyze reactions, evolved from nucleotide building blocks without sophisticated biological machinery. Our research suggests that phase-separated condensates—naturally occurring mesoscopic clusters of oligonucleotides—may have created a unique environment that mediated selection pressures favoring certain sequences. Using nonequilibrium thermodynamics, we explore conditions under which phase separation and intersequence interactions generate such pressures. We find that nonequilibrium driving via sequence fragmentation determines whether more or less cooperatively interacting sequences are selected. Our findings open up promising avenues to study how nonequilibrium physics and phase separation can select specific, potentially functional sequences. Nonequilibrium selection pressures were proposed for forming oligonucleotides with rich functionalities encoded in their sequences, such as catalysis. Since phase separation was shown to direct various chemical processes, we ask whether condensed phases can provide mechanisms for sequence selection. To answer this question, we use nonequilibrium thermodynamics and describe the reversible oligomerization of different monomers to sequences at nondilute conditions prone to phase separation. We find that as sequences form, their interactions can trigger phase separation, which in turn enriches some sequences while depleting others. Our main result is that phase separation creates a selection pressure leading to specific sequence patterns when fragmentation maintains the system away from equilibrium. When fragmentation is slow, alternating sequences that interact more cooperatively with their surroundings are preferred. When fragmentation is fast, sequences with longer repeating motifs capable of more specific interactions are selected instead. Our finding that out-of-equilibrium condensed phases can provide a selection mechanism highlights their potential as versatile hubs for the evolution of functional sequences, a question relevant to the molecular origin of life and de novo life.

3. Metastability and ripening of multi-component liquid mixtures

   Giacomo Bartolucci and Fabrizio Olmeda

   arXiv, Apr 2026

2025

1. Phase Behavior of Cacio e Pepe Sauce

   Giacomo Bartolucci, Daniel Maria Busiello, Matteo Ciarchi, and 5 more authors

   Physics of Fluids, Apr 2025

   Abs DOI

   “Pasta alla Cacio e pepe” is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect texture and creaminess of the sauce can be challenging. In this study, we systematically explore the phase behavior of Cacio e pepe sauce, focusing on its stability at increasing temperatures for various proportions of cheese, water, and starch. We identify starch concentration as the key factor influencing sauce stability, with direct implications for practical cooking. Specifically, we delineate a regime where starch concentrations below 1% (relative to cheese mass) lead to the formation of system-wide clumps, a condition determining what we term the “Mozzarella Phase” and corresponding to an unpleasant and separated sauce. Additionally, we examine the impact of cheese concentration relative to water at a fixed starch level, observing a lower critical solution temperature that we theoretically rationalized by means of a minimal effective free-energy model. We further analyze the effect of a less traditional stabilizer, trisodium citrate, and observe a sharp transition from the Mozzarella Phase to a completely smooth and stable sauce, in contrast to starch-stabilized mixtures, where the transition is more gradual. Finally, we present a scientifically optimized recipe based on our findings, enabling a consistently flawless execution of this classic dish.

2. Critical transition between intensive and extensive active droplets

   Jonathan Bauermann, Giacomo Bartolucci, Job Boekhoven, and 2 more authors

   Physical Review X, Apr 2025
3. Theory of reversed ripening in active phase separating systems

   Jonathan Bauermann, Giacomo Bartolucci, Christoph A Weber, and 1 more author

   Physical Review Letters, Apr 2025
4. Theory of Non-Dilute Binding and Surface Phase Separation Applied to Membrane-Binding Proteins

   Xueping Zhao, Daxiao Sun, Giacomo Bartolucci, and 3 more authors

   eLife, Jun 2025

   Abs DOI

   Surface binding and surface phase separation of cytosolic scaffold proteins on lipid membranes are involved in many cellular processes, such as cell signaling, cell adhesion, and cortex regulation. However, the interplay between surface binding and surface phase separation is poorly understood. In this work, we study this interplay by deriving a general thermodynamic model and applying it to in vitro reconstitution experiments of membrane-binding proteins involved in tight junction initiation. Our theory extends the classical surface binding isotherm to account for non-dilute and heterogeneous conditions where components can phase separate. We use our theory to demonstrate how surface phase separation is governed by the interaction strength among membrane-bound scaffold proteins and their binding affinity to the membrane surface. Comparing the theory to reconstitution experiments, we show that tuning the oligomerization state of the adhesion receptors in the membrane controls surface phase transition and patterning of the scaffold protein ZO1. These findings suggest a fundamental role of the interplay between non-dilute surface binding and surface phase separation in forming the tight junction. More broadly, our work highlights non-dilute surface binding and surface phase separation as a common organizational principle for membrane-associated structures in living cells.

5. Localized control of protein phase separation via membrane binding

   Isabel LuValle-Burke, Giacomo Bartolucci, Daxiao Sun, and 3 more authors

   bioRxiv, Jun 2025

2024

1. The Interplay between Biomolecular Assembly and Phase Separation

   Giacomo Bartolucci, Ivar S. Haugerud, Thomas C. T. Michaels, and 1 more author

   eLife, May 2024

   Abs DOI

   Many biological functions and dysfunctions rely on two fundamental processes, molecular assembly and the formation of condensed phases such as biomolecular condensates. Condensed phases generally form via phase separation, while molecular assemblies are clusters of molecules of various sizes, shapes, and functionality. We developed a theory that relies on thermodynamic principles to understand the interplay between molecular assembly and phase separation. We propose two prototypical classes of protein interactions and characterize their different equilibrium states and relaxation dynamics. We obtain results consistent with recent in vitro experimental observations of reconstituted proteins, including anomalous size distribution of assemblies, the gelation of condensed phases, and the change in condensate volume during ageing. Our theory provides the framework to unravel the mechanisms underlying physiological assemblies essential for cellular function, and aberrant assemblies that are associated with several neurodegenerative disorders.

2023

1. Sequence Self-Selection by Cyclic Phase Separation

   Giacomo Bartolucci, Adriana Calaça Serrão, Philipp Schwintek, and 7 more authors

   Proceedings of the National Academy of Sciences, Oct 2023

   Abs DOI

   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 dense phase through base-pairing. Our mechanism also enables initially weakly biased pools to enhance their sequence bias or to replace the previously most abundant sequences as the cycles progress. Our findings provide an example of a selection mechanism that may have eased screening for auto-catalytic self-replicating oligonucleotides.

2. Formation of Liquid Shells in Active Droplet Systems

   Jonathan Bauermann, Giacomo Bartolucci, Job Boekhoven, and 2 more authors

   Physical Review Research, Dec 2023

   Abs DOI

   We study a chemically active binary mixture undergoing phase separation and show that under nonequilibrium conditions, stable liquid spherical shells can form via a spinodal instability in the droplet center. A single liquid shell tends to grow until it undergoes a shape instability beyond a critical size. In an active emulsion, many stable and stationary liquid shells can coexist. We discuss conditions under which liquid shells are stable and dominant as compared to regimes where droplets undergo shape instabilities and divide.

3. Liquid Spherical Shells Are a Non-Equilibrium Steady State of Active Droplets

   Alexander M. Bergmann, Jonathan Bauermann, Giacomo Bartolucci, and 6 more authors

   Nature Communications, Oct 2023

   Abs DOI

   Liquid-liquid phase separation yields spherical droplets that eventually coarsen to one large, stable droplet governed by the principle of minimal free energy. In chemically fueled phase separation, the formation of phase-separating molecules is coupled to a fuel-driven, non-equilibrium reaction cycle. It thus yields dissipative structures sustained by a continuous fuel conversion. Such dissipative structures are ubiquitous in biology but are poorly understood as they are governed by non-equilibrium thermodynamics. Here, we bridge the gap between passive, close-to-equilibrium, and active, dissipative structures with chemically fueled phase separation. We observe that spherical, active droplets can undergo a morphological transition into a liquid, spherical shell. We demonstrate that the mechanism is related to gradients of short-lived droplet material. We characterize how far out of equilibrium the spherical shell state is and the chemical power necessary to sustain it. Our work suggests alternative avenues for assembling complex stable morphologies, which might already be exploited to form membraneless organelles by cells.

2021

1. Controlling Composition of Coexisting Phases via Molecular Transitions

   Giacomo Bartolucci, Omar Adame-Arana, Xueping Zhao, and 1 more author

   Biophysical Journal, Nov 2021

   Abs DOI

   Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely unexplored how the behavior of phase-separating systems with molecular transitions differs between thermodynamic equilibrium and cases in which the detailed balance of the molecular transition rates is broken because of the presence of fuel. Here, we present a model of a phase-separating ternary mixture in which two components can convert into each other. At thermodynamic equilibrium, we find that molecular transitions can give rise to a lower dissolution temperature and thus reentrant phase behavior. Moreover, we find a discontinuous thermodynamic phase transition in the composition of the droplet phase if both converting molecules attract themselves with similar interaction strength. Breaking the detailed balance of the molecular transition leads to quasi-discontinuous changes in droplet composition by varying the fuel amount for a larger range of intermolecular interactions. Our findings showcase that phase separation with molecular transitions provides a versatile mechanism to control properties of intracellular and synthetic condensates via discontinuous switches in droplet composition.

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

   Xueping Zhao, Giacomo Bartolucci, Alf Honigmann, and 2 more authors

   New Journal of Physics, Dec 2021

   Abs DOI

   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.

2018

1. Transition Path Theory from Biased Simulations

   Giacomo Bartolucci, Simone Orioli, and Pietro Faccioli

   The Journal of Chemical Physics, Aug 2018

   DOI