@article{21235, abstract = {The condensation of charged polymers is an important driver for the formation of biomolecular condensates. Recent experiments suggest that this mechanism also controls the clustering of eukaryotic chromosomes during the late stages of cell division. In this process, interchromosome attraction is driven by the condensation of cytoplasmic RNA and Ki-67, a charged intrinsically disordered protein that coats the chromosomes as a brush. Attraction between chromosomes has been shown to be specifically promoted by a localized charged patch on Ki-67, although the physical mechanism remains unclear. To elucidate this process, we combine coarse-grained simulations and analytical theory to study the RNA-mediated interaction between charged polymer brushes on the chromosome surfaces. We show that the charged patch on Ki-67 leads to interchromosome attraction via RNA bridging between the two brushes, whereby the RNA preferentially interacts with the charged patches, leading to stable, long-range forces. By contrast, if the brush is uniformly charged, bridging is basically absent due to complete adsorption of RNA onto the brush. Moreover, the RNA dynamics becomes caged in presence of the charged patch while remaining diffusive with uniform charge. Our work sheds light on the physical origin of chromosome clustering, while also suggesting a general mechanism for cells to tune work production by biomolecular condensates via different charge distributions.}, author = {Sorichetti, Valerio and Robin, Paul and Palaia, Ivan and Hernandez-Armendariz, Alberto and Cuylen-Haering, Sara and Šarić, Anđela}, issn = {2835-8279}, journal = {PRX Life}, number = {3}, publisher = {American Physical Society}, title = {{Charge distribution of the coating brush drives interchromosome attraction}}, doi = {10.1103/41fd-r847}, volume = {3}, year = {2025}, } @article{21256, abstract = {Collagen IV is one of the main components of the basement membrane, a layer of material that lines the majority of tissues in multicellular organisms. Collagen IV molecules assemble into networks, providing stiffness and elasticity to tissues and informing cell and organ shape, especially during development. In this work, we develop two coarse-grained models for collagen IV molecules that retain biochemical bond specificity and coarse grain at different length scales. Through molecular-dynamics simulations, we test the assembly and mechanics of the resulting networks and measure their response to strain in terms of stress, microscopic alignment, and bond dynamics. Within the basement membrane, collagen IV networks rearrange by molecule turnover, which affects tissue organization and can be linked with enzyme activity. Here we explore network rearrangements via bond remodeling, the process of breaking and remaking of bonds between network molecules. We then investigate the effects of active (enzymatic) bond remodeling. We find that this nonequilibrium remodeling allows a network to keep its integrity under strain, while relaxing fully over a variety of timescales, a dynamic response that is unavailable to networks undergoing equilibrium remodeling.}, author = {Meadowcroft, Billie and Sorichetti, Valerio and Ratajczyk, Eryk and Perez Verdugo, Fernanda L and Khalilgharibi, Nargess and Mao, Yanlan and Palaia, Ivan and Šarić, Anđela}, issn = {2835-8279}, journal = {PRX Life}, publisher = {American Physical Society}, title = {{Nonequilibrium remodeling of collagen IV networks in Silico}}, doi = {10.1103/gdd5-rnh7}, volume = {3}, year = {2025}, } @article{20477, abstract = {An electric double-layer capacitor (EDLC) stores energy by modulating the spatial distribution of ions in the electrolytic solution that it contains. We determine the mean-field timescales for planar EDLC relaxation to equilibrium after a potential difference is applied. We tackle first the fully symmetric case, where positive and negative ionic species have the same valence and diffusivity, and then the general, more complex, asymmetric case. Depending on the applied voltage and salt concentration, different regimes appear, revealing a remarkably rich phenomenology relevant for nanocapacitors.}, author = {Palaia, Ivan and Asta, Adelchi J. and Dutta, Megh and Warren, Patrick B. and Rotenberg, Benjamin and Trizac, Emmanuel}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {14}, publisher = {American Physical Society}, title = {{Charging dynamics of electric double-layer nanocapacitors in mean field}}, doi = {10.1103/72b9-c8cq}, volume = {135}, year = {2025}, } @article{20483, abstract = {A parallel plate capacitor containing an electrolytic solution is the simplest model of a supercapacitor or electric double-layer capacitor. Using both analytical and numerical techniques, we solve the Poisson-Nernst-Planck equations for such a system, describing the mean-field charging dynamics of the capacitor, when a constant potential difference is abruptly applied to its plates. Working at constant total number of ions, we focus on the physical processes involved in the relaxation and, whenever possible, give its functional shape and exact time constants. We first review and study the case of a symmetric binary electrolyte, where we assume the two ionic species to have the same charges and diffusivities. We then relax these assumptions and present results for a generic strong (i.e fully dissociated) binary electrolyte. At low electrolyte concentration, the relaxation is simple to understand, as the dynamics of positive and negative ions appear decoupled. At higher electrolyte concentration, we distinguish several regimes. In the linear regime (low voltages), relaxation is multiexponential, it starts by the buildup of the equilibrium charge profile and continues with neutral mass diffusion, and the relevant timescales feature both the average and the Nernst-Hartley diffusion coefficients. In the purely nonlinear regime (intermediate voltages), the initial relaxation is slowed down exponentially due to increased capacitance, while bulk effects become more and more evident. In the fully nonlinear regime (high voltages), the dynamics of charge and mass are completely entangled and, asymptotically, the relaxation is linear in time. We finally discuss nonideal behavior in real capacitors and provide conditions for which mean-field is expected to hold.}, author = {Palaia, Ivan and Asta, Adelchi J. and Dutta, Megh and Warren, Patrick B. and Rotenberg, Benjamin and Trizac, Emmanuel}, issn = {2470-0053}, journal = {Physical Review E}, number = {3}, publisher = {American Physical Society}, title = {{Poisson-Nernst-Planck charging dynamics of an electric double-layer capacitor: Symmetric and asymmetric binary electrolytes}}, doi = {10.1103/p4dg-snqf}, volume = {112}, year = {2025}, } @article{13971, abstract = {When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases.}, author = {Grober, Daniel and Palaia, Ivan and Ucar, Mehmet C and Hannezo, Edouard B and Šarić, Anđela and Palacci, Jérémie A}, issn = {1745-2481}, journal = {Nature Physics}, pages = {1680--1688}, publisher = {Springer Nature}, title = {{Unconventional colloidal aggregation in chiral bacterial baths}}, doi = {10.1038/s41567-023-02136-x}, volume = {19}, year = {2023}, } @article{11340, abstract = {Like-charge attraction, driven by ionic correlations, challenges our understanding of electrostatics both in soft and hard matter. For two charged planar surfaces confining counterions and water, we prove that, even at relatively low correlation strength, the relevant physics is the ground-state one, oblivious of fluctuations. Based on this, we derive a simple and accurate interaction pressure that fulfills known exact requirements and can be used as an effective potential. We test this equation against implicit-solvent Monte Carlo simulations and against explicit-solvent simulations of cement and several types of clays. We argue that water destructuring under nanometric confinement drastically reduces dielectric screening, enhancing ionic correlations. Our equation of state at reduced permittivity therefore explains the exotic attractive regime reported for these materials, even in the absence of multivalent counterions.}, author = {Palaia, Ivan and Goyal, Abhay and Del Gado, Emanuela and Šamaj, Ladislav and Trizac, Emmanuel}, issn = {1520-5207}, journal = {Journal of Physical Chemistry B}, number = {16}, pages = {3143--3149}, publisher = {American Chemical Society}, title = {{Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring}}, doi = {10.1021/acs.jpcb.2c00028}, volume = {126}, year = {2022}, } @article{11400, abstract = {By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.}, author = {Palaia, Ivan and Šarić, Anđela}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {19}, publisher = {AIP Publishing}, title = {{Controlling cluster size in 2D phase-separating binary mixtures with specific interactions}}, doi = {10.1063/5.0087769}, volume = {156}, year = {2022}, } @article{12108, abstract = {The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein–membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation.}, author = {Meadowcroft, Billie and Palaia, Ivan and Pfitzner, Anna Katharina and Roux, Aurélien and Baum, Buzz and Šarić, Anđela}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {26}, publisher = {American Physical Society}, title = {{Mechanochemical rules for shape-shifting filaments that remodel membranes}}, doi = {10.1103/PhysRevLett.129.268101}, volume = {129}, year = {2022}, }