{"title":"Direct computations of viscoelastic moduli of biomolecular condensates.","authors":"Samuel R Cohen, Priya R Banerjee, Rohit V Pappu","doi":"10.1063/5.0223001","DOIUrl":null,"url":null,"abstract":"<p><p>Biomolecular condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model that leverages information regarding intra- and inter-chain contacts, which we extract from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations of phase separation. The key ingredient of the generalized Rouse model is a graph Laplacian that we compute from equilibrium MMC simulations. We compute two flavors of graph Laplacians, one based on a single-chain graph that accounts only for intra-chain contacts, and the other referred to as a collective graph that accounts for inter-chain interactions. Calculations based on the single-chain graph systematically overestimate the storage and loss moduli, whereas calculations based on the collective graph reproduce the measured moduli with greater fidelity. However, in the long time, low-frequency domain, a mixture of the two graphs proves to be most accurate. In line with the theory of Rouse and contrary to recent assertions, we find that a continuous distribution of relaxation times exists in condensates. The single crossover frequency between dominantly elastic vs dominantly viscous behaviors does not imply a single relaxation time. Instead, it is influenced by the totality of the relaxation modes. Hence, our analysis affirms that viscoelastic fluid-like condensates are best described as generalized Maxwell fluids. Finally, we show that the complex shear moduli can be used to solve an inverse problem to obtain the relaxation time spectra that underlie the dynamics within condensates. This is of practical importance given advancements in passive and active microrheology measurements of condensate viscoelasticity.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":null,"pages":null},"PeriodicalIF":3.1000,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11374380/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Physics","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1063/5.0223001","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0
Abstract
Biomolecular condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model that leverages information regarding intra- and inter-chain contacts, which we extract from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations of phase separation. The key ingredient of the generalized Rouse model is a graph Laplacian that we compute from equilibrium MMC simulations. We compute two flavors of graph Laplacians, one based on a single-chain graph that accounts only for intra-chain contacts, and the other referred to as a collective graph that accounts for inter-chain interactions. Calculations based on the single-chain graph systematically overestimate the storage and loss moduli, whereas calculations based on the collective graph reproduce the measured moduli with greater fidelity. However, in the long time, low-frequency domain, a mixture of the two graphs proves to be most accurate. In line with the theory of Rouse and contrary to recent assertions, we find that a continuous distribution of relaxation times exists in condensates. The single crossover frequency between dominantly elastic vs dominantly viscous behaviors does not imply a single relaxation time. Instead, it is influenced by the totality of the relaxation modes. Hence, our analysis affirms that viscoelastic fluid-like condensates are best described as generalized Maxwell fluids. Finally, we show that the complex shear moduli can be used to solve an inverse problem to obtain the relaxation time spectra that underlie the dynamics within condensates. This is of practical importance given advancements in passive and active microrheology measurements of condensate viscoelasticity.
期刊介绍:
The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance.
Topical coverage includes:
Theoretical Methods and Algorithms
Advanced Experimental Techniques
Atoms, Molecules, and Clusters
Liquids, Glasses, and Crystals
Surfaces, Interfaces, and Materials
Polymers and Soft Matter
Biological Molecules and Networks.