Time-dependent material properties of aging biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations

AR Tejedor, R Collepardo-Guevara… - The Journal of …, 2023 - ACS Publications
Biomolecular condensates are important contributors to the internal organization of the cell
material. While initially described as liquid-like droplets, the term biomolecular condensates …

Progressive polymer deformation induced by polar activity and the influence of inertia

AR Tejedor, J Ramírez, M Ripoll - Physical Review Research, 2024 - APS
Polar activity is shown here to induce a progressive local deformation of linear polymer
chains, making a clear distinction between head and tail, while the overall chain …

Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates

A R. Tejedor, A Aguirre Gonzalez… - ACS Central …, 2024 - ACS Publications
Biomolecular condensates composed of highly charged biomolecules, such as DNA, RNA,
chromatin, and nucleic-acid binding proteins, are ubiquitous in the cell nucleus. The …

Delayed excitations induce polymer loo** and coherent motion

A Goychuk, D Kannan, M Kardar - Physical Review Letters, 2024 - APS
We consider inhomogeneous polymers driven by energy-consuming active processes which
encode temporal patterns of athermal kicks. We find that such temporal excitation programs …

Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates

A Feito, I Sanchez-Burgos, I Tejero… - PLOS Computational …, 2025 - journals.plos.org
Intracellular liquid–liquid phase separation (LLPS) of proteins and nucleic acids is a
fundamental mechanism by which cells compartmentalize their components and perform …

Spiral and helical formation of passive and active polymers with stiffness heterogeneity in a spherical cavity

R Yan, S Liu, N Zhao - Soft Matter, 2025 - pubs.rsc.org
Biomolecules usually adopt ubiquitous circular structures which are important for their
functionality. Based on three-dimensional Langevin dynamics simulations, we investigate …

Generalized Langevin equation for a tagged monomer in a Gaussian semiflexible polymer

X Durang, C Lim, JH Jeon - The Journal of Chemical Physics, 2024 - pubs.aip.org
In this study, we present a comprehensive analysis of the motion of a tagged monomer
within a Gaussian semiflexible polymer model. We carefully derived the generalized …

Collective behavior of active filaments with homogeneous and heterogeneous stiffness

C Zhao, R Yan, N Zhao - The Journal of Chemical Physics, 2024 - pubs.aip.org
The collective dynamics of active biopolymers is crucial for many processes in life, such as
cellular motility, intracellular transport, and division. Recent experiments revealed …

DROPP: Structure-Aware PCA for Ordered Data: A General Method and its Applications in Climate Research and Molecular Dynamics

A Beer, O Palotás, A Maldonado… - 2024 IEEE 40th …, 2024 - ieeexplore.ieee.org
Ordered data arises in many areas, eg, in molec-ular dynamics and other spatial-temporal
trajectories. While data points that are close in this order are related, common dimensionality …

Phase behaviour of hnRNPA1 low-complexity domain mutants described by different sequence-dependent models

A Feito, I Sanchez-Burgos, I Tejero, E Sanz, A Rey… - bioRxiv, 2024 - biorxiv.org
Intracellular liquid-liquid phase separation (LLPS) of proteins and nucleic acids represents a
fundamental mechanism by which cells compartmentalise their material and fulfill biological …