RT info:eu-repo/semantics/masterThesis
T1 Towards Long-Timescale Molecular Dynamics of Cytoplasmic Subdomains: Modeling Crowding, Polydispersity, and Pairwise Interactions
A1 Vargas Chaverri, María Ximena
A2 Universidad de Valladolid. Facultad de Ciencias
K1 Diffusion coefficient
K1 MSD
K1 Cytoplasm
K1 Molecular Dynamics
K1 Polydispersity
AB The cell cytoplasm is a crowded environment that is host to a variety of macromolecules. The motionsof these molecules deviate from simple Brownian statistics, yet the physical origin of the heavy-tailed,non-Gaussian step-length distributions reported in the live-cell experiments remains unclear. This workpresents a fully automated, colloidal molecular dynamics framework in LAMMPS to assert whethersize polydispersity by itself can cause such heterogeneity. Proteins and complexes are representedas rigid, colloidal spheres (log-normal distributed radii from 2 to 40 nm) and are packed at 25-45%volume fractions and evolved for up to 0.5 ms with Langevin dynamics. A Python code is developedthat fully automates the process of creating a simulation setup, from generating overlap-free initialconfigurations, to calculating all N(N + 1)/2 cutoff distances (where N is the number of differentradii present in the simulation) for the colloid pair coefficients. Strong-scaling benchmark and efficientneighbor list parameters optimization resulted in reaching a performance of ≈ 420 µs of simulationtime per one day of real time.When the colloid potential Hamaker constant is set to 10−5eV the colloids behave as hard spheres:diffusion coefficients follow the inverse-radius Stokes-Einstein trend and retain Brownian motion statistics across all crowding levels. Raising A above 0.1 eV introduces short-range attraction that leavessmall particles almost unchanged but doubles the long-time diffusivity of the largest particles and,crucially, produces the exponential tails in the log-probability of the step-lengths - mirroring the experimental results. Thus, polydispersity and steric crowding alone insufficient. Weak inter-colloidalattractions are likely essential for the observed cytoplasmic heterogeneity
YR 2025
FD 2025
LK https://uvadoc.uva.es/handle/10324/77887
UL https://uvadoc.uva.es/handle/10324/77887
LA eng
NO Departamento de Química Física y Química Inorgánica
DS UVaDOC
RD 20-sep-2025