Persona:
Torre Rodríguez, Jaime Arturo de la

Foto de perfil
Dirección de correo electrónico
ORCID
0000-0002-1657-0820
Fecha de nacimiento
Proyectos de investigación
Unidades organizativas
Puesto de trabajo
Apellidos
Torre Rodríguez
Nombre de pila
Jaime Arturo de la
Nombre

Filtros

2024 - 20252
Restablecer filtros

Ajustes

Fecha de inicio: 2010 × search.filters.applied.f.itemDepartamento: Física fundamental ×

Resultados de la búsqueda

Mostrando 1 - 2 de 2
  • Miniatura
    Publicación
    Unraveling internal friction in a coarse-grained protein model
    (AIP Publishing, 2025-03-19) Monago Díaz, Carlos Sebastián; Torre Rodríguez, Jaime Arturo de la; Delgado-Buscalioni, Rafael
    Understanding the dynamic behavior of complex biomolecules requires simplified models that not only make computations feasible but also reveal fundamental mechanisms. Coarse-graining (CG) achieves this by grouping atoms into beads, whose stochastic dynamics can be derived using the Mori–Zwanzig formalism, capturing both reversible and irreversible interactions. In liquid, the dissipative bead–bead interactions have so far been restricted to hydrodynamic couplings. However, friction does not only arise from the solvent but, notably, from the internal degrees of freedom missing in the CG beads. This leads to an additional “internal friction” whose relevance is studied in this contribution. By comparing with all-atom molecular dynamics (MD), we neatly show that in order to accurately reproduce the dynamics of a globular protein in water using a CG model, not only a precise determination of elastic couplings and the Stokesian self-friction of each bead is required. Critically, the inclusion of internal friction between beads is also necessary for a faithful representation of protein dynamics. We propose to optimize the parameters of the CG model through a self-averaging method that integrates the CG dynamics with an evolution equation for the CG parameters. This approach ensures that selected quantities, such as the radial distribution function and the time correlation of bead velocities, match the corresponding MD values.
  • Miniatura
    Publicación
    Stochastic Dissipative Euler’s equations for a free body
    (De Gruyter Brill, 2024-11-05) Torre Rodríguez, Jaime Arturo de la; Sánchez Rodríguez, Jesús; Español Garrigos, José
    Intrinsic thermal fluctuations within a real solid challenge the rigid body assumption that is central to Euler’s equations for the motion of a free body. Recently, we have introduced a dissipative and stochastic version of Euler’s equations in a thermodynamically consistent way (European Journal of Mechanics – A/Solids 103, 105,184 (2024)). This framework describes the evolution of both orientation and shape of a free body, incorporating internal thermal fluctuations and their concomitant dissipative mechanisms. In the present work, we demonstrate that, in the absence of angular momentum, the theory predicts that the principal axes unit vectors of a body undergo an anisotropic Brownian motion on the unit sphere, with the anisotropy arising from the body’s varying moments of inertia. The resulting equilibrium time correlation function of the principal eigenvectors decays exponentially. This theoretical prediction is confirmed in molecular dynamics simulations of small bodies. The comparison of theory and equilibrium MD simulations allow us to measure the orientational diffusion tensor. We then use this information in the Stochastic Dissipative Euler’s Equations, to describe a non-equilibrium situation of a body spinning around the unstable intermediate axis. The agreement between theory and simulations is excellent, offering a validation of the theoretical framework