Related papers: Accurate structure-based coarse-graining leads to …
A computational tool for coarse-graining nonlinear systems of ordinary differential equations in time is discussed. Three illustrative model examples are worked out that demonstrate the range of capability of the method. This includes the…
We introduce Coarse-Grained Nonlinear Dynamics, an efficient and universal parameterization of nonlinear system dynamics based on the Volterra series expansion. These models require a number of parameters only quasilinear in the system's…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
Grain boundaries dramatically affect the properties of polycrystalline materials because of differences in atomic configuration. To fully understand the relationship between grain boundaries and materials properties, systematic studies of…
Hybrid multiscale modelling has emerged as a useful framework for modelling complex biological phenomena. However, when accounting for stochasticity in the internal dynamics of agents, these models frequently become computationally…
We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
Coarse graining is an important ingredient in many multi-scale continuum-discrete solvers such as CFD--DEM (computational fluid dynamics--discrete element method) solvers for dense particle-laden flows. Although CFD--DEM solvers have become…
Coarse-grained (CG) models are simplified representations of soft matter systems that are commonly employed to overcome size and time limitations in computational studies. Many approaches have been developed to construct and parametrise…
We propose and illustrate an approach to coarse-graining the dynamics of evolving networks (networks whose connectivity changes dynamically). The approach is based on the equation-free framework: short bursts of detailed network evolution…
A first step towards implementing a notion of coarse graining in an intrinsically Lorentzian, discrete quantum- gravity approach, namely causal set quantum gravity is taken. It makes use of an abstract notion of scale, based on counting the…
We present a new multiphase-field theory for describing pattern formation in multi-domain and/or multi-component systems. The construction of the free energy functional and the dynamic equations is based on criteria that ensure mathematical…
We use confocal microscopy and time-resolved light scattering to investigate plasticity in a col- loidal polycrystal, following the evolution of the network of grain boundaries as the sample is submitted to thousands of shear deformation…
The macroscopic properties of materials that we observe and exploit in engineering application result from complex interactions between physics at multiple length and time scales: electronic, atomistic, defects, domains etc. Multiscale…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
Recent computer simulations reveal several intriguing features in the evolution of properties of amorphous solids subjected to repeated cyclic shear deformation. These include the divergence of the number of cycles to reach steady states as…
Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a…
Two very basic constructions involving experimental procedures are the formation of coarse-grained versions of experiments, and the formation of branching sequential experiments. The latter allow for the conditioning of states on the…
Fluctuating hydrodynamics provides a quantitative, large-scale description of many-body systems in terms of smooth variables, with microscopic details entering only through a small set of transport coefficients. Although this framework has…
We present an effective evolution equation for a coarse-grained distribution function of a long-range-interacting system preserving the symplectic structure of the non-collisional Boltzmann, or Vlasov, equation. We first derive a general…