The discrete fracture model (DFM) has been widely used in the simulation of fluid flow in fractured porous media. Traditional DFM uses the so-called hybrid-dimensional approach to treat fractures explicitly as low-dimensional entries (e.g. line entries in 2D media and face entries in 3D media) on the interfaces of matrix cells and then couple the matrix and fracture flow systems together based on the principle of superposition with the fracture thickness used as the dimensional homogeneity factor. Because of this methodology, DFM is considered to be limited on conforming meshes and thus may raise difficulties in generating high quality unstructured meshes due to the complexity of fracture's geometrical morphology. In this paper, we clarify that the DFM actually can be extended to non-conforming meshes without any essential changes. To show it clearly, we provide another perspective for DFM based on hybrid-dimensional representation of permeability tensor to describe fractures as one-dimensional line Dirac delta functions contained in permeability tensor. A finite element DFM scheme for single-phase flow on non-conforming meshes is then derived by applying Galerkin finite element method to it. Analytical analysis and numerical experiments show that our DFM automatically degenerates to the classical finite element DFM when the mesh is conforming with fractures. Moreover, the accuracy and efficiency of the model on non-conforming meshes are demonstrated by testing several benchmark problems. This model is also applicable to curved fracture with variable thickness.

Single-cell (sc)RNA-seq, together with RNA velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. Here, we introduce an analytical framework dynamo (https://github.com/aristoteleo/dynamo-release), which infers absolute RNA velocity, reconstructs continuous vector fields that predict cell fates, employs differential geometry to extract underlying regulations, and ultimately predicts optimal reprogramming paths and perturbation outcomes. We highlight dynamo’s power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically labeled human hematopoiesis scRNA-seq dataset. Furthermore, differential geometry analyses reveal mechanisms driving early megakaryocyte appearance and elucidate asymmetrical regulation within the PU.1-GATA1 circuit. Leveraging the least-action-path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. Finally, in silico perturbations predict cell-fate diversions induced by gene perturbations. Dynamo, thus, represents an important step in advancing quantitative and predictive theories of cell-state transitions.

It is known that many (upper) cluster algebras possess different kinds of good bases which contain the cluster monomials and are parametrized by the tropical points of cluster Poisson varieties. For a large class of upper cluster algebras (injective-reachable ones with full rank coefficients), we describe all of its bases with these properties. Moreover, we show the existence of the generic basis for them. In addition, we prove that Bridgeland's representation theoretic formula is effective for their theta functions (weak genteelness). Our results apply to (almost) all well-known cluster algebras arising from representation theory or higher Teichmüller theory, including quantum affine algebras, unipotent cells, double Bruhat cells, skein algebras over surfaces, where we change the coefficients if necessary so that the full rank assumption holds.

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