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This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology,(More)
Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical(More)
It is well known that information is encoded in the frequency or amplitude of Ca2+ signal and then decoded by target protein. However, few models considered both the encoding and decoding procedures of Ca2+ signal. In this work, aminimal Li–Rinzel model is coupled with a phosphorylation–dephosphorylation cycle model, which is used to investigate information(More)
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics, and transport is one of the most challenging tasks in biological science. In the present work, persistent homology is, for the first time, introduced for extracting molecular topological fingerprints (MTFs) based on the persistence(More)
Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with(More)
Elliptic partial differential equations (PDEs) are widely used to model real-world problems. Due to the heterogeneous characteristics of many naturally occurring materials and man-made structures, devices, and equipments, one frequently needs to solve elliptic PDEs with discontinuous coefficients and singular sources. The development of high-order elliptic(More)
Geometric, topological and graph theory modeling and analysis of biomolecules are of essential importance in the conceptualization of molecular structure, function, dynamics, and transport. On the one hand, geometric modeling provides molecular surface and structural representation, and offers the basis for molecular visualization, which is crucial for the(More)
Elastic materials are ubiquitous in nature and indispensable components in man-made devices and equipments. When a device or equipment involves composite or multiple elastic materials, elasticity interface problems come into play. The solution of three dimensional (3D) elasticity interface problems is significantly more difficult than that of elliptic(More)
Elasticity theory is an important component of continuum mechanics and has had widely spread applications in science and engineering. Material interfaces are ubiquity in nature and man-made devices, and often give rise to discontinuous coefficients in the governing elasticity equations. In this work, the matched interface and boundary (MIB) method is(More)
The emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is(More)