Over recent decades, we have gained detailed knowledge of many processes involved in root growth and development. However, with this knowledge come increasing complexity and an increasing need for mechanistic modeling to understand how those individual processes interact. One major challenge is in relating genotypes to phenotypes, requiring us to move beyond the network and cellular scales, to ...

Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics, and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as th...

Theoretical models of the human heart valves are useful tools for understanding and characterizing the dynamics of healthy and diseased valves. Enabled by advances in numerical modeling and in a range of disciplines within experimental biomechanics, recent models of the heart valves have become increasingly comprehensive and accurate. In this paper, we first review the fundamentals of native he...

We present a multiscale model for numerical simulations of dynamics of crystalline solids. The method combines the continuum nonlinear elasto-dynamics model, which models the stress waves and physical loading conditions, and molecular dynamics model, which provides the nonlinear constitutive relation and resolves the atomic structures near local defects. The coupling of the two models is achiev...

One of the most significant challenges faced by hydrogeologic modelers is the disparity between the spatial and temporal scales at which fundamental flow, transport, and reaction processes can best be understood and quantified (e.g., microscopic to pore scales and seconds to days) and at which practical model predictions are needed (e.g., plume to aquifer scales and years to centuries). While t...

Multiscale modeling is a tool aimed at combining mathematical descriptions of different process scales into a single, properly tailored scale integration hierarchy allowing for reliable modeling and simulation. This concept has already been successfully applied in deriving accurate state variable distributions for processes that exhibit full spatiotemporal variation and thus do not allow for th...

The accurate parameterization of moist convection presents a major challenge for the accurate prediction of weather and climate through numerical models. Superparameterization is a promising recent alternative strategy for including the effects of moist convection through explicit turbulent fluxes calculated from a cloud-resolving model. Basic scales for cloud-resolving modeling are the microsc...

The objective of this work is to develop a multiscale modeling tool of copolymers with long chains. We propose an enhanced coarse-graining method of thermoplastic polyurethane (TPU) with three beads. The proposed coarse-graining provides an accurate molecular modeling tool to keep the molecular interaction together with computational efficiency. The coarse-grained model with three beads is furt...