Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment. Whole-cell models have great potential to transform bioscience, bioengineering, and medicine. However, numerous challenges remain to achieve whole-cell models....

There is an almost unlimited number of metal-organic frameworks (MOFs). This creates exciting opportunities but also poses a problem: how do we quickly find the best MOFs for a given application? Molecular simulations have advanced sufficiently that many MOF properties - especially structural and gas adsorption properties - can be predicted computationally, and molecular modeling techniques are...

Morphogenesis and axonal targeting are key processes during development that depend on complex interactions at molecular, cellular and tissue level. Mathematical modeling is essential to bridge this multi-scale gap in order to understand how the emergence of large structures is controlled at molecular level by interactions between various signaling pathways. We summarize mathematical modeling a...

This thesis presents an ab initio study of biological molecules using first-principles molecular dynamics. Density functional theory and Car-Parrinello molecular dynamics are used in the computational modeling of the water molecules and the amyloidforming peptide GNNQQNY derived from the yeast prion protein Sup35. The Young's modulus of the fibril obtained from the ab initio method is larger th...

We previously described a tic-tac-toe playing molecular automaton, MAYA-II, constructed from a molecular array of deoxyribozyme-based logic gates, that uses oligonucleotides as inputs and outputs. We are now developing an ensemble modeling tool for high-throughput oligonucleotide input and logic gate designs. The modeling tool is based on exhaustive reconstruction of both intended and unintende...

The Extensible Computational Chemistry Environment (Ecce) is a suite of distributed applications that are integrated as a comprehensive problem solving environment for computational chemistry. Ecce provides scientists with an easily used graphical user interface to the tasks of setting up complex molecular modeling calculations, distributed use of high performance computers, and scientific visu...