Natural Frequencies of Diatom Shells: Alteration of Eigenfrequencies Using Structural Patterns Inspired by Diatoms

Diatoms have delicate and complex shells showing different lightweight design principles that have already been applied to technical products improving the mechanical properties. In addition, diatom inspired structures are expected to significantly affect the vibration characteristics, i.e., the eigenfrequencies. Directed eigenfrequency shifts are of great interest for many technical applications to prevent undesired high vibration amplitudes. Therefore, numerous complex diatom inspired dome structures primarily based on combs, ribs, and bulging patterns were constructed and their eigenfrequencies were numerically studied. Different structural patterns were identified to significantly affect eigenfrequencies. The results were compared to dome structures equipped with rib patterns in combination with a common structural optimization tool. The study indicates that a combination of (1) selecting diatom inspired structural patterns that strongly affect eigenfrequencies, and (2) adapting them to the boundary conditions of the technical problem is an efficient method to design diatom inspired lightweight solutions with high eigenfrequencies.

A cell-centered, agent-based framework that enables flexible environment granularities

BACKGROUND

Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell's perspective may offer new insights. Agent-based models lend themselves to model from an individual perspective, and existing agent-based models generally utilize a regular lattice-based environment. A framework which utilizes a cell's perspective in an off-lattice environment could improve the overall understanding of biological phenomena.

RESULTS

We present an agent-based, discrete event framework, with a demonstrative focus on biomimetic agents. The framework was first developed in 2-dimensions and then extended, with a subset of behaviors, to 3-dimensions. The framework is expected to facilitate studies of more complex biological phenomena through exploitation of a dynamic Delaunay and Voronoi off-lattice environment. We used the framework to model biological cells and to specifically demonstrate basic biological cell behaviors in two- and three-dimensional space. Potential use cases are highlighted, suggesting the utility of the framework in various scenarios.

CONCLUSIONS

The framework presented in this manuscript expands on existing cell- and agent-centered methods by offering a new perspective in an off-lattice environment. As the demand for biomimetic models grows, the demand for new methods, such as the presented Delaunay and Voronoi framework, is expected to increase.

Solvation studies of a zinc finger protein in hydrated ionic liquids

The solvation of the zinc finger protein with the PDB-ID “5ZNF” in hydrated ionic liquids was studied at varying water content. 1-Ethyl-3-methylimidazolium and trifluoromethanesulfonate were the cation and anion, respectively. The protein stability as well as the solvation structure, the shell dynamics and the shell resolved dielectric properties were investigated by means of molecular dynamics simulations. The lengths of the respective trajectories extended up to 200 nanoseconds in order to cover the complete solvent dynamics. Considering the above mentioned properties as a function of the water content they all exhibit a maximum or minimum at the very same mole fraction. While the exact value x(H(2)O) = 0.927 depends on the underlying force field, its origin may be traced back to the competition between the van der Waals and the electrostatic energy of the protein as well as to the transition from aqueous dielectric screening to ionic charge screening with decreasing water content. The parameter-free Voronoi decomposition of space served as a basis for the analysis of most results. In particular, solvation shells were naturally inferred from this concept. In addition to the molecular analysis a mesoscopic view is given in terms of dielectric properties. Thereby, the net dielectric constant is decomposed into contributions from the protein, the first and second solvation shells as well as the bulk. Cross-terms between these components are given, too.