Design and analysis of nucleic acid reaction pathways

Nucleic acids are a useful substrate for engineering at the molecular level. Designing the detailed energetics and kinetics of interactions between nucleic acid strands remains a challenge. Building on previous algorithms to characterize the ensemble of dilute solutions of nucleic acids, we present a design algorithm that allows optimization of structural features and binding energetics of a test tube of interacting nucleic acid strands. We extend this formulation to handle multiple thermodynamic states and combinatorial constraints to allow optimization of pathways of interacting nucleic acids. In both design strategies, low-cost estimates to thermodynamic properties are calculated using hierarchical ensemble decomposition and test tube ensemble focusing. These algorithms are tested on randomized test sets and on example pathways drawn from the molecular programming literature. To analyze the kinetic properties of designed sequences, we describe algorithms to identify dominant species and kinetic rates using coarse-graining at the scale of a small box containing several strands or a large box containing a dilute solution of strands.

Design, Fabrication, and Mechanical Property Analysis of 3D Nanoarchitected Materials

Recent developments in micro- and nanoscale 3D fabrication techniques have enabled the creation of materials with a controllable nanoarchitecture that can have structural features spanning 5 orders of magnitude from tens of nanometers to millimeters. These fabrication methods in conjunction with nanomaterial processing techniques permit a nearly unbounded design space through which new combinations of nanomaterials and architecture can be realized. In the course of this work, we designed, fabricated, and mechanically analyzed a wide range of nanoarchitected materials in the form of nanolattices made from polymer, composite, and hollow ceramic beams. Using a combination of two-photon lithography and atomic layer deposition, we fabricated samples with periodic and hierarchical architectures spanning densities over 4 orders of magnitude from ρ=0.3-300kg/m³ and with features as small as 5nm. Uniaxial compression and cyclic loading tests performed on different nanolattice topologies revealed a range of novel mechanical properties: the constituent nanoceramics used here have size-enhanced strengths that approach the theoretical limit of materials strength; hollow aluminum oxide (Al₂O₃) nanolattices exhibited ductile-like deformation and recovered nearly completely after compression to 50% strain when their wall thicknesses were reduced below 20nm due to the activation of shell buckling; hierarchical nanolattices exhibited enhanced recoverability and a near linear scaling of strength and stiffness with relative density, with E∝ρ^1.04 and σy∝ρ^1.17 for hollow Al₂O₃ samples; periodic rigid and non-rigid nanolattice topologies were tested and showed a nearly uniform scaling of strength and stiffness with relative density, marking a significant deviation from traditional theories on “bending” and “stretching” dominated cellular solids; and the mechanical behavior across all topologies was highly tunable and was observed to strongly correlate with the slenderness λ and the wall thickness-to-radius ratio t/a of the beams. These results demonstrate the potential of nanoarchitected materials to create new highly tunable mechanical metamaterials with previously unattainable properties.