Mapping behavioral specifications to model parameters in synthetic biology

With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal design specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified design constraints are robustly satisfied. In this work we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction. The method is general and can hence be incorporated in a pipeline for the rational forward design of arbitrary devices in synthetic biology

Large Area Synthesis of a Nanoporous Two-Dimensional Polymer at the Air/Water Interface

We present the synthesis of a two-dimensional polymer at the air/water interface and its nm-resolution imaging. Trigonal star, amphiphilic monomers bearing three anthraceno groups on a central triptycene core are confined at the air/water interface. Compression followed by photopolymerization on the interface provides the two-dimensional polymer. Analysis by scanning tunneling microscopy suggests that the polymer is periodic with ultrahigh pore density

A Two-Dimensional Polymer from the Anthracene Dimer and Triptycene Motifs

A two-dimensional polymer (2DP) based on the dimerization of anthraceno groups arranged in a triptycene motif is reported. A photoinduced polymerization is performed in the crystalline state and gives a lamellar 2DP via a crystal-to-crystal (but not single-crystal to single-crystal) transformation. Solvent-induced exfoliation provides monolayer sheets of the 2DP. The 2DP is considered to be a tiling, a mathematical approach that facilitates structural elucidation