Computational design of the sequence and structure of a protein-binding peptide

The de novo design of protein-binding peptides is challenging because it requires the identification of both a sequence and a backbone conformation favorable for binding. We used a computational strategy that iterates between structure and sequence optimization to redesign the C-terminal portion of the RGS14 GoLoco motif peptide so that it adopts a new conformation when bound to Gα(i1). An X-ray crystal structure of the redesigned complex closely matches the computational model, with a backbone root-mean-square deviation of 1.1 ?.     

Measurements of roughness noise

Experiments have been performed on the roughness noise produced by a two-dimensional turbulent wall jet boundary layer flowing over short fetches of sandpaper roughness. A range of rough surface sizes were studied from hydrodynamically smooth through fully rough. Velocity measurements were made to document the form of the wall jet boundary layer and the influence of the roughness upon it. Acoustic measurements showed background noise levels to be very low so that the sound produced by the rough surfaces could be clearly detected with signal to noise ratios as large as 20 dB. Even hydrodynamically smooth roughness was found to produce noise, conclusively indicating the presence of scattering as a source mechanism. Variations of the roughness noise spectra with flow speed and roughness size are found to be inconsistent with any simple parameter scaling. Boundary layer wall pressure fluctuation measurements made within the roughness fetches reveal a spectral form quite different than the roughness noise, and fluctuation levels some 50-70 dB higher. Despite these differences the wall pressure and roughness noise are found to be very simply related, at least at lower frequencies (<6 kHz). The roughness noise spectrum varies closely as the product of the wall pressure spectrum, the frequency squared, and the mean-square roughness height. This is the scaling predicted by scattering theory and implies a major simplification to the problem of roughness noise prediction for stochastic surfaces.     

Perfect imaging of hypersurfaces via transformation optics

Conventional optical imaging systems suffer from the presence of many imperfections, such as spherical aberrations, astigmatism, or coma. If the imaging system is corrected for spherical aberrations and fulfills the Abbe sine condition, perfect imaging is guaranteed between two parallel planes but only in a small neighborhood of the optical axis. It is therefore worth asking for optical systems that would allow for perfect imaging between arbitrary smooth surfaces without restrictions in shape or extension. In this Letter, we describe the application of transformation optics to design refractive index distributions that allow perfect, aberration-free imaging for various imaging configurations in R(n). A special case is the imaging between two extended parallel lines in R(2), which leads to the well-known hyperbolic secant index distribution that is used for the fabrication of gradient index lenses.     

Multiscale dynamics in communities of phase oscillators

We investigate the dynamics of systems of many coupled phase oscillators with heterogeneous frequencies. We suppose that the oscillators occur in M groups. Each oscillator is connected to other oscillators in its group with "attractive" coupling, such that the coupling promotes synchronization within the group. The coupling between oscillators in different groups is "repulsive," i.e., their oscillation phases repel. To address this problem, we reduce the governing equations to a lower-dimensional form via the ansatz of Ott and Antonsen, Chaos 18, 037113 (2008). We first consider the symmetric case where all group parameters are the same, and the attractive and repulsive coupling are also the same for each of the M groups. We find a manifold L of neutrally stable equilibria, and we show that all other equilibria are unstable. For M?≥?3, L has dimension M?-?2, and for M?=?2, it has dimension 1. To address the general asymmetric case, we then introduce small deviations from symmetry in the group and coupling parameters. Doing a slow/fast timescale analysis, we obtain slow time evolution equations for the motion of the M groups on the manifold L. We use these equations to study the dynamics of the groups and compare the results with numerical simulations.     

Topology and material orientation optimization based on evolution equations

Many modern high-performance materials have inherent anisotropic elastic properties and its local material orientation can be considered to be an additional design variable for the topology optimization [1–3]. We extend our previous model for topology optimization with variational controlled growth [4–6] for linear elastic anisotropic materials, for which the material orientation is introduced as an additional design variable. We solve the optimization problem purely with the principles of thermodynamics by minimizing the Gibbs energy. (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Tailored Solution-Based N-heterotriangulene Thin Films: Unravelling the Self-Assembly

The ability of a series of bridged triarylamines, so-called N-heterotriangulenes, to form multilayer-type 2D-extended films via a solution-based processing method was examined using complementary microscopic techniques. We found that the long-range order, crystallinity, and layer thickness decisively depend on the nature of the substituents attached to the polycyclic backbone. Owing to their flat core unit, compounds exhibiting a carbonyl unit at the bridge position provide a superior building block as compared to thioketone-bridged derivatives. In addition, nature and length of the peripheral substituents affect the orientation of the aromatic core unit within highly crystalline films. Hence, our results stress the significance of a suitable molecular framework and provide deeper understanding of structure formation in 2D-confined surroundings for such compounds.