Searching for the Pareto frontier in multi-objective protein design.

The goal of protein engineering and design is to identify sequences that adopt three-dimensional structures of desired function. Often, this is treated as a single-objective optimization problem, identifying the sequence-structure solution with the lowest computed free energy of folding. However, many design problems are multi-state, multi-specificity, or otherwise require concurrent optimization of multiple objectives.

Genetic background and environmental conditions drive metabolic variation in wild type and transgenic soybean (Glycine max) seeds.

The metabolic profiles and composition of storage reserves of agricultural crop seeds are strongly regulated by heritable and environmental factors. Yet, very little is known about the genetic and environmental determinants of adaptive metabolic variation amongst wild type as well as transgenic seed populations derived from the same genetic background, grown under natural field conditions. The goal of the current study was to investigate the effects of natural environmental conditions on wild type and transgenic soybean seeds expressing a feedback-insensitive form of cystathionine γ-synthase, a methionine main regulatory enzyme.

Efficient Isothermal Titration Calorimetry Technique Identifies Direct Interaction of Small Molecule Inhibitors with the Target Protein.

Protein-protein interactions (PPI) play a critical role in regulating many cellular processes. Finding novel PPI inhibitors that interfere with specific binding of two proteins is considered a great challenge, mainly due to the complexity involved in characterizing multi-molecular systems and limited understanding of the physical principles governing PPIs. Here we show that the combination of virtual screening techniques, which are capable of filtering a large library of potential small molecule inhibitors, and a unique secondary screening by isothermal titration calorimetry, a label-free method capable of observing direct interactions, is an efficient tool for finding such an inhibitor.

Exploring the complexity of quantum control optimization trajectories.

The control of quantum system dynamics is generally performed by seeking a suitable applied field. The physical objective as a functional of the field forms the quantum control landscape, whose topology, under certain conditions, has been shown to contain no critical point suboptimal traps, thereby enabling effective searches for fields that give the global maximum of the objective. This paper addresses the structure of the landscape as a complement to topological critical point features.

Efficient retrieval of landscape Hessian: forced optimal covariance adaptive learning.

Knowledge of the Hessian matrix at the landscape optimum of a controlled physical observable offers valuable information about the system robustness to control noise. The Hessian can also assist in physical landscape characterization, which is of particular interest in quantum system control experiments. The recently developed landscape theoretical analysis motivated the compilation of an automated method to learn the Hessian matrix about the global optimum without derivative measurements from noisy data.

Control of nitromethane photoionization efficiency with shaped femtosecond pulses.

The applicability of adaptive femtosecond pulse shaping is studied for achieving selectivity in the photoionization of low-density polyatomic targets. In particular, optimal dynamic discrimination (ODD) techniques exploit intermediate molecular electronic resonances that allow a significant increase in the photoionization efficiency of nitromethane with shaped near-infrared femtosecond pulses. The intensity bias typical of high-photon number, nonresonant ionization is accounted for by reference to a strictly intensity-dependent process.

Adaptive niche radii and niche shapes approaches for niching with the CMA-ES.

While the motivation and usefulness of niching methods is beyond doubt, the relaxation of assumptions and limitations concerning the hypothetical search landscape is much needed if niching is to be valid in a broader range of applications. Upon the introduction of radii-based niching methods with derandomized evolution strategies (ES), the purpose of this study is to address the so-called niche radius problem. A new concept of an adaptive individual niche radius is applied to niching with the covariance matrix adaptation evolution strategy (CMA-ES).