Structural and functional profile of phytases across the domains of life.

Phytase enzymes are a crucial component of the natural phosphorus cycle, as they help make phosphate bioavailable by releasing it from phytate, the primary reservoir of organic phosphorus in grain and soil. Phytases also comprise a significant segment of the agricultural enzyme market, used primarily as an animal feed additive. At least four structurally and mechanistically distinct classes of phytases have evolved in bacteria and eukaryotes, and the natural diversity of each class is explored here using advances in protein structure prediction and functional annotation.

Automated fitting of transition state force fields for biomolecular simulations.

The generation of surrogate potential energy functions (PEF) that are orders of magnitude faster to compute but as accurate as the underlying training data from high-level electronic structure methods is one of the most promising applications of fitting procedures in chemistry. In previous work, we have shown that transition state force fields (TSFFs), fitted to the functional form of MM3* force fields using the quantum guided molecular mechanics (Q2MM) method, provide an accurate description of transition states that can be used for stereoselectivity predictions of small molecule reactions. Here, we demonstrate the applicability of the method for fit TSFFs to the well-established Amber force field, which could be used for molecular dynamics studies of enzyme reaction.

A Phosphine-Mediated Dearomative Skeletal Rearrangement of Dianiline Squaraine Dyes.

A phosphorus(III)-mediated dearomatization of -substituted dianiline squaraine dyes results in an unusual skeletal rearrangement to provide exotic, highly conjugated benzofuranone and oxindole scaffolds bearing a C3 side chain comprised of a linear conflagration of an enol, a phosphorus ylide, and 2,4-disubstituted aniline. Employing experimental and computational analysis, a mechanistic evaluation revealed a striking dependence on the acidity of the aniline substituent. Notably, the rearrangement adducts underwent rapid and complete reversion to the parent squaraine in the presence of a Brønsted acid.

Recent developments in the PySCF program package.

PySCF is a Python-based general-purpose electronic structure platform that supports first-principles simulations of molecules and solids as well as accelerates the development of new methodology and complex computational workflows. This paper explains the design and philosophy behind PySCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PySCF as a development environment.

Compressing physics with an autoencoder: Creating an atomic species representation to improve machine learning models in the chemical sciences.

We define a vector quantity which corresponds to atomic species identity by compressing a set of physical properties with an autoencoder. This vector, referred to here as the elemental modes, provides many advantages in downstream machine learning tasks. Using the elemental modes directly as the feature vector, we trained a neural network to predict formation energies of elpasolites with improved accuracy over previous works on the same task.

Evaluation of the effect of the accordion suturing technique on wound lengths in breast cancer surgery: a randomised clinical trial.

Background: Cosmetic outcomes and scar lengths remain important considerations in breast cancer surgery. Suturing techniques should decrease scar tissue formation and provide good cosmetic results. The use of an accordion suturing technique may result in decreased surgical wound lengths and better cosmetic outcomes.

Accelerating Realtime TDDFT with Block-Orthogonalized Manby-Miller Embedding Theory.

Realtime time-dependent density-functional theory (RT-TDDFT) is one of the most practical techniques available to simulate electronic dynamics of molecules and materials. Promising applications of RT-TDDFT to study nonlinear spectra and energy transport demand simulations of large solvated systems over long time scales, which are computationally quite costly. In this paper, we apply an embedding technique developed for ground-state SCF methods by Manby and Miller to accelerate realtime TDDFT.

Optimal feature selection applied to multispectral fluorescence imaging.

Recent rapid developments in multi-modal optical imaging have created a significant clinical demand for its in vivo--in situ application. This offers the potential for real-time tissue characterization, functional assessment, and intra-operative guidance. One of the key requirements for in vivo consideration is to minimise the acquisition window to avoid tissue motion and deformation, whilst making the best use of the available photons to account for correlation or redundancy between different dimensions.

Molecular and functional characterization of inositol trisphosphate receptors during early zebrafish development.

Fluctuations in cytosolic Ca(2+) are crucial for a variety of cellular processes including many aspects of development. Mobilization of intracellular Ca(2+) stores via the production of inositol trisphosphate (IP(3)) and the consequent activation of IP(3)-sensitive Ca(2+) channels is a ubiquitous means by which diverse stimuli mediate their cellular effects. Although IP(3) receptors have been well studied at fertilization, information regarding their possible involvement during subsequent development is scant.