MP-NeRF: A massively parallel method for accelerating protein structure reconstruction from internal coordinates

The conversion of proteins between internal and cartesian coordinates is a limiting step in many pipelines, such as molecular dynamics simulations and machine learning models. This conversion is typically carried out by sequential or parallel applications of the Natural extension of Reference Frame (NeRF) algorithm. This work proposes a massively parallel NeRF implementation which, depending on the polymer length, achieves speedups between 400 and 1200× over the previous state-of-the-art. It accomplishes this by dividing the conversion into three main phases: parallel composition of the monomer backbone, assembly of backbone subunits, and parallel elongation of sidechains; and by batching these computations into a minimal number of efficient matrix operations. Special emphasis is placed on reusability and ease of use. We open source the code (available at https://github.com/EleutherAI/mp_nerf ) and provide a corresponding python package.     

Ab initio quantum chemistry on the Cray T3E massively parallel supercomputer: II

Gaussian-94 is the series of electronic structure programs. It is an integrated system to model a broad range of molecular systems under a variety of conditions, performing its calculations from the basic laws of quantum chemistry. This new version includes methods and algorithms for scalable massively parallel systems such as the Cray T3E supercomputer. In this study, we discuss the performance of Gaussian using large number of processors. In particular, we analyze the scalability of methods such as Hartree–Fock and density functional theory (DFT), including first and second derivatives. In addition, we explore scalability for CIS, MP2, and MCSCF calculations. Scalability and speedups were investigated for most of the examples with up to 64 process elements. A single-point energy calculation (B3-LYP/6-311++G3df,3p) was tested with up to 512 process elements. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1053–1063, 1998     

Cellulolytic and Xylanolytic Enzymes from Yeasts: Properties and Industrial Applications

Lignocellulose, the main component of plant cell walls, comprises polyaromatic lignin and fermentable materials, cellulose and hemicellulose. It is a plentiful and renewable feedstock for chemicals and energy. It can serve as a raw material for the production of various value-added products, including cellulase and xylanase. Cellulase is essentially required in lignocellulose-based biorefineries and is applied in many commercial processes. Likewise, xylanases are industrially important enzymes applied in papermaking and in the manufacture of prebiotics and pharmaceuticals. Owing to the widespread application of these enzymes, many prokaryotes and eukaryotes have been exploited to produce cellulase and xylanases in good yields, yet yeasts have rarely been explored for their plant-cell-wall-degrading activities. This review is focused on summarizing reports about cellulolytic and xylanolytic yeasts, their properties, and their biotechnological applications.     

Thiocoumarins: From the Synthesis to the Biological Applications

Coumarin is a privilege scaffold in medicinal chemistry. Coumarin derivatives are still an emerging class of highly potent pharmaceutical drugs, best known in the field of antimicrobials and anticoagulants. Thiocoumarins are a particular class of coumarins in which one or two of the oxygen atoms are replaced by a sulfur. They are chemically subdivided in three groups: Thiocoumarins, 2-thioxocoumarins, and dithiocoumarins. This review emphasizes the rationale behind the synthesis and biological applications of the most relevant publications related to this family of compounds. Particular attention has been given to their potential as drug candidates, with particular emphasis in the last 5 years. This article is based on the most relevant information collected from multiple electronic databases, including SciFinder, Pubmed, Espacenet, and Mendeley.     

Designing State-of-the-Art Gas Sensors: From Fundamentals to Applications

Gas sensors are crucial in environmental monitoring, industrial safety, and medical diagnostics. Due to the rising demand for precise and reliable gas detection, there is a rising demand for cutting-edge gas sensors that possess exceptional sensitivity, selectivity, and stability. Due to their tunable electrical properties, high-density surface-active sites, and significant surface-to-volume ratio, nanomaterials have been extensively investigated in this regard. The traditional gas sensors utilize homogeneous material for sensing where the adsorbed surface oxygen species play a vital role in their sensing activity. However, their performance for selective gas sensing is still unsatisfactory because the employed high temperature leads to the poor stability. The heterostructures nanomaterials can easily tune sensing performance and their different energy band structures, work functions, charge carrier concentration and polarity, and interfacial band alignments can be precisely designed for high-performance selective gas sensing at low temperature. In this review article, we discuss in detail the fundamentals of semiconductor gas sensing along with their mechanisms. Further, we highlight the existed challenges in semiconductor gas sensing. In addition, we review the recent advancements in semiconductor gas sensor design for applications from different perspective. Finally, the conclusion and future perspectives for improvement of the gas sensing performance are discussed.     

壳聚糖基生物医用材料及其应用研究进展

壳聚糖是一种极具发展潜力的天然生物材料,其在生物医学领域的研究和应用越来越受到重视。阐述了壳聚糖及其衍生物作为生物医用材料的特性,介绍了壳聚糖基生物医用材料的应用现状和发展趋势。     

Revisiting the Physicochemical Properties and Applications of Deep Eutectic Solvents

Recently, deep eutectic solvent (DES) or ionic liquid (IL) analogues have been considered as the newest green solvent, demonstrating the potential to replace harsh volatile organic solvents. DESs are mainly a combination of two compounds: hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD), which have the ability to interact through extensive hydrogen bonds. A thorough understanding of their physicochemical properties is essential, given their successful applications on an industrial scale. The appropriate blend of HBA to HBD can easily fine-tune DES properties for desired applications. In this context, we have reviewed the basic information related to DESs, the two most studied physicochemical properties (density and viscosity), and their performance as a solvent in (i) drug delivery and (ii) extraction of biomolecules. A broader approach of various factors affecting their performance has been considered, giving a detailed picture of the current status of DESs in research and development.     

多功能磁性纳米粒的合成、修饰及生物医学应用

多功能磁性纳米粒由于其独特的性质而受到广泛的关注。磁性纳米粒可以与荧光探针、生物靶向分子或抗肿瘤药物等相结合实现磁性纳米粒的多功能化,因此在多模式成像、癌症的靶向诊断与治疗中有较好的应用前景。本文介绍了磁性纳米粒的合成以及多功能磁性纳米粒的构建方法,重点介绍了核壳型、哑铃型和组合杂化型三种不同类型多功能磁性纳米粒的合成方法。多功能磁性纳米粒通常具有粒径小、超顺磁性以及荧光等独特性质,在此基础上对纳米粒表面进行稳定化和靶向性修饰后即可在多模式成像、特异性靶向药物输送、基因转染等生物医学领域得到应用。最后指出了当前研究中需要解决的问题。     

Hierarchically Porous Organic Materials Derived From Copolymers: Preparation and Electrochemical Applications

Abstract

Compared to conventional porous materials with a uniform pore size distribution, hierarchical ones containing interconnected macro-, meso-, and micropores have greatly enhanced material performance due to the increased specific surface area and mass transfer. Copolymer is a good candidate used for construction of such hierarchically porous structures, resulting from its tunable segment composition, unique phase separation, and self-assembly, etc. Hierarchically porous materials derived from copolymers can be served as a versatile support for many reactive molecules. Furthermore, hierarchically porous carbon materials (HPCMs) can also be prepared by carbonization of copolymers, one segment of which is converted to carbon while the other segment is responsible for the pore formation after its removal by pyrolysis. The obtained hierarchically porous copolymers or carbon materials have promising electrochemical applications especially in energy conversion and storage. In the present review, recent advances in preparation of hierarchically porous materials (HPMs) derived from copolymers are reviewed, and their electrochemical applications in supercapacitors, lithium-ion batteries, fuel cells, electrochemical biosensors, and electrocatalysis are also introduced. The rational design and control for the hierarchically porous microstructures are described deeply from the molecular level. Also, the relationship between the micro-structure and the electrochemical performance is revealed. This review can provide us a better understanding of both theory and experiment for the preparation of hierarchically porous organic materials and their electrochemical applications.     

A Review on Gold Nanotriangles: Synthesis,Self-Assembly and Their Applications

Gold nanoparticles (AuNPs) with interesting optical properties have attracted much attention in recent years. The synthesis and plasmonic properties of AuNPs with a controllable size and shape have been extensively investigated. Among these AuNPs, gold nanotriangles (AuNTs) exhibited unique optical and plasmonic properties due to their special triangular anisotropy. Indeed, AuNTs showed promising applications in optoelectronics, optical sensing, imaging and other fields. However, only few reviews about these applications have been reported. Herein, we comprehensively reviewed the synthesis and self-assembly of AuNTs and their applications in recent years. The preparation protocols of AuNTs are mainly categorized into chemical synthesis, biosynthesis and physical-stimulus-induced synthesis. The comparison between the advantages and disadvantages of various synthetic strategies are discussed. Furthermore, the specific surface modification of AuNTs and their self-assembly into different dimensional nano- or microstructures by various interparticle interactions are introduced. Based on the unique physical properties of AuNTs and their assemblies, the applications towards chemical biology and sensing were developed. Finally, the future development of AuNTs is prospected.     

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano‐objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano‐objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. © 2013 Wiley Periodicals, Inc.     

Two-Dimensional Black Phosphorus: Preparation,Passivation and Lithium-Ion Battery Applications

As a new type of single element direct-bandgap semiconductor, black phosphorus (BP) shows many excellent characteristics due to its unique two-dimensional (2D) structure, which has great potential in the fields of optoelectronics, biology, sensing, information, and so on. In recent years, a series of physical and chemical methods have been developed to modify the surface of 2D BP to inhibit its contact with water and oxygen and improve the stability and physical properties of 2D BP. By doping and coating other materials, the stability of BP applied in the anode of a lithium-ion battery was improved. In this work, the preparation, passivation, and lithium-ion battery applications of two-dimensional black phosphorus are summarized and reviewed. Firstly, a variety of BP preparation methods are summarized. Secondly, starting from the environmental instability of BP, different passivation technologies are compared. Thirdly, the applications of BP in energy storage are introduced, especially the application of BP-based materials in lithium-ion batteries. Finally, based on preparation, surface functionalization, and lithium-ion battery of 2D BP, the current research status and possible future development direction are put forward.     

The Strength of the Macromonomer Strategy for Complex Macromolecular Architecture: Molecular Characterization,Properties and Applications of Polymacromonomers

The efficiency of the macromonomer (MM) synthetic strategy for the creation of nonlinear complex macromolecular architectures (miktoarm stars, α,ω‐branched polymers, random/exact comb and graft copolymers, dendritic polymers, molecular brushes) is reviewed. In addition, the solution/bulk properties and the potential applications of polymacromonomers (PMM), as well as new synthetic ideas are presented. The synthesis of macromonomers and living polymacromonomers in situ leads to many novel linear and nonlinear structures, as for example PMM‐b‐PS‐b‐PMM, (PS)₂PMM. The use of multichlorosilylstyrenes as monomer/linking agents opens new ways for structures with multichain macromonomeric building blocks.

The use of multichlorosilylstyrenes as monomer/linking agents opens new ways for structures having multichain macromonomeric building blocks.     

One‐ and Two‐Photon Absorption: Physical Principle and Applications

We introduce the principle and applications of one‐photon absorption (OPA) and two‐photon absorption (TPA) controlled by external electric fields. The physical mechanism of OPA and TPA are firstly introduced, which can visually promote thoroughly understanding of principle and physical analysis. Secondly, the applications of different molecules in OPA and TPA with and without external electric field are introduced in detail. The effect of the external electric field on the charge transfer during the absorption process is also exemplified. Furthermore, the external electric field on the molecular orbital wave function is visualized through the charge transfer process in the excited state transitions. The purpose of this review is to deepen the understanding of the types of charge transfer under linear and non‐linear absorption in different systems.     

Exploring the Research Progress about the Applications of Cyclodextrins and Nanomaterials in Electroanalysis

Cyclodextrins and nanomaterials are widely used in the achievement of powerful platforms in supramolecular chemistry and nanotechnology. The relatively hydrophobic internal cavity of the CDs selectively retains molecules having the proper geometry, while the hydrophilic exterior allows CDs to improve the dispersibility and molecular recognition. The nanomaterials provide higher surface area, good conductivity, and electrocatalytic effect. The use of nanomaterials and CDs in electrochemical sensors’ design allows the development of a large variety of devices, explaining the increasing number of papers in the last years that are discussed in this review.     

PRIRODA-04: a quantum-chemical program suite. New possibilities in the study of molecular systems with the application of parallel computing

Main characteristics are described of the PRIRODA quantum-chemical program suite designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing. A number of examples of calculations are presented.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 804–810, March, 2005.     

Self‐Assembled Fluorescent Nanoparticles from π‐Conjugated Small Molecules: En Route to Biological Applications

Since the development of supramolecular chemical biology, self‐organised nano‐architectures have been widely explored in a variety of biomedical applications. Functionalized synthetic molecules with the ability of non‐covalent assembly in an aqueous environment are typically able to interact with biological systems and are therefore especially interesting for their use in theranostics. Nanostructures based on π‐conjugated oligomers are particularly promising as theranostic platforms as they bear outstanding photophysical properties as well as drug loading capabilities. This Feature Article provides an overview on the recent advances in the self‐assembly of intrinsically fluorescent nanoparticles from π‐conjugated small molecules such as fluorene or perylene based chromophores for biomedical applications.

     

Harnessing the Electrophilicity of Keteniminium Ions: A Simple and Straightforward Entry to Tetrahydropyridines and Piperidines from Ynamides

An efficient, modular and straightforward entry to tetrahydropyridines and piperidines is reported. This reaction is based on a formal intramolecular hydroalkylation of readily available, properly substituted ynamides which, upon simple activation under acidic conditions, generate highly reactive activated keteniminium ions whose reactivity can be finely controlled to induce a remarkably efficient [1,5]‐hydride shift from unactivated C?H bonds and trigger a cationic cyclization which is complete within minutes.     

A Novel Neutral Carrier for Uranyl Ion Based on a Commercially Available Aminophosphate Derivative: Evaluation in Membrane Electrodes and Nuclear Safeguards Applications

The construction and performance characteristics of uranyl membrane electrodes based on cheap and commercially available amino(trimethyl)phosphate are described. The influence of various membrane constituents on the potentiometric responses of the prepared membrane electrodes has been studied. Optimized membrane electrodes exhibited performance characteristics comparable with those based on high cost and commercially available ionophores. Selectivity studies indicated that the developed membrane electrodes are selective towards uranyl ion over a large number of cations including the well‐known uranyl ion interferents (e.g., Fe³⁺, Th⁺⁴). The analytical utility of the proposed membrane electrode has been demonstrated through its application in nuclear safeguards verification purposes.