The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations between them have become routine in chemistry, new developments have pushed the frontier in the field to high-throughput calculations. Chemical relations may be created by a search for specific molecular properties in a molecular design attempt, or they can be defined by a set of elementary reaction steps that form a chemical reaction network. The software modules of SCINE have been designed to facilitate such studies. The features of the modules are (i) general applicability of the applied methodologies ranging from electronic structure (no restriction to specific elements of the periodic table) to microkinetic modeling (with little restrictions on molecularity), full modularity so that SCINE modules can also be applied as stand-alone programs or be exchanged for external software packages that fulfill a similar purpose (to increase options for computational campaigns and to provide alternatives in case of tasks that are hard or impossible to accomplish with certain programs), (ii) high stability and autonomous operations so that control and steering by an operator are as easy as possible, and (iii) easy embedding into complex heterogeneous environments for molecular structures taken individually or in the context of a reaction network. A graphical user interface unites all modules and ensures interoperability. All components of the software have been made available as open source and free of charge.
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http://dx.doi.org/10.1063/5.0206974 | DOI Listing |
Mol Syst Biol
January 2025
Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.
With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation.
View Article and Find Full Text PDFWorld J Microbiol Biotechnol
January 2025
Institute of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1 St, Rzeszow, 35-310, Poland.
Phthalic acid esters are widely used worldwide as plasticizers. The high consumption of phthalates in China makes it the world's largest plasticizer market. The lack of phthalic acid ester's chemical bonding with the polymer matrix facilitates their detachment from plastic products and subsequent release into the environment and causes serious threats to the health of living organisms.
View Article and Find Full Text PDFNat Commun
January 2025
Lab of Low-Dimensional Materials Chemistry, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontier Science Center of the Materials Biology and Dynamic Chemistry, Shanghai Engineering Research Center of Hierarchical Nanomaterials, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, China.
Reactive oxygen species (ROS) is promising in cancer therapy by accelerating tumor cell death, whose therapeutic efficacy, however, is greatly limited by the hypoxia in the tumor microenvironment (TME) and the antioxidant defense. Amplification of oxidative stress has been successfully employed for tumor therapy, but the interactions between cancer cells and the other factors of TME usually lead to inadequate tumor treatments. To tackle this issue, we develop a pH/redox dual-responsive nanomedicine based on the remodeling of cancer-associated fibroblasts (CAFs) for multi-pronged amplification of ROS (ZnPP@FQOS).
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
Department of Chemical, Metallurgical and Materials Engineering (Polymer Division), Institute of NanoEngineering Research (INER), Tshwane University of Technology, Pretoria, South Africa.
This work investigates the adhesive property of Soy Protein Isolate(SPI)polymer solution by studying mechanical properties of composites formed using waste wood granules and SPI solutions. To improve the adhesive strength of SPI solution, Carboxymethyl Cellulose Sodium(NaCMC)was mixed (in the weight ratios of 9:1 and 8:2) due to its strong gel formation capabilities. The adhesive performance of these composites was further investigated in the presence and absence of non-toxic additives, including sorbitol (SOR) and stearic acid (SA).
View Article and Find Full Text PDFEnviron Pollut
January 2025
Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China. Electronic address:
Heavy metal (HM) contamination poses significant global environmental threats, impacting ecosystems, public health, and sustainable development. Fungi, as eco-friendly alternatives to chemical treatments, have the potential to reduce HM bioavailability in contaminated soils while promoting plant growth. However, current fungal remediation methods face limitations in efficiency, long-term effectiveness, and the ability to address combined contamination, particularly with naturally occurring strains.
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