We discuss how to include our recently proposed thermopotentiostat technique [Deissenbeck et al. 2021, 126, 136803] into any existing molecular dynamics (AIMD) package. Using thermopotentiostat AIMD simulations in the canonical NVTΦ ensemble at a constant electrode potential, we compute the polarization bound charge and dielectric response of interfacial water from first principles.
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http://dx.doi.org/10.1021/acs.jctc.2c00959 | DOI Listing |
Adv Biotechnol (Singap)
January 2025
Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
Enzymes are the cornerstone of biocatalysis, biosynthesis and synthetic biology. However, their applicability is often limited by low substrate selectivity. A prime example is the bifunctional linalool/nerolidol synthase (LNS) that can use both geranyl diphosphate (GPP) and farnesyl diphosphate (FPP) to produce linalool and nerolidol, respectively.
View Article and Find Full Text PDFJ Mol Model
January 2025
Department of Mechanical Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 807, Taiwan.
Context: To address the severe fuel crisis and environmental pollution, the use of lightweight metal materials, such as AZ alloy, represents an optimal solution. This study investigates the mechanical behavior and deformation mechanism of AZ alloys under uniaxial compressive using molecular dynamics (MD) simulations. The influence of various compositions, grain sizes (GSs), and temperatures on the compressive stress, the ultimate compressive strength (UCS), compressive yield stress (CYS), Young's modulus (E), shear strain, phase transformation, dislocation distribution, and total deformation length is thoroughly examined.
View Article and Find Full Text PDFJ Mol Model
January 2025
College of Chemical Engineering, Fuzhou University, Fuzhou, 350116, People's Republic of China.
Context: The rotating arc plasma technique for the synthesis of nitrogen-doped graphene capitalizes on the distinctive attributes of plasma, presenting a straightforward, efficient, and catalyst-free strategy for the production of nitrogen-doped graphene. However, experimental outcomes generally fail to elucidate the atomic-level mechanism behind this process. Our research utilizes molecular dynamics simulations to explore theoretically the formation of radicals during the plasma-driven reaction between methane (CH₄) and nitrogen (N₂).
View Article and Find Full Text PDFJ Phys Chem A
January 2025
College of Physics Science and Technology, Yangzhou University, Yangzhou 225009, China.
Developing high-performance solar cells is a practical way to improve clean energy conversion efficiency. However, the performance of solar cells faces challenges such as fast carrier combination, poor stability, and limited solar light harvesting. Herein, we propose a strategy by decorating periodic holes in two-dimensional (2D) porous carbon-nitrogen (CN) materials with a zero-dimensional (0D) semiconducting (ZnO) cluster.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
Water dynamics are investigated in binary osmolyte-water mixtures, exhibiting a microscopic heterogeneity driven by molecular aggregation, on the basis of molecular dynamics (MD) simulation studies. The protecting osmolyte TMAO molecules in solution are evenly dispersed without the formation of noticeable osmolyte aggregates, while the denaturant TMU molecules aggregate readily, generating microscopic heterogeneity in the spatial distribution of component molecules in TMU-water mixtures. A combined study of MD simulation with graph theoretical analysis and spatial inhomogeneity measurement with -values in the two osmolyte solutions revealed that the translational and rotational motions of water in the microheterogeneous environment of TMU-water mixtures are less hindered than those in the homogeneous media of TMAO-water mixtures.
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