Coarse-grained molecular simulation has become a popular tool for modeling simple and complex fluids alike. The defining aspects of a coarse grained model are the force field parameters, which must be determined for each particular fluid. Because the number of molecular fluids of interest in nature and in engineering processes is immense, constructing force field parameter tables by individually fitting to experimental data is a futile task. A step toward solving this challenge was taken recently by Mejía et al., who proposed a correlation that provides SAFT-γ Mie force field parameters for a fluid provided one knows the critical temperature, the acentric factor and a liquid density, all relatively accessible properties. Building on this, we have applied the correlation to more than 6000 fluids, and constructed a web application, called "Bottled SAFT", which makes this data set easily searchable by CAS number, name or chemical formula. Alternatively, the application allows the user to calculate parameters for components not present in the database. Once the intermolecular potential has been found through Bottled SAFT, code snippets are provided for simulating the desired substance using the "raaSAFT" framework, which leverages established molecular dynamics codes to run the simulations. The code underlying the web application is written in Python using the Flask microframework; this allows us to provide a modern high-performance web app while also making use of the scientific libraries available in Python. Bottled SAFT aims at taking the complexity out of obtaining force field parameters for a wide range of molecular fluids, and facilitates setting up and running coarse-grained molecular simulations. The web application is freely available at http://www.bottledsaft.org . The underlying source code is available on Bitbucket under a permissive license.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.jcim.6b00149 | DOI Listing |
Sci Rep
December 2024
Weather Program Office, Ocean and Atmospheric Research, NOAA, Silver Spring, MD, USA.
Tropical cyclone risks are expected to increase with climate change. One such risk is extreme ocean waves generated by surface winds from these systems. We use synthetic databases of both historical (1980-2017) and future (2015-2050) tropical cyclone tracks to generate wind fields and force a computationally efficient wave model to estimate significant wave heights across all global tropical cyclone basins.
View Article and Find Full Text PDFSmall
December 2024
Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
The ocean wave energy is considered one of the most promising forms of marine blue energy due to its vast reserves and high energy density. However, traditional electromagnetic power generation technology suffers from drawbacks such as high maintenance costs, heavy structures, and low conversion efficiency, which restricts its application range. The triboelectric nanogenerator (TENG) uses Maxwell displacement current as its internal driving force, which can efficiently convert irregular, low-frequency, and dispersed mechanical energy into electrical energy.
View Article and Find Full Text PDFInt J Biol Macromol
December 2024
Department of Chemistry and Chemical Sciences, Central University of Himachal Pradesh, Dharamshala, Kangra 176206, India. Electronic address:
In the present study, we prepared Gum Acacia-cl-Acrylic acid-co-itaconic acid (GA-cl-AA-co-IA) hydrogels by free radical crosslink polymerization method for the efficient removal of Rhodamine-B (RhB) dye. The hydrogels were further characterized by different characterization techniques: Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), Atomic force microscopy (AFM), Brunuer-Emmett-Teller (BET) and field emission scanning electron microscopy (FE-SEM) to confirm synthesis. The synthesis parameters were optimized by swelling studies, which were performed by gravimetric analysis method.
View Article and Find Full Text PDFJACS Au
December 2024
Freie Universität Berlin, Physics Department, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany.
Vibrational Stark effect (VSE) spectroscopy has become one of the most important experimental approaches to determine the strength of noncovalent, electrostatic interactions in chemistry and biology and to quantify their influence on structure and reactivity. Nitriles (C≡N) have been widely used as VSE probes, but their application has been complicated by an anomalous hydrogen bond (HB) blueshift which is not encompassed within the VSE framework. We present an empirical model describing the anomalous HB blueshift in terms of H-bonding geometry, i.
View Article and Find Full Text PDFACS Appl Electron Mater
December 2024
CEITEC, Brno University of Technology, Purkyňova 123, 61200 Brno, Czech Republic.
To satisfy the needs of the current technological world that demands high performance and efficiency, a deep understanding of the whole fabrication process of electronic devices based on low-dimensional materials is necessary for rapid prototyping of devices. The fabrication processes of such nanoscale devices often include exposure to an electron beam. A field effect transistor (FET) is a core device in current computation technology, and FET configuration is also commonly used for extraction of electronic properties of low-dimensional materials.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!