Two new charge-scaling methods for efficient modeling of the solvated macromolecular environment in hybrid QM/MM calculations of biological reactions are presented. The methods are extensions of the variational electrostatic projection (VEP) method, and allows a subset of atomic charges in the external environment to be adjusted to mimic, in the active dynamical region, the electrostatic potential and field due to the large surrounding macromolecule and solvent. The method has the advantages that it offers improved accuracy, does not require the use of a three-dimensional grid or auxiliary set of fitting points, and requires only minor molecular simulation code modifications. The VEP-cs and VEP-RVM+cs methods are able to attain very high accuracy (relative force errors of 10(-7) or better with appropriate choice of control parameters), and take advantage of a recently introduced set of high-order discretization schemes and Gaussian exponents for boundary element solvation and VEP methods. The methods developed here serve as potentially powerful tools in the arsenal of computational techniques used in multiscale computational modeling problems.
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http://dx.doi.org/10.1002/jcc.20318 | DOI Listing |
Chemphyschem
November 2024
Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
Soft Matter
November 2024
Department of Physics, Bilkent University, Ankara 06800, Turkey.
We predict the thermodynamic behavior of bulk electrolytes from an ionic hard-core (HC) size-augmented self-consistent formalism incorporating asymmetrically the short- and long-range ion interactions their virial and cumulant treatment, respectively. The characteristic splitting length separating these two ranges is obtained from a variational equation solved together with the Schwinger-Dyson (SD) equations. comparison with simulation results from the literature, we show that the asymmetric treatment of the distinct interaction ranges significantly extends the validity regime of our previously developed purely cumulant-level Debye-Hückel (DH) theory.
View Article and Find Full Text PDFIEEE J Biomed Health Inform
October 2024
Falls are one of the most serious health risks faced by older adults worldwide, and they can have a significant impact on their physical and mental well-being as well as their quality of life. Detecting falls promptly and accurately and providing assistance can effectively reduce the harm caused by falls to older adults. This paper proposed a noncontact fall detection method based on the human electrostatic field and a VMD-ECANet framework.
View Article and Find Full Text PDFSci Rep
October 2024
RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
The electroconvection of liquid crystals is a typical example of a dissipative structure generated by complicated interactions between three factors: convective flow, structural deformation, and the migration of charge carriers. In this study, we found that the periodic structural deformation of a cholesteric liquid crystal propagates in space, like a wave, under an alternating-current electric field. The existence of convection and charge carriers was confirmed by flow-field measurements and dielectric relaxation spectroscopy.
View Article and Find Full Text PDFJ Chem Inf Model
September 2024
Department of Computer Science, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan.
Generating drug candidates with desired protein-ligand interactions is a significant challenge in structure-based drug design. In this study, a new generative model, IEV2Mol, is proposed that incorporates interaction energy vectors (IEVs) between proteins and ligands obtained from docking simulations, which quantitatively capture the strength of each interaction type, such as hydrogen bonds, electrostatic interactions, and van der Waals forces. By integrating this IEV into an end-to-end variational autoencoder (VAE) framework that learns the chemical space from SMILES and minimizes the reconstruction error of the SMILES, the model can more accurately generate compounds with the desired interactions.
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