Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space, one is then able to sample efficiently and reconstruct the free energy landscape. In methods such as metadynamics, the quality of these collective variables plays a key role in convergence efficiency. Unfortunately in many systems of interest it is not possible to identify an optimal collective variable, and one must deal with the nonideal situation of a system in which some slow modes are not accelerated. We propose a two-step approach in which, by taking into account the residual multiscale nature of the problem, one is able to significantly speed up convergence. To do so, we combine an exploratory metadynamics run with an optimization of the free energy difference between metastable states, based on the recently proposed variationally enhanced sampling method. This new method is well parallelizable and is especially suited for complex systems, because of its simplicity and clear underlying physical picture.
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http://dx.doi.org/10.1021/acs.jctc.9b00032 | DOI Listing |
Environ Sci Technol
January 2025
Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China.
Membrane distillation (MD) efficiently desalinizes and treats high-salinity water as well as addresses the challenges in handling concentrated brines and wastewater. However, silica scaling impeded the effectiveness of MD for treating hypersaline water and wastewater. Herein, the effects of humic acid (HA) on silica scaling behavior during MD are systematically investigated.
View Article and Find Full Text PDFHeliyon
January 2025
Department of Chemistry, School of Physical Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana.
Zeolite was successfully synthesized using a mixture of kaolinite clay (which served as the alumina source) and rice husk ash (silica source). The aim of this work was to synthesize highly efficient zelolite to remove methyle blue dye from aqueous solution. The synthesized adsorbent was characterised using Fourier Transform Infrared (FTIR) spectroscopy, powder x-ray diffraction (PXRD) analysis, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and pH at the point of zero charge (pHpzc).
View Article and Find Full Text PDFJ Taibah Univ Med Sci
December 2024
Universitas Nasional, Department of Biology, South Jakarta, Indonesia.
Objectives: Dementia, a growing concern globally, affects more than 55 million people-a number projected to rise to 152 million by 2050. Current medications target Alzheimer's disease, the most prevalent form of dementia. This study investigated L.
View Article and Find Full Text PDFActa Pharm Sin B
December 2024
State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Accurate receptor/ligand binding free energy calculations can greatly accelerate drug discovery by identifying highly potent ligands. By simulating the change from one compound structure to another, the relative binding free energy (RBFE) change can be calculated based on the theoretically rigorous free energy perturbation (FEP) method. However, existing FEP-RBFE approaches may face convergence challenges due to difficulties in simulating non-physical intermediate states, which can lead to increased computational costs to obtain the converged results.
View Article and Find Full Text PDFAdv Sci (Weinh)
January 2025
School of Physics, Zhejiang University, Hangzhou, 310058, PR China.
The self-assembly of intrinsically disordered proteins (IDPs) into condensed phases and the formation of membrane-less organelles (MLOs) can be considered as the phenomenon of collective behavior. The conformational dynamics of IDPs are essential for their interactions and the formation of a condensed phase. From a physical perspective, collective behavior and the emergence of phase are associated with long-range correlations.
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