Structure and thermodynamics of a 2D Lennard-Jones hexagonal fluid [0.03%]
二维Lennard-Jones六方流体的结构和热力学性质
Anže Hubman,Tomaz Urbic
Anže Hubman
The thermodynamic and structural properties of the 2D hexagonal soft-sites fluid are examined by integral equation theory benchmarked against extensive Monte Carlo simulations. Hexamers are built of six equal Lennard-Jones segments. Site-si...
Mohammad Moulod,Saeed Moghaddam
Mohammad Moulod
Understanding the nature of water transport in nanoscale is of high importance. Graphene properties such as mass flow rate, stability, filtration efficiency, and selectivity have been studied in various fields. It is a widely held view that...
Molecular dynamics free energy simulations of ATP:Mg2+ and ADP:Mg2+ using the polarizable force field AMOEBA [0.03%]
采用可极化势AMOEBA进行ATP:Mg2+和ADP:Mg2+分子动力学自由能模拟
Brandon Walker,Zhifeng Jing,Pengyu Ren
Brandon Walker
ATPases and GTPases are two important classes of protein that play critical roles in energy transduction, cellular signaling, gene regulation and catalysis. These proteins use cofactors such as nucleoside di and tri-phosphates (NTP, NDP) an...
Conformational fingerprints in the modelling performance of MIA-QSAR: a case for SARS-CoV protease inhibitors [0.03%]
构象指纹在MIA-QSAR建模性能中的作用——以SARS-CoV蛋白酶抑制剂为例
Joyce K Daré,Daniela R Silva,Teodorico C Ramalho et al.
Joyce K Daré et al.
Multivariate image analysis applied to quantitative structure-activity relationships (MIA-QSAR) has proved to be a high-performance 2D tool for drug design purposes. Nonetheless, MIA-QSAR strategy does not efficiently incorporate conformati...
The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation [0.03%]
分子模拟在金属有机框架气体存储和分离中的作用与发展展望
Arni Sturluson,Melanie T Huynh,Alec R Kaija et al.
Arni Sturluson et al.
Metal-organic frameworks (MOFs) are highly tuneable, extended-network, crystalline, nanoporous materials with applications in gas storage, separations, and sensing. We review how molecular models and simulations of gas adsorption in MOFs ha...
Tomaz Urbic
Tomaz Urbic
The structures and properties of biomolecules like proteins, nucleic acids, and membranes depend on water. Water is also very important in industry. Overall, water is unusual substance with more than 70 anomalous properties. The understandi...
Gerhard König,Bernard R Brooks,Walter Thiel et al.
Gerhard König et al.
In this work we employ simple model systems to evaluate the relative performance of two of the most important free energy methods: The Zwanzig equation (also known as "Free energy perturbation") and Bennett's acceptance ratio method (BAR). ...
Xiya Lu,Dong Fang,Shingo Ito et al.
Xiya Lu et al.
Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computatio...
Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace [0.03%]
利用迭代子空间的直接反转加速加权直方图分析方法
Cheng Zhang,Chun-Liang Lai,B Montgomery Pettitt
Cheng Zhang
The weighted histogram analysis method (WHAM) for free energy calculations is a valuable tool to produce free energy differences with the minimal errors. Given multiple simulations, WHAM obtains from the distribution overlaps the optimal st...
Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review [0.03%]
生物分子自由能计算的无约束增强采样方法综述
Yinglong Miao,J Andrew McCammon
Yinglong Miao
Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampli...