相关论文: Implementing Reactivity in Molecular Dynamics Simu…
The particle contact model is important for powder simulations. Although several contact models have been proposed, their validity has not yet been well established. Therefore, we perform molecular dynamics (MD) simulations to clarify the…
Molecular simulations are essential tools in computational chemistry, enabling the prediction and understanding of molecular interactions and thermodynamic properties of biomolecules. However, traditional force fields face significant…
Classical empirical force fields have dominated biomolecular simulation for over 50 years. Although widely used in drug discovery, crystal structure prediction, and biomolecular dynamics, they generally lack the accuracy and transferability…
Electrostatic field matching (EFM) has recently appeared as a novel physics-inspired paradigm for data generation and transfer using the idea of an electric capacitor. However, it requires modeling electrostatic fields using neural…
Accurate and efficient simulation of infrared (IR) and Raman spectra is essential for molecular identification and structural analysis. Traditional quantum chemistry methods based on the harmonic approximation neglect anharmonicity and…
Electronic polarization and dispersion are decisive actors in determining interaction energies between molecules. These interactions have a particularly profound effect on excitation energies of molecules in complex environments, especially…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
A path integral ground state approach has been used to estimate the ground-state energy and structural properties of hydrogen fluoride molecules pinned to a one-dimensional lattice. In the simulations, the molecules are assumed to be rigid,…
Force matching is an established technique to generate effective potentials for molecular dynamics simulations from first-principles data. This method has been implemented in the open source code potfit. Here, we present a review of the…
Biomolecular thermodynamics and spectroscopy depend on relative conformer energies, local curvatures, and collective dipole fluctuations on the potential-energy surface. Conventional molecular mechanics force fields enable large-scale…
Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…
The efficient simulation of fluid-structure interactions at zero Reynolds number requires the use of fast summation techniques in order to rapidly compute the long-ranged hydrodynamic interactions between the structures. One approach for…
The effects of electromagnetic fields (EMF) have been widely debated concerning their role in chemical reactions. Reactions usually took hours or days to complete, and have been shown to happen a thousand times faster using EMF radiations.…
We present a computational method for solving the coupled problem of chemical transport in a fluid (blood) with binding/unbinding of the chemical to/from cellular (platelet) surfaces in contact with the fluid, and with transport of the…
Atomic Force Microscopy (AFM) operating in the frequency modulation mode with a metal tip functionalized with a CO molecule images the internal structure of molecules with an unprecedented resolution. The interpretation of these images is…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
Force-matched water models provide a practical route from first-principles reference data to long classical and path-integral molecular simulations. Previous flexible four-site potentials in the spirit of q-TIP4P/F showed that fitting…
A simple effective model for the intermediate-density regime is constructed from the high-density effective theory of quantum chromodynamics (QCD). In the effective model, under a renormalization-group (RG) scaling towards low momenta, the…
Although aqueous electrolytes are among the most important solutions, the molecular simulation of their intertwined properties of chemical potentials, solubility and activity coefficients has remained a challenging problem, and has…
ReaxFF provides a method to model reactive chemical systems in large-scale molecular dynamics simulations. Here, we developed ReaxFF parameters for phosphorus and hydrogen to give a good description of the chemical and mechanical properties…