Related papers: Ab initio machine learning simulation of calcium c…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
This work constructs an advanced force field, the Completely Multipolar Model (CMM), to quantitatively reproduce each term of an energy decomposition analysis (EDA) for aqueous solvated alkali metal cations and halide anions and their ion…
While molecular dynamics (MD) is a very useful computational method for atomistic simulations, modeling the interatomic interactions for reliable MD simulations of real materials has been a long-standing challenge. In 2007, Behler and…
In this work, we propose a linear machine learning force matching approach that can directly extract pair atomic interactions from ab initio calculations in amorphous structures. The local feature representation is specifically chosen to…
Climate emergency has led to the investigation of CO$_{2}$ valorization routes. A competitive process included in this framework is the catalytic CO$_{2}$ cycloaddition to epoxides, to produce cyclic carbonates. Halide-based Ionic liquids…
Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
We propose a mathematical model describing the process of filling the pores of a building material with lime water solution with the goal to improve the consistency of the porous solid. Chemical reactions produce calcium carbonate which…
Proteins' fuzziness are features for communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene…
The acceleration of material property calculations while maintaining ab initio accuracy (1 meV/atom) is one of the major challenges in computational physics. In this paper, we introduce a Python package enhancing the computation of (finite…
Machine learning (ML) methods are being used in almost every conceivable area of electronic structure theory and molecular simulation. In particular, ML has become firmly established in the construction of high-dimensional interatomic…
We simulate the liquid silicon surface with first-principles molecular dynamics in a slab geometry. We find that the atom-density profile presents a pronounced layering, similar to those observed in low-temperature liquid metals like Ga and…
The fundamental understanding of intermolecular interactions of ionic liquids with water represents a vital extent in predicting ionic liquid properties. Intermolecular or noncovalent interactions were studied for 1,3-dimethyl imidazolium…
Polymer-derived ceramics combine the thermal stability of ceramics with the versatile properties of carbon domains, but modeling their atomic-scale evolution during processing remains elusive due to the limitations of traditional…
In this paper, we study chain melting state in the commensurate host-guest structure of calcium. We trained a NN (neural network) force field with DeepMD-kit, and by implementing classical simulations, we found that the convergence of…
Despite the widespread use of zeolites in chemical industry, their formation process is not fully understood due to the complex and heterogeneous structure of traditional synthesis media. Hydrated silicate ionic liquids (HSILs) have been…
Amorphous calcium carbonate (ACC) has been widely found in biomineralization, both as a transient precursor and a stable phase, but how organisms accurately control its formation and crystallization pathway remains unclear. Here, we aim to…
Equilibrium relationships involving solids are based on bulk thermodynamic properties that concern ideal crystals of infinite size. However, real processes towards equilibrium imply development of finite molecular-scale entities. The…