Related papers: Maximum entropy mediated liquid-to-solid nucleatio…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
It is important to study contact angle of a liquid on a solid surface to understand its wetting properties, capillarity and surface interaction energy. While performing transient molecular dynamics (MD) simulations it requires calculating…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
We demonstrate a strategy for simulating wide-range X-ray scattering patterns, which spans the small- and wide scattering angles as well as the scattering angles typically used for Pair Distribution Function (PDF) analysis. Such simulated…
We develop a maximum relative entropy formalism to generate optimal approximations to probability distributions. The central results consist in (a) justifying the use of relative entropy as the uniquely natural criterion to select a…
We build a comprehensive methodology for the fast computation of entropy across both solid and liquid phases. The proposed method utilizes a single trajectory of molecular dynamics (MD) to facilitate the calculation of entropy, which is…
We have recently developed a breakthrough methodology for rapidly computing entropy in both solids and liquids by integrating a multiscale entropy approach (known as zentropy theory) with molecular dynamics (MD) simulations. This approach…
We develop the method of Maximum Entropy (ME) as a technique to generate approximations to probability distributions. The central results consist in (a) justifying the use of relative entropy as the uniquely natural criterion to select a…
As with many parts of the natural sciences, machine learning interatomic potentials (MLIPs) are revolutionizing the modeling of molecular crystals. However, challenges remain for the accurate and efficient calculation of sublimation…
We explore the use of the method of Maximum Entropy (ME) as a technique to generate approximations. In a first use of the ME method the "exact" canonical probability distribution of a fluid is approximated by that of a fluid of hard…
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the…
Reactive molecular dynamics (MD) simulation is performed using a reactive force field (ReaxFF). To this end, we developed a new method to optimize the ReaxFF parameters based on a machine learning approach. This approach combines the…
Molecular dynamics simulations of water, liquid beryllium fluoride and silica melt are used to study the accuracy with which the entropy of ionic and molecular liquids can be estimated from atom-atom radial distribution function data. All…
Liquid water is fundamentally important, and its accurate computer simulation has been the driving force for myriad methodological developments. Ab initio molecular dynamics with forces obtained from density functional theory (DFT) is now a…
Many species, from single-cell bacteria to advanced animals, use molecular communication (MC) to share information with each other via chemical signals. Although MC is mostly studied in microscale, new practical applications emerge in…
We propose a new molecular simulation framework that combines the transferability, robustness and chemical flexibility of an ab initio method with the accuracy and efficiency of a machine learned force field. The key to achieve this mix is…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
In the research of condensed matter, atomistic dynamic simulations play a crucial role, particularly in revealing dynamic processes, phase transitions and thermodynamic statistics macroscopic physical properties in systems such as solids…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…