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We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and principal thermodynamic properties of a model solution consisting of NaCl salt dissolved in methanol solvent. Four united atom force fields…
To leverage the redundancy between the electronic structure computed at each step of first-principles molecular dynamics, we present a data-driven modeling framework for Kohn-Sham Density Functional Theory that bypasses the explicit…
Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping…
Owing to the advances in computational techniques and the increase in computational power, atomistic simulations of materials can simulate large systems with higher accuracy. Complex phenomena can be observed in such state-of-the-art…
Hypothesis A prototypical modelling approach is required for a full characterisation of the static and equilibrium dynamical properties of confined ionic liquids (ILs), in order to gain predictive power of properties that are difficult to…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This…
The dynamical properties of liquid lithium at several thermodynamic states near the triple point have been studied within the framework of the mode-coupling theory. We present a self-consistent scheme which, starting from the knowledge of…
We develop an approach to liquid thermodynamics based on collective modes. We perform extensive molecular dynamics simulations of noble, molecular and metallic liquids and provide the direct evidence that liquid energy and specific heat are…
The first step in the construction of a regression model or a data-driven analysis, aiming to predict or elucidate the relationship between the atomic scale structure of matter and its properties, involves transforming the Cartesian…
The answers to many unsolved problems lie in the intractable chemical space of molecules and materials. Machine learning techniques are rapidly growing in popularity as a way to compress and explore chemical space efficiently. One of the…
This computational experiment demonstrates that chain melting in lipids is a molecular process. BOMD is certainly the best method to reproduce such dynamics properties, since the electronic contributions to the various molecular structures…
We present a theory to predict the structure and thermodynamics of mixtures of colloids of different diameters, building on our earlier work [J. Chem. Phys. 145, 074904 (2016)] that considered mixtures with all particles constrained to have…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Large language models (LLMs) have demonstrated broad utility across molecular domains, spanning drug discovery and materials design. Analyzing LLMs' latent representations is crucial for elucidating their underlying mechanisms, improving…
Machine-learned interatomic potentials (MLIPs) show promise in accurately describing the physical properties of materials, but there is a need for a higher throughput method of validation. Here, we demonstrate using that MLIPs and molecular…
Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…