Related papers: Condensed-phase molecular representation to link s…
We present a detailed description of semi-quantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian…
Spherically-symmetric atom-centered descriptors of atomic environments have been widely used for constructing potential or free energy surfaces of atomistic and colloidal systems and to characterize local structures using machine learning…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Atomistic simulations of heat transport in complex materials are costly and hard to converge. This has led to the development of several noise-reduction techniques applicable to equilibrium molecular-dynamics (MD) simulations. We analyze…
The purpose of this paper is to introduce Condensed-Matter-Laboratory (CML) application for simulating solids and nanostructures and calculating different properties of them by density functional theory and using Green's function theory in…
Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with…
Condensed-phase spectral line shapes encode the strength and timescale of interactions between molecules and their environments, yet these ideas are often difficult to introduce at the undergraduate level due to their reliance on formal…
Molecular graphs generally contain subgraphs (known as groups) that are identifiable and significant in composition, functionality, geometry, etc. Flat latent representations (node embeddings or graph embeddings) fail to represent, and…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…
Modeling plasmas in terms of atoms or ions is theoretically appealing for several reasons. When it is relevant, the notion of atom or ion in a plasma provides us with an interpretation scheme of the plasma's microscopic structure. From the…
We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically…
We investigate thermal fluctuations in a smectic A phase of an amphiphile-solvent mixture with molecular dynamics simulations. We use an idealized model system, where solvent particles are represented by simple beads, and amphiphiles by…
The integration of molecular and natural language representations has emerged as a focal point in molecular science, with recent advancements in Language Models (LMs) demonstrating significant potential for comprehensive modeling of both…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
The thermodynamic properties of systems with long-range interactions is still an ongoing challenge, both from the point of view of theory as well as computer simulation. In this work we study a model system, a Coulomb gas confined inside a…
Thermoresponsive polymer architectures have become integral building blocks of 'smart' functional materials in modern applications. For a large range of developments, e.g., for drug delivery or nanocatalytic carrier systems, the selective…
Large-scale molecular representation methods have revolutionized applications in material science, such as drug discovery, chemical modeling, and material design. With the rise of transformers, models now learn representations directly from…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
The designer's preoccupation to reduce the energy needs and get a better thermal quality of ambiances helped in the development of several packages simulating the dynamic behaviour of buildings. This paper shows the adaptation of a method…