Related papers: Systematic Builder for All-Atom Simulations of Pla…
Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation.…
The single-centre convergent close-coupling approach to ion-atom collisions has been extended to model collisions involving arbitrary multi-electron atoms and partially stripped ions. This is accomplished by generating a set of target…
Hexahedral meshes are widely used in simulation pipelines, yet automatic generation remains challenging for complex CAD geometries. Polycube-based hexahedral meshing is a representative approach due to its regular, parameterization-friendly…
We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and…
In this study, a new alternative model algorithm has been proposed for assembling amorphous structures, unifying the bosonic paradigm applicable at low temperatures with crystalline models relevant at room and higher temperatures. Physical…
Particle acceleration in relativistic shocks of electron-positron plasmas with proton admixture is investigated through two-dimensional (2D) particle-in-cell (PIC) simulations. The upstream plasma, with a bulk Lorentz factor of $10$ and a…
Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…
We describe a phenomenological model for molecular hydrogen formation suited for applications in galaxy formation simulations, which includes on-equilibrium formation of molecular hydrogen on dust and approximate treatment of both its…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
Understanding the modification of jets and high-$p_T$ probes in small systems requires the integration of soft and hard physics. We present recent developments in extending the JETSCAPE framework to build an event generator, which includes…
Engineering atomic-scale structures allows great manipulation of physical properties and chemical processes for advanced technology. We show that the B atoms deployed at the centers of honeycombs in boron sheets, borophene, behave as nearly…
This paper is devoted to the construction of a new fast-to-evaluate model for the prediction of 2D crack paths in concrete-like microstructures. The model generates piecewise linear cracks paths with segmentation points selected using a…
The development of new manufacturing techniques such as 3D printing have enabled the creation of previously infeasible chemical reactor designs. Systematically optimizing the highly parameterized geometries involved in these new classes of…
Twisted van der Waals heterostructures have latterly received prominent attention for their many remarkable experimental properties, and the promise that they hold for realising elusive states of matter in the laboratory. We propose that…
The boson peak (BP), a low-energy excess in the vibrational density of states over the phonon Debye contribution, is usually identified as one of the distinguishing features between ordered crystals and amorphous solid materials. Despite…
The detailed investigation of electronic and magnetic properties of polymeric coordination materials with accurate ab initio quantum mechanical methods is often computationally extremely demanding because of the large number of atoms in the…
Fabrication of custom-built heterostructures based on stacked 2D materials provides an effective method to controllably tune electronic and optical properties. To that end, optimizing fabrication techniques for building these…
High-harmonic generation (HHG) in condensed-matter systems is both a source of fundamental insight into quantum electron motion and a promising candidate to realize compact ultraviolet and ultrafast light sources. Here we argue that the…
We present a combined phase field and cohesive zone formulation for hydrogen embrittlement that resolves the polycrystalline microstructure of metals. Unlike previous studies, our deformation-diffusion-fracture modelling framework accounts…
Atomic diffusion affects the properties of various engineering materials, which predominantly occur in the polycrystalline state. A rigorous description of polycrystalline diffusion must therefore account for crystallographic defects,…