Related papers: Molecular Tools for Non-Planar Surface Chemistry
Particle-based simulations are an essential tool for the study of biochemical systems for scales between molecular/Brownian dynamics and the reaction-diffusion master equation. These simulations utilise proximity-based reaction conditions…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not…
We present two new tools for studying and modelling metal absorption lines in the circumgalactic medium. The first tool, dubbed ``NMF Profile Maker'' (NMF$-$PM), uses a non-negative matrix factorization (NMF) method and provides a robust…
Selected theoretical developments in modeling of deposition of submicrometer size (submicron) particles on solid surfaces, with and without surface diffusion, of interest in colloid, polymer, and certain biological systems, are surveyed. We…
In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated…
Imaging individual conformational instances of generic, inhomogeneous, transient or intrinsically disordered protein systems at the single molecule level in situ is one of the notable challenges in structural biology. Present techniques…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Discrete rearranging patterns include cellular patterns, for instance liquid foams, biological tissues, grains in polycrystals; assemblies of particles such as beads, granular materials, colloids, molecules, atoms; and interconnected…
The homoepitaxial growth of Si on Si(100) covered by a resist mask is a necessary technological step for the fabrication of donor-based quantum devices with scanning tunneling microscope lithography. In the present work, the chlorine…
Electrochemical 3D printing of conductors with microscale resolution holds a great promise for a wide range of applications, but the choice of suitable metals for these technologies remains limited. Most efforts so far have been focused on…
Within the paradigm of metamaterials and metasurfaces, electromagnetic properties of composite materials can be engineered by shaping or modulating their constituents, so-called meta-atoms. Synthesis and analysis of complex-shape meta-atoms…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Molecule-surface interaction is key to many physical and chemical processes at interfaces. Here, we show that the dynamics of single molecules on a surface under ultrahigh vacuum can be resolved using fluorescence imaging. By adapting…
Semiconductor devices are scaled down to the level which constituent materials are no longer considered continuous. To account for atomistic randomness, surface effects and quantum mechanical effects, an atomistic modeling approach needs to…
Current in vivo microscopy allows us detailed spatiotemporal imaging (3D+t) of complete organisms and offers insights into their development on the cellular level. Even though the imaging speed and quality is steadily improving,…
Structurally and chemically complex materials such as amorphous metallosilicates underpin major catalytic and separation technologies, yet their intrinsic complexity challenges reliable atomistic modeling under realistic conditions.…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Tight binding molecular dynamics simulations, with a non orthogonal basis set, are performed to study the fragmentation of carbon fullerenes doped with up to six silicon atoms. Both substitutional and adsorbed cases are considered. The…
Inversion symmetry eliminates the second-order nonlinear responses in materials commonly used in silicon photonics with electric-dipole approximation. The lack of effective methods to induce the second-order nonlinearity in silicon photonic…