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The structural and dynamical properties of four silicate liquids (silica, rhyolite, a model basalt and enstatite) are evaluated by ab initio molecular dynamics simulation using the density functional theory and are compared with classical…
Mixed-species growth models are needed as a synthesis of ecological knowledge and for guiding forest management. Individual-tree models have been commonly used, but the difficulties of reliably scaling from the individual to the stand level…
The growth of thin amorphous hydrogenated carbon films (a-C:H) on diamond (111) surface from the bombardment of CH2 radicals is studied using molecular dynamics simulations. The structural analysis shows that the local structure (e.g., the…
Processes on different length scales affect the dynamics of chain molecules. In this work, we focus on structures on the scale of a monomer and investigate polyolefins, i.e. hydrocarbon chains with different small scale architectures. We…
Some of the materials are more affected by oxidation than others. To elucidate the oxidation-induced degradation mechanisms in transition metal chalcogenides, the chemical effects in single layer MoS$_2$ and MoTe$_2$ were studied in situ in…
We propose a model based on quantum molecular dynamics (QMD) incorporated with statistical decay model (SDM) to describe various nuclear reactions in an unified way. In this first part of the work, the basic ingredients of the model are…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
The transient quantum statistical properties of the atoms and molecules in an atom-molecule BEC system are investigated by obtaining a third-order perturbative solution of the Heisenberg's equations of motion corresponding to the…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
In a single molecule assay, the motion of a molecular motor is often inferred from measuring the stochastic trajectory of a large probe particle attached to it. We discuss a simple model for this generic set-up taking into account…
The origin of biological motion can be traced back to the function of molecular motor proteins. Cytoplasmic dynein and kinesin transport organelles within our cells moving along a polymeric filament, the microtubule. The motion of the…
Estimating rate coefficients from complex chemical reactions is essential for advancing detailed chemistry. However, the stiffness inherent in real-world atmospheric chemistry systems poses severe challenges, leading to training instability…
Shape transformations of amphiphilic molecular assemblies induced by chemical reaction are studied using coarse-grained molecular simulations. A binding reaction between hydrophilic and hydrophobic molecules is considered. It is found that…
The quality of astrochemical models is highly dependent on reliable binding energy (BE) values that consider the morphological and energetic variety of binding sites on the surface of ice-grain mantles. Here, we present the Binding Energy…
Three dimensional models that account for chemistry are useful tools to predict the chemical composition of (exo)planet and brown dwarf atmospheres and interpret observations of future telescopes. Recent Juno observations of the NH3…
We simulate the granulation process of solid spherical particles in the presence of a viscous liquid in a horizontal rotating drum by using molecular dynamics simulations in three dimensions. The numerical approach accounts for the cohesive…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
Five recently developed chemical kinetics mechanisms for ammonia oxidation are analysed and compared, in the context of homogeneous adiabatic autoignition. The analysis focuses on the ignition delay and is based on the explosive mode that…
We study a model for a two-mode atomic-molecular Bose--Einstein condensate. Starting with a classical analysis we determine the phase space fixed points of the system. It is found that bifurcations of the fixed points naturally separate the…
To study the chemical evolution during the formation of molecular clouds, we model three types of clouds with different density structures: collapsing spherical, collapsing ellipsoidal, and static spherical profiles. The collapsing models…