Related papers: Multiscale modeling strategy to solve fullerene fo…
Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…
To understand the phenomenon of fullerene growth during its synthesis, an attempt is made to model a minimum energy growth route using a semi-empirical quantum mechanics code. C2 addition leading to C60 was modelled and three main routes,…
Molecular Mechanics describes molecules as particle configurations interacting via classical potentials. These {\it configurational energies} usually consist of the sum of different phenomenological terms which are tailored to the…
The classical nucleation theory finds the rate of nucleation proportional to the monomer concentration raised to the power, which is the `critical nucleaus size', ${n_c}$. The implicit assumption, that amyloids nucleate in the same way, has…
The production mechanism of (anti)nuclei in ultrarelativistic hadronic collisions is under debate in the scientific community. Two successful models used for the description of the experimental measurements are the statistical hadronization…
The formation and proliferation of protein aggregates play a central role in a number of devastating neuro-degenerative diseases. Many experimental studies indicate that the ability of existing aggregates to replicate is a key property in…
We consider a composite medium, which consists of a homogeneous matrix containing a statistically homogeneous set of multimodal spherical inclusions. This model is used to represent the morphology of heterogeneous solid propellants (HSP)…
The problem of hadronic cluster production in quark-hadron phase transition in heavy-ion collisions is studied by cellular automata. Previous result on the scaling behavior is extended to include variation in the drift speed. It is also…
Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach facilitates combining data from…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
Stochastic process discovery is concerned with deriving a model capable of reproducing the stochastic character of observed executions of a given process, stored in a log. This leads to an optimisation problem in which the model's parameter…
From an experimental point of view, clear signatures of multifragmentation have been detected by different experiments. On the other hand, from a theoretical point of view, many different models, built on the basis of totally different and…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
The development of mechanistic models of biological systems is a central part of Systems Biology. One major task in developing these models is the inference of the correct model parameters. Due to the size of most realistic models and their…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of…
Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…
We analyze the role of shake-off and of the final state interactions in inelastic processes in the fullerene shell which follow ionization of the caged atom. We demonstrate that in the broad interval of the photon energies the process is…
Complex organic molecules, such as propylene (CH3CHCH2), are detected in molecular clouds (such as TMC1) with high fractional abundances (~2.10^{-9}, relative to hydrogen) that cannot be explained by gas-phase chemical reactions under…
Morphologies of adsorbed molecular films are of interest in a wide range of applications. To study the epitaxial growth of these systems in computer simulations requires access to long time and length scales and one typically resorts to…