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This study presents a coarse-grained molecular dynamics simulation model to investigate the process of oxidative aging in polymers. The chemical aging effect is attributed to the auto-oxidation mechanism, which is initiated by radicals,…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
In contrast to proteins much less attention has been focused on development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force…
This work presents a novel framework governing the development of an efficient, accurate, and transferable coarse-grained (CG) model of a polyether material. The proposed framework combines the two fundamentally different classical…
Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher-resolution reference, making the CG model chemically specific.…
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
Analysis of molecular scale interactions and chemical structure offers an enormous opportunity to tune material properties for targeted applications. However, designing materials from molecular scale is a grand challenge owing to the…
Discrete mesoscale network models, in which explicitly modeled polymer chains are replaced by implicit pairwise potentials, are capable of predicting the macroscale mechanical response of polymeric materials such as elastomers and gels,…
Multiscale simulations facilitate the efficient exploration of large spatiotemporal scales in chemical and physical systems, yet particle-based simulations become prohibitively expensive at time and length scales beyond the molecular level.…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
In this publication we introduce SAMPLE, a structure search approach for commensurate organic monolayers on inorganic substrates. Such monolayers often show rich polymorphism with diverse molecular arrangements in differently shaped unit…
Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
Simulations have acted as a cornerstone to understand MOF/polymer interface structure, however, no molecular-level simulation has yet been performed at the nanoparticle scale. In this work, a hybrid MARTINI/Force Matching (FM) force field…
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
The adsorption of polymer and surfactant molecules onto colloidal particles or droplets in solution can be characterized non-destructively by scattering techniques. In a first part, the general framework of Dynamic Light Scattering, Small…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…