Related papers: Molecular dynamics simulation of polymer helix for…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Parallel Molecular Dynamics simulations are conducted for describing growth on surfaces with different kind of roughness: a perfect ordered crystalline flat graphite surface, a disordered rough graphite surface and flat surface with an…
Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…
We study equilibrium properties of polymer films and droplets on a solid substrate employing particle-based simulation techniques (Molecular Dynamics) and a continuum description. Parameter-passing techniques are explored that facilitate a…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…
The mobility of polymer chains in perfect polyethylene (PE) crystal was calculated as a function of temperature and chain length through Molecular dynamics (MD) in united atom approximation. The results demonstrate that the chain mobility…
We present a simple and efficient method to simulate three-dimensional, complex-shaped, interacting bodies. The particle shape is represented by Minkowski operators. A time-continuous interaction between these bodies is derived using simple…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
We perform molecular dynamics simulations on an interacting electron gas confined to a cylindrical surface and subject to a radial magnetic field and the field of the positive background. In order to study the system at lowest energy states…
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid…
The presence of ordered structures such as helices in collapsed states of polymer chains is still an open question challenging physics and biology. In this work, we present a potential model for polymer chains with monomers that are not…
This study focuses on comparing the individual polymer chain dynamics in an entangled polymeric liquid under different shear and extension rates. Polymer chains under various shear rates and extension rates were simulated using a…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
Magnetic gels with embedded micro/nano-sized magnetic particles in crosslinked polymer networks can be actuated by external magnetic fields, with changes in their internal microscopic structures and macroscopic mechanical properties. We…
Helices are not generic outcomes of polymer collapse. Collapsed conformations of semiflexible polymers with isotropic attractions typically form globules, toroids, or rod-like structures, as seen in simulations and described by…