We demonstrate that hierarchical backmapping strategies incorporating generic blob-based models can equilibrate melts of high-molecular-weight polymers, described with chemically specific, atomistic models. The central idea is first to represent polymers by chains of large soft blobs (spheres) and efficiently equilibrate the melt on large scales. Then, the degrees of freedom of more detailed models are reinserted step by step. The procedure terminates when the atomistic description is reached. Reinsertions are feasible computationally because the fine-grained melt must be re-equilibrated only locally. We consider polystyrene (PS) which is sufficiently complex to serve method development because of stereo-chemistry and bulky side groups. Our backmapping strategy bridges mesoscopic and atomistic scales by incorporating a blob-based, a moderately coarse-grained (CG), and a united-atom model of PS. We demonstrate that the generic blob-based model can be parameterised to reproduce the mesoscale properties of a specific polymer - here PS. The moderately CG model captures stereo-chemistry. To perform backmapping we improve and adjust several fine-graining techniques. We prove equilibration of backmapped PS melts by comparing their structural and conformational properties with reference data from smaller systems, equilibrated with less efficient methods.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1039/c8sm01830h | DOI Listing |
J Phys Chem B
February 2024
Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States.
While the excess chemical potential is the key quantity in determining phase diagrams, its direct computation for high-density liquids of long polymer chains has posed a significant challenge. Computationally, the excess chemical potential is calculated using the Widom insertion method, which involves monitoring the change in internal energy as one incrementally introduces individual molecules into the liquid. However, when dealing with dense polymer liquids, inserting long chains requires generating trial configurations with a bias that favors those at low energy on a unit-by-unit basis: a procedure that becomes more challenging as the number of units increases.
View Article and Find Full Text PDFFront Bioinform
November 2023
Leibniz Institute of Photonic Technology e.V., Member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany.
In this study, we introduce Blob-B-Gone, a lightweight framework to computationally differentiate and eventually remove dense isotropic localization accumulations (blobs) caused by artifactually immobilized particles in MINFLUX single-particle tracking (SPT) measurements. This approach uses purely geometrical features extracted from MINFLUX-detected single-particle trajectories, which are treated as point clouds of localizations. Employing clustering, we perform single-shot separation of the feature space to rapidly extract blobs from the dataset without the need for training.
View Article and Find Full Text PDFSoft Matter
September 2023
School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Recently, the study of long, slender living worms has gained attention due to their unique ability to form highly entangled physical structures, exhibiting emergent behaviors. These organisms can assemble into an active three-dimensional soft entity referred to as the "blob", which exhibits both solid-like and liquid-like properties. This blob can respond to external stimuli such as light, to move or change shape.
View Article and Find Full Text PDFFront Neurorobot
August 2023
Research Institute of Electrical Communication, Tohoku University, Sendai, Japan.
Worms often aggregate through physical connections and exhibit remarkable functions such as efficient migration, survival under environmental changes, and defense against predators. In particular, entangled blobs demonstrate versatile behaviors for their survival; they form spherical blobs and migrate collectively by flexibly changing their shape in response to the environment. In contrast to previous studies on the collective behavior of worm blobs that focused on locomotion in a flat environment, we investigated the mechanisms underlying their adaptive motion in confined environments, focusing on tubificine worm collectives.
View Article and Find Full Text PDFSoft Matter
March 2023
School of Physics, Georgia Institute of Technology, Atlanta, GA 30318, USA.
The design of amorphous entangled systems, specifically from soft and active materials, has the potential to open exciting new classes of active, shape-shifting, and task-capable 'smart' materials. However, the global emergent mechanics that arise from the local interactions of individual particles are not well understood. In this study, we examine the emergent properties of amorphous entangled systems in an collection of u-shaped particles ("smarticles") and in living entangled aggregate of worm blobs ().
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!