ESPResSo++: A modern multiscale simulation package for soft matter systems

2013 ◽  
Vol 184 (4) ◽  
pp. 1129-1149 ◽  
Author(s):  
Jonathan D. Halverson ◽  
Thomas Brandes ◽  
Olaf Lenz ◽  
Axel Arnold ◽  
Staš Bevc ◽  
...  
Keyword(s):  
Soft Matter ◽  
Multiscale Simulation ◽  
Simulation Package

Multiscale simulation for soft matter: Application to wormlike micellar solution

2013 ◽  
Author(s):  
Takahiro Murashima ◽  
Masatoshi Toda ◽  
Toshihiro Kawakatsu
Keyword(s):  
Micellar Solution ◽  
Soft Matter ◽  
Multiscale Simulation

scholarly journals Multiscale simulation of soft matter systems

2010 ◽  
Vol 144 ◽  
pp. 9-24 ◽  
Author(s):  
Christine Peter ◽  
Kurt Kremer
Keyword(s):  
Soft Matter ◽  
Multiscale Simulation

Systematic Coarse Graining of Biomolecular and Soft-Matter Systems

MRS Bulletin ◽  
2007 ◽  
Vol 32 (11) ◽  
pp. 929-934 ◽  
Author(s):  
Gary S. Ayton ◽  
Will G. Noid ◽  
Gregory A. Voth
Keyword(s):  
High Resolution ◽  
Soft Matter ◽  
Coarse Graining ◽  
Multiscale Simulation ◽  
Atomic Scale ◽  
Coarse Grained ◽  
Statistical Mechanical ◽  
Transfer Of Information ◽  
Very High

AbstractCoarse-grained modeling is a key component in the field of multiscale simulation. Many biomolecular and otherwise complex systems require the characterization of phenomena over multiple length and time scales in order to fully resolve and understand their behavior. These different scales range from atomic to near macroscopic dimensions, and they are generally not independent of one another, but instead coupled. That is, phenomena occurring at atomic length scales have an effect at macroscopic dimensions and vice versa. Systematic transfer of information between these different scales represents a core challenge in the field of multiscale simulation. Coarse-grained modeling works at an intermediate resolution that can bridge the very high resolution (atomic) scale to the very low resolution (macroscopic) scale. As such, a significant challenge is the development of a systematic methodology whereby coarse-grained models can be derived from their high-resolution atomistic-scale counterpart. Here, a systematic theoretical and computational methodology will be described for developing coarse-grained representations of biomolecular and other soft-matter systems. At the heart of the methodology is a variational statistical mechanical algorithm that uses forcematching of atomistic molecular dynamics data to a coarse-grained representation. A theoretical analysis of the coarse-graining methodology will be presented, along with illustrative applications to membranes, peptides, and carbohydrates.

ESPResSo—an extensible simulation package for research on soft matter systems

2006 ◽  
Vol 174 (9) ◽  
pp. 704-727 ◽  
Author(s):  
H.J. Limbach ◽  
A. Arnold ◽  
B.A. Mann ◽  
C. Holm
Keyword(s):  
Soft Matter ◽  
Simulation Package

Allosteric regulation of GPCR Rhodopsin by soft matter

2020 ◽  
Author(s):  
Nipuna Weerasinghe ◽  
Steven Fried ◽  
Anna Eitel ◽  
Andrey Struts ◽  
Suchithranga Perera ◽  
...  
Keyword(s):  
Soft Matter ◽  
Allosteric Regulation

Natural Killer Cell Inspired AIE Nanoterminator for Blood-Brain-Barrier Crossing via Tight-Junction Modulation and NIR-II Gliomas Theranostics

2020 ◽  
Author(s):  
Guanjun Deng ◽  
Xinghua Peng ◽  
Zhihong Sun ◽  
Wei Zheng ◽  
Jia Yu ◽  
...  
Keyword(s):  
Natural Killer Cell ◽  
Natural Killer ◽  
Intracellular Signaling ◽  
Soft Matter ◽  
Tumor Imaging ◽  
Nk Cell ◽  
Killer Cell ◽  
Light Illumination ◽  
Blood Brain ◽  
Intracellular Signaling Cascade

Nature has always inspired robotic designs and concepts. It is conceivable that biomimic nanorobots will soon play a prominent role in medicine. In this paper, we developed a natural killer cell-mimic AIE nanoterminator (NK@AIEdots) by coating natural kill cell membrane on the AIE-active polymeric endoskeleton, PBPTV, a highly bright NIR-II AIE-active conjugated polymer. Owning to the AIE and soft-matter characteristics of PBPTV, as-prepared nanoterminator maintained the superior NIR-II brightness (quantum yield ~8%) and good biocompatibility. Besides, they could serve as tight junctions (TJs) modulator to trigger an intracellular signaling cascade, causing TJs disruption and actin cytoskeleton reorganization to form intercellular “green channel” to help themselves crossing Blood-Brain Barriers (BBB) silently. Furthermore, they could initiatively accumulate to glioblastoma cells in the complex brain matrix for high-contrast and through-skull tumor imaging. The tumor growth was also greatly inhibited by these nanoterminator under the NIR light illumination. As far as we known, The QY of PBPTV is the highest among the existing NIR-II luminescent conjugated polymers. Besides, the NK-cell biomimetic nanorobots will open new avenue for BBB-crossing delivery.

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