Zobrazeno 1 - 10
of 27
pro vyhledávání: '"Antti-Pekka Hynninen"'
Publikováno v:
Lecture Notes in Computer Science ISBN: 9783319460789
ISC Workshops
ISC Workshops
All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in ter
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::950420f38c20ac868e98ff09b2de3a98
https://pubmed.ncbi.nlm.nih.gov/29202130
https://pubmed.ncbi.nlm.nih.gov/29202130
Publikováno v:
Journal of Computational Chemistry
We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the pre
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::828c083a1198a71d3c71cfe2b2ff641b
https://doi.org/10.1002/jcc.23501
https://doi.org/10.1002/jcc.23501
Autor:
Robert K. Prud'homme, Athanassios Z. Panagiotopoulos, Ting Chen, Ioannis G. Kevrekidis, Antti-Pekka Hynninen
Publikováno v:
The Journal of Physical Chemistry B. 112:16357-16366
We present a coarse-grained, implicit solvent model for polystyrene-b-poly(ethylene oxide) in aqueous solution and study its assembly kinetics using Brownian dynamics simulations. The polymer is modeled as a chain of freely jointed beads interacting
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9c097dd585838011ae1e7c271e737b28
https://doi.org/10.1021/jp805826a
https://doi.org/10.1021/jp805826a
Publikováno v:
Molecular Physics. 106:2039-2051
A review of simulation studies of phase equilibria and free energies for systems dominated by coulombic interactions is presented. Phase transitions occur for ionic systems in the strong-coupling limit realized in low-dielectric constant solvents, at
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::30a8d22909ebb797d346ab4b43665f19
https://doi.org/10.1080/00268970802112160
https://doi.org/10.1080/00268970802112160
Autor:
Gregg T. Beckham, Antti-Pekka Hynninen, Michael F. Crowley, Mark R. Nimlos, James F. Matthews
Publikováno v:
Journal of chemical theory and computation. 7(7)
We present a coarse-grain (CG) simulation model for aqueous solutions of β-d-glucose, cellobiose, and cellotetraose, based on atomistic simulation data for each system. In the model, three spherical beads are used to represent glucose, and a single
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e3bcdfdb27de40607d400a4b7cda707a
https://pubmed.ncbi.nlm.nih.gov/26606485
https://pubmed.ncbi.nlm.nih.gov/26606485
Publikováno v:
The Journal of chemical physics. 131(6)
We study by computer simulations the stability of various crystal structures in a binary mixture of large and small spheres interacting either with a hard sphere or a screened-Coulomb potential. In the case of hard-core systems, we consider structure
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2f67fcd55a8e4b235627218af758ef56
https://pubmed.ncbi.nlm.nih.gov/19691406
https://pubmed.ncbi.nlm.nih.gov/19691406
Publikováno v:
The journal of physical chemistry. B. 113(18)
We have used atomistic simulations to study the role of electrostatic screening and charge correlation effects in self-assembly processes of ionic surfactants into micelles. Specifically, we employed grand canonical Monte Carlo simulations to investi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4d9f6914a4c29ab414a62b6abf4e8eb2
https://pubmed.ncbi.nlm.nih.gov/19361177
https://pubmed.ncbi.nlm.nih.gov/19361177
Publikováno v:
The journal of physical chemistry. B. 112(44)
We propose a method for parametrization of implicit solvent models for the simulation of the self-assembly of ionic surfactants into micelles. The parametrization is carried out in two steps. The first step involves atomistic molecular dynamics simul
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe246823df952d36db492fe6a8c0aa77
https://pubmed.ncbi.nlm.nih.gov/18844395
https://pubmed.ncbi.nlm.nih.gov/18844395
Publikováno v:
Physical review letters. 98(19)
We calculate the full phase diagram of spherical charged colloidal particles using Monte Carlo free energy calculations. The system is described using the primitive model, consisting of explicit hard-sphere colloids and point counterions in a uniform
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4866891a06e2b2cdea94581ce7db8123
https://pubmed.ncbi.nlm.nih.gov/17677666
https://pubmed.ncbi.nlm.nih.gov/17677666
Autor:
Job H. J. Thijssen, Antti-Pekka Hynninen, Marjolein Dijkstra, E. C. M. Vermolen, Alfons van Blaaderen
Publikováno v:
Nature materials. 6(3)
Three-dimensional photonic crystals, or periodic materials, that do not allow the propagation of photons in all directions with a wavelength in the visible region have not been experimentally fabricated, despite there being several potential structur
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c7d1a7ab471f47e9d9c660b56edc409d
https://pubmed.ncbi.nlm.nih.gov/17330079
https://pubmed.ncbi.nlm.nih.gov/17330079