Matches in SemOpenAlex for { <https://semopenalex.org/work/W2489840895> ?p ?o ?g. }
Showing items 1 to 85 of
85
with 100 items per page.
- W2489840895 endingPage "569a" @default.
- W2489840895 startingPage "569a" @default.
- W2489840895 abstract "The rate of unfacilitated diffusion of solutes through a lipid bilayer is an important factor in cell signaling, toxicology, and pharmacokinetics. The solubility-diffusion model allows the permeability coefficient of a solute to be calculated using molecular dynamics simulations [1]. This method requires only the potential of mean force and diffusion coefficient of the solute along the transmembrane axis. Accurate calculation of the transmembrane diffusion coefficient profile has proven difficult because the diffusivity depends strongly on the position of the solute in the membrane and converges slowly. Hummer proposed a simple method to calculate position-dependent diffusivity from the position-autocorrelation function of a restrained molecular dynamics simulations, but the values calculated in the lipid tail region can have large uncertainties and are sensitive to the method of integration, etc. We show that long-time correlations of the solute within the membrane are the cause of these issues. An alternative method based on the Laplace transform of the velocity autocorrelation function avoids this issue and provides a straightforward and reliable method of calculating transmembrane diffusion coefficient profiles. This method will facilitate calculation of the rates of unfacillitated membrane permeation. Our implementation of this method is available for free online [5].[1] Marrink, Berendsen, J. Phys. Chem., 1994, 98, 4155, http://dx.doi.org/10.1021/j100066a040.[2] Riahi, Rowley, J. Am. Chem. Soc., 2014, 136, 15111 http://dx.doi.org/10.1021/ja508063s.[3] Hummer, New J. Phys. 2005, 7, 34, http://dx.doi.org/10.1088/1367-2630/7/1/034.[4] Woolf and Roux. J. Am. Chem. Soc. 1994, 116, 5916, http://dx.doi.org/10.1021/ja00092a048.[5] GitHub: https://github.com/RowleyGroup/ACFCalculator." @default.
- W2489840895 created "2016-08-23" @default.
- W2489840895 creator A5031800998 @default.
- W2489840895 creator A5060557743 @default.
- W2489840895 creator A5065514882 @default.
- W2489840895 date "2016-02-01" @default.
- W2489840895 modified "2023-09-27" @default.
- W2489840895 title "Calculating Transmembrane Diffusivity" @default.
- W2489840895 doi "https://doi.org/10.1016/j.bpj.2015.11.3045" @default.
- W2489840895 hasPublicationYear "2016" @default.
- W2489840895 type Work @default.
- W2489840895 sameAs 2489840895 @default.
- W2489840895 citedByCount "0" @default.
- W2489840895 crossrefType "journal-article" @default.
- W2489840895 hasAuthorship W2489840895A5031800998 @default.
- W2489840895 hasAuthorship W2489840895A5060557743 @default.
- W2489840895 hasAuthorship W2489840895A5065514882 @default.
- W2489840895 hasBestOaLocation W24898408951 @default.
- W2489840895 hasConcept C105795698 @default.
- W2489840895 hasConcept C121332964 @default.
- W2489840895 hasConcept C121864883 @default.
- W2489840895 hasConcept C134306372 @default.
- W2489840895 hasConcept C14036430 @default.
- W2489840895 hasConcept C147597530 @default.
- W2489840895 hasConcept C170493617 @default.
- W2489840895 hasConcept C185592680 @default.
- W2489840895 hasConcept C203496682 @default.
- W2489840895 hasConcept C24530287 @default.
- W2489840895 hasConcept C33923547 @default.
- W2489840895 hasConcept C37668627 @default.
- W2489840895 hasConcept C39944091 @default.
- W2489840895 hasConcept C41625074 @default.
- W2489840895 hasConcept C5297727 @default.
- W2489840895 hasConcept C55493867 @default.
- W2489840895 hasConcept C59593255 @default.
- W2489840895 hasConcept C69357855 @default.
- W2489840895 hasConcept C78458016 @default.
- W2489840895 hasConcept C86803240 @default.
- W2489840895 hasConcept C97355855 @default.
- W2489840895 hasConcept C97937538 @default.
- W2489840895 hasConceptScore W2489840895C105795698 @default.
- W2489840895 hasConceptScore W2489840895C121332964 @default.
- W2489840895 hasConceptScore W2489840895C121864883 @default.
- W2489840895 hasConceptScore W2489840895C134306372 @default.
- W2489840895 hasConceptScore W2489840895C14036430 @default.
- W2489840895 hasConceptScore W2489840895C147597530 @default.
- W2489840895 hasConceptScore W2489840895C170493617 @default.
- W2489840895 hasConceptScore W2489840895C185592680 @default.
- W2489840895 hasConceptScore W2489840895C203496682 @default.
- W2489840895 hasConceptScore W2489840895C24530287 @default.
- W2489840895 hasConceptScore W2489840895C33923547 @default.
- W2489840895 hasConceptScore W2489840895C37668627 @default.
- W2489840895 hasConceptScore W2489840895C39944091 @default.
- W2489840895 hasConceptScore W2489840895C41625074 @default.
- W2489840895 hasConceptScore W2489840895C5297727 @default.
- W2489840895 hasConceptScore W2489840895C55493867 @default.
- W2489840895 hasConceptScore W2489840895C59593255 @default.
- W2489840895 hasConceptScore W2489840895C69357855 @default.
- W2489840895 hasConceptScore W2489840895C78458016 @default.
- W2489840895 hasConceptScore W2489840895C86803240 @default.
- W2489840895 hasConceptScore W2489840895C97355855 @default.
- W2489840895 hasConceptScore W2489840895C97937538 @default.
- W2489840895 hasIssue "3" @default.
- W2489840895 hasLocation W24898408951 @default.
- W2489840895 hasOpenAccess W2489840895 @default.
- W2489840895 hasPrimaryLocation W24898408951 @default.
- W2489840895 hasRelatedWork W1989524298 @default.
- W2489840895 hasRelatedWork W1992173619 @default.
- W2489840895 hasRelatedWork W2016929027 @default.
- W2489840895 hasRelatedWork W2021210841 @default.
- W2489840895 hasRelatedWork W2027790859 @default.
- W2489840895 hasRelatedWork W2045145768 @default.
- W2489840895 hasRelatedWork W2063651676 @default.
- W2489840895 hasRelatedWork W2067544869 @default.
- W2489840895 hasRelatedWork W2107317356 @default.
- W2489840895 hasRelatedWork W2148109030 @default.
- W2489840895 hasRelatedWork W2567650562 @default.
- W2489840895 hasRelatedWork W3104716259 @default.
- W2489840895 hasVolume "110" @default.
- W2489840895 isParatext "false" @default.
- W2489840895 isRetracted "false" @default.
- W2489840895 magId "2489840895" @default.
- W2489840895 workType "article" @default.