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membrane-channel
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A computational fluid dynamics (CFD) approach to modeling of pervaporation in thin membrane channels
, Article CHISA 2006 - 17th International Congress of Chemical and Process Engineering, Prague, 27 August 2006 through 31 August 2006 ; 2006 ; 8086059456 (ISBN); 9788086059457 (ISBN) ; Shayegh, M ; Azad, R. R ; Sharif University of Technology
2006
Abstract
A comprehensive model for pervaporation in thin membrane channels was developed to study the effect of changing temperature and concentration on mass flux. This model consists of momentum, energy and species mass balances along and across the membrane in the flow channel. A computational fluid dynamics (CFD) code was written in C++ programming language to solve the coupled non-linear transport equations in the channel by finite volume method. The Semi-Implicit Pressure Link Equation (SIMPLE) CFD algorithm is used to modify the dependent variables in each of the iterations. The effect of variation of temperature and concentration on transport and thermodynamic properties were considered by...
Study of the Gating Mechanism of Mechanosensitive Membrane Channels
,
M.Sc. Thesis
Sharif University of Technology
;
Nejat Pishkenari, Hoessein
(Supervisor)
;
Zohour, Hassan
(Supervisor)
;
Jamali, Yousef
(Co-Advisor)
Abstract
Mechanosensitive membrane channels are indispensable part of cells that sense and respond to mechanical signals. Hence, malfunction of these channels may cause various diseases. Despite numerous studies of these channels, there are still many unanswered questions surrounding these channels and their gating mechanism. Although there have been valuable experimental studies in this field, the need for modelling and computational studies are still felt since experiments face many limitations in this area. Thus, a channel that its crystallographic structure has been recently determined was chosen and studied using computational tools. In this study, gating of the channel under surface tension has...
The role of mscl amphipathic n terminus indicates a blueprint for bilayer-mediated gating of mechanosensitive channels
, Article Nature Communications ; Volume 7 , 2016 ; 20411723 (ISSN) ; Cortes, D. M ; Cox, C. D ; Rohde, P. R ; Liu, W ; Deitmer, J. W ; Bavi, O ; Strop, P ; Hill, A. P ; Rees, D ; Corry, B ; Perozo, E ; Martinac, B ; Sharif University of Technology
Nature Publishing Group
2016
Abstract
The bacterial mechanosensitive channel MscL gates in response to membrane tension as a result of mechanical force transmitted directly to the channel from the lipid bilayer. MscL represents an excellent model system to study the basic biophysical principles of mechanosensory transduction. However, understanding of the essential structural components that transduce bilayer tension into channel gating remains incomplete. Here using multiple experimental and computational approaches, we demonstrate that the amphipathic N-terminal helix of MscL acts as a crucial structural element during tension-induced gating, both stabilizing the closed state and coupling the channel to the membrane. We...
Gating and conduction of nano-channel forming proteins: A computational approach
, Article Journal of Biomolecular Structure and Dynamics ; Volume 31, Issue 8 , 2013 , Pages 818-828 ; 07391102 (ISSN) ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
2013
Abstract
Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used...