| 1. |
- Lyubartsev, Alexander P., et al.
(författare)
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Force Field Development for Lipid Membrane Simulations
- 2016
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Ingår i: Biochimica et Biophysica Acta - Biomembranes. - : Elsevier BV. - 0005-2736 .- 1879-2642. ; 1858:10, s. 2483-2497
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Tidskriftsartikel (refereegranskat)abstract
- With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Rog.
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| 2. |
- Lyubartsev, Alexander P., et al.
(författare)
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Recent development in computer simulations of lipid bilayers
- 2011
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Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 7:1, s. 25-39
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Forskningsöversikt (refereegranskat)abstract
- Rapid development of computer power during the last decade has made molecular simulations of lipid bilayers feasible for many research groups, which, together with the growing general interest in investigations of these very important biological systems has lead to tremendous increase of the number of research on the computational modeling of lipid bilayers. In this review, we give account of the recent progress in computer simulations of lipid bilayers covering mainly the period of the last 5 years, and covering several selected subjects: development of the force fields for lipid bilayer simulations, studies of the role of lipid unsaturation, the effect of cholesterol and other inclusions on properties of the bilayer, and use of coarse-grained models.
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| 3. |
- Rabinovich, Alexander L., et al.
(författare)
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Bond orientation properties in lipid molecules of membranes : molecular dynamics simulations
- 2014
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Ingår i: 25th IUPAP Conference on Computational Physics (CCP2013). - : Institute of Physics (IOP).
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Konferensbidrag (refereegranskat)abstract
- Atomistic molecular dynamics simulations have been carried out for 16 different fully hydrated phosphatidylcholine lipid bilayers, having 16 or 18 carbon atoms in fully saturated sn-1 chain and from 18 to 22 carbon atoms in sn-2 chain with different degree of unsaturation, with the purpose to investigate the effect of unsaturation on physical properties of lipid bilayers. Special attention has been paid to profiles of C-C and C-H bond order parameters of lipid molecules and the orientational fluctuations of these bond vectors. It was shown that the study of anisotropy degree of bond orientations probability distributions allows distinguishing extended regions with different types of angular fluctuations of bonds in a membrane formed by lipid molecules with unsaturated chains.
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| 4. |
- Rabinovich, Alexander L., et al.
(författare)
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Unperturbed hydrocarbon chains and liquid phase bilayer lipid chains : a computer simulation study
- 2018
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Ingår i: European Biophysics Journal. - : Springer Science and Business Media LLC. - 0175-7571 .- 1432-1017. ; 47:2, s. 109-130
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Tidskriftsartikel (refereegranskat)abstract
- In this work, the properties of saturated and unsaturated fatty acid acyl chains 16:0, 18:0, 18:1(n-9)cis, 18:2(n-6)cis, 18:3(n-3)cis, 18:4(n-3)cis, 18:5(n-3)cis, 20:4(n-6)cis, 20:5(n-3)cis and 22:6(n-3)cis in a bilayer liquid crystalline state and similar hydrocarbon chains (with CH terminal groups instead of C=O groups) in the unperturbed state characterised by a lack of long-range interaction were investigated. The unperturbed hydrocarbon chains were modelled by Monte Carlo simulations at temperature K; sixteen fully hydrated homogeneous liquid crystalline phosphatidylcholine bilayers containing these chains were studied by molecular dynamics simulations at the same temperature. To eliminate effects of the simulation parameters, the molecular dynamics and Monte Carlo simulations were carried out using the same structural data and force field coefficients. From these computer simulations, the average distances between terminal carbon atoms of the chains (end-to-end distances) were calculated and compared. The trends in the end-to-end distances obtained for the unperturbed chains were found to be qualitatively similar to those obtained for the same lipid chains in the bilayers. So, for understanding of a number of processes in biological membranes (e.g., changes in fatty acid composition caused by environmental changes such as temperature and pressure), it is possible to use, at least as a first approximation, the relationships between the structure and properties for unperturbed or isolated hydrocarbon chains.
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| 5. |
- Abdulla, Parosh Aziz, et al.
(författare)
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Verification of Probabilistic Systems with Faulty Communication
- 2002
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Many protocols are designed to operate correctly even in the case where the underlying communication medium is faulty. To capture the behaviour of such protocols, lossy channel systems (LCS) \citeAbJo:lossy:IC have been proposed. In an LCS the communication channels are modelled as FIFO buffers which are unbounded, but also unreliable in the sense that they can nondeterministically lose messages. Recently, several attempts \citeBaEn:plcs,ABIJ:problossy have been made to study probabilistic Lossy Channel Systems (PLCS) in which the probability of losing messages is taken into account. In this paper, we consider a variant of PLCS which is more realistic than those studied in \citeBaEn:plcs,ABIJ:problossy. More precisely, we assume that during each step in the execution of the system, each message may be lost with a certain predefined probability. We show that for such systems the following model checking problem is decidable: to verify whether a given property definable by finite state ømega-automata holds with probability one. We also consider other types of faulty behavior, such as corruption and duplication of messages, and insertion of new messages, and show that the decidability results extend to these models.
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| 7. |
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| 8. |
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| 9. |
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| 10. |
- Rabinovich, A. L., et al.
(författare)
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Computer Simulation of Lipid Membranes : Methodology and Achievements
- 2013
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Ingår i: POLYMER SCIENCE SERIES C. - 1811-2382. ; 55:1, s. 162-180
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Forskningsöversikt (refereegranskat)abstract
- Rapid development of computer power during the last decade has made molecular simulations of lipid bilayers feasible for many research groups, which, together with the growing general interest in investigations of these very important biological systems has lead to tremendous increase of the number of research on the computational modeling of lipid bilayers. In this review, we give account of the recent progress in computer simulations of lipid bilayers covering mainly the period of the last 7 years, and covering only several selected subjects: methodological (development of the force fields for lipid bilayer simulations, use of coarse-grained models) and scientific (studies of the role of lipid unsaturation, and the effect of cholesterol and other inclusions on properties of the bilayer).
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