The Influence of Bilayer Composition on the Gel to Liquid Crystalline Transition

Debnath, Ananya; Ayappa, K. G.; Kumaran, V.; Maiti, Prabal K.

doi:10.1021/jp901551d

Cited by 32 publications

(49 citation statements)

References 65 publications

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“…Similar increase in the membrane thickness has been observed in DPD simulations of polymer free bilayers 12 as well as in united atom models of mixed surfactant membranes with explicit ions and water. 28 Several mechanisms for this swelling have been proposed in the literature and summarized within the context of observations in DPD simulations by Kranenburg and Smit. 12 Figure 5 illustrates the density distributions for the solvent and bilayer particles at two different temperatures and different grafting fractions for N p = 10.…”

Section: A Influence Of Grafted Polymer On Bilayer Melting Transitionmentioning

confidence: 99%

Melting and mechanical properties of polymer grafted lipid bilayer membranes

Thakkar

Ayappa

2011

The Journal of Chemical Physics

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The influence of polymer grafting on the phase behavior and elastic properties of two tail lipid bilayers have been investigated using dissipative particle dynamics simulations. For the range of polymer lengths studied, the L(c) to L(α) transition temperature is not significantly affected for grafting fractions, G(f) between 0.16 and 0.25. A decrease in the transition temperature is observed at a relatively high grafting fraction, G(f) = 0.36. At low temperatures, a small increase in the area per head group, a(h), at high G(f) leads to an increase in the chain tilt, inducing order in the bilayer and the solvent. The onset of the phase transition occurs with the nucleation of small patches of thinned membrane which grow and form continuous domains as the temperature increases. This region is the co-existence region between the L(β)(thick) and the L(α)(thin) phases. The simulation results for the membrane area expansion as a function of the grafting density conform extremely well to the scalings predicted by self-consistent mean field theories. We find that the bending modulus shows a small decrease for short polymers (number of beads, N(p) = 10) and low G(f), where the influence of polymer is reduced when compared to the effect of the increased a(h). For longer polymers (N(p) > 15), the bending modulus increases monotonically with increase in grafted polymer. Using the results from mean field theory, we partition the contributions to the bending modulus from the membrane and the polymer and show that the dominant contribution to the increased bending modulus arises from the grafted polymer.

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Section: A Influence Of Grafted Polymer On Bilayer Melting Transitionmentioning

confidence: 99%

Melting and mechanical properties of polymer grafted lipid bilayer membranes

Thakkar

Ayappa

2011

The Journal of Chemical Physics

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“…In view of its biological relevance [26 -33], most simulation studies have focused on the characterisation of the LC phase, but some have also considered the GL phase [29,34 -38]. Statistical [39] and coarse-grained [6,40] models have been used to study the GL $ LC phase transition, but atomistic MD simulations that systematically investigate this process are relatively scarce [38,41].…”

Section: Introductionmentioning

confidence: 99%

Phase-transition properties of glycerol-monopalmitate lipid bilayers investigated by molecular dynamics simulation: influence of the system size and force-field parameters

Laner

Horta

Hünenberger

2013

Molecular Simulation

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Phase-transition properties of glycerol-1-monopalmitate (GMP) bilayers are investigated using explicit-solvent molecular dynamics (MD) simulations, initiated from structures appropriate for the gel (GL) or liquid crystal (LC) phases, and carried out at different hydration levels and temperatures. Building up on a previous study and based on 600 ns simulations, the influence of the system size and of the force field on the equilibrium thermodynamic and dynamic parameters of the bilayers in the GL and LC phases, as well as on the temperature T m and properties of the GL $ LC phase transition, are analysed. Qualitatively speaking, the results agree with the available experimental data for the area per lipid in the two phases and for the phase-transition temperatures at the three hydration levels irrespective of the selected model parameters. They also suggest that the total number of hydrogen bonds formed between a lipid headgroup and its environment is essentially constant, amounting to about four in both the LC and the GL phases. Quantitatively speaking, the dependence of T m on the hydration level is found to be non-systematic across the different combinations of model parameters. This results in part from a sensitivity of the results on the system size and force-field parameters but also from the limited accuracy of the bracketing approach employed here to estimate T m . Finally, a simple kinetic model is proposed to account for the timescales of the transitions. This model involves enthalpy and entropy increases of about 26 kJ mol 21 and 83 J mol 21 K 21 per lipid, upon going from the GL to the LC phase. The transition state is associated with activation parameters corresponding to 13% and 11%, respectively, of these values along the GL ! LC transition, resulting in an activation free energy of about 0.3 kJ mol 21 per lipid at T m .

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“…Contact formation (cyclization) between the ends of a long polymer has been intensely studied both experimentally [1,2] and theoretically [3,4,5,6,7,8,9]. More recently, the kinetics of loop formation has become increasingly important largely because of its relevance to DNA looping [10,11] as well as protein [12,13,14,15,16,17,18,19] and RNA folding [20].…”

Section: Introductionmentioning

confidence: 99%

Kinetics of Loop Formation in Polymer Chains

et al. 2008

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We investigate the kinetics of loop formation in ideal flexible polymer chains (the Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is tau(c) approximately tau(0)N(2) (where tau(0) is a microscopic time scale and N is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when a, the capture radius for contact formation, exceeds b, the average distance between two connected beads. Simulations also show that when a < b, tau(c) approximately N(alpha)(tau), where 1.5 < alpha(tau) < or = 2 in the range 7 < N < 200 used in the simulations. By using a diffusion coefficient that is dependent on the length scales a and b (with a < b), which captures the two-stage mechanism by which looping occurs when a < b, we obtain an analytic expression for tauc that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly effected when interactions between monomers are taken into account. Remarkably, for N < 100, the values of tau(c) decrease by more than 2 orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for tau(c) to a power law in N (tau(c) approximately N(alpha)(tau)) show that alpha(tau) varies from about 2.4 in a good solvent to about 1.0 in poor solvents. The effective exponent alpha(tau) decreases as the strength of the attractive monomer-monomer interactions increases. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain. The time for contact formation between beads that are interior to the chain in good solvents changes nonmonotonically as the loop length varies. In contrast, the variation in interior loop closure time is monotonic in poor solvents. The implications of our results for contact formation in polypeptide chains, RNA, and single-stranded DNA are briefly outlined.

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The Influence of Bilayer Composition on the Gel to Liquid Crystalline Transition

Cited by 32 publications

References 65 publications

Melting and mechanical properties of polymer grafted lipid bilayer membranes

Melting and mechanical properties of polymer grafted lipid bilayer membranes

Phase-transition properties of glycerol-monopalmitate lipid bilayers investigated by molecular dynamics simulation: influence of the system size and force-field parameters

Kinetics of Loop Formation in Polymer Chains

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