We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.

Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in one domain of the ripple is found to be that of a splayed gel; in the other domain the lipids are gel-like and fully interdigitated. In the concave part of the kink region between the domains the lipids are disordered. The results are consistent with the experimental information available and provide an atomic-level model that may be tested by further experiments. molecular dynamics simulation ͉ structural model L ipid bilayers are studied widely as models for biological membranes (1). Biological membranes have many components. The complexity of the biological membrane facilitates a wide range of functionalities. Among these, order-disorder transitions within the lipid matrix are believed to play a crucial role in the regulation of protein function (2). Single-component phosphatidylcholine (lecithin) lipid aggregates in water, however, already show rich phase behavior (3). Upon cooling lecithin bilayers from the liquid crystalline (L ␣ ) state to a temperature below the main transition temperature, x-ray studies have revealed the formation of rippled bilayers (4-8). This phase is denoted P ␤ Ј. Upon further cooling below the pretransition temperature, a gel phase is found in which the lipid tails are fully stretched and ordered in a hexagonal array, with a uniform tilt with respect to the bilayer normal. This phase is denoted L ␤ Ј. X-ray studies of the P ␤ Ј phase have been used to obtain the ripple length ( r ), the stacking repeat distance (d), and the oblique angle (␥), as shown in Fig. 1 (5). The ripple is asymmetric (sawtooth-like) and consists of a major domain (M domain) and a minor domain (m domain) (6), connected by a kink. Several theories have been developed to explain the appearance of this kink. These theories either emphasize the packing frustration caused by the difference in steric requirements between the head groups and the tails of the lipids or emphasize the interaction between neighboring bilayers (for reviews, see refs. 5 and 9). Because the ripple phase is intermediate between the fluid and gel phases, study of its properties contributes to our understanding of the balance of forces within the lipid matrix and the resulting molecular organization. These insights are likely to be relevant to order-disorder transitions in a wider sense.The organization of the lipids in the domains of the ripple is unknown (10). It is generally agreed that the thickness of the lipid layer differs in the two domains (6). From x-ray scattering data the thickness of the bilayer in the M domain is found to be comparable to that found in the L ␤ Ј phase. The thickness of the bilayer in the m domain is found to be considerably smaller. It is consistent with the thickness found in the L ␣ phase, but there is no clear evid...

A two-dimensional nonlocal version of continuum crystal plasticity theory is proposed, which is based on a statistical-mechanics description of the collective behavior of dislocations coupled to standard small-strain crystal continuum kinematics for single slip. It involves a set of transport equations for the total dislocation density ÿeld and for the net-Burgers vector density ÿeld, which include a slip system back stress associated to the gradient of the net-Burgers vector density. The theory is applied to the problem of shearing of a two-dimensional composite material with elastic reinforcements in a crystalline matrix. The results are compared to those of discrete dislocation simulations of the same problem. The continuum theory is shown to be able to pick up the distinct dependence on the size of the reinforcing particles for one of the morphologies being studied. Also, its predictions are consistent with the discrete dislocation results during unloading, showing a pronounced Bauschinger e ect. None of these features are captured by standard local plasticity theories.

The tension-driven gating process of MscL from Mycobacterium tuberculosis, Tb-MscL, has been addressed at near-atomic detail using coarse-grained molecular dynamics simulations. To perform the simulations, a novel coarse-grained peptide model based on a thermodynamic parameterization of the amino-acid side chains has been applied. Both the wild-type Tb-MscL and its gain-of-function mutant V21D embedded in a solvated lipid bilayer have been studied. To mimic hypoosmotic shock conditions, simulations were performed at increasing levels of membrane tension approaching the rupture threshold of the lipid bilayer. Both the wild-type and the mutant channel are found to undergo significant conformational changes in accordance with an irislike expansion mechanism, reaching a conducting state on a microsecond timescale. The most pronounced expansion of the pore has been observed for the V21D mutant, which is consistent with the experimentally shown gain-of-function phenotype of the V21D mutant.

We have recently proposed a nonlocal continuum crystal plasticity theory for single slip, which is based on a statistical-mechanics description of the collective behavior of dislocations in two dimensions. In the present paper we address the extension of the theory from single slip to multiple slip. Continuum dislocation dynamics in multiple slip is defined and coupled to the small-strain framework of conventional continuum crystal plasticity. Dislocation nucleation, the material resistance to dislocation glide and dislocation annihilation are included in the formulation. Various nonlocal interaction laws between different slip systems are considered on phenomenological grounds. To validate the theory we compare with the results of dislocation simulations of two boundary value problems. One problem is simple shearing of a crystalline strip constrained between two rigid and impenetrable walls. Key features are the formation of boundary layers and the size dependence of the response in the case of symmetric double slip. The other problem is bending of a single crystal strip under double slip. The bending moment versus rotation angle and the evolution of the dislocation structure are analyzed for different slip orientations and specimen sizes.

We have recently proposed a nonlocal continuum crystal plasticity theory that is based on a statistical-mechanics description of the collective behaviour of dislocations. Kinetic equations for the dislocation density fields have been derived from the equation of motion of individual dislocations and have been coupled to a continuum description of single slip. Dislocation nucleation, the material resistance to dislocation glide and dislocation annihilation are included in the formulation. The theory is applied, in this paper, to the problem of bending of a single-crystal strip in plane strain, using parameter values obtained previously from fitting to discrete dislocation results of a different boundary value problem. A numerical solution of the problem is obtained using a finite element method. The bending moment versus rotation angle and the evolution of the dislocation structure are analysed for different orientations and specimen sizes with due consideration of the role of geometrically necessary dislocations. The results are compared to those of discrete dislocation simulations of the same problem. Without any additional fitting of the parameters, the continuum theory is able to describe the dependence on slip plane orientation and on specimen size.

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