Molecular dynamics study of vesicle deformation mechanisms

Lipid bilayer membranes are known to form various structures like large sheets or vesicles. When both bilayer leaflets have equal composition, membranes preferentially form flat sheets or spherical vesicles. However, vesicles with a wide variety of shapes, including ellipsoids, discoids, pear-shaped, cup-shaped and budded vesicles, have been shown experimentally. Such shapes were predicted theoretically from energy minimization of continuous sheets as well. We show, using coarse-grained molecular dynamics simulations, how relatively small asymmetry in composition between the two leaflets may result in spontaneously curved bilayers and all these vesicle shapes. Three types of bilayer asymmetry are considered. Firstly, the situation where the headgroup-solvent interaction and thus the lipid packing alters due to a change in pH or ion-concentration of the vesicle interior/exterior (A). Secondly, where asymmetry arises from phase separation of two lipid types (B). And thirdly, where asymmetry arises from growth of one of the bilayer leaflets by incorporation of additional lipids from the solvent (C)

Directional interactions in semiflexible single-chain polymer folding

Precise control over folded conformations of synthetic polymers is highly desirable in the development of functional nanomaterials for diverse applications. Introducing monomers capable of strong intramolecular hydrogen bonding is a promising route to achieve this control. In the present work we report the use of Wang–Landau Monte Carlo simulations of coarse-grained copolymers to explore the design parameters of these systems on their pathway to collapse. The highly directional nature of hydrogen-bonded supramolecular interactions is modelled by a directional non-bonded potential while a harmonic bending potential is used to take into account the flexibility of the polymer chain, thus making it possible to look at the interplay of both factors. The introduction of directional interactions in the copolymer chain leads to a sharper coil-globule collapse when compared to homopolymers composed of isotropic interacting beads only. Simultaneously, some of the stiffness-dependent structural properties become exacerbated when directional beads are present. Finally, from the heat capacity profiles for the different chain stiffness values we are able to distinguish the prevalence of the collapse of the backbone for highly flexible chains, while as chain stiffness increases folding of the co-polymer due to the directional interactions becomes the dominant feature

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide

Coarse Grained Molecular Dynamics

No abstract

Catalyst nano-particle size dependence of Fischer-Tropsch reaction

Computational catalytic studies indicate that the elementary reactions that constitute the Fischer-Tropsch reaction strongly dependent on the structure of the catalyst reaction center. Recent experimental evidence is available that for metallic Fischer-Tropsch catalysts as Co or Ru the very small metallic particles show altered catalytic performance. To distinguish between changes in the relative concentration of reaction centres, changes in chemical reactivity, or rate controlling steps, transient SSITKA data are extremely useful. Here, we present kinetics simulations to extract molecular kinetic information from SSITKA data. We have applied such simulations to interpret published experimental SSITKA data on nano-particle size dependent Fischer-Tropsch (FT) kinetics. The FT catalytic cycle consists of four essential reaction steps. Their relative size determines activity as well as selectivity. The simulated SSITKA indicate three different regimes with different kinetic behaviour, where the two fundamental regimes to distinguish are the monomer formation limit and the chain growth limit. Particle size changes shift kinetics from one to the other regime. We note different effects of supports and choice of metal composition on changes in elementary rates or relative number of reactive centers when the particle size is decreased in the nanometer regime

Chain growth by CO insertion in the Fischer–Tropsch reaction

The molecular kinetics of the mechanism of chain growth through CO insertion of the Fischer–Tropsch reaction is analyzed. The maximum chain growth within the CO insertion chain growth model is predicted if the rate of CO activation to give the C1 species that initiates chain growth balances the rate of chain growth termination. The overall rate of chain growth, determined by the elementary rates of CO insertion, hydrogen-transfer reaction steps, and CO bond cleavage, has to be fast compared to the rate of methanation and the rate of chain growth termination, which gives an oxygenate or hydrocarbon product. However, estimates of rate constants based on quantum-chemical data predict low chain growth within this CO insertion mechanism, which is mainly caused by the relatively slow rate of CO insertion into the growing chain compared to the rate of product desorption. Such a high barrier for CO insertion is consistent with oxygenate formation through the carbide mechanism pathway. A comparison of the derived expressions for CO consumption shows that the rate of chain growth is limiting within the mechanism of chain growth through CO insertion, whereas within the carbide mechanism it is rate controlled by the rate of CO to CHx monomer formation

Computer simulations of cellular group selection reveal mechanism for sustaining cooperation

We present a computer simulation of group selection that is inspired by proto-cell division. Two types of replicating molecules, cooperators and defectors, reside inside membrane bound compartments. Cooperators pay a cost for other replicators in the cell to receive a benefit. Defectors pay no cost and distribute no benefits. The total population size fluctuates as a consequence of births and deaths of individual replicators. Replication requires activated substrates that are generated at a constant rate. Our model includes mutation between cooperators and defectors and selection on two levels: within proto-cells and between proto-cells. We find surprising similarities and differences between models with and without cell death. In both cases, a necessary requirement for group selection to favor some level of cooperation is the continuous formation of a minimum fraction of pure cooperator groups. Subsequently these groups become undermined by defectors, because of mutation and selection within cells. Cell division mechanisms which generate pure cooperator groups more efficiently are stronger promoters of cooperation. For example, division of a proto-cell into many daughter cells is more powerful in enhancing cooperation than division into two daughter cells. Our model differs from previous studies of group selection in that we explore a variety of different features and relax several restrictive assumptions that would be needed for analytic calculations

Estimating ground-state properties of quantum dot arrays using a local Thomas-Fermi-Dirac approximation

PACS. 85.35.Be Quantum well devices (quantum dots, quantum wires, etc.) – 71.10.Ca Electron gas, Fermi gas,

Lipid acrobatics in the membrane fusion arena

In this review, we describe the recent contribution of computer simulation approaches to unravel the molecular details of membrane fusion. Over the past decade, fusion between apposed membranes and vesicles has been studied using a large variety of simulation methods and systems. Despite the variety in techniques, some generic fusion pathways emerge that predict a more complex picture beyond the traditional stalk–pore pathway. Indeed the traditional path-way is confirmed in particle-based simulations, but in addition alternative path-ways are observed in which stalks expand linearly rather than radially, leading to inverted-micellar or asymmetric hemifusion intermediates. Simulations also suggest that the first barrier to fusion is not the formation of the stalk, but rather, the formation of a lipid bridge consisting of one or two lipids only. Fusion occurring during the fission process involves other intermediates, however, and is not just fusion reversed. Finally, recent progress in simulations of peptide and protein-mediated fusion shows how fusion proceeds in a more biologically relevant scenario

Coarse-grained modelling of urea-adamantyl functionalized poly(propylene imine) dendrimers

To investigate the behaviour of poly(propylene imine) dendrimers -- and urea-adamantyl functionalized ones -- in solution using molecular dynamics simulations, we developed a coarse grained model to tackle the relatively large system sizes and time scales needed. Harmonic bond and angle potentials were derived from atomistic simulations using an iterative Boltzmann inversion scheme, modified to incorporate Gaussian fits of the bond and angle distributions. With the coarse grained model and accompanying force field simulations of generations 1 to 7 of both dendrimer types in water were performed. They compare favourably with atomistic simulations and experimental results on the basis of size, shape, monomer density, spacer back-folding and atomic form factor measurements. These results show that the structural dynamics of these dendrimers originate from flexible chains constrained by configurational and spatial requirements. Large dendrimers are more rigid and spherical, while small ones are flexible, alternatively rod-like and globular