Towards hybrid molecular simulations

In many biology, chemistry and physics applications molecular simulations can be used to study material and process properties. The level of detail needed in such simulations depends on the application. In some cases quantum mechanical simulations are indispensable. However, traditional ab-initio methods, usually employing plane waves or a linear combination of atomic orbitals as a basis, are extremely expensive in terms of computational as well as memory requirements. The well-known fact that electronic wave functions vary much more rapidly near the atomic nuclei than in inter-atomic regions calls for a multi-resolution approach, allowing one to use low resolution and to add extra resolution only in those regions where necessary, so limiting the costs. This is provided by an alternative basis formed of wavelets. Using such a wavelet basis, a method has been developed for solving electronic structure problems that has been applied successfully to 2D quantum dots and 3D molecular systems. In other cases, it suffices to use effective potentials to describe the atomic interaction instead of the use of the electronic structure, enabling the simulation of larger systems. Molecular dynamics simulations with such effective potentials have been used for a systematic study of surface wettability influence on particle and heat flow in nanochannels, showing that the effects at the solid-gas interface are crucial for the behavior of the whole nanochannel. Again in other cases even coarse grained models can be used where the average behavior of several atoms is combined into a single particle. Such a model, refraining from as much detail as possible while maintaining realistic behavior, has been developed for lipids and with this model the dynamics of membranes and vesicle formation have been studied in detail. A disadvantage of molecular dynamics simulations with effective potentials is that no reactions are possible. Therefore a new method has been developed, where molecular dynamics is coupled with stochastic reactions. Using this method, both unilamellar and multilamellar vesicle formation, and vesicle growth, bursting, and healing are shown. Still larger systems can be simulated using other methods, like the direct simulation Monte Carlo method. However, as shown for nanochannels, these methods are not always accurate enough. But, exploiting again that the finest level of detail is often only needed in part of the domain, a hybrid method has been developed coupling molecular dynamics, where needed for accuracy, and direct simulation Monte Carlo, where possible in order to speed up the calculation. Further development of such hybrid simulations will further increase molecular simulation’s scientific role

Bill 150: The Green Energy Act: An Analysis of Green Energy Politics in Ontario

This paper examines the Green Energy Act (GEA) and the economic circumstances that enabled the bill to become law in Ontario. An analysis of electrical power research, planning, and recommendations over the past forty years was conducted. The findings reveal that a variety of changes led to the approval of the GEA, including an environmentally conscious value shift and the economic recession, and the coincidence of these factors allowed forty years of government funded energy research to culminate in a publicly supported piece of legislation

Smart Solutions: Smart Grid Demokit

Treball desenvolupat dins el marc del programa 'European Project Semester'.The purpose of this report is to justify the design choices of the smart grid demo kit. Something had to be designed to make a smart grid clear for people who have little knowledge about smart grids. The product had to be appealing and clear for people to understand. And eventually should be usable, for example, on an information market. The first part of the research consisted of looking how to shape the whole system. How the 'tiles' had to look to be interactive for users and what they should feature. One part of this was doing research to get to know more about the already existing knowledge amount users. Another research investigated what appeals the most to the users. After this, a concept was created in compliance with the group and the client. The concept consists of hexagonal tiles, each with a different function: houses, solar panels, wind turbines, factories and energy storages. These tiles are all different parts of a smart grid. When combining these tiles, it can be made clear to users how smart grids work. The tiles are fabricated using a combination of 3D printing and laser cutting. The tiles have laser cut symbols on top of them to show what part of the smart grid they are. Digital LED strips are on top of the tiles to show the direction of the energy flow, and the colors indicate if the tile is producing or consuming power from the grid. The tiles are connected to each other by the so called “grid blocks”. These blocks make up the central power grid and are also lighting up by LED strips. Each tile is equipped with a microcontroller which controls the LED strips and makes it possible for the different tiles to “talk” with each other. Using this, the central tile knows which tiles are connected to the system. The central tile controls all tiles and runs the simulation of the smart grid. For further development of the project, it can be investigated how to control and adjust the system from an external system, for example by a tablet. The final product consists of five tiles connected by seven grid blocks which show how a smart grid works

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)

Coarse Grained Molecular Dynamics Simulations of the Fusion of Vesicles Incorporating Water Channels

As the dynamics of the cell membrane and the working mechanisms of proteins cannot be readily asserted at a molecular level, many different hypotheses exist that try to predict and explain these processes, for instance vesicle fusion. Therefore, we use coarse grained molecular dynamics simulations to elucidate the fusion mechanism of vesicles. The implementation of this method with hydrophilic and hydrophobic particles is known for its valid representation of bilayers. With a minimalistic approach, using only 3 atom types, 12 atoms per two-tailed phospholipids and incorporating only a bond potential and Lennard-Jones potential, phospholipid bilayers and vesicles can be simulated exhibiting authentic dynamics. We have simulated the spontaneous full fusion of both tiny (6 nm diameter) and larger (13 nm diameter) vesicles. We showed that, without applying constraints to the vesicles, the initial contact between two fusing vesicles, the stalk, is initiated by a bridging lipid tail that extends from the membrane spontaneously. Subsequently it is observed that the evolution of the stalk can proceed via two pathways, anisotropic and radial expansion, which is in accordance with literature. Contrary to the spherical vesicles of in vitro experiments, the fused vesicles remain tubular since the internal volume of these vesicles is too small compared to their membrane area. While the lipid bilayer has some permeability for water, it is not high enough to allow for the large flux required to equilibrate the vesicle content in the time accessible to our simulations. To increase the membrane permeability, we incorporate proteinaceous water channels, by applying the coarse grained technique to aquaporin. Even though incorporating water channels in the vesicles does significantly increase water permeability, the vesicles do not become spherical. Presumably the lipids have to be redistributed as well

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