Facilitate SIMD-Code-Generation in the Polyhedral Model by Hardware-aware Automatic Code-Transformation

Although Single Instruction Multiple Data (SIMD) units are available in general purpose processors already since the 1990s, state-of-the-art compilers are often still not capable to fully exploit them, i.e., they may miss to achieve the best possible performance. We present a new hardware-aware and adaptive loop tiling approach that is based on polyhedral transformations and explicitly dedicated to improve on auto-vectorization. It is an extension to the tiling algorithm implemented within the PluTo framework. In its default setting, PluTo uses static tile sizes and is already capable to enable the use of SIMD units but not primarily targeted to optimize it. We experimented with different tile sizes and found a strong relationship between their choice, cache size parameters and performance. Based on this, we designed an adaptive procedure that specifically tiles vectorizable loops with dynamically calculated sizes. The blocking is automatically fitted to the amount of data read in loop iterations, the available SIMD units and the cache sizes. The adaptive parts are built upon straightforward calculations that are experimentally verified and evaluated. Our results show significant improvements in the number of instructions vectorized, cache miss rates and, finally, running times

Mesoscale modelling of polyelectrolyte electrophoresis

The electrophoretic behaviour of flexible polyelectrolyte chains ranging from single monomers up to long fragments of hundred repeat units is studied by a mesoscopic simulation approach. Abstracting from the atomistic details of the polyelectrolyte and the fluid, a coarse-grained molecular dynamics model connected to a mesoscopic fluid described by the Lattice Boltzmann approach is used to investigate free-solution electrophoresis. Our study demonstrates the importance of hydrodynamic interactions for the electrophoretic motion of polyelectrolytes and quantifies the influence of surrounding ions. The length-dependence of the electrophoretic mobility can be understood by evaluating the scaling behavior of the effective charge and the effective friction. The perfect agreement of our results with experimental measurements shows that all chemical details and fluid structure can be safely neglected, and a suitable coarse-grained approach can yield an accurate description of the physics of the problem, provided that electrostatic and hydrodynamic interactions between all entities in the system, i.e., the polyelectrolyte, dissociated counterions, additional salt and the solvent, are properly accounted for. Our model is able to bridge the single molecule regime of a few nm up to macromolecules with contour lengths of more than 100 nm, a length scale that is currently not accessible to atomistic simulations.Comment: 23 pages, 9 figures, to be presented at Faraday Discussion 14

Non-equilibrium molecular dynamics study of an amphiphilic model system

Diese Doktorarbeit untersucht das Verhalten von komplexenFluidenunter Scherung, insbesondere den Einfluss von Scherflüssenauf dieStrukturbildung.Dazu wird ein Modell dieser entworfen, welches imRahmen von Molekulardynamiksimulationen verwendet wird.Zunächst werden Gleichgewichtseigenschaften dieses Modellsuntersucht. Hierbei wird unter anderem die Lage desOrdnungs--Unordnungsübergangs von derisotropen zur lamellaren Phase der Dimere bestimmt.Der Einfluss von Scherflüssen auf diese lamellare Phase wirdnununtersucht und mit analytischen Theorien verglichen. Die Scherung einer parallelen lamellaren Phase ruft eineNeuausrichtung des Direktors in Flussrichtung hervor.Das verursacht eine Verminderung der Schichtdicke mitsteigender Scherrateund führt oberhalb eines Schwellwertes zu Ondulationen.Ein vergleichbares Verhalten wird auch in lamellarenSystemengefunden, an denen in Richtung des Direktors gezogen wird.Allerdings wird festgestellt, dass die Art der Bifurkationenin beidenFällen unterschiedlich ist.Unter Scherung wird ein Übergang von Lamellen parallelerAusrichtung zu senkrechter gefunden.Dabei wird beoachtet, dass die Scherspannung in senkrechterOrientierungniedriger als in der parallelen ist.Dies führt unter bestimmten Bedingungen zum Auftreten vonScherbändern, was auch in Simulationen beobachtet wird. Es ist gelungen mit einem einfachen Modell viele Apsekte desVerhalten vonkomplexen Fluiden wiederzugeben. Die Strukturbildung hängt offensichtlich nurbedingt von lokalen Eigenschaften der Moleküle ab.This thesis is concerned with the behavior of complex fluidsunder shear flows, especially the influence on structureformation.A model of such fluid is developed, which is later used inthe scopeof molecular dynamics (MD) simulations.First equilibrium properties of model are investigated.Then order--disorder transition of a dimer--melt is locatedandinfluence of shear on the lamellar phase is studied.Results are compared to appropriate analytical theories. Shear on parallel oriented lamellae causes a flow alignmentof the director.This alignment leads to a shrinkage in the layer thicknessand above a certain threshold to undulation of the layers.A similar behavior is also found in dilatation simulationsbut thebifurcation at the onset is here different.A transition from a parallel to a perpendicular orientationis alsofound. The shear stress of the perpendicular oriented sampleis lowerthan the shear stress found in the parallel orientation atsame strain rates. This may lead to shear bands which are observed as acoexistence of isotropic and perpendicular regionsexhibitingdifferent local strain rates.This thesis succeeds in describing the essential physics ofspecialcomplex fluids under shear flow with a simple andcomputationalefficient model

A new model for simulating colloidal dynamics

We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of spherical colloidal particles. The solvent is modeled on the level of the lattice-Boltzmann method while the molecular dynamics is done for the solute. The coupling between the two is implemented through a frictional force acting both on the solvent and on the solute, which depends on the relative velocity. A spherical colloidal particle is represented by interaction sites at its surface. We demonstrate that this scheme quantitatively reproduces the translational and rotational diffusion of a neutral spherical particle in a liquid and show preliminary results for a charged spherical particle. We argue that this method is especially advantageous in the case of charged colloids.Comment: For a movie click on the link below Fig

Investigating Interactions of Biomembranes and Alcohols: A Multiscale Approach

We study the interaction of lipid bilayers with short chain alcohols using molecular dynamics on different length scales. We use detailed atomistic modeling and modeling on the length scale where an alcohol is just an amphiphilic dimer. Our strategy is to calibrate a coarse--grained model against the detailed model at selected state points at low alcohol concentration and then perform a wider range of simulations using the coarse--grained model. We get semiquantitative agreement with experiment for the major observables such as order parameter and area per molecule. We find a linear increase of area per molecule with alcohol concentration. The alcohol molecules in both system descriptions are in close contact with the glycerol backbone. Butanol molecules can enter the bilayer to some extent in contrast to the behavior of shorter alcohols. At very high alcohol concentrations we find clearly increased interdigitation between leaflets.Comment: 14 pages, 6 figure

Interoperable job submission and management with GridSAM, JMEA, and UNICORE

Achieving interoperability between Grid infrastructures is required by all us-ers consuming computing time for projects spanning across Grid domain boundaries. Standards naturally evolve slowly and on Grid level only a few have been proposed and widely accepted so far, among them JSDL. This pa-per describes how GridSAM which supports JSDL in combination with JMEA can be used to submit jobs to a UNICORE infrastructure and hence how the number of Grid projects accessible via GridSAM can be increased right now

Polyhedral vesicles

Polyhedral vesicles with a large bending modulus of the membrane such as the gel phase lipid membrane were studied using a Brownian dynamics simulation. The vesicles exhibit various polyhedral morphologies such as tetrahedron and cube shapes. We clarified two types of line defects on the edges of the polyhedrons: cracks of both monolayers at the spontaneous curvature of monolayer $C_{\text {0}}<0$, and a crack of the inner monolayer at $C_{\text {0}}\ge0$. Around the latter defect, the inner monolayer curves positively. Our results suggested that the polyhedral morphology is controlled by $C_{\text {0}}$.Comment: 4 pages, 5 figure

Toy amphiphiles on the computer: What can we learn from generic models?

Generic coarse-grained models are designed such that they are (i) simple and (ii) computationally efficient. They do not aim at representing particular materials, but classes of materials, hence they can offer insight into universal properties of these classes. Here we review generic models for amphiphilic molecules and discuss applications in studies of self-assembling nanostructures and the local structure of bilayer membranes, i.e. their phases and their interactions with nanosized inclusions. Special attention is given to the comparison of simulations with elastic continuum models, which are, in some sense, generic models on a higher coarse-graining level. In many cases, it is possible to bridge quantitatively between generic particle models and continuum models, hence multiscale modeling works on principle. On the other side, generic simulations can help to interpret experiments by providing information that is not accessible otherwise.Comment: Invited feature article, to appear in Macromolecular Rapid Communication

Rheology of Lamellar Liquid Crystals in Two and Three Dimensions: A Simulation Study

We present large scale computer simulations of the nonlinear bulk rheology of lamellar phases (smectic liquid crystals) at moderate to large values of the shear rate (Peclet numbers 10-100), in both two and three dimensions. In two dimensions we find that modest shear rates align the system and stabilise an almost regular lamellar phase, but high shear rates induce the nucleation and proliferation of defects, which in steady state is balanced by the annihilation of defects of opposite sign. The critical shear rate at onset of this second regime is controlled by thermodynamic and kinetic parameters; we offer a scaling analysis that relates the critical shear rate to a critical "capillary number" involving those variables. Within the defect proliferation regime, the defects may be partially annealed by slowly decreasing the applied shear rate; this causes marked memory effects, and history-dependent rheology. Simulations in three dimensions show instead shear-induced ordering even at the highest shear rates studied here. This suggests that the critical shear rate shifts markedly upward on increasing dimensionality. This may in part reflect the reduced constraints on defect motion, allowing them to find and annihilate each other more easily. Residual edge defects in the 3D aligned state mostly point along the flow velocity, an orientation impossible in two dimensions.Comment: 18 pages, 12 figure

Optimizing end-labeled free-solution electrophoresis by increasing the hydrodynamic friction of the drag-tag

We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles. It is specifically shown that the label's drag coefficient is determined by its hydrodynamic size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hydrodynamic drag than the other label types. The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.Comment: 32 pages, 11 figures, submitted to Macromolecule