Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D < n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved.

The CACTOS Vision of Context-Aware Cloud Topology Optimization and Simulation

Recent advances in hardware development coupled with the rapid adoption and broad applicability of cloud computing have introduced widespread heterogeneity in data centers, significantly complicating the management of cloud applications and data center resources. This paper presents the CACTOS approach to cloud infrastructure automation and optimization, which addresses heterogeneity through a combination of in-depth analysis of application behavior with insights from commercial cloud providers. The aim of the approach is threefold: to model applications and data center resources, to simulate applications and resources for planning and operation, and to optimize application deployment and resource use in an autonomic manner. The approach is based on case studies from the areas of business analytics, enterprise applications, and scientific computing.

Energy-Aware Rate and Description Allocation Optimized Video Streaming for Mobile D2D Communications

The proliferation problem of video streaming applications and mobile devices has prompted wireless network operators to put more efforts into improving quality of experience (QoE) while saving resources that are needed for high transmission rate and large size of video streaming. To deal with this problem, we propose an energy-aware rate and description allocation optimization method for video streaming in cellular network assisted device-to-device (D2D) communications. In particular, we allocate the optimal bit rate to each layer of video segments and packetize the segments into multiple descriptions with embedded forward error correction (FEC) for realtime streaming without retransmission. Simultaneously, the optimal number of descriptions is allocated to each D2D helper for transmission. The two allocation processes are done according to the access rate of segments, channel state information (CSI) of D2D requester, and remaining energy of helpers, to gain the highest optimization performance. Simulation results demonstrate that our proposed method (named OPT) significantly enhances the performance of video streaming in terms of high QoE and energy saving.

Joint Optimization of Area Spectral Efficiency and Delay over PPP Interfered Ad-Hoc Networks

To evaluate the performance of the co-channel transmission based communication, we propose a new metric for area spectral efficiency (ASE) of interference limited ad-hoc network by assuming that the nodes are randomly distributed according to a Poisson point processes (PPP). We introduce a utility function, U = ASE/delay and derive the optimal ALOHA transmission probability p and the SIR threshold τ that jointly maximize the ASE and minimize the local delay. Finally, numerical results have been conducted to confirm that the joint optimization based on the U metric achieves a significant performance gain compared to conventional systems.

Ab initio simulation of charged slabs at constant chemical potential

We present a practical scheme for performing ab initio supercell calculations of charged slabs at constant electron chemical potential mu, rather than at constant number of electrons N-e. To this end, we define the chemical potential relative to a plane (or "reference electrode") at a finite distance from the slab (the distance should reflect the particular geometry of the situation being modeled). To avoid a net charge in the supercell, and thus make possible a standard supercell calculation, we restore the electroneutrality of the periodically repeated unit by means of a compensating charge, whose contribution to the total energy and potential is subtracted afterwards. The "constant mu" mode enables one to perform supercell calculation on slabs, where the slab is kept at a fixed potential relative to the reference electrode. We expect this to be useful in modeling many experimental situations, especially in electro-chemistry. (C) 2001 American Institute of Physics.

Analytical description of stochastic field-Line wandering in magnetic turbulence

A nonperturbative nonlinear statistical approach is presented to describe turbulent magnetic systems embedded in a uniform mean magnetic field. A general formula in the form of an ordinary differential equation for magnetic field-line wandering (random walk) is derived. By considering the solution of this equation for different limits several new results are obtained. As an example, it is demonstrated that the stochastic wandering of magnetic field-lines in a two-component turbulence model leads to superdiffusive transport, contrary to an existing diffusive picture. The validity of quasilinear theory for field-line wandering is discussed, with respect to different turbulence geometry models, and previous diffusive results are shown to be deduced in appropriate limits.

Laser-Driven Proton Beams: Acceleration Mechanism, Beam Optimization, and Radiographic Applications

This paper reviews recent experimental activity in the area of optimization, control, and application of laser accelerated proton beams, carried out at the Rutherford Appleton Laboratory and the Laboratoire pour l’Utilisation des Lasers Intenses 100 TW facility in France. In particular, experiments have investigated the role of the scale length at the rear of the plasma in reducing target-normal-sheath-acceleration acceleration efficiency. Results match with recent theoretical predictions and provide information in view of the feasibility of proton fast-ignition applications. Experiments aiming to control the divergence of the proton beams have investigated the use of a laser-triggered microlens, which employs laser-driven transient electric fields in cylindrical geometry, enabling to focus the emitted
protons and select monochromatic beam lets out of the broad spectrum beam. This approach could be advantageous in view
of a variety of applications. The use of laser-driven protons as a particle probe for transient field detection has been developed and
applied to a number of experimental conditions. Recent work in this area has focused on the detection of large-scale self-generated magnetic fields in laser-produced plasmas and the investigation of fields associated to the propagation of relativistic electron both on the surface and in the bulk of targets irradiated by high-power laser pulses.

Using simulation to assess cardiac first-responder schemes exhibiting stochastic and spatial complexities

A Monte-Carlo simulation-based model has been constructed to assess a public health scheme involving mobile-volunteer cardiac First-Responders. The scheme being assessed aims to improve survival of Sudden-Cardiac-Arrest (SCA) patients, through reducing the time until administration of life-saving defibrillation treatment, with volunteers being paged to respond to possible SCA incidents alongside the Emergency Medical Services. The need for a model, for example, to assess the impact of the scheme in different geographical regions, was apparent upon collection of observational trial data (given it exhibited stochastic and spatial complexities). The simulation-based model developed has been validated and then used to assess the scheme's benefits in an alternative rural region (not a part of the original trial). These illustrative results conclude that the scheme may not be the most efficient use of National Health Service resources in this geographical region, thus demonstrating the importance and usefulness of simulation modelling in aiding decision making.

Optimization of heat transfer characteristics, flow distribution, and reaction processing for a microstructured reactor/heat-exchanger for optimal performance in platinum catalyzed ammonia oxidation

The present work is focused on the demonstration of the advantages of miniaturized reactor systems which are essential for processes where potential for considerable heat transfer intensification exists as well as for kinetic studies of highly exothermic reactions at near-isothermal conditions. The heat transfer characteristics of four different cross-flow designs of a microstructured reactor/heat-exchanger (MRHE) were studied by CFD simulation using ammonia oxidation on a platinum catalyst as a model reaction. An appropriate distribution of the nitrogen flow used as a coolant can decrease drastically the axial temperature gradient in the reaction channels. In case of a microreactor made of a highly conductive material, the temperature non-uniformity in the reactor is strongly dependent on the distance between the reaction and cooling channels. Appropriate design of a single periodic reactor/heat-exchanger unit, combined with a non-uniform inlet coolant distribution, reduces the temperature gradients in the complete reactor to less than 4degreesC, even at conditions corresponding to an adiabatic temperature rise of about 1400degreesC, which are generally not accessible in conventional reactors because of the danger of runaway reactions. To obtain the required coolant flow distribution, an optimization study was performed to acquire the particular geometry of the inlet and outlet chambers in the microreactor/heat-exchanger. The predicted temperature profiles are in good agreement with experimental data from temperature sensors located along the reactant and coolant flows. The results demonstrate the clear potential of microstructured devices as reliable instruments for kinetic research as well as for proper heat management in the case of highly exothermic reactions. (C) 2002 Elsevier Science B.V. All rights reserved.

Influence of test methodology and probe geometry on nanoscale fatigue mechanisms of diamond-like carbon thin film

The aim of this paper is to investigate the mechanism of nanoscale fatigue using nano-impact and multiple-loading cycle nanoindentation tests, and compare it to previously reported findings of nanoscale fatigue using integrated stiffness and depth sensing approach. Two different film loading mechanism, loading history and indenter shapes are compared to comprehend the influence of test methodology on the nanoscale fatigue failure mechanisms of DLC film. An amorphous 100 nm thick DLC film was deposited on a 500 μm silicon substrate using sputtering of graphite target in pure argon atmosphere. Nano-impact and multiple-load cycle indentations were performed in the load range of 100 μN to 1000 μN and 0.1 mN to 100 mN, respectively. Both test types were conducted using conical and Berkovich indenters. Results indicate that for the case of conical indenter, the combination of nano-impact and multiple-loading cycle nanoindentation tests provide information on the life and failure mechanism of DLC film, which is comparable to the previously reported findings using the integrated stiffness and depth sensing approach. However, the comparison of results is sensitive to the applied load, loading mechanism, test-type and probe geometry. The loading mechanism and load history is therefore critical which also leads to two different definitions of film failure. The choice of exact test methodology, load and probe geometry should therefore be dictated by the in-service tribological conditions, and where necessary both test methodologies can be used to provide better insights of failure mechanism. Molecular dynamics (MD) simulations of the elastic response of nanoindentation is reported, which indicates that the elastic modulus of the film measured using MD simulation was higher than that experimentally measured. This difference is attributed to the factors related to the presence of material defects, crystal structure, residual stress, indenter geometry and loading/unloading rate differences between the MD and experimental results.

Defining Simulation Intent

Defining Simulation Intent involves capturing high level modelling and idealisation decisions in order to create an efficient and fit-for-purpose analysis. These decisions are recorded as attributes of the decomposed design space.

An approach to defining Simulation Intent is described utilising three known technologies: Cellular Modelling, the subdivision of space into volumes of simulation significance (structures, gas paths, internal and external airflows etc.); Equivalencing, maintaining a consistent and coherent description
of the equivalent representations of the spatial cells in different analysis models; and Virtual Topology, which offers tools for partitioning and de-partitioning the model without disturbing the manufacturing oriented design geometry. The end result is a convenient framework to which high level analysis attributes can be applied, and from which detailed analysis models can be generated
with a high degree of controllability, repeatability and automation. There are multiple novel aspects to the approach, including its reusability, robustness to changes in model topology and the inherent links created between analysis models at different levels of fidelity and physics.

By utilising Simulation Intent, CAD modelling for simulation can be fully exploited and simulation work-flows can be more readily automated, reducing many repetitive manual tasks (e.g. the definition of appropriate coupling between elements of different types and the application of boundary conditions). The approach has been implemented and tested with practical examples, and
significant benefits are demonstrated.