Hermes Summer School in Materials Modelling Hi there! Hermes 2016 - a unique international summer school organised by PhD students from around the UK (Imperial College London, Birmingham, Sheffield, Cambridge) and abroad - will take place in July next year. It will bring together cutting edge materials modelling and world class science communication. It will also provide a networking opportunity and the chance to meet the invited speakers in an informal setting. Our confirmed speakers on materials modelling methods are Prof. Kurt Kremer (Max Planck Institute for Polymer Research), Prof. Nicola Spaldin (ETH Zürich), Prof. Sauro Succi (Istituto per le Applicazioni del Calcolo). Further, we have an excellent lineup of science communication speakers, including Craig Carter (Massachusetts institute of Technology), Piero Vitelli (Island 41) and Lulu Pinney (Freelance Infographer), with a key focus on presenting data in an effective and comprehensible manner. Hereby participants will learn the art of communicating science to a wide range of audiences - a skill of growing importance in both scientific research and in the public domain. The event takes place from 27-31 July 2016 at Cumberland Lodge (a former Royal Palace located in Great Windsor Park, Greater London, UK ). Applications are now open, with an early bird deadline of 28 February 2016. For more information see our video http://www.youtube.com/watch?v=FjL8v4rGQpg and our website http://hermessummerschool.org . We would welcome any applications from early stage researchers that have a keen interest in materials modelling, science communication and would enjoy the one-of-a-kind atmosphere in the countryside with like minded people. If you have any questions, please contact us at contactus@hermessummerschool.org . Best wishes, Hermes Team
IJSPM 1004 CONTENTS PAGE.pdf Int. J. Simulation and Process Modelling Vol. 10, No. 4, 2015 Contents 307 Structural optimisation and analysis of internally heat integrated reactive distillation column Shoushi Bo, Jian Wang, Lanyi Sun, Fei Bai and Kang He 315 Android malware detection based on permission combinations Zenghui Liu, Yingxu Lai and Yinong Chen 327 Engineering-oriented simulation platform for laminar cooling process of hot rolled strips Jinxiang Pian, Zhen Wang, Yunlong Zhu, Tianyou Chai and Jiejia Li 334 Customer order fulfilment in mass customisation context – an agent-based approach Khaled Medini 350 A virtualisation simulation environment for data centre Chia-Jung Chen and Rong-Guey Chang 360 Modelling the complexity of emergency department operations using hybrid simulation Norazura Ahmad, Noraida Abdul Ghani, Anton Abdulbasah Kamil and Razman Mat Tahar 372 Simulation and analysis of water concentration in the proton exchange membrane Shizhong Chen, Zhongxian Xia, Shiyu Xing, Xuyang Zhang and Yuhou Wu 383 Contents Index 385 Keywords Index 389 Author Index
CellDesigner http://celldesigner.org/index.html (The models can be generated by manual and simulated with built-in tools ). More tools: http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix Summary: http://sbml.org/SBML_Software_Guide/SBML_Software_Summary Well, I think most of the biological modelling tools would support SBML(Systems Biology Markup Language). The SBML website provides a long list of software. This should be the full list, at least a great list to start with.
今天是MMM2012 SINGAPORE的第一天，原来在BROWN University 的 William Curtin 教授作了第一个报告，这是我听到的最好好的报告之一。他的主题是：Perspective on multiscale materials modelling: Why, What, How, Who, Where and so what? 我主要理解2点 （1）What is multiscale material modelling? Wiki: In engineering , mathematics , physics , meteorology and computer science , multiscale modeling is the field of solving physical problems which have important features at multiple scales, particularly multiple spatial and(or) temporal scales. Important problems include scale linking (Baeurle 2009 , de Pablo 2011 , Knizhnik 2002 , Adamson 2007 ). （2）This internal conference on multiscale material modelling was First held in 2002, after 10 years, what we get? We have key understanding: there are two key points: Different scales information passing and concurrent coupling.for scale information passing, for Lower scale: what is the key information needed to pass up；for higher scale: Theory can accept the appropriate lower-scale information.
The protein-protein docking workflow in Rosetta could be described as following: 1. Low resolution docking command: docking_protocol.linuxgccrelease @flags docking.log This step will create large number of initial pose e.g. 10,000 for full sampling. To fasten the whole process, poses without sidechain would be wise for this step especially if you want to sample even a larger population. 2. Clustering pose command: cluster.linuxgccrelease @flags-cluster cluster.log Clustering was used for largest population pose recognition which usually represent the most likely protein binding mode. The best scored pose in the largest clustered group would be used as the input of next step. 3. Initial pose refinement command: relax.linuxgccrelease @flags relax.log Initial docking in 1st step is a rigid body docking without sidechain and the 2nd would build full atom poses. There are many unfavorable sidechain conformation or atom clashes in the poses comes from step 2. So this step would make the pose much more favorable in energy level. 4. High resolution docking command: docking_protocol.linuxgccrelease @flags2 docking2.log To confirm the docking results, small perturbations can be introduced for such purpose. In this step, thousands of perturbed pose can be generated and the best one can be identified as final docking results according to the scoring function in Rosetta. Tips: Some protocols in Rosetta could support parallel job running, users could use MPI for such kind tasks so that the whole workcould be finished much faster.
Citation: Cavaleri L., Alves J.-H.G.M., Ardhuin F., Babanin A., Banner M., Belibassakis K., Benoit M., (...), Young I. Wave modelling - The state of the art (2007) Progress in Oceanography ,75(4),pp.603-674. Abstract This paper is the product of the wave modelling community and it tries to make a picture of the present situation in this branch of science, exploring the previous and the most recent results and looking ahead towards the solution of the problems we presently face. Both theory and applications are considered. The many faces of the subject imply separate discussions. This is reflected into the single sections, seven of them, each dealing with a specific topic, the whole providing a broad and solid overview of the present state of the art. After an introduction framing the problem and the approach we followed, we deal in sequence with the following subjects: (Section) 2, generation by wind; 3, nonlinear interactions in deep water; 4, white-capping dissipation; 5, nonlinear interactions in shallow water; 6, dissipation at the sea bottom; 7, wave propagation; 8, numerics. The two final sections, 9 and 10, summarize the present situation from a general point of view and try to look at the future developments. Keywords: Wind waves; Windwave generation; Wavewave interaction; Wave propagation; Wave dissipation; Wavecurrent interaction; Numerics Article Outline 1. Introduction 2. Brief review of windwave generation 2.1. Linear theory 2.2. Nonlinear effects 2.3. Gustiness 2.4. Open issues 2.4.1. Damping of low-frequency swells 2.4.2. Momentum transfer for high wind speeds 2.4.3. Quality of modelled wind fields 3. Modelling nonlinear four-wave interactions in discrete spectral wave models 3.1. Theory 3.2. Solution methods 3.3. Properties 3.4. Development in computational methods 3.5. Inter-comparison of computational methods 3.6. Questions and actions 4. Spectral dissipation in deep water 4.1. Theoretical and experimental research of physics of the spectral dissipation 4.1.1. Spectral dissipation due to wave breaking 4.1.2. Waveturbulence interactions 4.1.3. Wavewave modulations 4.2. Modelling the spectral dissipation function 5. Nonlinear interactions in shallow water waves 5.1. Nonlinearity in shallow water 5.2. Deterministic models: time-domain and spectral-domain 5.3. Stochastic models 5.4. Dissipation and wave breaking in shallow water 5.5. Open problems 6. Bottom dissipation 6.1. Wave energy dissipation due to bottom friction 6.1.1. Common formulations for spectral wave models: waves only 6.1.2. Common formulations for spectral wave models: waves and currents 6.1.3. Bottom roughness models for movable beds 6.2. Energy dissipation due to wavebottom interaction 6.3. Discussion and outstanding problems 7. Wave propagation 7.1. Dispersion, geometrical optics and the wave action equation 7.2. Limitations of geometrical optics: diffraction, reflection and random scattering 7.3. Waves over varying currents, nonlinear wave effects and the advection velocity 7.4. Waves blocking 7.5. Unsteady water depths and currents 7.6. Waves in the real ocean 8. Numerics and resolution in large-scale wave modelling 8.1. A description of the problem 8.1.1. Error due to the numerical scheme for geographic propagation on a grid 8.1.2. Diffusion 8.1.3. Numerical dispersion 8.1.4. Combined effect of diffusion and dispersion 8.1.5. Error due to the numerical scheme for spectral propagation 8.1.6. Error due to coarse geographic resolution 8.1.7. Error due to coarse spectral resolution 8.1.8. Errors in source term integration 8.2. Existing solutions 8.2.1. Improved numerical schemes for propagation on a grid 8.2.2. Alternatives to the finite difference schemes on a grid 8.2.3. Addressing error due to coarse geographic resolution 8.2.4. Garden sprinkler effect correction methods 8.2.5. Errors in source term integration 8.3. Relative importance of problem 8.3.1. Error due to the numerical scheme for geographic propagation 8.3.2. Argument 8.3.3. Counter-argument 8.3.4. Error due to the numerical scheme for spectral propagation 8.3.5. Geographic resolution 8.3.6. Spectral resolution 8.3.7. Source term integration 8.4. Future solutions 8.4.1. The numerical scheme for geographic propagation 8.4.2. Geographic resolution 8.4.3. Spectral resolution 8.4.4. Errors in source term integration 8.5. Numerics and resolution: problems particular to finite depth and high resolution applications 9. Where we are 10. Where to go Acknowledgements References
标签: Modelling
