Simulation and Modeling

Simulation and Modeling

  • Troestler Christophe added an answer:
    What is the best TeX editor for LaTeX?
    Give your opinion especially on your experience whether good or bad on TeX editors like LEd, TeXMaker, TeXStudio, Notepad++, WinEdt (Paid), ....

    Some quick ref.
  • Ali Gelali added an answer:
    Radially averaged power spectral density (PSD) in 3D space?
    Most people plot PSD with time series data at some space and MATLAB has a function for it. Is there any inbuilt function or file exchange function which could be used with 2D and 3D data with its grids to get power spectral density?
    Ali Gelali · Islamic Azad University Kermanshah Branch

    Hi Dear

  • Dennis Schmitz added an answer:
    How can I create a power law filter in matlab ( 1/f^x )?
    Eventually what I need is a power law noise with adjustable exponent (x) between 2 and 3, so I'm planning to filter the white noise with this filter.
    Dennis Schmitz · Terumo

    I have spent the past several days working on a high quality pink noise generator, and have misgivings about the rigor of any method that tries to scale fft output and then transform it back. (These misgivings are mostly based on the unhappy reaction of Dr. Burrus (of Parks and Burrus) whenever anyone suggested it.)

    I found this reference:

    which makes a solid case for using a filter over white noise to produce 1/f noise.

    There are links to C code and Matlab code. Also, attached is Python code that implements their algorithm directly (I'm not the author, but is freely distributable).

  • Hakeem Niyas added an answer:
    Does anyone use COMSOL Multiphysics for simulation?
    Is anyone working in this area - Electromagnetism, Heat transfer and CFD.
    Hakeem Niyas · Indian Institute of Technology Guwahati

    I am working on CFD & HT

  • Muhammad Zakarya added an answer:
    How to simulate a trusted cloud computing platform?
    Does anyone know any tools that can be used to simulate Trusted Cloud Computing models. Can we simulate this one in CloudSim? or do we need to create our own API for CloudSim for the support of trusted computing? Your comments would be highly appreciated.
    Muhammad Zakarya · Abdul Wali Khan University Mardan

    still there is an option to implement your own security algorithms in cloudsim. I think its very easy to consider in event driven programming

  • Arafat A. Bhuiyan added an answer:
    Which computer language (C, Fortran, Visual basic) is faster in the CFD using FEM? Do any of them work with VBE?
    I'm working on a CFD project using FEM, the time elapsed for every run is high to get results. Now I'm using MATLAB but I want to change coding language. Which program do you suggest?
    Arafat A. Bhuiyan · Swinburne University of Technology

    Fortran is the appropriate

  • Hoskoti L added an answer:
    I need tutorial materials in modeling and simulation of wave propagation(Lamb,P,S and Ultrasonic) using ANSYS. Thanks in advance
    Modeling and simulation of Acoustics wave propagation

    Find the attachment .

    I hope i will be helpful to you

  • Sankar Padmanabhan added an answer:
    Why most transaction in ieee accept modelling and simulation?
    Computer simulation and modelling on networks
    Sankar Padmanabhan · Jerusalem College of Engineering

    It should contain some novelty in  the research work

  • Fabio Mavelli added an answer:
    How can I implicate two sets of differential equations with different time scaling simultaneously (second and millisecond) in Matlab R2013a simulink?
    We have two sets of differential equations for neuron dynamics and astrocyte Ca2+ oscillations but with different time scales (Di Garbo 2009). Is it correct that for simulation of these sets simultaneously you must use integrators with 1000 coefficient for rescaling one set?
    Fabio Mavelli · Università degli Studi di Bari Aldo Moro

    of course, you can approximate the ODE set by decoupling the equations, but my suggestion is firstly try a MATLAB numerical procedure for stiff ODE set that could solve easily your problem

  • Andrea Presciutti added an answer:
    What is the difference between average irradiance and instant solar irradiance and their maximum value?

    I want to know what is the maximum solar irradiance (W/meter square) in India and when do we get solar irradiation of 1000 W/meter square.

    Andrea Presciutti · Università degli Studi di Perugia

    1365 W/m2 is the solar costant that can change from 1350 to 1367 W/m2 and such value is measured in the space (out of the atmosphere)

  • Amare Teklay asked a question:
    How is complexity science applied in economics?

    I am an economist by training but I have never been satisfied with my choice-I wish I studied the natural science for my bachelors. Recently, I have seen complexity science as an interdisciplinary field which knows little or no boundary among all relevant aspects of a problem. Can anyone help me learn more about it? In particular, I am looking for information on the best book to read as a beginner; best researchers to get in touch with or even best programs such as short courses to take etc.
    If you're a economist, I don't mean economics is bad, but my preference is different. 

  • Sepideh Moshtagh added an answer:
    During metabolism of thiobacilli, why does the network become infeasible when sulfur is added?

    I am about to reconstruct a metabolic network for a chemelithiautotroph thiobacillus. It uses Co2 as the carbon source and Thiosulfate as the energy source. I have setted a central metabolsim for this micro organism inculding Calvin cycle (The dark part), TCA cycle, Glycolysis and other common pathway but when in comes to sulfur metabolsim in which Thiosulfate is consumed and terationathe is produced then terathionate oxidizes and so on. When I add sulfur metabolsim network become infeasible and there is no link between central metabolsim and sulfur. I'd be very thankful if anyone could help me.

    Sepideh Moshtagh · Iran University of Science and Technology

    Hello Jack

    Thanks a lot for answering my question,I used the following reaction to create a link between sulfur metabolism and central metabolism but it did not work


    the p/o ration for this organism is 1.12.

    Due to the infeasibility I can not expand the network now it just includes central metabolism and 4 reaction of sulfur metabolism one for thiosulfate exchange,2 for thiosulfate oxidation and one for tetrathionate conversion to sulfate and sulfur

  • Rita Pizzi asked a question:
    Contributions to a Frontier Research Topic on NCC

    I was proposed as  Topic Editor of a Frontiers Research Topic , and I am searching for contributions to the following subject:

    Computational methods to explore Neural Correlates of Consciousness.

    Frontiers joined the Nature Publishing Group in 2013.

    If you are interested in co-hosting this Research Topic or in proposing contributions, please contact me. 


  • Hamzeh Noor added an answer:
    Which model is best in predicting reservoir sedimentation due to the effect of land use and land cover change?
    Using different models except SWAT model.
    Hamzeh Noor · Tarbiat Modares University
      It depends on your goal.
    Your search for distributied model or a lamp on? or event base or continuous model? Your goal,  available data, scenario which you are considering change in model, determine the model
  • Ljubomir Jacić added an answer:
    Are you interested in Modelling and Simulation?
    The Spring Simulation Multi-Conference 2015 (SpringSim'15) brings leading experts in various domains of Modeling and Simulation together.
    Ljubomir Jacić · Technical College Požarevac
    You are welcome dear @Gregory!
  • Ruchi Tiwari added an answer:
    Is self-citation good for showing the continuity of the research and avoiding self plagiarism? Please share your experience and thought.
    Self citation can help paper reviewers to check on the history of the author(s) and research topics.

    Any comment or opinion are welcome.

  • Luc-Andre Gregoire added an answer:
    Can we use matrix converters for simultaneous ac-dc transmission systems?
    hvdc systems
    Luc-Andre Gregoire · École de Technologie Supérieure
    Matrix converter usually comes with bulky filter which could be troublesome in HVDC application. Also there is no DC-bus in matrix converter.

    If it is AC-AC converter, "Generalised analytical methods and current-energy
    control design for modular multilevel cascade
    converter" from Yun Wan shows such an application using modular multilevel converter you could achieve similar (see fig 3c)
  • Yónatan Calderón Pérez added an answer:
    Does anyone have any suggestions for a Monte Carlo Simulation of electron Solid interaction (~1-30 KeV range)?
    I am trying to use experimental optical data to find the inelastic scattering cross sections for different materials. I am also aware of the pyPENELOPE program which does the same. But I'm writing it from scratch and implementing it on a GPU. I've read a couple of papers by Fernandez-Varea, Salvat et. al. and Penn etc. but they are not instructional. I was wondering if anybody had inputs on this.
    Yónatan Calderón Pérez · Autonomous University of Barcelona
    I have no experience with the other softwares mentioned, but i can tell you that geant4 includes a very precise physics list for low energy electrons.

    Here's a link:
  • Kevin R Keane added an answer:
    What are the new mathematical foundations for assessing and aggregating risks?
    Many of the current methods for assessing risks depends on probabilities and events as randomly distributed occurences. This does not fit with intentional acts that can be persistent, reoccuring, focused etc. I am looking for any new work on providing new methods for assessing events that are not randomly distributed and for aggregating such risks. A closely related topic would be any new work on aggregating very low probability or rare events. Does anyone have a pointer or suggestions for who to look at and where to look?
    Kevin R Keane · University at Buffalo, The State University of New York
    I’m not familiar with your domain, so I’ll make some general comments on dealing with “rare” events that happen too often.

    Perhaps the “rare” events occur too often with respect to a particular proposed probability model. A mixture model, entertaining other distributions or parameterizations, would allow various component models in the mixture to address various modes of reality (non-intentional events, intentional events, …)

    If you believe events group in time or location (or some other dimension), you might want to entertain models similar to MRFs used in computer vision. An approach to constructing maximum entropy probability models to replicate observed statistical characteristics is discussed in:

    Zhu, Song Chun, Yingnian Wu, and David Mumford. "Filters, random fields and maximum entropy (FRAME): Towards a unified theory for texture modeling." International Journal of Computer Vision 27.2 (1998): 107-126.
  • Anteneh Ayanso added an answer:
    How much data is too much data?
    Conant's Rule (5 x the overall-state-set-size) gives us an effective minimum dataset size in order to be able to claim statistical significance for results based on analyzing the dataset. What I'm looking for is at the other end: is there a measure that will tell me when I'm using *too* much data, such that the effects I'm looking for are likely to be drowned in the data mass? What would I look for in the literature discussing this consideration?
    Anteneh Ayanso · Brock University
    Depends on the purpose and method of analysis
  • Virendra Yadav added an answer:
    For ns2, which version of linux can I use to facilitate the manipulation of ns2?
    Because of the existence of many operating systems in linux, I can't decide alone, so please help me. My processor is the intel(R) pentium(R)Dual CPU T 2310 @ 1.46GHz 1.47 GHz.
    Virendra Yadav · ABES Engineering College
    you can use linux mint or Ubuntu
    just type sudo apt-get install NS2
    after that sudo apt-get install x graph
  • Luca Belmonte added an answer:
    How do you extract the force constants for angles using GAMESS (US)?
    I would like to map QM output (a GAMESS (US) job) in a new residue, not mapped in the CHARMM FF.
    Finding the Bonds/force constant is an easy task to do, and I already done. But I miss the angle/dihedral parameters.
    I found a section of wavenumber in cm^-1. Anyhow, I am not sure it is right to use those parameters.

    I have already checked the "Parameterizing a Novel Residue" tutorial and other tutorial, but no explanations are provided. I also searched the web, maybe I am just missing some link.

    Can anyone help? Can anyone suggest one (or more) reference?
    Luca Belmonte · Università degli Studi di Trento
    Thank you! That's what I was looking for!

  • Hicham Chibane added an answer:
    Which is the most proper Design of Experiments for the optimization of a process?
    My main concern is on the advantages of choosing Box-Behnken, Central Composite or other. They all appear in various articles, so what are the advantages of each method, and which did you choose in your work?
    Hicham Chibane · University of Tours
    I agree with all the authors, Response surface modeling is most suited for optimizing.
  • Faris Oghanna added an answer:
    For meshing complex geometries using numerical modelling softwares which contributes more, CPU or RAM or both?
    Meshing is difficult for complex geometries with a low/medium end workstations. Which has the major share in meshing - CPU or RAM or a combination of both?
    Faris Oghanna · The Nielsen Company
    I would say you will need enough ram, especially if you are going to use other applications while the analysis is running, but the processor speed more crucial. At the same time don't forget the complexity and the size of the software you are using. All that will be very limited if you are using parallel programing and computers as they have more than one processors and it also depends on how these processors are linked.
    I used to use fluent package for my fluid dynamics symmetrical and non-symmetrical geometries, it used to take a lot of time and even when I used my own program, then later when I moved my own program to parallel programming and used supercomputer just took couple minutes to run the same complex geometry using finite volume and element meshes.

    Faris Oghanna
  • Sergei Sergeenkov added an answer:
    How to calculate direct correlation function between colloids?
    I would like to calculate dcf between colloidal particles, which would help me to calculate the effective potential between colloids.
    Sergei Sergeenkov · Universidade Federal da Paraíba
    Good for you, Moez.
  • Serge Grabtchak added an answer:
    Is anybody working on steady-state photoconductivity measurements of GaN materials and thin films?
    Is there any simulation software available for PC simulations?
    Serge Grabtchak · University of Prince Edward Island
    Not sure if that such software exists because it would require adapting a particular model for your needs. I'd recommend you going a different path by acquiring knowledge on photoconductivity phenomena in semiconductors, studying various models and then developing the model you need (coding it in any language, Matlab etc.) The book I'd recommend for this purpose is by R.Bube, "Photoelectronic properties of semiconductors"
  • Roman Šperka added an answer:
    Which multi-agent platform is suitable for system of systems modeling?
    According to your experience, what is the best multi-agent platform for modeling system of systems?
    Roman Šperka · Silesian University in Opava
    We are using JADE in our research.
  • Sepideh Moshtagh added an answer:
    Does anyone know where I can get a tutorial for using Cobra Toolbox?
    I need a tutorial for using Cobra Toolbox
    Sepideh Moshtagh · Iran University of Science and Technology
    thank you Ahil
  • Anupam Singh added an answer:
    Could someone please explain the random seed number of autodock/vina?
    My docking results on the same grid and the same machine are different. For the same grid both the Windows and Linux systems also give different a docking energy. I read that the system generates this random seed number that might be a possible cause of differences. Could someone explain me what these random seed numbers are and how they affect the docking results?
    Anupam Singh · Jawaharlal Nehru Centre for Advanced Scientific Research
    Hi Ashmit,
    I have also faced the same problem earlier but its not a problem rather how the data is being handled. As Paul has already described it excellently. I will just add a simple understanding to it. The random number generator is here used to sample the different orientations of the ligand and if you provide sufficient amount of sample space you will end up in the same binding orientation. Try checking the binding orientation of the top results. You might find that the ligand is in the same orientation in both linux and windows results. I hope this answers the question "the role of random seed numbers in docking results". So I will suggest to perform docking use the same system configuration.

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