# Simulation and Modeling

• Peter T. Breuer added an answer:
Can we use pre-dominance in EFSM control dependency?
Dominance relationships are used in compilers and Extended Finite State Machines (EFSM). In compilers, they indicate which statements are necessarily executed before others while in EFSM, they are used in determining control dependence between transitions. Pre-dominance and Post-dominance are the two types of dominance relationship. Kindly, I have a question regarding control dependency. in all the articles I have read so far, the post-dominance is always mentioned for control dependency in EFSM. My question is " can we use pre-dominance instead of post-dominance in EFSM control dependency? If yes, what are the conditions for determining the control dependence between two transitions in EFSM". Thank you in advance.
Peter Breuer · University of Birmingham
I'm afraid that's too confused to follow as is. Firstly, one does not "execute" nodes in a control graph. Secondly, program control graphs are abstract images of a program (which is a FSM) in which almost all the information has been suppressed, and yes they are also a FSM but the correspondence is not what I'd call particularly wonderful. Their "states" are just instruction addresses. I don't know what you consider the inputs and outputs as being. Are there any? So you'll have to try harder to say what you mean for me. Tell me first of all exactly what you mean by a finite state machine. I mean something like a finite set of states S, a finite set of inputs I and outputs O, a set of transitions T in SxIxOxS ... oh, and an initial state s0 in S, and maybe a final state sN in S too. You can think of that as a lot of little circles s0,s1,s2,... for every state in S, with circles s1,s2 joined by arrows with an i above the arrow and an o below the arrow whenever (s1,i,o,s2) is in T. And there could be two circles around the s0, and sN could be coloured black. Is that what you are imagining too? Now tell me what you mean in terms of that imagery. I _think_ what you mean by a predominance relation is essentially that which holds between a state s1 and all the transitions t such that there is some I/O i and o and next state s2 with t=(s1,i,o,s2) in the allowed set of transitions T. It's the map from a state to the set of transitions that may originate at that state. Or maybe it's between s1 and the set of the i such that there is some o and next state s2 with (s1,i,o,s2) in the set of transitions T. Or maybe it's between s1 and the set of s2 such that there is some I/O i and o with (s1,i,o,s2) in T. Anyway, I'd be grateful if you'd say! I thought you meant that last option. I described what I meant informally last answer, and told you informally what I expected you meant, and that got us nowhere :(, so now I'm asking for more formality, so that there will be no wibbling around and we can be sure we understand each other :).
• Thabet Slimani 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. http://en.wikipedia.org/wiki/Comparison_of_TeX_editors
Thabet Slimani · Taif University
TexnicCenter
• Nilesh S Kanhe added an answer:
Is FORTRAN an outdated programming language?
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Nilesh Kanhe · University of Pune
I agree with The Haroldo Sir; The Simplicity towards the solving complicated problems is the beauty of FORTRAN.
• Pradosh K. Roy added an answer:
How could the 1/f^x power spectrum be generated by interacting point processes?
When we measure neural population activity, its power spectrum behaves like the 1/f^x power law, where 2<x<4. This activity is a reflection of neuronal spiking activity such that each neuron can be modelled as a point process. To understand how the neurons interact within the network I'd like to understand how the 1/f^x spectrum can be generated by interacting point processes and what kind of interaction defines the exponent x value. More details: - The point processes (aka spike trains), are poisson-like processes - The rate is ~10-100Hz. - We have ~100000 processes (aka neurons) - We define some kind of interaction kernel (positive/negative) - When we sum up all processes and compute the power spectrum we have 1/f behaviour, at least in 10-100Hz range with any exponent that is not constant.
Pradosh K. Roy · Asia Pacific Institute of Information Technology (APIIT)
Dr. Nev - Of course the neuro-biological signal is multifractal i.e. it is represented by Dq vs q spectrum , rather than a single fractal dimension. My experiments with epicentral patterns prior and after a major earthquake reveals startling behavior of the Dq vs q spectrum. Reprint is available freely in Researchgate website. Dr Podvalny is looking for the process also and in this context the paper by Keshner is very helpful. I have again gone through Keshner's paper after 20 years (again thanks to Dr.Nev) and recollected that we could model the intracranial EEG data in terms of long range memory of the system.
• Dmitri Chubarov added an answer:
Does anyone work on the normal cloud models and cloud generator?
"Cloud models are effective tools for uncertain transition between a linguistic term of a qualitative concept and its quantitative description. In short, it is a model of the uncertain transition between qualitatives and quantitatives."
Dmitri Chubarov · Institute of Computational Technologies
Sure someone does. Just see how many papers cite the original papers by Li Deyi. Google scholar finds over 200 such papers, though coming mostly from China and a few papers from Eastern Europe and, well, Iran. Since many papers that use cloud theory are written in a variety of the English language that is very difficult to understand, the concept is not widely known in Europe and the US. I myself struggle to understand it. Once I had to refuse to review a paper that used cloud theory precisely because it was close to totally incomprehensible.
• Habib Sedehi asked a question:
Churn problem analysis, modelling and simulation for Mobile Telecommunications?
Any successful case studies or System Dynamics simulation models (or alternative modelling approaches) to support Telecom operators, in order to manage customer behaviour and control attrition rate (churning) in mobile telephony market?
• Irshad Baig added an answer:
Does anyone know any software to predict 3D structure of ssDNA aptamer (30mer oligonucleotide)?
I am trying to study DNA (ligand)-Protein (receptor) Interaction by molecular docking, hence i need .pdb file format for DNA as ligand?. I would highly appreciate if you could please lend your valuable suggestions/advice to me.
Irshad Baig · Hanyang University
Dear Dr Campbell. Thank you for your kind suggestion. I have tried UNA-fold web server (Mfold) , however it is confined to secondry structure of DNA oligonucleotide. As you suggested, I would try for academic license of UNA Fold, if it gives various parameters to build reliable 3D model of DNA oligonucleotide ( in hair/pin loop structure form). Thank you. Best regards, Irshad
• Daniel Roach added an answer:
How to build a force field for materials? Who knows the (WO3)n 's force field?
I want to use GULP as a classical code to predict WO3 clusters structures, but the problem is that I don't have the force field of my clusters
Daniel Roach · University of Salford
Hi Zahed, When you use GULP to solve these kinds of structures, you want to consider very carefully what you are using the potential for. Now, you say that you want to predict clusters - the cluster calculation will frequently give very different structure predictions for bulk, and there is a paper that might help - Pirovano, M. S. Islam, R. Vannier, G. Nowogrocki, G. Mairesse,Solid State Ionics, 140 2001) 115. or you can start with the bulk WO3 potentials given in the UCL potential library - http://www.ucl.ac.uk/klmc/Potentials/ # # ISLAM(III) library - collection of potentials based # # MS Islam, S Lazure, RN Vannier, G Nowogrocki and G Mairesse # J Mater Chem 8(3) 655-660 (1998) # # Fitted for Bi2WO6 # NB check cutoffs # species Bi core 8.51 Bi shel -5.51 W core 0.11 W shel 5.89 O core 0.04 O shel -2.04 buckingham Bi shel Bi shel 24244.50 0.3284 0.0 0.0 12.0 Bi shel O shel 49529.35 0.2223 0.0 0.0 12.0 W shel O shel 767.43 0.4386 0.0 0.0 12.0 O shel O shel 9547.96 0.2192 32.0 0.0 12.0 spring Bi 359.55 W 7.69 O 6.3 Personally, I would give them both a go and see what the difference is! Hope this helps, Daniel.
• J. P. Torreglosa added an answer:
Block Error Message
Why do I get this Error message while I start the simulation, the error in the transfer function block: the message is: at time 0.0 is Inf or NaN. Stopping simulation. There may be a singularity in the solution. If not, try reducing the step size (either by reducing the fixed step size or by tightening the error tolerances)
J. Torreglosa · Universidad de Jaén
You can "trick" the start of your model. Use a Switch block with a Clock in its control input and select a Threshold for the switch of a negligible quantity of time. In the upper input of the switch, connect the same input that you already have in your transfer function. In the lower one, connect a constant which is the innitial condition. You can also try the "Initial condition block" instead of the commented above.
• Ganesh Kumar Seeniraj added an answer:
Where can I get hydraulic and mechanical circuit simulation done?
I have a reasonably complex experimental electro-mechanical hydraulic system (using water medium) design I would like to have simulated (to include pressure and flowrate versus time response, valve operation - steady state and transient) before I spend a lot on hardware to build it. If anyone has any connections/suggestions, please let me know.
Ganesh Kumar Seeniraj · Purdue University
Barry, Have you looked at LMS's AMESim software? It is perfect for the application you mentioned and it has a wide range of sub-models to build your system with varying levels of complexity. Let me know if you know more info on AMESim. Ganesh
• T. P M Goumans added an answer:
How to add a diffuse function in Amsterdam Density Functional (ADF)?
What is the keyword? Some details are anticipated.
T. Goumans · Scientific Computing & Modelling NV
Dear Hongguang, Indeed set up in ADF-GUI should work automatically, but if you want to run via the command line you will need to define the directory of the basis type, e.g. AUG/ADZP or ET/ET-QZ3P-1DIFFUSE. We will try to make the manual more clear on this. Fedor
• Jeffrey Potoff added an answer:
How to create pressure differences across the membrane during membrane protein simulation ?
Using NAMD, I want to simulate aquaporin channel in POPC membrane. To induce the water flow, pressure difference across the membrane is needed. I am stuck with this point. Could you please suggest how to do it?
Jeffrey Potoff · Wayne State University
Build your system with AQP embedded in the membrane. Equilibrate as needed. Then use steered molecular dynamics to pull a water molecule through the channel. Once you get it started, water will move through AQP readily. There is no need for a two bilayer system, nor would using one achieve what you are trying to do.
• Sanat Kumar Tiwari asked a question:
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?
• Heiko Kern added an answer:
Does anyone know examples where software agents have been used for social simulation?
I am looking for examples where multi-agent system frameworks (software agent templates) have been used to define the agents of social simulation models. To give you an example of what I am looking for here is a presentation that I recently gave to my colleagues from the NIBS Network (mainly Economists): http://www.cs.nott.ac.uk/~pos/gtmssig/slides/gtmssigSiebers2013-09-13v3.pdf Many thanks to everyone who answered so far :).
Heiko Kern · University of Leipzig
We use software agents for simulation of viral effects in Facebook. Please see the following link for our article: https://www.researchgate.net/publication/235907490_An_Agent-Based_Simulation_of_Viral_Marketing_Effects_in_Social_Networks
• Dimitrios G Tsalikakis asked a question:
Does anyone work with Cell Electrophysiology Simulation Environment Plus (CESE Plus) by Simulogic, software platform?
I am looking for someone who has experience with Cell Electrophysiology Simulation Environment Plus (CESE Plus).
• N. Kheirabadi added an answer:
Empirical Tight-Binding Method vs. Empirical Pseudopotentials Method: Pros and cons?
In your experience which one is better in terms of ease of programming and computational efficiency: TBM or EPM?
N. Kheirabadi · Islamic Azad University Tehran North Branch
Hi. I think that it is depended on the structure you are studying. You can search in papers and find the best method according to previous results.
• Sergey Ostroumov added an answer:
Parallel Computing - can anyone help?
Does anyone know how I can assign to 2 processors on a dual core computer for the combination of Simpson's rule (y[n+2]-y[n]=(h/3)*(f[n+2]+4f[n+1]+f[n])) and two-step Adams Moulton method (y[n+2]-y[n+1]=(h/12)*(5f[n+2]+8f[n+1]-f[n])) to solve ordinary differential equations to produce results for y[n+1] and y[n+2] simultaneously from each processor using Maple, Matlab or Mathematica?
Sergey Ostroumov · Åbo Akademi University
Dear Ehigie, I agree with Ulrich that if you are interested in the result it is much simpler to implement the algorithm in, e.g., C with separate threads. Then, these threads can be bound to specific cores by using cpu affinity. For instance, Linux OS allows you to directly set the affinity by invoking 'sched_setaffinity' while in windows you can do a similar operation by invoking 'SetThreadAffinityMask'.
• Farij Ehtiba added an answer:
Mannasim patch file for ns2.35
I have installed ns2.35 simulator to simulate a wireless sensor network routing protocol, but, they told me that I need a mannasim patch file to add, for correct working ns2. So please, if you can help me and tell me how to do that, if someone can give me the patch and how to add it?
Farij Ehtiba · University of Science Malaysia
Hello All, Could you please send me the steps for installing MannaSim on ns-2.35. I would like to simulate video stream over WSNs. If there is any other method to simulate it, Please help me. Thank you, your help is appreciated. email : f_ehtiba@yahoo.com
• Dinesh Gandhi 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. Thanks M.M.Noor
Dinesh Gandhi · Indian Council of Medical Research
I also agree with Afaq Ahmed's answer.
• Hamed Haghshenas added an answer:
Need help with pdb2gmx command in GROMACS
I am trying pdb2gmx command for MD simulation. but the output of pdb2gmx is not working properly in-case of multiple chains. the output file of pdb2gmx >>> .pdb or .gro was not generated. ERROR MSG: WARNING: atom HH21 is missing in residue ARG 215 in the pdb file You might need to add atom HH21 to the hydrogen database of building block ARG in the file aminoacids.hdb (see the manual) WARNING: atom HH22 is missing in residue ARG 215 in the pdb file You might need to add atom HH22 to the hydrogen database of building block ARG in the file aminoacids.hdb (see the manual) ------------------------------------------------------- Program pdb2gmx_d, VERSION 4.5.6 Source code file: pdb2top.c, line: 1489 Fatal error: There were 30 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "It is Lunchtime" (A.R. Van Buuren) Using the Gromos43a1 force field in directory gromos43a1.ff Reading 3.pdb... Read ' KINASE', 1711 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 1 blocks of water and 571 residues with 1711 atoms chain #res #atoms 1 'A' 227 1670 2 ' ' 41 41 (only water) Reading residue database... (gromos43a1) Processing chain 1 'A' (1670 atoms, 227 residues) Identified residue LEU27 as a starting terminus. Identified residue THR261 as a ending terminus. Start terminus LEU-27: NH3+ End terminus THR-261: COO- Checking for duplicate atoms.... Now there are 1666 atoms. Deleted 4 duplicates. Generating any missing hydrogen atoms and/or adding termini. Now there are 227 residues with 2086 atoms
Hamed Haghshenas · Shahrekord University
Dear Nitin, I don't understand what you exactly mean? If you have problem with multiple chains you must edit your pdb file with a text editor and remove extra chains before starting pdb2gmx.otherwise send your pdb file to my email (naghshejahan68@yahoo.com).I will make your necessary files. best HAH
• Trung Kien Vu 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.
Trung Kien Vu · University of Ulsan
Ubuntu 10.04
• Marek Wojciech Gutowski added an answer:
What is concept of negative infinitey to positive infinity limit in integration?
How we can define -ve to + ve infinity concept.
Marek Gutowski · Institute of Physics of the Polish Academy of Sciences
I suppose that both f_1 and f_2 polynomials are real functions (all coefficients of f_1(x) and f_2(x) are real). In such a case the requested integral may be calculated as a sum of integrals taken on sections of a real line ended on zeroes of the denominator f_2(x) and (-infinity, smallest zero of f_2] and [largest zero of_2, +infinity). All those partial results of integration have to be finite to get a meaningful result. If they are infinite, but of the same sign, then your result is infinite with the same sign. Otherwise the result is non-existent. More generally, and maybe more in spirit of your original question: the integral from minus infinity to plus infinity is a limit of an integral from 'a' to 'b' taken when 'a' tends to minus infinity and 'b' tends to plus infinity independently. That is to say you shouldn't set 'a'=a0 - ct and 'b'=b0 + ct, where a0, b0 and c>0 are constants, and compute the above limit when t goes to infinity. Such a limit, if exists, is called "principal value" but is *not* the true integral you are looking for.
• Edoardo A Di Napoli added an answer:
Should the current peer-review process be revolutionized?
Recently the submission of a scientifically bogus paper to a large number of peer-reviewed journals (http://www.cbc.ca/news/technology/bogus-science-paper-reveals-peer-review-s-flaws-1.2054004) revealed how the current peer-review process is broken. As one commentator simply put it "... First, and foremost, we need to get past the antiquated idea that the singular act of publication – or publication in a particular journal – should signal for all eternity that a paper is valid, let alone important. Even when people take peer review seriously, it is still just represents the views of 2 or 3 people at a fixed point in time. To invest the judgment of these people with so much meaning is nuts. And its far worse when the process is distorted – as it so often is – by the desire to publish sexy papers, or to publish more papers, or because the wrong reviewers were selected, or because they were just too busy to do a good job. ..". This is a very serious problem which should be addressed by the scientific community in a time where proliferation of papers is omnipresent and the assessment of their validity overwhelming.
Edoardo Di Napoli · Forschungszentrum Jülich
Michael, thanks for the contribution. The article is quite interesting and propose a partial solution to the current issue to the peer-review process. It is partial because is a post-processing solution allowing readers to comment on published papers. You may object that an author could post his paper on an open access archive where the open peer review process could start. Such a solution would be feasible but only if a large community of people would agree to such a process. Is the scientific community ready for this? By looking at the frenzies with which many authors of scientific manuscript fraction their results in order to have more papers it does not seem likely. There is unfortunately quite a bit of resistance while the standard peer-review process is deteriorating quite dramatically. Overall one has the sensation that many authors are not realizing that we are navigating on a sinking ship. Perhaps we should let it sink in order to hope for a new system.
• Gajendra PS Raghava added an answer:
Freeware for Simulation
question for the group - What freeware simulation tools do use m particularly interested in those with natural resource focus that have some kind of visualization component
Gajendra Raghava · Institute of Microbial Technology
I will suggest to visit following sites for information related to drug design using freeware http://osddlinux.osdd.net/ http://crdd.osdd.net/ http://www.imtech.res.in/raghava/
• Yalin Chen added an answer:
What's interesting tool for modeling
I've tried to develop process model using neural network, can anyone suggest me interesting software tool for such modeling?
Yalin Chen · Nanjing University of Finance and Economics
Why not use Pajek?
• G. F. Zhang asked a question:
Can I use dataflow and actor oriented programming in modeling and simulation software development?
Modeling and simulation software face end users in many specific domain, such as environmental science and physics. In those domains, module, component, service, and agent-related technologies are adopted widely. To use those existing blocks, I want to use dataflow and actor oriented programming technologies to improve the efficiency of development. But because the dataflow and actor oriented programming are used in low levels of computer systems, such as circuit design, static scheduling or digital signal processing, I wonder whether it is efficient for high level applications such as software development.
• Dhirendra Singh added an answer:
Do you know any real example of use of agent-based models by decision-makers?
These last years, I have developed many models to tackle real problems, but until now none of them have been used in real situations by decision-makers. I am curious to know if some of you have heard about examples of agent-based models that are actually used by decision-makers (city-planners, environmental health and safety manager, etc.) and not only by researchers/modelers.
Dhirendra Singh · RMIT University
We have had two government funded projects where agent-based simulation was used by the emergency services in Australia. The first was around simulating bushfire evacuation for the town of Breamlea in collaboration with the Country Fire Authority. The second was around the use of sandbagging for urban flooding in the inner-Melbourne suburb of Elwood, in collaboration with the local council and the State Emergency Service. Some details here: https://sites.google.com/site/rmitagents/projects/nccarf We have just also received government and industry funding for a larger three year project combining social science and planning expertise, where we will use agent-based simulation for modelling housing choices people make, in the context of sustainable urban development in Australia. Best regards,
• Ananth Saradhi added an answer:
interested in semiconductor optoelectronic device simulation
interested in semiconductor optoelectronic device simulation
Ananth Saradhi · Birla Institute of Technology and Science Pilani
Yes.

#### About Simulation and Modeling

The focus of this group are the methods and tools for modeling and simulation.