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  • Ya-Zhou Shi added an answer in PDB:
    How to create a pdb file of the standard RNA triplex?

    Hi, all.

    I need a pdb file of RNA triplex to  do Molecular dynamics simulations. Do you know what  software or method can be used to create structures of a (the) standard RNA triplex? Thanks a lot.

    Ya-Zhou Shi · Wuhan University

    To Gustaf D Olsson,

    Thank you very much for your answer. As you said, there are some DNA/RNA structure generators available in more than one software package, such as NAB tool in Amber package. However, these tools can usually be used to generate dsRNA/dsDNA , and it is still difficult for them to produce a RNA/DNA triplex from sequences.

    Thanks again.

  • Matt Novacevski asked a question in Population Growth:
    How are small towns around the world working to retain their identity in the face of pressures associated with growth and globalisation?

    The idea of a distinct identity has been raised as an important part of small towns maintaining their liveability - particularly those in areas experiencing population growth.  I'm interested in views on how identity is reflected and developed in small towns, testing the relationship between a community's identity and how liveability it is and case studies on initiatives that have been taken to bolster/develop the identity of small towns (population <20,000 people).

  • Arvind Bharani R.S asked a question in Kalanchoe:
    Friends Do u have any idea about th plant Kalanchoe pinnata and its therapeutic applications ?

     Friends i would like to know the details about the plant Kalanchoe pinnata , its therapeutic and pharmaceutical applications

    regarding the extraction processes and isolation of compounds from it .

  • Anubhav Sharma added an answer in MATLAB:
    Is there anyone who can help me in writing a MATLAB code?

    Hello everyone,

    I am doing research in signal processing but I am facing a problem in writing a MATLAB code of computing AM & FM bandwidths of analytic signal.

    Is there anyone in this community who can help me with that? Please refer to point no. D on page no. 3 of the research paper attached here.

    Thanking in advance.

    Anubhav Sharma,
    MNIT, Jaipur

    Anubhav Sharma · Malaviya National Institute of Technology Jaipur


    You are not getting my point.Please sir go through point no. D on page 3 of attach pdf.

  • Jiansheng Wei added an answer in Magnesium Alloys:
    How can I make ultra-fine twins in magnesium alloys by the forging method?

    I have tried so many times but couldn't succeed. For large mechanical properties, fine twins are required in magnesium alloys.

    Jiansheng Wei · Central South University

    Dr. Roven,

    Thanks for tips above. I am working on AZ80, yes foring, MDF, large stain plus inter-annealling. My problem lies the temperature range for the occurence of the precipitation, 300°C, you start to see them in one hour,  200°C, it only takes 5min, so basically I cannot avoid them, plus there is temperature drop when foring using a machine big enough to produce a bulk.

    Foring at 300, easy to produce piles of twins, lots paper on it, but when dynamic precipitation happens at large scale, no twins at all, from my data.

    So I start to deal with it, and try use them as toolkit to produce small twins. Any suggestions on this idea?

  • Zhen Sun added an answer in Intervertebral Disc:
    Do annulus fibrosus (AF) cells need oxygen to be functional in the intervertebral disc?

    Hi, I am doing research in intervertebral disc cells. Studies have demonstrated that nucleus pulposus (NP) cells need anoxia environment to approach functional capacity  in the disc for collagen 2 secrection. However, do the annulus fibrosus (AF) cells behavior in the same way or they need oxygen to function well in the disc as they are in the outer region anatomically? I am waiting for your precious opinions about this issue. 

    Zhen Sun · Fourth Military Medical University

    I think collagen types in more linked with cell types rather than oxygen concentration. However, my point is that is AF cells need higher oxygen concentration than NP cells to function well.

  • Rajnikant Namdeo added an answer in Proteins:
    I would like to plot protein contact maps. Could anyone suggest suitable tools?

    My protein is 476 residues. I would like to plot the map only for specific regions and mention it in the input thus choosing the residues i wish to calculate the contacts for. Does anyone know of any server /standalone programs for same?

    Rajnikant Namdeo · IBI Biosolutions

    Use the radius tool available in SPDBV. It will display the region falling in selected radius only. Further you can save a PDB file of displayed residues or a JPG also.       

  • Peter T Breuer added an answer in Personal Computer:
    What is the difference in your solution?

    Please see this paper:


    The solution for linear programming problems with bounded variables and a single linear combination constraint is given. Necessary and sufficient conditions for the existence of a feasible solution and for a bounded optimum are derived. This solution is used for constructing a simple 0(n) space and 0(n log n) time algorithm where n is the number of variables. The algorithm has been implemented successfully on a personal computer for problems with thousands of variables.


    Yoav Raz

    Peter T Breuer · Birmingham City University

    Indeed, but the change needs to be grammatically correct [What makes THE/A difference ...  nouns used in a non-generic sense have articles!]

    The real problem is that nobody has the slightest idea what you mean. What solution? Solution to what?

    I guess that you have a better algorithm for something than the world - or think you do. What is the problem? Is your algorithm faster? Less space-intensive? What? Are you talking about complexity analysis, range of applicable situations? What?

    "linear programming problems with bounded variables and a single linear combination constraint "

    sounds odd to me! I've never met a LP problem with only one constraint, and I have no idea what a "combination" constraint is. If the constraint is itself linear (as "LP" implies), I don't see how to code more than one constraint into it. Is it possible? Why not tell us?

    And if this is any good .. why are you asking us instead of publishing?

    And what do you mean by "the solution"? Surely an LP problem with only constraints and no objective function to minimize usually has many solutions (if not none), not one.

  • What to do if you believe that your supervisor is wrong?
    In doing research, in most cases your supervisor is right. But not always. What is the criterion if any? Should you do what you believe is wrong?
    Virendra Kumar Saxena · National Geophysical Research Institute

    If you want to continue your research work please Don't believe your supervisor is wrong only you think in this regards. With mutual understanding solve the issue if any and go ahead.

  • Graeme Smith added an answer in Consciousness:
    Is Will free, or does freedom exist without the presence of a Force of Will?

    Since Libett's work, there are many people who have questioned the idea of free will, since the fact that much of the work done before a decision is preconscious and consciousness only seems to come into play at a late stage in the process, calling into question the assumption that conscious choice is a factor in will.

    Others have asked if the idea of Will itself is questionable, in that it seems to assume a force that has a causal relationship to decisions. This is even more in question due to work done on attribution of blame that suggests that attribution is dependent on a kludge that links actions to previous steps in thinking whether or not they are actually causal.

    Many books have been published on this topic because it has legal and philosophical connotations, what is your opinion, and what is it based on.

    Glad to see you made it Luder.

  • Roland Iosif Moraru added an answer in Chimpanzee:
    What makes us human?

    Just looking at our DNA won't tell us – the human genome is 99% identical to a chimpanzee's and, for that matter, 50% to a banana's. We do, however, have bigger brains than most animals – not the biggest, but packed with three times as many neurons as a gorilla (86bn to be exact).

    A lot of the things we once thought distinguishing about us – language, tool-use, recognising yourself in the mirror – are seen in other animals.

    Roland Iosif Moraru · University of Petrosani

    Dear Andras

    Yes, a well developed memory is important. I also appreciate your interpretation on tolerance, as "self -defense and a reaction of intelligence". I will reflect more to this.

  • Ravi Kant Upadhyay added an answer in Solanine:
    Can any one give me an extraction method of solanine from potatoes?

    can any one give me an extraction method of solanine from potatoes?

    Ravi Kant Upadhyay · Deen Dayal Upadhyaya Gorakhpur University

    Bisolvent extraction method and colorimetric method are used for the determination of solanine and solanidine from potatoes. A high-performance thin-layer chromatographic (HPTLC) method is also used to determine the glycoalkaloids alpha-solanine and alpha-chaconine in potatoes. Alpha-solanine and alpha-chaconine are extracted from dehydrated potatoes with boiling methanol-acetic acid (95 + 5, v/v). The analytes are separated on a Silica Gel 60 F254 HPTLC plate by a saturated mixture of dichloromethane-methanol-water-concentrated ammonium hydroxide (70 + 30 + 4 + 0.4, v/v), which is used for vertical development of the plate up to a distance of 85 mm. For visualization, the plate is dipped 3 times into a modified Carr-Price reagent, 20% (w/v) antimony(III) chloride in acetic acid-dichloromethane (1 + 3, v/v), and subsequently heated on a hot plate at 105 degrees C for 5 min.

  • Zohreh Abdollahi added an answer in Spin Coating:
    Can we use SEM to see particular colloidal nanoparticles?

    We are researching Pt, Pd, PtPd colloidal nanoparticles for catalysis and we want to characterize them. The sample preparation is simply to deposit them on Si and spin-coating. We were wondering if SEM would be able to see these nanoparticles. The mean size of these nanoparticles is about 5 nm. Is there any way to use SEM to get an image of these nanoparticles?


    Zohreh Abdollahi · University of Sydney

    I have observed particle size ~20nm using TEM and STEM but with difficulty. I think for 5nm you need TEM with very high resolution.

  • How do you do static and dynamic simulations in Fluent?

    I need a quick step by step guide to perform static and dynamic simulation for blood flow in an artery in Fluent. I am a total novice with the software and the topic, and the user's guide is really complicated for me.

    Ricardo Vicente de Paula Rezende · Federal University of Santa Catarina

    Dear Patricia, if I understood you are begin in computational fluid mechanics, isn't?  All the  answers are very helpful to you. But is fundamental to have a solid, or at least, a minimal knowledge about the theory. I advise you to study also the Finite Volume Method, some topics about linear Álgebra to understand how the solver works. This  will give a solid fundament to your work, and you will be more confident with your future results. ANSYS CFX is other good and easier than  FLUENT to use.  Avoid to use a commercial simulator as a 'black box' .

    You can decribe you problem in more details as geometry, conditions , what do you want as velocity profiles,  pressure drop, forces,  drug delivery, etc? The setup can be easy or a hard. 

    If you have  theoretical questions, you can contact me in box. I 'll be happy to help you in what you need. I've attached a paper  regarding to blood cells flow into a capillary vessel. It is in Portuguese, but is easy to translate and any doubt, you may ask me. 


  • Peng Li added an answer in SEM/EDX:
    Is SEM-EDX a good way for the characterization Sulfur content in nanomaterials?

    Is there any good way to determine the Sulfur content in composite nanomaterials?

    For example, Metal-organic framework has been used as support for a wide range of functional materials (catalyst, enzyme, quantum dot and lighter harvester). The most important characterization for such kind of composite nanomaterials is where the functional materials locate in parent MOF materials. More specifically,, how much catalytic sites have been incorporated or loaded per each metal-cluster-node in MOF materials. SEM-EDX technique can give a general idea to look at the distribution of the loading materials along a single nanoparticle of MOF.

    Is there any limit for such kind of characterization method? For example, If I would like to look at the sulfur content (catalyst contains sulfur) in this nanomaterials. 

    Peng Li · Northwestern University

    Thank you for your suggestion!  I have tested my sample using both SEM-EDX and ICP-OES. The sulfur content results from two different methods are exactly the same with only 1% difference.   

  • How can I measure the extent to which supply and demand factors affect the volatility of a time series?

    Apart from estimating the volatility of electricity prices, I would like to find out how much of it may be attributed to either supply or demand factors. However, I am still looking for empirical methods that I can possibly apply.

  • What are the methods to identify and manage the New Product Introduction Risks in multi-tier OEM and Supplier environments?

    Assessing program and product level risks from huge list of tier1 suppliers is a tough thing. Many times, potential risks related component failures at suppliers side, changes in their product or process design, inability of suppliers to meet the schedule, etc are not even known to OEM program managers.

    What Will be the Realizable solution to effectively identify risk early from the huge list of tier1 suppliers for them to monitor and control the overall program risks throughout the NPI program?

    Geen Paul V · Computational Research Laboratories

    Thank you Stanley Kam Sing Wong  and  Gopinath. R. for your valuable viewpoints.

    To be more specific I would like to add that: 

    Assessing program and product level risks from huge list of tier1 suppliers is a tough thing.  Many times, potential risks related component failures at suppliers side, changes in their product or process design, inability of suppliers to meet the schedule, etc are not even known to OEM program managers.

    What Will be the Realizable solution to effectively identify risk early from the huge list of tier1 suppliers for them to monitor and control the overall program risks throughout the NPI program?

  • Noorulain Hyder asked a question in Anti Depressant:
    Tds dosing in anti depressant activity reference ?

    kindly tell me the reference for tds dosing for tested unknown antidepressant in mice ? as i have all the references giving the tested compound in OD DOSE 

  • Salah Eldeen Gasim added an answer in Simulink:
    It is normal to measure voltage magnitude of a terminal in an electrical circuit in MATLAB/SIMULINK, but how to measure the voltage angle?

    Measuring voltage angle of a terminal (point) in an electrical circuit.

    Salah Eldeen Gasim · Sudan University of Science and Technology

    That has helped me a lot. Thank you for your time. Your help is highly appreciated.        I will refer to you again. Thank you.

  • Ramkumar Ponnuraj asked a question in Poloxamer:
    Will Nanoparticles aggregate if compressed as tablets?

    Dear All, 

    We had prepared Nanoparticles and we plan to compress into tablets for oral route delivery. This is to increase the Bioavailability of the drug. 

    There are many articles states that Nanoparticles can be compressed into tablets and provide via oral route. 

    But let me know whether these Nanoparticles will aggregate when compressed to tablets of will they stay as nanoparticles when the tablet disintegrate in the GI fluid. 

    Anyhow We will cross check this with SEM of the disintegrated tablet but want to know whether it will? 

    Also let me know any options like addition of excipients in the tablet that allow the nanoparticles to stay seperate after the tablet disintegrate in the GI fluid. 

    We also use Poloxamer in nanoparticles prepearation to avoid this problem. 

    Your suggestions will help me a bit. 

    Thanks in advance 

  • Give an example of the following question in topology?

    Let X be any finite set and let A, B be subsets of X such that

    A is a preopen set and a union of semiclosed set, and

    B is also a preopen set and a union of semiclosed set. But A \cap B does not belong to preopen set.

    For information, a subset P of X is preopen if P \subseteq Int(Cl(P)) and a subset S of X is semiclosed if Int(Cl(S)) \subseteq S.

    Dr Nimmagadda Venkata Nagendram · Acharya Nagarjuna University

    Let X be any finite set and let A, B be subsets of X such that

    A is a preopen set and a union of semiclosed set, and

    B is also a preopen set and a union of semiclosed set. But A \cap B does not belong to preopen set.

    A cap B does not belong to preopen set because you should take  X as infinite but not finite set that is why so make subsets are of an infinite set X it contains all union intersection and complement preopen sets in a preopen sets vice vers for closed set are in pre closed sets surely. ....Dr N VNagendram

  • Mayank Agarwal added an answer in Autodock:
    How do you use Autodock for structure based screening in the absence of any known ligand?


    My enzyme does not have any known ligand. It interacts with other proteins though. I wanted to do virtual screening. I know amino acids that are important for binding. But I do not know any ligand.

    Can anybody let me know how can I use Autodock for structure based virtual screening in absence of a ligand?



    Mayank Agarwal · Madhav Institute of Technology and Science

    For virual screening you can upload the protein on http://www.scfbioiitd.res.in/software/drugdesign/raspd2.jsp   and can choose any one of the 4 method for finding out the potent inhibitors of the target protein.

    After finding the potent inhibitor you  can continue with the autodock for docking.

  • What is the physical cause of photoluminescence in a plasmonic nanocomposite?

    Specifically, I'm referring to spherical noble metal nanoparticles within an optically transparent glass. The papers I have read seem to gloss over the underlying physics. This is really a two-part question:

    1) Since the wavenumbers of light and the plasmon must be equal (dependent on the plasma frequency) for plasmon/polariton coupling, why is absorption observed over a range of wavelengths, rather than a narrow band?

    2) If I am understanding correctly, the plasma frequency is constant (dependent on electron density, particle size, etc). In the case of the nanocomposite, how is the absorbed wavelength different from the emitted wavelength? Where does the energy go? Is it lost as heat in the metal nanoparticle? If that is the case, how can the frequency of oscillation of the plasmon be less than the plasma frequency?

    Any help is appreciated.

    Serge Grabtchak · University of Prince Edward Island


    I strongly recommend you to look at the article ("Continuum..") I mentioned because you'll see plasmonic signatures in NPs resembling the broad band luminescence. Of course, under different excitation conditions. 

  • Bhawanisingh G Desai added an answer in Iran:
    Can anyone name the specimen of this belemnite found in the Toarcian-Bajocian in Kerman, Iran?

    This specimen found in the Badamu formation.

    Bhawanisingh G Desai · Pandit Deen Dayal Petroleum University

    It is difficult to identify as some of its features are not visible as they are embedded in the rock. 

  • Raihana Bahru asked a question in MWCNT:
    How to measure the zeta potential of MWCNT- dimethylformamide solutions?

    Dimethylformamide dilute with deionized water.  How to calculate the dielectric constant? Refractive Index? for the dispersant.

  • Do you have a recommendation for survey for Latinas and breast cancer prevention that examines structural, enabling, and individual level factors?

    looking for validated survey to examine factors that enable and impede breast cancer screening as well as measure breast cancer and prevention knowledge.

  • Megha Budhwani asked a question in Tissue Sectioning:
    Has anyone used the SK1 clone CD8 antibody for IHC on formalin fixed paraffin embedded tissue sections?

    Its recommended for Flow but has just one old reference for IHC-P. As this is going to be used for very precious human tissue sections, I wanted to be absolutely sure before trying it on our very few work up samples.

  • Ying Han asked a question in Mariculture:
    Does anyone have the knowledge of how to test the toxicity of mariculture sediment?

    HI everybody, I wonder if the high concentration of ammonia, heavy metal, antibiotics, carbon resources and phosphate is toxic to microbial community down there. Can anyone share your way to test the toxicity of any kind of sediments? It will be better if you recommend some articles.