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  • Justin Lemkul added an answer in Gromacs:
    How to get the topology file for the alkylated or modified DNA?

    I am trying to run molecular dynamics simulation in Gromacs for the modified DNA, alkylated at the different nitrogen base positions. I have the PDB file. I know force field will nor recognize the modified part. Would you please help me out how to treat the modified part in the DNA in molecular dynamics simulation. Thank you

    Justin Lemkul

    You have to parametrize the new residue.



    Adding an alkyl substituent should be fairly straightforward, but there will be charge calculations to carry out as well as some new bonded parameters.

  • Winston T Richards added an answer in Autopsy:
    In burns fatalities, why do we relate soot particles in the respiratory tract to antemortem burns? Is there really any correlation or a coincidence?

    A practice that goes on from autopsy to autopsy in burnt or charred bodies is an effort to find soot particles in respiratory tract and then to opine that the cause of death is antemortem burns.

    Is this correct? Do we really have any sure gross autopsy finding of antemortem burns in charred or even other burnt bodies where death occurs with in short time? Why do we correlate soot particles to antemortem burns?

    Soot particle only suggest that the person was alive during fire rather than burning from fire. This distinction is hardly made by anybody. Rather most of deaths occur from smoke inhalation (reason for soot) while the body being burnt after death (when flames reach the body) and the converse is also true that in self immolation or where clothes of live person catch fire (like in explosions or flash fires) soot particles are even rare to be found and we don't have any finding of antemortem burns where death occurs shortly from burns.Red Hyperemic zone requires considerable time (as seen in hospital admission deaths mostly) and may also be produced within an hour after death.

    Any comments or suggestions.

    Winston T Richards

    It seems as though the presence of soot particles in the respiratory tract is only an indication of actively breathing in smoke. A person could die from hypoxia during the fire and then they could suffer burns as the flames and heat contacted their body. They could also suffer burn injuries first and then die. In each case the inhalation of smoke wouldn't identify when they were burned. 

  • Gwendolyn Amos added an answer in Cold War:
    Thinking outside the box: Who will win the next cold war?

    There has been two paradigm shifts recently, one in the former red socialist countries, and one in the former pure capitalist countries, if you think outside the box these two shifts have the structures that  will be key to the future cold war....Has anybody thought about what this future paradigm clash structure is or will be? Has anybody wondered who will win the next cold war this time around and why?

    Gwendolyn Amos

    No one. In reality there are no "winners" to any war.  Just those who have succeeded in advancing their own cause.  However, answering your question as you would like, I would say it would most likely be the socialists.  Socialists are successfully pushing their agenda in countries around the world, and are making great headway in America, even.  It is not to say that capitalist are not taking a stand, but too many people do not want capitalism, anymore - they want change, but when they receive the change for which they vote, they fight that, too.

  • Yaser Alaiwi added an answer in ProCAST:
    ProCast numerical simulation?

    What is the best way to approach the casting simulation with the ProCast software? There is a lack of information about how to get started, even in the net! Anyone who knows more about it, please answer me!

    Yaser Alaiwi

    You can use ProCast to prepare the simulation boundary conditions and after solving the problem you can see the results using ESI Visual environment.

  • Gwendolyn Amos added an answer in Political Sociology:
    Does the level of democracy in a country affect people involvement in the public affairs and their contribution to their community?

    Does the level of democracy ( political freedom and civil liberties) in a country affect people involvement in the public affairs and their contribution to their community?

    Any Empirical evidence?

    Gwendolyn Amos

    The lack of democracy forces citizens to take a backseat to government.  The amount of democracy present in a government allows more participation from the citizens.  Democracy is a force of support for the people, willing and able to participate and make the democracy stronger for themselves.  The lack of participation in democratic governments also stems from the lack of desire, or thought of an individual vote not counting, decreases the level of democracy in that government, thus participation.  The two concepts; democracy and participation, are inter-mingled.

  • Md.Ferdous Wahid asked a question in Structural Engineering:
    What will be the most significant topic in future in structural engieering for a PhD? " Reliability analysis of structure" how the topic is for a PhD

    I have few publications on this topic, but I am going to apply for a PhD position. Now I am confused about that: what topic should I select. I want to select a topic which will be most significant for structural engineering in future. I love these three topics:- Relisbility Analysis of Structure; Tall Building ; Structural Dynamics.  Please provide me some informationa.

  • Patrick Freeze added an answer in Soil Science:
    What is the best method to determine mineral nitrogen in a compost sample with an ultraviolet– visible spectrophotometer?

    I looking for method to determine only the amount of mineral nitrogen (NH4, NO3, NO2) but not of organic nitrogen in a compost sample. 

    For exemple : the Nessler method 

    Patrick Freeze

    I don't do a lot of work with nitrogen but the way I've done it in the lab was determining the total N through combustion.  Then we determine the organic N through a mineralization incubation study.  That is the organic N fraction.  Then we subtract that from the total value and the difference is the inorganic N fraction. 

    What's your email?  I can send you a few methods I have and you can see what is best for your study.  The one I outlined is probably the easiest and most basic.  

  • Muhammad Saiful Islam asked a question in Engines:
    How could I justify the sample size of my research? How many projects should I survey?

    I am going to conduct a survey among the experts who are working in power plant construction projects in my country. So far I know, construction of 30 mega projects are going on. The targeted experts are 7-categories, for example, contractors, sub-contractors, vendors, project director (PD), project manager (PM), site engineer, and consulting engineer (or consultant). The other variables are project size in terms of power generation capacity, budget, project location, experts' experience (year), and academic qualification. Please suggest me in a precise way to save my time? I am now in a critical moment. I have a presentation just after couple of weeks. Thank you for your patience and time. 

  • Eric Ariel L. Salas added an answer in Landsat:
    Is it possible to download natural colour images for Landsat 8 for whole earth?

    I can find the multi band data on USGS, but the natural colour images are more relevant. If it is not possible to download Landsat 8 natural colour images, I would have to proceed with using RGB bands to create natural colour composite. Any insights are appreciated.

    Eric Ariel L. Salas

    This is what Maria V. Kozlova is referring to:

  • Avery Meeker asked a question in Shorebirds:
    What birds are under-researched in Southwest Costa Rica?

    Preferably mid to high elevation (no sea or shorebirds).

  • Muhammad Saiful Islam added an answer in Sample Size:
    How many sample size do I need?


    I am little bit worried about the selection of sample size of my current research. There are approximately 30 projects in my research field and 5 categories of experts are my target to conduct a questionnaire survey. Therefore, 150 is the population size. However, there are other variables like project size, respondents experience, academic qualification, occupations etc. Do you know, how I could calculate the sample size and justify the number of sample size? If you have any relevant literature, I will be very thankful to you. 

    Muhammad Saiful Islam

     Dear Mr. Jim,

    Many thanks for your suggestions. Actually, I will conduct survey among the experts who are working in power plant construction projects in my country. So, it is in a specific domain. So far I know, construction of 30 mega projects are going on. The targeted experts are 7-categories, for example, contractors, sub-contractors, vendors, project director (PD), project manager (PM), site engineer, and consulting engineer (or consultant). The other variables are project size in terms of power generation capacity, budget, project location, experts' experience (year), and academic qualification. Could you please suggest me in a precise way to save my time? I am now in a critical moment. I have a presentation just after couple of weeks. Thank you for your patience and time. 

  • Campbell Reece added an answer in Cell Culture Techniques:
    How to seed cells in triplicates, in 6-well plate?


    I want to seed my cells in triplicates in six well plate (due to density issue)

    There are six groups for my experiment and I need 18 wells in total.

    How should I seed them? I've heard that there are plate variations and you cannot put data in a single graph if the cells are seeded in different plates...

    Should I seed..for example

    Control 1 Vehicle 1  Treatment 1

    Control 2 Vehicle 2 Treatment 2

    Control 3 Vehicle 3 Treatment 3

     in separate plates?

    Or Control 1, 2, 3, Vehicle 1, 2, 3 in one plate and

    treated groups 1, 2, 3 in a separate plate?

    Thank you very much

    Campbell Reece

    Thanks Hina, that's the answer I was looking for!

  • António Maximiano Fernandes added an answer in Allergy and Clinical Immunology:
    What are the receptors for the following mediators produced by mast cell and eosinophils following allergic reaction?

     mast cell :- PAF, Histamine, LTC4, LTDA

     eosinophils: LTC4, LTD4, PAF.

    Specifically receptors found in the air pathways(lungs)

    António Maximiano Fernandes


    Histamine: H2 receptor in lung airway

    PAF: PAF receptor

    LTC4: cys-LT-selective receptors

    LTDA?(what mean)

    + 1 more attachment

  • Motomichi Koyama added an answer in Materials Physics:
    What is the most reliable interfacial energy of FCC/HCP at around 300 K in high Mn austenitic steels?

    What is the most reliable interfacial energy of FCC/HCP at around 300 K in high Mn austenitic steels? or if there is a paper clearly showing chemical composition dependence of that, please tell me.

    Motomichi Koyama

    Dear Mr Geissler

    Thank you for the clear answer. In fact the interfacial energy has been an important issue to thermodynamically calculate stacking fault energy. But the value is set as fitting parameter in most cases. Your answer and work are more theoretical and convincing. I greatly appreciate you.


  • Geeta Ajit added an answer in Literature:
    How Literature can be evaluated to be a reliable source of knowledge ?

    Literature has been considered ancient source of knowledge but with the advent of science and technology, People have started doubting its reliability, How we can revive its supremacy ?

    Geeta Ajit

    Literature gives an account of the life of the times in which it was written. It is through literature, that we know in detail of how the life was lived in the past. Even in imaginative fiction, as we chaff through the work, we get insight of situations of how people lived their lives, their attitudes and thought process.

    Besides, history has a way of repeating itself. Through the study of literature, we can get an insight on the impact various events had on the lives of common people and the mark it left on the psyche of common man.

  • Emimal Jabason asked a question in Longitudinal:
    What is Cross Sectional and longitudinal MRI?

    Can anyone please differentiate the cross sectional and longitudinal MRI? Thanks

  • Shanmugaraj V S Kalyanasundaram asked a question in Linux programming:
    I want to write a linux program ?

    which will modify file names. The script is dedicated to lowerizing (-l)
    file names, uppercasing (-u) file names or internally calling sed
    command with the given sed pattern which will operate on file names.
    Changes may be done either with recursion (-r) or without it. Write a
    second script, named modify_examples, which will lead the tester of the
    modify script through the typical, uncommon and even incorrect scenarios
    of usage of the modify script.

  • Eiji Kinoshita added an answer in Western Blot:
    Accuracy of Phos-tag gels
    Is anyone working with Phos-tag gels? I have just started out working with them and I understand that with such gels, the protein marker is not an accurate indication of the weight of the protein of interest. However, after blotting for my protein interest, it seems that the darkest bands seen are in the range of 25- 35kDa where in theory, it should have been seen at around 60 - 70kDa. Is this some non specific binding of the primary Ab or is there more to the phos tag gel that I do not know about.
    Eiji Kinoshita

    Hi, Davide.

    Yes! As you mentioned, genomic DNA in the lysate sample sometimes interferes in electrophoresis. We usually use benzoase, which is directly added in a sample-loading buffer, for the analysis of Phos-tag SDS-PAGE.

    Best wishes!


  • Niloufar Khoshbakht added an answer in Adina:
    For 2D contact modeling in ADINA ,does any one know how to consider the effect of friction ?

    I tried different coefficients of friction (Extrermums) and no changes occurred in results.

    Good to know the target is rigid.

    Niloufar Khoshbakht

    Dr Shil'ko,I've modeled a single laminated bamboo dowel connection.The compressive loading is applied parallel-to-grain direction.And I'm looking at shear stress results and tensile stress/strain perpendicular to the grain around the bolt hole.I assumed steel bolt as rigid target.

    no changes occurs  in results by changing coeff. of friction.I'm not sure this  is due  the nature of the problem,since it seems by increasing the load, slip happens in contact surface.I've also seen in the literature that results changes by changing coeff.of friction.I don't know whether I've missed any key parameter in my ADINA model or not?

  • Sami Althwab added an answer in Enzymatic Assay:
    Help with a calculation of triglyceride amount in liver tissue?

    I extracted liver tissue (~100 mg) using Folch method and evaporated the solvent mixture and resuspended the lipid in 600 ul of dH2O (with triton x100). Then, I determined the concentration of triglyceride using an enzymatic assay. For this determination, I used only 4 ul from the 600 ul, and the TG concentration was 130.5 mg/dL. Now, I need to convert the amount (mg/dl) to umol/g and to mg/g?? Any help on this conversion would be greatly appreciated..

    Sami Althwab

    Thank you all for these helpful solutions.. I now have a good idea about this  calculation.. Thomas, yes I have the exact weight of the tissue  (100.8mg), and the total volume of the kit reaction was 120 ul. According to the kits we use, yes the enzymatic assay hydrolyzes all neutral lipids TG, DG, and MG, and the TG molecular weight is 885.4 g/mol. 

  • Ahmed Eid asked a question in Macro:
    How to deal with macros files in Jmol-Nbo Visualization Helper and apply it on my molecule ?

    How to deal and applay  macros files on my molecule to show the orbitals from output file of NBO ?

    Or any program to show the orbitals from NBO output file ?


  • Cleiton Freitas added an answer in ARM Microcontroller:
    Is it possible to program an ARM microcontroller by MATLAB to work as an ADC?

    to whom may concern!


    I am working on a project witch I need an 8 channel ADC by ARM microcontroller Xmega xx. As I know nothing about programming an ARM microcontroller, I've decided to program it by MATLAB.

    Is there any way to convert MATLAB code to program this microcontroller? Infact I mean without installing MATLAB itself on the microcontroller to compile the program.

    Cleiton Freitas

    take a look at the following link:

    It seams like you can program an arm microcontroller form matlab/symulink code. Unfortunately, I don't think it'll be easier than programming the microcontroller directly.

  • Yeongdong Lee added an answer in Chemical Vapor Deposition:
    How to clean the quartz tube used for CVD synthesis of MoS2?

    How to clean the quartz tube used for CVD synthesis of MoS2 using sulfur and MoO3 powder?

    The quartz tube was covered by Sulfur and MoS2(black). 

    Also, alumina boat was covered by Sulfur and MoS2.

    1. How do I clean the quartz tube and alumina boat?

    Following post suggested that Nitric acid is effectivly clean the tube. 


    I'm afraid that S + HNO3 leads to formation of NO2 which is toxic although cleaning would be processed in fume hood.

    2. Is it proper to use of HNO3 for cleaning of quartz and alumina boat?

    Thank you very much.

    Yeongdong Lee

    Thank you for your valuable answers. It help a lot. I'll try it.

  • Azzam K Almosallami added an answer in General Relativity:
    Universe is static!!! Yes or no?

    Space of Universe is static! Yes or no?

    Question: Are there any observations that do not fit into the model static space of Universe, are there any theoretical obstacles to the existence of such a model?

    I assume that the Universe is eternal, infinite and static, it is not expanded and not curved, it is possible to construct a preferred inertial frame of reference in which the CMBR is most isotropic. The matter in this space evolves, but the average density of matter and energy (in large enough volumes) fluctuate within a rather broad range.
    The light in this model is "tired", the speed of light depends on the optical density intergalactic medium. Gravity is also "tired" t.i. weakens a little faster R2. The energy of destroying matter goes into the surrounding vacuum. The excess energy from the vacuum give rise to new particles of matter.

    I state that all the observed cosmological effects can be explained in such a Static Model of the Universe.
    See attached "Basic_Cosmological_Formula_1_En.pdf"

    Dear colleagues, I do not ask, what are the problems faced by other theories (though I would be interested in your opinion on that. The General theory of relativity is not applicable to the entire space of the Universe).

    Azzam K Almosallami

    Dear Erkki J. Brändas,

    Read this attached letter again from an expert in relativity and math. There are no the comments you say. It is discussed too much.

    The only criticism of my theory is the reciprocity principle after long discussion, and now you understand well  what is the meaning of the reciprocity principle. It is only objectivity and continuity. The fact is, there is no objectivity and continuity in macro world. Because of that quantum and GR do not merge, and there is no way to be merged under objectivity and continuity. 

  • Rakhshan Roohi added an answer in ENVI/IDL:
    Has someone worked with Envi IDL in order to calculate SEBAL Algorithm?

    I want to know how i can set a programme about SEBAL algorithm.

    Rakhshan Roohi


    First thing is that do you have access to SEBAL algorithms? I have not used Envi IDL, however, following the principle of SEBAL, I have done all the modelling for surface energy fluxes using ArcGIS model builder and have developed a Surface Energy Balance Algorithms for Rainfed Agriculture (SEBARA). This approach is more flexible and give you a better control over input parameters, especially when you are working in water limited areas. I would suggest to use ArcGIS model builder if you do not have prior experience of any language. 

  • Bibhuti B Sahu added an answer in Laser Spectroscopy:
    Have anyone ever had an issue with Ar ion gun?

    The sputter gun I use, instead of cleaning sample surface, deposits C atoms.

    Bibhuti B Sahu

    This is probably due to higher gas temperature in the plasma. You have to minimize heating which can leads to C contenet. In this case add a small content of N2 gas along with Ar.

  • Renaud Lancelot added an answer in Linear Equation:
    How important is the order of the variables in a linear regression?

    For (x1, x2, ... , xn) the predicted value y* of y is given by the linear equation:

    y* = a+ a1x1 + a2x2 + ... + anxn. 

    However, the result seems to be different, when the order of variables in different.

    Renaud Lancelot

    The result is always the same, in the sense that you're always solving the same equation. By the way, the predicted values do not depend on the order of predictors n the equation. However, differences appear when you make the so-called sequential analysis of variance, ie adding one term after the other, and computing residual df and sum of squares at each step. That's the reason why you should not use such sequential anova for testing the statistical significance of model coefficients.

  • Bibhuti B Sahu added an answer in Electron Attachment:
    Are there resources for plasma afterglow ion recombination?

    Looking for good resources for plasma afterglow recombination chemistry, specifically hollow cathode discharges and electron attachment cross sections and time profiles. Books, articles, anything really. Thanks!

    Bibhuti B Sahu

    A plasma afterglow (also afterglow) is the radiation emitted from a plasma after the source of ionization is removed. The external electromagnetic fields that sustained the plasma glow are absent or insufficient to maintain the discharge.

    A plasma afterglow can either be a temporal, due to an interrupted plasma source, or a spatial one, due to a remote plasma source.

    In the afterglow, plasma-generated species de-excite and participate in secondary chemical reactions that tend to form stable species.

    Recombination of ions (atomic or molecular) with electrons is an important loss process ofcharged particles in low-temperature plasmas. Molecular ions can after collision with electron dissociate to neutral products (dissociative recombination – DR, typical rate coefficient αDR ≈ 10−7 cm3s−1). In environments with low number density of neutral particles and electrons, atomicions can recombine via radiative or dielectronic recombination. Both processes are orders of magnitude slower than the dissociative recombination.

    If the environment where recombination takes place contains other particles of sufficient number densities, other recombination processes are possible. After the collision of electron e− with an ion A+ a neutral excited intermediate state is formed. Further collision with another particle can stabilize this complex and finish the recombination process.

  • Jonathan Wilson added an answer in Gender Studies:
    Are there any research studies on the evolution of stick figures throughout history?

    There is very little evidence that stick figures have changed over time, gender is usually depicted by hair or shapes, but has that evolved from ancient cave drawings that depict the first stick figures?

    Jonathan Wilson

    I am looking at the evolution from this perspective :

    If female stick figures are (today) often drawn with longer hair than male, what about time periods where men wore wigs, or i.e.. Viking stick figures where males had long hair as did females.......How where stick figures differentiated male v. female in different cultures, geographic locations, time periods?