User:Fuse809

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Please read the section on my philosophies before writing on my talk page as it will probably answer some questions you have about my work and how you should reply.

My real name is Brenton Horne, I am interested in mathematics, pharmacy, physics and medicine and am a second year pharmacy student at James Cook University Townsville campus as of 2014. I live in Townsville, Queensland, Australia :The current date and time in Townsville is Saturday 1 November, 01:51.[1]

I do 3D and 2D chemical structure images, if you have one you'd like to request, feel free to on my talk page. I also attempt IPA keys on pages with names sufficiently difficult for pronunciation to be a problem with the help of this page. Likewise I also attempt translations of drug info using Google Translate. For instance a summary of product characteristics (SPC) for piritramide may be found here and a translation of a SPC for tilidine may be found here.

I am a Christian, albeit an unconventional one, for instance I believe that this excerpt from the Apocalypse of Peter to be correct:

And I asked him and said unto him, "Lord, allow me to speak your word concerning the sinners: 'It were better for them if they had not been created.'" The Saviour answered and said to me, "Peter, why do you say this, that is, that not to have been created would have been better for them? You resist God; you would not have more compassion than he for his image: for he has created them and brought them forth out of not being. Now, because you have seen the lamentation which shall come upon the sinners in the last days, your heart is troubled; but I will show thee their works, whereby they have sinned against the Most High.

Likewise I think the commandment to love each other is above all other commandments, other than love your God, as Jesus said (John 13:34-40), consequently I have nothing against homosexuals, transsexuals, bisexuals, members of other religions (provided their religions are based on love), etc.

I am currently working on a Wiki on drugs of abuse and their relative harms, their mechanisms of action, their legality, and assorted other little facts about them; it may be found here.

My chemical structures[edit]

I create structural images to satisfy everyone, not just me. I try to use the structures provided by ChemSpider or PubChem just to ensure reliability. The software I use for chemical structure drawing is:

  • MarvinSketch/ChemSpider/PubChem (for the production of MOL files), ChemSketch (to create WMF files in ACS style) and then Scribus to convert the WMF to a SVG file (these are the images with 2DACS tags).
  • MarvinSketch (with settings according to WP:Chem/Structures) to create SVG files. (2DCSD tag). Sometimes I do these images wrong the first time in that I do not crop them as well as I can and when I upload a better scaled cropped version I give it the tag 2DCSDS. Sometimes I accidentally draw the opioids in a less conventional way, so when I fix this I give them the tag 2DCSDT.
  • MarvinSketch (to create SDF files) → OpenBabel (SDF->PDB; also adds hydrogens with this tool) → QuteMol (PDB->GIF). (3Dan tag). Unfortunately these images do not display double bonds in a way distinct from single bonds and hence I'm now favouring the 3DanJ images.
  • I also create 3D animated GIF files of drug molecules using Jmol (to create usually about 60 PNG images spaced 3 degrees apart) and GIMP to animate them into gif files. (3DanJ tag). This is the code I use to create these images:
background white;##
name = "./images/Work0000.png";
nFrames = 60;
nDegrees =6 ;
thisFrame = 0;
width = 539;
height = 260;
 
message loop;
thisFrame = thisFrame + 1;
fileName = name.replace("0000","" + ("0000" + thisFrame)[-4][0]);
rotate y @ndegrees;
frame next; # only use this if you have a multiframe file.
refresh;
write image @width @height @fileName;
if (thisFrame < nFrames);goto loop;endif;
  • I create 3D animated pictures of biomolecules, most often joined with their respective ligand(s) using the PDB files found here, Jmol and then PhotoScape or GIMP to convert these PNG images to GIF format. I usually colour shapely, unless doing so will make the ligand(s) difficult to see. I have now decided to use the name PDBID3DanJ for these images; for instance, https://en.wikipedia.org/wiki/File:3NT13DanJ.gif for this protein-ligand complex 3NT1.

I upload all these images to commons now, as per the request by Leyo on my talk page. For a comprehensive list of images I've uploaded see Commons:Special:ListFiles/Fuse809.

My philosophies about Wikipedia[edit]

I have ten philosophies when it comes to Wikipedia:

  • The five pillars of Wikipedia are the law.
  • Style guides are the guidelines, if you stray from them, in a way that isn't well-justified, you better have a good reason and if you do not you should not be surprised if somebody, yes, including myself, reverts your edits.
  • Consensus is the legislator. If you show me consensus against what I did I will admit I was wrong and never do it again!
  • If you make any changes to a page then the burden of proof for any additions you make is ON YOU. If you do not manage to keep to this standard then people (including myself) may and should feel no guilt in reverting your edits!
  • If you have a problem with my work, please don't just stop there, tell me specifically what is wrong. I have seen some people not bother to give me any specifics and I have deleted their comments from my talk page as I did ask them, repeatedly, what specifically they wanted me to change, but they didn't bother to. Otherwise, answer me, what good does your criticism do if you don't even bother telling me what is specifically wrong? I am willing to accept people challenging the way I draw structures and edit Wikipedia, I may even thank you for it and admit I was wrong! But if and only if they're willing to actually have a conversation with me and not just dump on me. After all, I think that's what a psychiatrist is for.
  • I only create structural images and replace those on Wikipedia articles if and only if I see the picture there are inferior quality, most often due to the distance between bonds, their angles, or sometimes because the previous image wasn't cropped. I only replace them with images that are acceptable according to WP:CSDG.
  • Primary sources DO NOT belong in the lead, unless there's a good reason for it. The reasoning is simple, if the experts can't agree on the validity of the info in primary sources enough to sit down and write a review article on it then why should we mention it in Wikipedia articles as fact? Plus, of course, secondary sources do take into account unpublished results, whereas primary sources usually do not unless they have an extensive and unbiased introductory section. I do not have a problem if you use primary sources and then say the info from it is pure conjecture or if you use the Introduction section of primary sources to support your info (as the intro is by definition a minireview, in effect).
  • International Nonproprietary Names (INNs) should always be the title used for drug articles. This is a change I have argued for the articles: amfetamine, dexamfetamine, metamfetamine, etc. But for some reason everybody seems to favour the more conventional spelling (i.e. ones that include the letters "ph").
  • Something is better than nothing; I would rather some information be on an article from a primary source, than there be no information, whatsoever. Like I understand, for some things like alternative medicine, where some user might have a rant about how good the stuff is with little, if any, high-quality evidence, and I can understand why you should, definitely, remove those sort of rants but I would rather you put something than nothing when it comes to alternative medicine articles. Like, for acetylcarnitine, I think we should mention the putative antidepressant and analgesic properties, even if we say it is purely conjecture.
  • "The Devil is in the details" is very true. This is why I am so pedantic. People tend to be very obsessed with the big details, hence it can be very easy to miss the little, yet important details.

My preferences[edit]

I absolutely adore Wikipedia's in-built referencing style, especially for medicine, mostly because it is so exhaustive, that is, it lists PMIDs, PMCs, DOIs (and gives these identifiers hyperlinks to the respective page associated with them) and other URLs, if free full-text is available and the format of said URL if applicable. I personally think that every article would be far better if we just used the in-built referencing style, plus the rp operator, when referencing books.

I dislike BKChem-created structural images, mostly as I know personally the tool is pretty basic and most of the images look pretty scrappy to me at least. But I am trying to avoid replacing images solely for this reason, usually due to the fact there is empty, unused space in the image, which is typical of BKChem images.

Although I realize many members of WikiProject Medicine disapprove of Medscape/eMedicine I do sometimes use it, usually when it gives one information that's difficult to come across in other secondary sources. I realize it changes and while I am all for it being knocked out of articles in which the information contained therein can be just as easily found in a static secondary source, I still favour it over primary sources or no information at all. I tend to find that eMedicine tends to be pretty static and accurate. Like there's the odd minor grammatical or spelling errors that pop up and get amended but usually the information stays pretty static unless it should be updated as it is out-of-date.

My profiles[edit]

Website title Link Comment
Blogger Link My blog for medicine-related matters. Disclaimer: NOT for personal medical information.
Facebook Link Feel free to send me a friend request, I will likely accept. Just tell me that this is how you found my profile, as otherwise I may find your request a little odd. All I ask is do not offend any of my friends and think before you tag me in anything.
Google+ Link None.
StackExchange Link None.

Comments on my sandboxes[edit]

Sandbox number (hyperlinked) Comments
1 Using to create a section on flavonoids
2 Cancers in Australia.
3 Blood cancers in Australia.
4 Antineoplastic table I created.
5 Lisdexamfetamine page edit.
6 Comparison of accepted autoimmune diseases.
7 Renal cell carcinoma page edit.
8 A page I use to create a reference list for something I'm working on.
9 The opioids.
10 Table of the opioids.

Helpful links for Wikipedia[edit]

Introduction[edit]

Pages[edit]

Uploads[edit]

Citing sources[edit]

Behaviour[edit]

Other guidelines and policies[edit]

Help[edit]

Plus, if you would like help and can't find guidance anywhere else, you can always leave {{help me}} enclosed on your talk page.

Medicine[edit]

Wikilinks[edit]

External links[edit]

Social media

Meta page

PubMed searches
PubMed searches you need to go to this page before you can implement the instructions below:

  • For a search for review articles from the past 5 years: basically edit the search line such that it looks like this. (Hidden the image as it's too large to comfortably fit here).
  • For a search for free review articles from the past years: do what is shown in the above image but add after [pdat]: " AND free full text[sb]".

PubMed Health search for systematic reviews, you need to go to this page:

  • For a search for systematic reviews from the past 5 years: edit the search line such that it looks like this. Then, after clicking "search" and being directed to your search page select the systematic reviews option in this image.

PubMed Central search for free reviews from the past 5 years:

  • Go here. Replace the "Term" field in this search with the drug/disease of your choice.

Trip database secondary evidence search

  • Go here. Then, edit the highlighted "Term" field in this image, after editing the search bar such that it appears the way it does in this image.

Cochrane collaboration review article search

  • Go to this page. Edit the highlighted "Term" field in this image after adjusting the settings such that it appears the way it does in this screenshot. You may add additional parameters to your search by pressing the encircled "+" to the left of the search boxes.

Chemistry[edit]

Mathematics[edit]


Proof that a projectile will travel in a parabola[edit]

Note: this is using some basic energy conservation laws of physics.
Assumptions: acceleration due to gravity (g=\frac{GM}{r^2}) does not vary substantially with position along the trajectory. Air resistance is negligible and wind is non-existent.

Figure 1: A parabolic trajectory.

With the Hamiltonian:

Figure 2: William Rowan Hamilton (1805-1865), the Irish physicist and mathematician after whom the Hamiltonian is named.
\mathcal{H}=T+V

also known as the total energy of the system. Where T is kinetic energy (\frac{mv^2}{2}); V is potential energy (mgy). where: v^2=\dot{x}^2+\dot{y}^2 and v is the velocity.

\mathcal{H}=\frac{mv^2}{2}+mgy

Re-expressing v as a function of y[edit]

Basic energy conservation laws state that the Hamiltonian should be static, assuming a lack of drag. Therefore, H at one time should equal H at another time. So let us take t=0 where y=0 and v=v0 and equate it to the variable form of the Hamiltonian. That is:

\therefore \ \ \ \ \frac{mv_0^2}{2}=\frac{mv^2}{2}+mgy

\ \ \ v^2=v_0^2-2gy

\therefore \ \ \ \ \ \ \ \ v=\sqrt{v_0^2-2gy}

Expressing y in terms of x[edit]

Let, y be a function of x. That is let:

y=y(x)

\therefore using the chain rule we get:

\dot{y}=\frac{dy}{dt}=y'(x)\dot{x}

Where: \dot{x}=\frac{dx}{dt}; \ \dot{y}=\frac{dy}{dt}; \ y'(x)=\frac{dy}{dx}

It follows with the substitution of this expression into our first expression for v2 we get:

v^2=\dot{x}^2 (1+(y'(x))^2)

Equating results for v[edit]

Equating this expression with what we got from the law of conservation of energy we get:

v_0^2-2gy=\dot{x}^2 (1+(y'(x))^2)

As there is no forces in the x direction we can safely assume that \dot{x} is constant, letting this constant be v_{0,x} we can rearrange this equation to get:

\ v_{0,y}^2 - v_{0,x}^2 (y'(x))^2 = 2gy

with some rearrangement we get:

(y'(x))^2 = \frac{v_{0,y}^2-2gy}{v_{0,x}^2}

Identifying the ratio of the y and x velocities as \tan{\theta} where \theta is the launch angle of the projectile we get:

First order differential equation for y

(y'(x))^2 = \tan^2{\theta} - \frac{2gy}{v_{0,x}^2}

Taking the square root of both sides gives:

y'(x)=\pm \sqrt{\tan^2{\theta} - \frac{2gy}{v_{0,x}^2}}

Solving our first-order differential equation for y[edit]

Dividing through by the RHS and integrating with respect to x gives:

\pm \int \frac{dy}{\sqrt{\tan^2{\theta} - \frac{2gy}{v_{0,x}^2}}} = x+C

Integrating by substitution with: u=\tan^2{\theta}-\frac{2gy}{v_{0,x}^2}, du=-\frac{2g}{v_{0,x}^2} dy, \therefore dy=-\frac{v_{0,x}^2}{2g} du

\frac{v_{0,x}^2}{2g}\int u^{-1/2} du = \pm x + C

Solving this integral gives:

\therefore \ \ \ \ \ \ \ \ \ \ \ \ \ \frac{v_{0,x}^2}{g} \sqrt{u} = \pm x + C

Squaring both sides and rearranging, gives:

\therefore \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ u = \frac{g^2}{v_{0,x}^4} (\pm x+C)^2

Back-substituting again gives:

\therefore \ \ \ \ \ \ \tan^2{\theta}-\frac{2gy}{v_{0,x}^2} = \frac{g^2}{v_{0,x}^4} (\pm x+C)^2

Then with some rearranging:


 \ \frac{2gy}{v_{0,x}^2} = \tan^2{\theta}-\frac{g^2}{v_{0,x}^4} (\pm x+C)^2

Our solution for y[edit]

Solution for y

 \ y=\frac{v_{0,y}^2}{2g}-\frac{g}{2v_{0,x}^2} (\pm x+C)^2

This equation is precisely the equation of a parabola, that is, y=ax^2+bx+c.

Drag and projectile motion[edit]

Figure 3: An example trajectory, the green line denotes the closest fit a parabola can give to the trajectory.

When drag is taken into consideration there are two major possible corrections to the force acting on an object, Stokes' and Newton. Stokes' gives the correction \vec{F}=-b\vec{v} whereas Newton gives \vec{F}=-av\vec{v}.[2] Therefore Newton's second law reduces to:
m\frac{d\vec{v}}{dt}=m\vec{g}-b\vec{v}-av\vec{v}

Letting: \beta=\frac{b}{m}; \ \alpha=\frac{a}{m}

\frac{d\vec{v}}{dt}=\vec{g}-\beta\vec{v}-\alpha v\vec{v}

Working in two dimensions (x and y), yields two equations:

\frac{dv_{x}}{dt}=-\beta v_x-\alpha \sqrt{v_x^2+v_y^2} v_x   (1)

\frac{dv_y}{dt}=-g-\beta v_y-\alpha \sqrt{v_x^2+v_y^2} v_y   (2)

Where v_{x}=\dot{x} and v_{y}=\dot{y} are the velocities in the x and y directions, respectively. These equations, being nonlinear coupled ordinary differential equations are impossible to solve in an exact (analytical) way, hence only numerical approximations are available. Letting, \alpha=0.016; \ \beta=1.024\times 10^{-5}; \ D=0.08; \ g=9.8; \ m = 0.1 kg; \ v_{0,x}=10; \ v_{0,y}=10 (refer to the [2] for the reasons for these choices) where the units are given here and t\in [0,1.92] and applying quadratic regression to the numerical solution gives the following MATLAB code and an estimate with a root mean square error of 0.068 metres.[2]

%dragcalc.m
clear all
options = odeset('RelTol',1e-10,'AbsTol',[1e-10 1e-10 1e-10 1e-10]);
 
%Using the ODE45 function http://www.mathworks.com.au/help/matlab/ref/ode45.html. 
 
[t,x]=ode45(@drag,[0 1.92],[0 10 0 10],options);
 
%Quadratic regression
N=length(t);
P=[ones(N,1) x(:,1) x(:,1).^2];
a=P\x(:,3); Pr=P*a; 
err=(Pr-x(:,3)); rms=sqrt(err'*err/N); 
 
%Plotting
plot(x(:,1),x(:,3),'r',x(:,1),Pr,'g')

Where the drag function is given by the following m file:

%drag.m
function dx=drag(t,x)
  g=9.8; alf=0.016; bet=1.024e-5; %alf=alpha; bet=beta
  dx(1,1)=x(2,1); %dx/dt
  dx(2,1)=-alf*sqrt(x(2,1)^2+x(4,1)^2)*x(2,1)-bet*x(2,1); %d^2x/dt^2
  dx(3,1)=x(4,1); %dy/dt
  dx(4,1)=-g-alf*sqrt(x(2,1)^2+x(4,1)^2)*x(4,1)-bet*x(4,1); %d^2y/dt^2
end

Proof that a satellite will travel in an elliptical path around a central mass[edit]

Figure 4: The elliptical orbit of a planet in orbit around the sun. The sun is at the focus of this ellipse.

Conservation of energy[edit]

Let the Hamiltonian (which is the total energy of the system) be:

\mathcal{H}=T+V

Where T and V are the kinetic and potential energies, respectively. Assuming we have the central mass at r=0 (the focus of the trajectory, although we do not know this quite yet as we are still to prove that the trajectory is elliptical in the first place), then:

\mathcal{H}=\frac{m}{2} \left( \dot{r}^2+r^2 \dot{\theta}^2 \right)-\frac{GMm}{r}

 

 

 

 

(1)

Where G is the gravitational constant, which is approximately, 6.6738\times 10^{-11} \ \textrm{N} \cdot \textrm{m}^2 \cdot \textrm{kg}^{-2}.[3] is the mass of the larger object, m is mass of the smaller object (like the particle in orbit). As always the dot above r or theta, indicates the derivative with respect to time, that is, the rate at which said coordinate changes with respect time. According to the law of the conservation of energy, this quantity should be static (i.e. constant) throughout the projectile's path.

Substitutions galore to make our job easier[edit]

Now it is time for some substitutions to make our lives easier. Let: \alpha^2 = \frac{2\mathcal{H}}{m}, \mu=GM. According to the law of the conservation of angular momentum L=m r^2 \dot{\theta}=\textrm{constant}; \ \dot{\theta} = \frac{L}{mr^2}; \ \therefore \ r^2 \dot{\theta}^2 = \frac{L^2}{m^2 r^2}. Let: \beta=\frac{L}{m}, which is also a constant, provided m is constant, then r^2 \dot{\theta}^2 = \frac{\beta^2}{r^2}.

Manipulating the Hamiltonian to get r dot[edit]

Multiplying (1) by \frac{2}{m}, gives:

\alpha^2 = \dot{r}^2+\frac{\beta^2}{r^2} - \frac{2\mu}{r}

\implies \dot{r}^2=\alpha^2 + \frac{2\mu}{r} - \frac{\beta^2}{r^2}

Extensive substitutions[edit]

To simplify this further, let: \rho=\frac{1}{r} then:

 \ \ \dot{\rho} = -\frac{\dot{r}}{r^2}

 

 

 

 

(2)

\therefore \ \ \ \dot{r}^2 = \alpha^2 + 2\mu\rho - \beta^2 \rho^2

Let us call this expression on the right-hand side f(\rho). We shall rearrange f so that it is easier for us to use later.

f(\rho) = -\beta^2 \left(\rho^2 - \frac{2\mu}{\beta^2} \rho - \frac{\alpha^2}{\beta^2} \right)

Let the expression in brackets be called g(\rho). Making some further substitutions: \gamma^2 = \frac{\alpha^2}{\beta^2} ; \ \nu = \frac{\mu}{\beta^2}; \ \xi = \rho-\nu; \ \xi^2 = \rho^2 + \nu^2 - 2\nu \rho. Then:

g(\rho) = \xi^2 - \nu^2 - \gamma^2

Let: \chi = \beta \xi; \ \kappa = \frac{\mu}{\beta^2} then:

f(\rho) = -\chi^2 + \kappa^2 + \alpha^2

Two final substitutions are required, let: \omega^2 = \kappa^2 + \alpha^2 and z = \frac{\chi}{\omega}.

Inverting this, for future reference, gives:

d\rho = \frac{\omega}{\beta} dz

 

 

 

 

(3)

Then:

f(\rho) = \omega^2 (1-z^2)

This, in turn gives:


\therefore \ \ \ \ \dot{r} = \pm \omega \sqrt{1-z^2}

 

 

 

 

(4)

Expressing theta in terms of rho[edit]

\theta ' = \frac{d\theta}{d\rho}

 = \frac{\dot{\theta}}{\dot{\rho}}

 

 

 

 

(5)

 \therefore \ \ \ \ \theta' = - \frac{\beta}{\dot{r}}

Integrating with respect to rho gives:

\ \ \theta = \mp \beta \int \frac{d\rho}{\dot{r}}

 

 

 

 

(6)

Substituting, into (6), (3) and (4) gives:

\ \ \theta = \mp \beta \int \frac{\omega}{\beta} \frac{dz}{\omega \sqrt{1-z^2}}

 

 

 

 

(7)

These constants cancel out, giving:

\ \ \theta=\pm \cos^{-1}{z}

 

 

 

 

(8)

Back-substituting z gives: z=\frac{\beta}{\omega}(\rho-\nu)

hence:

Solution for θ

\therefore \ \ \theta=\pm \cos^{-1}{\left(\frac{\beta}{\omega} (\rho-\nu) \right)}

Taking the cosine of both sides, multiplying by omega over beta and reversing sides gives:

\rho-\nu = \frac{\omega}{\beta} \cos \theta

\rho = \nu+\frac{\omega}{\beta} \cos \theta

re-expressing in terms of r:

Solution for r

r = \frac{r_0}{1+ e \cos \theta}

Where: r_0 = \frac{\beta^2}{\mu}; \ e=\frac{L}{m} \sqrt{\frac{1}{\beta^4}+\frac{2\mathcal{H}}{m\mu^2}}

Mathematics/Physics (Old)[edit]

Reference list[edit]

  1. ^ Calculated using Wikimedia Foundation Inc.. For more information see WP:CCT. To update time purge page cache.
  2. ^ a b c Taylor, JR (2005). "Chapter 2: Projectiles and Charged Particles" (PDF). Classical Mechanics. Sausalito, USA: University Science Books. ISBN 978-1891389221. 
  3. ^ Mohr, PJ; Taylor, BN; Newell, DB (2011). Baker, J; Douma, M; Kotochigova, S, ed. "The 2010 CODATA Recommended Values of the Fundamental Physical Constants" (Web Version 6.0)". Gaithersburg, MD: National Institute of Standards and Technology.