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February 08, 2010
10:41
Race is on to save UK’s only Roman chariot racetrack
» ‎ Past Horizons' Weblog - World Archaeology

When the white handkerchief dropped, the Ben Hurs of Colchester would have set off down Circular Road North, past the banked tiers of seats, turning left at Napier Road, their iron tyres gouging a deep rut in the track,and back up past St John’s gatehouse towards the water-spouting dolphin marking the end of the first [...]

10:06
Theory and Experiment in “Step” on Semiconductors
» ‎ Accelrys Blog

A recent news article by the University of Texas at Dallas (UTD) highlighted recent joint work by the Department of Materials Science and Engineering and Accelrys on critical surface reactions of Silicon. The research points the way to ”improve semiconductor devices’ performance in health care and solar power applications in particular.”

Who cares? Anybody who uses chips, solar cells, or any other device containing semiconductors (in other words, all of us.)

Insertion of Nitrogen atom is predicted to occur preferentially at the step edge of Si(111)

How does the latest research help? A typical semiconductor device consists of a metal oxide semiconductor layer (e.g., HfO2) deposited on a silicon substrate. As explained by co-author Dr. Mat Halls, formation of an SiO2interlayer between the silicon substrate and metal oxide can decrease semiconductor performance. One approach to solving this is to introduce a nitride barrier to prevent the growth of interfacial SiO2. The ability to introduce such heteroatoms into the topmost layers of Si affords additional opportunities to tune the surface properties by enhancing chemical reactivity at these sites to form functional surfaces. But how do you get the nitrogen to stick to the surface?

In the latest research, published in Nature Materials, used infra-red spectroscopy to explore the possible formation mechanisms of nitride on silicon surfaces terminated by hydrogen. Calculations using density functional theory (DFT) demonstrated how stepped edges are important to formation of the nitride layers. The reaction mechanism on the stepped surface provides a means of controlling the reaction. As the authors wrote: “The ability to control the reaction … enables the realization of applications … including sensing, electrical and thermal transport, and molecular computing.” This is a beautiful demonstration of the complementarity of theory and experiment. One can deal with facts, but requires interpretation. The other provides detailed explanations at the atomic level, but sometime requires an anchor to the “real world.” Together they can do more. Wouldn’t it be great if all viewpoints could be reconciled this well?

9:16
New Blog Round Up
» ‎ A Very Public Sociologist

It seems ages since I last did one of these. There are plenty of new and newish blogs doing the rounds at the moment readers can get their teeth into. Without further ado ...

First up is a rare departure for this blog. Normally I concentrate on socialist, Labour, feminist and Green blogging but just this once I'll allow a LibDem to slip through the net. But with good reason. Giles Wilkes' Freethinking Economist has rapidly established itself as one of the few must-read populist economics blogs out there (alongside the apparently defunct Duncan's Economics Blog and the ever-excellent Stumbling and Mumbling). I think that's reason enough for inclusion on this list!

Next on the conveyor belt of blogging goodies comes Red Rag, which is neither the blog-that-never-was that got Derek Draper into a spot of bother last year, nor the newish Tory-supporting effort that's recently been touted in Conservative blogging circles. This Red Rag is very much in the mode of an attack blog, aiming its fire at the easy ride the Tories get in the mainstream press. It also tries to make a nuisance of itself, such as this interesting piece on the Tories' treasurer, Michael Spence. If Red Rag gets an audience behind it, it could give the Tories a bit of a headache.

Reddebrek's Bowl is not a million miles away from my own blog in its intention. The author, 'Red Mike' writes "I'm a male 20 something politically active student who enjoys reading, long walks in the woods and being pretentious" and promises "an eclectic mix of Left leaning rants, pop cultural rambles and the odd grumble about the state of the telly and book world."

Time for a touch of greenery. Green Gabbles from Steve Gabb carries his personal musings about the Green party and green politics. His latest piece looks at Phillip Lee, the candidate who won the high profile open primary for the Tory safeseat of Bracknell and has since disappeared off the local political radar. Hopefully his inaction will see Labour and the Greens rack up decent votes. You can follow Steve on Twitter here.

This is another cheeky one stretching the definition of 'new' to the limit. Faithful to the Line has been going on and off since December 2008, and has recently started up again. Hopefully they will continue churning stuff out as the comment and opinion so far has been excellent. Show your encouragement by visiting, and visiting often.

The Novocastrian is the vehicle of Rob Carr, a "Labour supporting Christian living in Newcastle". If religion isn't your bag, don't worry. Rob doesn't do preaching. Instead his blog lately indulges attacks on the Tories, reflects on the John Terry saga, and some pretty revealing thoughts about weight and weight loss. You can follow Rob on Twitter here.

When you're an independent political activist, there is always a temptation to try and fish in the waters of anti-politics by projecting yourself as somehow new or fresh. Vote Gareth Allen does just that, claiming to offer a "new approach to politics". A pretty bold claim considering Gareth is standing on a number of social democratic policies. Nonetheless he typifies the kind of centre left voter/activist who Labour has alienated with its slavish submission to neoliberal dogma.

Time for another contribution from green politics. The collaborative blog, Bright Green Scotland does what you expect it to. It offers "news and analysis for Scotland's green and progressive movement" and covers quite a wide range of topics. You can follow BGS on Twitter here.

And now for the last blog this month. Wind From Nowhere is the platform of long time cpgb supporter and Weekly Worker writer, Eddie Ford. Like other cpgb bloggers (such as the legendary Milton Keynes Communists), the bulk of material consists of stuff Eddie or other comrades have written for the WW. That's not necessarily a bad thing (especially as the WW is generally the best written and least boring of the far left's official publications), but it can be much of a muchness as far as blogging is concerned.

And that is it for another month. If you know of any new left blog (i.e. less than a year old) that deserves a shout out, plug them in the comments box or write to me at the usual address.

4:35
Top online engineering degree online
» ‎ Chemical Engineering for Life

Well, some time back I received a mail sent by Betty Jones. He had newly posted an article(100 Eye-Opening Lectures on Future of Engineering) on his site. The article is on 100 engineering topics by different professionals, and each one followed by its respective excerpt. Among those, this one impressed me:

Aubrey de Grey says we can avoid aging
Inventions that slow or entirely halt the aging process have the potential to also cure humans of the many medical problems that settle in as one grows older.
The article is worth reading especially for all the engineering students.Here is the link: [toponlineengineeringdegree.com]
3:52
Professionls have answered my questions, still I'm in a dilemma
» ‎ Chemical Engineering for Life

My comment: Hi, your blog has always been interesting and cute. I’m a chemical engineering student.Could you please give me some advices for manipulating my engineering studies efficiently.Secondly, I’m interested in Alchemy.Could you please guide me regarding the same.

Gaussling said...
Hi Vinith, can’t help much with alchemy given that it faded out centuries ago. As a chemist, I’m reluctant to advise in regard to chemical engineering. But in regard to the chemical processing industry (CPI), you should decide where you would like the arc of your career to take you.
If you are business oriented, then you need to be sharp in the area of process economics and finance. If you want to be on the technical end, then you have to try to guess what part of the CPI you’ll end up in. Pharmaceuticals requires different skills than petroleum refining. Biotechnical engineering favors those with some knowledge of cell biology and microbiology. If you show good mechanical aptitude, you might end up being a plant engineer maintaining and installing equipment. You should have a good look in the mirror and decide on what really excites you about engineering – do you like to be out on the plant floor supervising or indoors planning? Perhaps you want to be a consulting engineer who flys in to solve specific problems. Before anyone can help you plan your studies, you need to look inward and decide what drew you to engineering and what do you love to do.
My comment:I'm a chemical engineering student and interested in rheology. Could you please give me any suggestions.
John said... I'd say you are off to a good start being in chemical engineering. (That's my background as well, only I ended up here without any planning.) Despite its importance across so many fields, you can't get a degree in rheology. It's the same way with thermodynamics - so useful across so many fields, but you can't get a degree in it. There aren't job postings for "Rheologists" but for people (engineers, mostly) with experience in rheology. And it's mostly engineers because fluid mechanics is an engineering subject that few "scientists" ever study. Studying polymers is a good entry point, as is food processing. Lastly, take as much math as you can handle. The mathematics behind much of rheology is the same mathematics used in Relativity Theory - tensor analysis. Taking the derivative of a vector is trivial; taking the derivative of a tensor is a nightmare.
I'm not able to decide which area of chemical engineering more interests me. Our choices design our fortune and I hope, I would make a good choice. On the whole, many areas like I'd mentioned in my profile-rheology, nanotechnology, microbiology etc. have influenced me.And yesterday, I read some chemical engineering matter on the net. Then I decided to become a freelancer.However, I'm in a dilemma whether to procure a job and go for working in an industrial sector directly after b.tech, or opt for higher studies and go for R & D in my interested area(s). Have some time to decide. Before that I should just complete doing my engineering.Lastly, I would like to thank all the chemical engineering and other professionals who were supportive and did care my presence(blog) on the net and responded to my queries.They have included my blog on their sites. I want to list them up: Chemical Professionals, Chemical Engineering, It's a micro world, The Chem Blog, Coronene Chemistry Blog, Smart Process Design .I'm also a big fan of Zaki, Profmaster and Dilantha.

January 23, 2010
14:31
Comment on 5 years of Mestrelab (year 5) - The present by accubs
» ‎ Comments for The Mestrelab Blog

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February 07, 2010

Permalink for 'Molecules & MongoDB - Numbers and Thoughts'

20:18

Molecules & MongoDB - Numbers and Thoughts

» ‎ So much to do, so little time

In my previous post I had mentioned that key/value or non-relational data stores could be useful in certain cheminformatics applications. I had started playing around with MongoDB and following Rich’s example, I thought I’d put it through its paces using data from PubChem.

Installing MongoDB was pretty trivial. I downloaded the 64 bit version for OS X, unpacked it and then simply started the server process:

1	$MONGO_HOME/bin/mongod --dbpath=$HOME/src/mdb/db

where $HOME/src/mdb/db is the directory in which the database will store the actual data. The simplicity is certainly nice. Next, I needed the Python bindings. With easy_install, this was quite painless. At this point I had everything in hand to start playing with MongoDB.

Getting data

The first step was to get some data from PubChem. This is pretty easy using via their FTP site. I was a bit lazy, so I just made calls to wget, rather than use ftplib. The code below will retrieve the first 80 PubChem SD files and uncompress them into the current directory.

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import glob, sys, os, time, random, urllib

def getfiles():
n = 0
nmax = 80
for o in urllib.urlopen('ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF/').read()
o = o.strip().split()[5]
os.system('wget %s/%s' % ('ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF/', o))
os.system('gzip -d %s' % (o))
n += 1
sys.stdout.write('Got n = %d, %sr' % (n,o))
sys.stdout.flush()
if n == nmax: return

This gives us a total of 1,641,250 molecules.

Loading data

With the MongoDB instance running, we’re ready to connect and insert records into it. For this test, I simply loop over each molecule in each SD file and create a record consisting of the PubChem CID and all the SD tags for that molecule. In this context a record is simply a Python dict, with the SD tags being the keys and the tag values being the values. Since i know the PubChem CID is unique in this collection I set the special document key “_id” (essentially, the primary key) to the CID. The code to perform this uses the Python bindings to OpenBabel:

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from openbabel import *
import glob, sys, os
from pymongo import Connection
from pymongo import DESCENDING

def loadDB(recreate = True):
conn = Connection()
db = conn.chem
if 'mol2d' in db.collection_names():
if recreate:
print 'Deleting mol2d collection'
db.drop_collection('mol2d')
else:
print 'mol2d exists. Will not reload data'
return
coll = db.mol2d

obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()

n = 0
files = glob.glob("*.sdf")
for f in files:
notatend = obconversion.ReadFile(obmol,f)
while notatend:
doc = {}
sdd = [toPairData(x) for x in obmol.GetData() if x.GetDataType()==PairData]
for entry in sdd:
key = entry.GetAttribute()
value = entry.GetValue()
doc[key] = value
doc['_id'] = obmol.GetTitle()
coll.insert(doc)

obmol = OBMol()
notatend = obconversion.Read(obmol)

n += 1
if n % 100 == 0:
sys.stdout.write('Processed %dr' % (n))
sys.stdout.flush()

print 'Processed %d molecules' % (n)

coll.create_index([ ('PUBCHEM_HEAVY_ATOM_COUNT', DESCENDING) ])
coll.create_index([ ('PUBCHEM_MOLECULAR_WEIGHT', DESCENDING) ])

Note that this example loads each molecule on its own and takes a total of 2015.020 sec. It has been noted that bulk loading (i.e., insert a list of documents, rather than individual documents) can be more efficient. I tried this, loading 1000 molecules at a time. But this time round the load time was 2224.691 sec - certainly not an improvement!

Note that the “_id” key is a “primary key’ and thus queries on this field are extremely fast. MongoDB also supports indexes and the code above implements an index on the PUBCHEM_HEAVY_ATOM_COUNT field.

Queries

The simplest query is to pull up records based on CID. I selected 8000 CIDs randomly and evaluated how long it’d take to pull up the records from the database:

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from pymongo import Connection

def timeQueryByCID(cids):
conn = Connection()
db = conn.chem
coll = db.mol2d
for cid in cids:
result = coll.find( {'_id' : cid} ).explain()

The above code takes 2351.95 ms, averaged over 5 runs. This comes out to about 0.3 ms per query. Not bad!

Next, lets look at queries that use the heavy atom count field that we had indexed. For this test I selected 30 heavy atom count values randomly and for each value performed the query. I retrieved the query time as well as the number of hits via explain().

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from pymongo import Connection

def timeQueryByHeavyAtom(natom):
conn = Connection()
db = conn.chem
coll = db.mol2d
o = open('time-natom.txt', 'w')
for i in natom:
c = coll.find( {'PUBCHEM_HEAVY_ATOM_COUNT' : i} ).explain()
nresult = c['n']
elapse = c['millis']
o.write('%dt%dt%fn' % (i, nresult, elapse))
o.close()

A summary of these queries is shown in the graphs below.

One of the queries is anomalous - there are 93K molecules with 24 heavy atoms, but the query is performed in 139 ms. This might be due to priming while I was testing code.

Some thoughts

One thing that was apparent from the little I’ve played with MongoDB is that it’s extremely easy to use. I’m sure that larger installs (say on a cluster) could be more complex, but for single user apps, setup is really trivial. Furthermore, basic operations like insertion and querying are extremely easy. The idea of being able to dump any type of data (as a document) without worrying whether it will fit into a pre-defined schema is a lot of fun.

However, it’s advantages also seem to be its limitations (though this is not specific to MongoDB). This was also noted in a comment on my previous post. It seems that MongoDB is very efficient for simplistic queries. One of the things that I haven’t properly worked out is whether this type of system makes sense for a molecule-centric database. The primary reason is that molecules can be referred by a variety of identifiers. For example, when searching PubChem, a query by CID is just one of the ways one might pull up data. As a result, any database holding this type of data will likely require multiple indices. So, why not stay with an RDBMS? Furthermore, in my previous post, I had mentioned that a cool feature would be able to dump molecules from arbitrary sources into the DB, without worrying about fields. While very handy when loading data, it does present some complexities at query time. How does one perform a query over all molecules? This can be addressed in multiple ways (registration etc.) but is essentially what must be done in an RDBMS scenario.

Another things that became apparent is the fact that MongoDB and its ilk don’t support JOINs. While the current example doesn’t really highlight this, it is trivial to consider adding say bioassay data and then querying both tables using a JOIN. In contrast, the NoSQL approach is to perform multiple queries and then do the join in your own code. This seems inelegant and a bit painful (at least for the types of applications that I work with).

Finally, one of my interests was to make use of the map/reduce functionality in MongoDB. However, it appears that such queries must be implemented in Javascript. As a result, performing cheminformatics operations (using some other language or external libraries) within map or reduce functions is not currently possible.

But of course, NoSQL DB’s were not designed to replace RDBMS. Both technologies have their place, and I don’t believe that one is better than the other. Just that one might be better suited to a given application than the other.

16:53
Getting Physical
» ‎ OChemOnline

Our first lab of the semester in “Introduction to Organic Chemistry” was a “physical properties” exploration activity. I incorporated some of the features that I like to include in experiments into this lab. The students were assigned either vanillin or camphor as their solid and limonene or ethyl lactate as their liquid. The four possible [...]

16:24
The Future of Soccer
» ‎ A Spoken Silence

The other day I was channel surfing, and I came across a gaming channel. The game they were playing was Fifa on the computer from what I could tell.

If you have ever watched a Star Craft tournament, it was very much like that. Two teammates play on one system, working together to crush their opposition, who sit at another system on the other side of the room. The team's consisted of blurry eyed Asians staring at their screens with a focus you normally see them direct at textbooks. They even wore the team shirts of the soccer teams they represented: Manchester United and Real Madrid.

The thing that truly disgusted me was the commentary. The commentators treated the tournament as if it were the real sport. Let me give you idea of what I witnessed.

"Ronaldo is dribbling down the field, but he has two men on him. Oh, he's crossing it and OH MY GOD, it's off the crossbar."

"It looks like we have an offsides, Jim. I don't know if that call is correct, but this is a computer, so I guess we'll have to accept it. There are problems with programming sometimes though."

"Manchester United is looking really strong today. Their footwork is impeccable in losing their defenders. I'm sure we'll see more interesting gameplay in the second half when both teams are warmed up."

"We have some incredible players on the field and I can't wait, Jim."

Really? Really? They argued about whether the computer judged the offsides correctly. They were talking about the dribbling down the field as if it was really happening. Congratulations! You pushed the arrow key in the correct direction. They talked about footwork, and discussed each goal in detail. They questioned whether the teams were getting warmed up properly. It was disgusting.

The actually playing of soccer is more difficult because of the physical prowess necessary to play the game. You almost have to be picked by God to play in the professionals. I remember a boy I played with who had practiced his skills to perfection, but his body was so weak he could only play half of the time.

The sport requires the entire body and mind to work as one to execute the tactics necessary to score on the opponents. The player cannot see the whole field, and he can only hope his 9 other teammates are doing what they should be. The body has to be capable to play at the level. Any athlete should be acknowledged on their physical prowess.

Computer games only require a sharp mind and fast fingers to exploit the programing. They often only consist of teams of 2. The morale of a team is not affected in computer games. Instead of relying on gut shots, one relies on the mathematics written into the game. Any hack with enough time and patience can pick up the controller and master it. I fear that someday this may become the future of soccer. As people get more overweight, people will play the computer game that gives them the illusion of playing the game perfectly instead of the real game.

I don't know. Watching the gaming network made me think.

15:31
RDF, Jena, Bioclipse, Eclipse, Zest: Mashups
» ‎ chem-bla-ics

Quite a while a go, I blogged about Zest in Bioclipse showing a bit of ONS Solubility data. I could not follow up on that until now, as I had yet to do a lot of RDF work in Bioclipse, so the screenshot back then was kind of a mockup.

Things are different now, and the Bioclipse-RDF functionality (using Jena) is released in Bioclipse 2.2 (see Semantic Web features in Bioclipse 2.2), and I got around to writing the graphical goodies for the following papers. Not submitted yet, but here's the screenshot showing a N3 file opened with a Zest-powered editor (read-only) and a plain text editor:

15:08
17 Ways to Reduce Likelihood of Pump Cavitation
» ‎ Chemical & Process Technology
In recent project, there was a topic being discussed. What are the measures can be considered to reduce the likelihood of pump cavitation ?. To answer to this question, we may need to understand some background about pump cavitation phenomenon. Previous posts as follow may probably provide some background information :
Recommended :- Subscribe FREE - Chemical Engineering- Tips on Succession in FREE Subscription
Key to ensure no detrimental cavitation is the ensure NPSHa is higher than NPSHr. One may have to take extra note that pump cavitation can exist eventhough NPSHa is above the NPSHr of a centrifugal pump. However, it suction energy is sufficient low (below 3% head drop) and will not results cavitation which is detrimental to pump internal (discussed in "Facts About NPSH - Cavitation Even NPSHa More than NPSHr ?". Therefore, two main parameters we may have to focus are NPSHa and NPSHr.
Increase NPSHaPrevious post "How to Increase NPSHa to a Pump ?" , several points have been highlighted. Will further expand. Following equation define NPSHa :

NPSHa = Hp + Hs - Hf - Hv - Hvp
where
Hp - pressure head
Hs - static head gain
Hf - frictional loss
Hv - velocity head
Hvp - vapor pressure headThe key is to increase Hp and Hs whilst decrease Hf, Hv and Hvp (1) Increase suction line size to reduce frictional loss (decrease Hf ) and velocity head (decrease Hv)
(2) Rearrange and /or redesign suction pipe work to minimise bends, valves and fittings to reduce frictional loss (decrease Hf )
(3) Reduce suction pipe length to reduce frictional loss (decrease Hf )
(4) Use smoother pipe (lower friction factor) to reduce frictional loss (decrease Hf ) e.g. SS instead of CS
(5) Raise suction vessel to increase static head (increase Hs )
(6) Lower pump elevation to increase static head (increase Hs)
(7) Increase pressure in suction vessel to increase suction pressure head (increase Hp) e.g. pressurize suction drum with inert gas
(8) Reduce fluid vapor pressure to decrease vapor pressure head (decrease Hvp) e.g. subcool fluid by dropping it temperature

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Decrease NPSHr Suction specific speed ( Nss) of a pump is a dimensionless number expressed as

Nss = ( N* Q ^0.5 ) / (NPSHr)^0.75
Where

Nss : Suction Specific speed
Q : Flow rate (gpm) at the Best Efficiency Point
N : Pump rotational speed (rpm)
NPSHr : Net Positive Suction Head required (ft)

(9) Use low speed pumpDecrease pump speed reduce NPSHr. Therefore use low speed pump required lower NPSHr.

(10) Use double suction impellerDouble suction impeller as shown in below image will reduce flow to each impeller by half and will reduce the NPSHr by approximately 36%-37%.

(11) Increase impeller eye area to minimize inlet pressure drop. The downside is introduction of suction recirculation. There shall be a balance in eye area selection.
(12) Use cavitation resistance material like SS (discussed in "Stainless Steel SS316 resist to CAVITATION ?"(13) Use Suction Inducer to streamline suction flow to pump and reduce suction pressure drop
Process TreatmentBesides above measures, process engineer may also consider other process measures :(14) Use of pump in series to reduce pump capacity of pump and reduce pump NPSHr(15) Use of booster pump to provide sufficient head for main pump NPSHr(16) Vortex in suction results vapor entrainment into liquid and lead to pump cavitation. Install vortex breaker at vessel outlet to avoid vapor entrainment (discussed in "Vortex Breaker to Avoid Vapor Entrainment") and;(17) Ensure sufficient liquid height above vessel outlet to avoid vapor entrainment (discussed in "Estimate Minimum Submergence to Avoid Vapor Entrainment"

Above listed the ways to minimize likelihood of pump cavitation by increasing NPSHa, reducing NPSHr and introducing process treatment.

Related Post

10:23
M45 Test Shot
» ‎ Phil's Astronomy Blog

M45 Test Shot
10:07
Testing Guiding with the CGEM
» ‎ Phil's Astronomy Blog

Testing Guiding with the CGEM

8:57
I'm positive
» ‎ Molecular Modeling Basics

Figure 4.2. 0.002 au isodensity surface with superimposed electrostatic potential of (a) Li⁺, (b) Na⁺, and (c) K⁺ ion. The maximum potential value is 0.8 au, and the level of theory is B3LYP/6-31G(d).
From Molecular Modeling Basics CRC Press, May 2010.

Here is an example of how computational chemistry can be used to enhance teaching at the general chemistry level.

Why does the ionization energy decrease on from Li to Na to K? That's the same as asking why the electron affinities decrease on going from Li⁺ to Na⁺ to K⁺.

Figure 4.2 show the ions colored by how positive they are at the surface (i.e. the electrostatic potential superimposed on the 0.002 isodensity surface). The darker the
color the more positive the ion, and it is clear that the Li+ ion is “more positive” than Na⁺, which is more positive than K⁺. Thus, more energy should be released when adding an electron to Li⁺ compared to Na⁺, and hence more energy is needed to remove an electron from Li
compared to Na (and similarly for K).

The reason why Li⁺ is “more positive” than Na⁺ or, more accurately, why the potential on the 0.002 au isodensity surface is more positive for Li⁺ than for Na⁺, is that the former is a smaller ion than the latter, so the surface is closer to the +1 charge at the center of the ion.

Figure 4.4. 0.002 au isodensity surface with superimposed electrostatic potential of (a) Li⁺, (b) Ne⁺, and (c) Na⁺ ion. The maximum potential value is 0.8 au, and the level of theory is B3LYP/6-31G(d).
From Molecular Modeling Basics CRC Press, May 2010.

This rationalization is, of course, only qualitative and is is not predictive of the ionization energies among different groups. For example, based on Figure 4.4 one would expect that Ne would have roughly the same ionization potential as Na, which is not true at all.

When making these figures it is very important to get the relative sizes of the ions correct, but this can be difficult since each image can be zoomed to an arbitrary size. The screencast below shows how to control this in MacMolPlt using the Manual Windows Parameter window.

The same point can also be made with a "quick-and-dirty" electrostatic potential, as shown in this interactive figure. Here the electrostatic potential is due to a plus one charge centered at the atom (rather than the nuclear charge and the electron density) and the surfaces are the spheres defined by empirical ionic radii. The Jmol script can be found here, and the mol2 files here, here, and here.

Click on the picture for an interactive version

8:42
Expenses: What is to be Done?
» ‎ A Very Public Sociologist

Elliot Morley, David Chaytor, Jim Devine. As Labour MPs go they're cards aren't they? It's not enough that they've allegedly swindled the system by submitting false expense claims *and* will be in receipt of at least £30k "relocation money" when they step down, but now the right honourable members have the cheek to pursue parliamentary privilege defence to avoid court action. In a society where the rich and powerful are litigious, this is an important democratic gain worth defending. So to see it dragged through the muck to defend the sullied reputations of men caught with their hands in the taxpayer's pocket is a sickening sight. You cannot but agree with Ruth Cox of the Hansard Society, who says
"If it is a defence against almost any action that an MP takes in parliament, in any relationship with their work, then I think that is going to be deeply damaging for the public. They will see that it is putting MPs above the public, giving them enhanced powers, making them essentially above the laws that they themselves make." (source)
Coming on top of the wider expenses crisis, if this defence is allowed and the trio of troughers emerge unscathed this will compound the widespread antipathy against 'official' politics. Not good news for the mainstream parties or the minor ones to their left, but it provides fertile environment for the far right.

What can be done to prevent a scandal like this from happening again? The anarchists have traditionally argued against seeking election on grounds that democracy in capitalist societies corrupts even the best representatives of the workers' movement. They have a point. I remember a Coventry SP comrade telling me of all the freebies and corporate invites that poured into Dave Nellist's office when he was elected to parliament in 1983. He turned them all down and, famously, only took the average wage of a Coventry skilled worker during the two terms he served.

Dave's example, as well as those of Militant's two other MPs and the Scottish Socialist Party's MSPs have provided the far left with a ready made answer to the expenses crisis. I'm sure many SP readers did their share of stalls calling for a workers' MP on a worker's wage at the height of the scandal (I certainly did a few). It sounds good and makes easily understood populist points, but how much of a solution is it?

The argument goes that limiting a MP's wage means s/he is not materially cut off from the people they represent. It's a lot easier to empathise with constituents who struggle to make ends meet if your income is not an order of magnitude higher. While this may be true the workers' wage, in and of itself, is problematic if uniformly applied. There is the wage cut argument (often picked up by Tories and other well-heeled members). If a MP's salary is not sufficiently attractive it will not draw in successful people from business, etc. I couldn't care less if business-types steered clear of the House of Commons (it's not like they're thin on the ground at the moment), but what about comparatively well paid sectors of the labour movement such as teachers, engineers, firefighters, social workers, etc? Some might be willing to take a wage cut for ideological reasons, but with kids to bring up and mortgages to pay off even a modest cut could be enough to put off otherwise dedicated activists. Second, implementing the average wage could exacerbate the already disgraceful situation regarding MPs' second jobs and, for some, make them even more willing to accept the gratuities business lavishes on our elected representatives.

An alternative favoured by George Galloway is to increase the salaries of MPs to the levels enjoyed by members of Congress in the United States. If they were paid a hefty salary out of which the cost of maintaining an office and employing staff was taken, everything would be above board. An unwieldy expenses system would be unnecessary, and MPs would be less likely to take on second jobs. But the problem of the income gap addressed by the average wage argument rears its head again.

Whatever the merits of the two income arguments, it's mistaken to present either as solutions that would banish the problem of institutionally corrupt politics altogether. Two reforms addressing the election and accountability of MPs would likely have more of an impact than either.

The Chartists were certainly onto something with their call for annual parliaments. They were entirely right that the more precarious position an MP is in, the more accountable they are to the electorate. I'm not sure if anyone has the appetite for a general election every year, but the implementation of mechanisms for recalling MPs could work just as well. This must go hand in hand with some form of proportional representation (see here). If political parties and MPs have to fight for every single vote no one will coast into parliament on the back of safe, geographically concentrated majorities (and as Left Foot Forward pointed out, the worst expenses offenders also happened to have the safest seats).

But for any improved system to work, it's not enough to engineer better constitutional arrangements. Politics needs to re-engage the millions of people who've been alienated from it these last 20 years. It's not a matter of educating the electorate or forcing citizenship classes on school kids. Parties need to eat humble pie and listen to the real problems of 'real' people, and pay big business and the mythological 'Middle England' less mind.

Image by Beau Bo D'Or.

5:35
Average time on Site: chem-bla-ics
» ‎ chem-bla-ics

Cameron freeded(?) on the Spanish and Dutch sticking around longest on his site. I've never used Google Analytics for that, but it's good time spent on procrastination: it makes nice graphics:

For what it's worth, the two visitors from Cuba spend most time on my site :) More seriously, the information on the site does not include any error bars, such as the standard deviation:

Most of use know that 4:24 for two visitors is not necessarily significantly different from 2:43 for one hundred visitors (actual numbers). Standard deviation information would have helped significantly here (pun intended :).

February 06, 2010
23:18
Perchance to Dream
» ‎ A Spoken Silence

I am alive, forum! By the power of fried chicken and an In 'n' Out burger, I finally have the energy to blog again. I was sick for the past week. I delivered a speech to my public speech class, which quickly turned it into a public humiliation class. After a humble ride home, I crawled into bed and slept for 12 hours straight. I awoke to read some manga and Norman Mailer's "The Naked and the Dead" for 5 hours and passed out for another 12 hours. With the sleep, I've had plenty of opportunity to dream of blog topics to talk about.

"To die, to sleep; To sleep, perchance to dream." Now, for the well-read, perhaps you may recognize the Shakespeare quote. It comes from the "To be or not to be" soliloquy by Hamlet. (Stop being a Hamlet, Andrew! Sorry, it was too good to pass up.) The phrase "Perchance to Dream" has been used as a title for a Twilight Zone episode, and even a Batman: The Animated Series episode. Both episodes challenged my perceptions of dreaming.

I watched the Batman: The Animated Series episode when I was about 10 years old. Bruce Wayne discovers himself in a life where he isn't Batman. His parents are alive. He's getting married to the love of his life Selina Kyle, who you probably know as Catwoman. In fact, there is another Batman protecting the city. He has a hard time relinquishing the drive to protect people, but he finally starts to settle into his peaceful life. He sits down to read the newspaper, but he can't. The text is all gibberish. In a frenzy, he flees his house and goes to the cemetery to confront Batman because Bruce knows Batman knows what is going on. I don't want to give away the ending, but needless to say, the ending for this episode blew my 10-year-old mind. I found the episode in parts on YouTube: part 1 and part 2. I think this a must-see for the Batman fan.

The Twilight Zone episode appeared more than 30 years earlier, and it contains another thought-provoking message about dreaming. A man goes to a psychiatrist to help him with a problem. The man has a weak heart, so he can't do anything too stressful. In his dreams, he is visited by a woman who makes him take thrilling rides, which make his heart want to burst. He knows the next time he falls asleep, it will be his last. Another incredible ending which will make you think. If you ever have the opportunity, I suggest you watch it. Sorry, I couldn't find the episode on YouTube for you.

Now, I've talked about two television series and their mischievous dealings with dreams. How does this concern me? Whenever I get sick, I have a perchance to dream.

In the 7th grade, we were required to read a book called "The Hero and the Crown". I was running a fever, so I was lying in bed trying to keep up with school work. I was reading the book, but I kept fading in and out of reality. The forest and shrubbery became more than words, I had become one with the book. I will never forget the description of the man's skin as "milky-white". It was all so vivid. Think Avatar 3-D, and kick it up a couple of notches. Unbeknownst to me, my fever had run up to 106 degrees. My mom rushed me to the emergency room, and I was fine.

Ever since, when I'm sick, I have a tendency to dream. Unlike "The Hero and the Crown" incident where I was forced into the book, I tend to have the capability to experiment with my dream. I was reading "The Naked and the Dead" which takes place in World War II in the Pacific campaign. I dreamt of the Pacific beaches that had to be stormed, how a life is held so precariously by Chance as a soldier creeps through the jungle growth, and attitudes of the men. I erase the story as I go, making it my own. It's a weird experience I cannot describe.

My manga chapters led my dream to wander in metropolises overrun by demons and their hunters. It was very reminiscent of Blade Runner. Santa Claus was on the corner trying to give Christmas cheer to the neo-tropolis. The style of dress was terse like the people who wore them. Action scenes unfolded in my mind. Each thrust and parry of the hunter's sword were performed to perfection. Vapor trails of bullets laced the scenery making into a grim artistic display of death. All of this played out in my mind while I rested. In fact, my dreaming is part of the reason for my long hours of sleeping. I want to see the ending. So, I sleep, perchance to dream of the next story.

Author's Note:
I did some reviewing of the forum, and would you believe I was wrong about the 100th post. We had written a 100 posts, but we hadn't published all of them. So, I guess you can say, I screwed up.

If you are interested in the endings for the Twilight Zone and Batman episodes, I can publish them in the comments section. Let me know if you want to hear more.

So, do you guys dream often? Stephanie told me she doesn't.

17:26
A Lesson from North Korea
» ‎ A Very Public Sociologist

Fed up with the love lives of footballers plastered all over our useless daily press? The Jucheist skivvies of the Dear Leader Kim Jong Il at the (North) Korean Central News agency show how sports stories ought to be treated by the media:
Pyongyang, February 5 (KCNA) -- The national football team of the Democratic People's Republic of Korea, qualified for the 2010 FIFA World Cup, embraces a lot of competent players.

Typical of them is Hong Yong Jo, famous for many scores he has made in international and local tournaments.

He, who has been interested in sports, especially football, from primary school days, is characterized by running fast, dribbling well, taking scoring positions in time and skillfully getting goals.

He has been active as a forward in many international tournaments.

He fully demonstrated his skill by scoring three goals in the home-and-home matches with Jordan at the third-phase preliminaries of the Asian region for the 2010 FIFA World Cup.

Hong, captain of the national team, was crowned with the title of People's Athlete last year.
Much, much better than the The Sun's hand-wringing hypocrisy.

16:39
Comment on 5 years of Mestrelab (year 5) - The present by point of sale software
» ‎ Comments for The Mestrelab Blog

point of sale software…

Rendezvous next-generation club system fully integrates every aspect of a club, from member accounts to meeting room scheduling to food & beverage management….

16:26
Molecular Medicine Tri-Conference 2010
» ‎ Practical Fragments

The first event on our 2010 calendar, the Molecular Medicine Tri-Conference 2010, was held in San Francisco earlier this week. There were fragment talks and a roundtable, as well as a number of vendors selling fragment libraries – we’ve recently noted how rapidly this area has expanded.

Michael Hennig presented a nice overview of the history and development of fragment-screening at F. Hoffmann-La Roche (Basel). Work done there back in the late 1990s relied on NMR and crystallographic screening of a library of 300 fragments, described in the seminal “needle-screening” publication in J. Med. Chem. Today that library has grown to 6000 compounds following a relaxed rule-of-3 (allowing in particular more hydrogen-bond acceptors and higher lipophilicity) and requiring at least one hydrogen bond donor or acceptor and at least one ring. Also, the primary screening technique is now surface-plasmon resonance (SPR), with crystallographic follow-up; the entire collection can be screened on a single Biacore instrument in four weeks.

Hennig shared two case studies, one on BACE-1, the other on chymase. In the second case, a dozen fragments were successfully co-crystallized with the enzyme, and all but one of these bound in the S1 pocket, revealing the importance of this site for binding. In response to a question about how widely FBDD is used at Roche, Hennig said that it is applied to all targets that are technically feasible.

In another talk, James Madden described fragment-based discovery at Evotec. An increasingly stringent series of assays (from high-throughput high-concentration functional assays, through SPR and/or ligand-detected NMR, and finally crystallography and/or protein-detected NMR) helps keep the number of compounds manageable at each step. Madden also presented two cases studies, BACE-1 (clearly a popular target for FBDD, perhaps due to its intractability to many other approaches) and PDE10a.

A fun talk with relevance beyond FBDD was “Examples of X-ray Bloopers”, by Edward Kesicki of the Infectious Disease Research Institute (IDRI) in Seattle, WA. He described several cautionary tales from his own experience. In one case, a chemist provided the structure of the wrong enantiomer to a crystallographer, who duly refined the data, resulting in weeks of confusion and time-consuming follow-up experiments. In two others, crystallographers inadvertently omitted methylene units in fitting electron density. We’ve previously commented on the dangers of taking crystallographic data at face value, and Kesicki also mentioned an effort by Stephen Warren of Gonzaga University to comb through and correct structures in the protein data bank. He has a lot of work to do: of the 1000 structures examined thus far, roughly 20% have problems with the ligands.

Finally, in a panel discussion on “medicinal chemistry drivers,” someone asked about the role of fragment-based drug discovery. Consistent with the idea that fragment approaches are becoming increasingly integrated with other lead-finding activities, Hing Sham of Elan said that he was neither pro-fragment nor anti-fragment – “it’s just another tool in the toolbox.”

15:10
Comment on 5 years of Mestrelab (year 5) - The present by conference software
» ‎ Comments for The Mestrelab Blog

conference software…

The Aloha point of sale software is a world-beating solution Point of Sale solution from NFS…

13:54
Two New Posts with ChEMBL Team
» ‎ ChEMBL - Open Access Drug Discovery And Medicinal Chemistry Data

We have recently been awarded an Innovative Medicines Initiative grant in the area of predictive toxicology - the project is called eTox. This is a very exciting project and will build an unprecedented collaborative database of rat toxicology data for a large number of clinical development candidates. It is also a chance to work in close collaboration with a network of some of the leading European academics, SMEs and pharmaceutical companies.

We have two posts available under this funding. The first is for a scientist with experience of datamining and analysis of data, preferably with good experience of bioinformatics or chemoinformatics. The second post is for an informatician to build a data repository, and then populate this with deposited curated toxicology data.

If you have any questions about the jobs, please feel free to mail us.

The deadline for applications is 14th March 2010.
5:45
2010 New Drug Approvals - Pt. III - Liraglutide (Victoza)
» ‎ ChEMBL - Open Access Drug Discovery And Medicinal Chemistry Data

Also approved in January is Liraglutide, on January 25th, under the trade name Victoza. Liraglutide, previously known as NN2211, is a glucagon-like peptide-1 (GLP-1) receptor agonist indicated as an adjunct to diet and exercise to improve glycemic control in adults with type 2 diabetes mellitus. People with this type of diabetes have difficulty making and using insulin.

Liraglutide works by activating the GLP-1 receptor (GLP-1R), which in turn stimulates the adenylyl cyclase pathway leading to insulin release in the presence of elevated glucose concentrations. GLP-1R is a class-II GPCR (also known as secretin receptor family). Liraglutide is the second GLP-1 agonist approved for the treatment of type 2 diabetes, after Exenatide (marketed as Byetta), which reached the market in 2005.

Liraglutide is an engineered form of the natural human GLP-1 peptide (one amino acid difference to the major circulating form of GLP-1, GLP-1(7-37), an arginine replaces a lysine at position 34), an additional modification is the addition of palmitic acid attached via a glutamic acid spacer at position 26. The molecular weight of Liraglutide is 3751.2 Da. Each standard dose contains 1.8mg of Liraglutide (equivalent to 480 nmol). Dosing is as a once daily subcutaneous (s.c.) injection.

Liraglutide has a plasma half-life of ~13 hr (far longer than the 2 min half life of the natural GLP-1 peptide). Slowing the fast degradation of GLP-1 is the basis of the therapeutic mechanism of the gliptin class of DPP-IV inhibitors). The absolute bioavailability of Liraglutide, after s.c. dosing is 55%, and has high plasma protein binding > 98%. The volume of distribution Vd is 0.07L/kg, with a clearance of 1.2 L/h.

Liraglutide has a boxed warning (risk of thyroid C-cell tumours).

Victoza is marketed by Novo Nordisk and the product website is http://www.victoza.com.
5:00
2010 New Drug Approvals - Pt. I - Tocilizumab (Actemra/RoActemra)
» ‎ ChEMBL - Open Access Drug Discovery And Medicinal Chemistry Data

The first FDA approval of this year is Tocilizumab, approved on January 8th, under the trade name Actemra. Tocilizumab is a first-in-class interleukin-6 (IL-6) receptor-inhibiting monoclonal antibody drug, and is indicated for the treatment of rheumatoid arthritis in adults who have had an inadequate response to one or more tumor necrosis factor (TNF) antagonist therapies. Rheumatoid arthritis is a chronic and debilitating, systematic inflammatory disorder, which affects principally synovial tissues.

Tocilizumab works by blocking the signalling of IL-6, an immune system soluble cytokine that is overproduced in patients with rheumatoid arthritis. Other biological therapies for RA include tumor necrosis factor-α (TNF-α) blockers (e.g, Golimumab), IL-1 blockers (e.g., Anakinra), monoclonal antibodies against B cells (e.g., Rituximab) and T cell costimulation inhibitors (e.g., Abatacept). However, all these act through binding to different target molecules. Others drugs with the same IL-6R binding mechanism as Tocilizumab are ALD518 and CNTO-136, which are currently reported to be in Phase II clinical trials.

Tocilizumab is a recombinant humanized anti-human IL-6 receptor monoclonal antibody of the immunoglobulin IgG1κ subclass. Tocilizumab binds specifically to both soluble and membrane-bound IL-6 receptors (sIL-6R and mIL-6R) - mIL-6R is also known as CD126. Tocilizumab has a molecular weight of ca. 148 kDa, with a volume of distribution of ~6.4L, a linear clearance of ~12.5 mL/h and a half-life up to 13 days. The recommended starting dosage is ~4 mg/kg followed by an increase to ~8 mg/kg based on clinical response, administrated as a single intravenous drip infusion over 1 hour, every 4 weeks. Interestingly, Tocilizumab, via blocking cytokine signalling can affect expression levels of a wide variety of CYP450 drug metabolizing enzymes, leading to the potential for drug-drug interactions.

The full prescribing information for Tocilizumab can be found here.

Tocilizumab has a boxed warning (Risk of serious infections).

Each light and heavy chain of Tocilizumab consists of 214 and 448 amino acids, respectively, and the four polypeptide chains are linked intra- and inter-molecularly by disulfide bonds.

The license holder of Tocilizumab is Genentech, Inc. and the product website is www.actemra.com.

4:04
A First Course in Probability 5Ed By Sheldon M. Ross
» ‎ Electronic Communication Engineering

Prentice Hall College Div 1997 | ISBN: 0137463146 | 514 pages | Djvu | 3,4 MB

This market-leading introduction to probability features exceptionally clear explanations of the mathematics of probability theory and explores its many diverse applications through numerous interesting and motivational examples. The outstanding problem sets are a hallmark feature of this book. Provides clear, complete explanations to fully explain mathematical concepts. Features subsections on the probabilistic method and the maximum-minimums identity. Includes many new examples relating to DNA matching, utility, finance, and applications of the probabilistic method. Features an intuitive treatment of probability—intuitive explanations follow many examples. The Probability Models Disk included with each copy of the book, contains six probability models that are referenced in the book and allow readers to quickly and easily perform calculations and simulations.

Download:
Link_1
Or
Link_2

0:35
Maybe a trend: U3, U6 unemployment down
» ‎ Chemjobber

While Big Pharma's Great Recession rolls on (with GSK layoffs, BMS salary freezes, AstraZeneca layoffs and Pfizer cutting its internal R&D budget), the bigger picture is coming a little clearer and is just a little better than last month's. These days, that's all we can hope for.

Today's BLS report indicates that the official unemployment rate (U3) for January 2010 was 9.7%, which is the lowest it's been since September 2009. It's also lower than December's rate of 10.0%. In addition, the broadest measure of unemployment (U6) is at 16.5% for January, which is lower than December's rate of 17.3% and lower still than October 2009's high of 17.5%.

One step in front of the other -- hopefully, Big Pharma will follow. Hopefully.

February 05, 2010
13:40
Wishing Him Well
» ‎ Liberal Arts and Minds

Wishing Jack strength and determination for a speedy recovery.

11:39
CPMG to Enhance Sharp Lines
» ‎ University of Ottawa NMR Facility Blog

The Carr - Purcell - Meiboom - Gill (CPMG) sequence is used to measure T2 relaxation times and more recently has made an impact in measuring the line shapes of very broad solid lines by breaking them up into spikelet patterns which mimic the static line shape. The very simple pulse sequence is shown here:During the (D2 - π -D2)n period the intensity of lines with short T2 (broad lines) diminishes much more quickly than that for lines with long T2 (sharp lines). The CPMG sequence is therefore useful for enhancing the sharp features in a spectrum by suppressing the broad features. This is demonstrated in the figure below. The top panel of the figure shows a portion of a conventional 500 MHz ¹H NMR spectrum of a polymer sample contaminated with small amounts of smaller molecules. The broad lines (truncated in the figure) are due to the polymer whereas the much smaller sharp lines are due to the impurities. The bottom panel of the figure shows the CPMG spectrum of the same sample with D2 = 4 msec and n = 32. One can see that the broad polymer lines are greatly suppressed and the smaller sharp lines are much more obvious.

11:13
PERMANENT #DM4082 Principal Consultant - IT Services Consultancy
» ‎ B2E Resourcing

Permanent - Principal Consultant – IT Service Business

Summary:

Our client is an IT Services Company, a major player in the industry. They offer the complete range of IT services - from consulting and outsourcing to focused technology and solutions. They work across most industries. This role is focused within their financial services division.

Role:

They are looking for a Consultant to start up a new practice within the Financial Services division based on the Solvency II European regulations for the Insurance industry. They will need to have a strong background in the Financial services and Insurance sectors a good understanding of risk and regulation and will be responsible for developing the practice

KEY skills/requirements:

The successful candidate will have the contacts and knowledge to find business and to develop the delivery capability in the area of Solvency II regulation.
.
They will have:

A blue chip consulting past with strong leadership, business development and delivery skills
In depth experience of system change programmes related to Solvency II
The drive and capability to get a new practice going within a large IT services business.

Logistics:

Salary: OTE package of £150,000
Location: London

Please contact David Meggitt for more information.

7:36
Overall Heat Transfer Coefficient
» ‎ Chemical Engineering for Life

The heat transfer coefficient is used in calculating the heat transfer by convection or phase change between a fluid and a solid.
$h = frac{Delta Q}{A cdot Delta T cdot Delta t}$ ------->(1)ΔQ = heat input or heat lost, Jh = heat transfer coefficient, W/(m²K)A = heat transfer surface area, m²ΔT = difference in temperature between the solid surface and surrounding fluid area, KΔt = time period, sThe overall heat transfer coefficient U is a measure of the overall ability of a series of conductive and convective barriers to transfer heat applied to heat exchangers.
Q = UAΔTLM----->(2) whereQ = heat transfer rate (W)U = overall heat transfer coefficient (W/(m²·K))A = heat transfer surface area (m²)ΔTLM = log mean temperature difference (K)Today process heat transfer class has been very interesting. HOD has discussed about heat exchangers. As you can see, the above formula( equation 2), could be used for calculating the overall heat transfer coefficient U. Actually, I got to know that there are even two other heat transfer coefficients, i.e, U subscript d and U subscript c. The former represents the heat transfer coefficients of fouling tubes and the latter that of clean tubes. Always coefficient of clean tubes is greater than the coefficient of fouling, as in case of the latter, scale formation takes place and heat loss occurs. A high jet stream is required to remove the dirt or scale-up in such kind of tubes.

Coming to the heat transfer rate in the above expression, it is determined by comparing the rates of heat transfer of two substances. For instance, if a substance is converted to another at a particular temperature, then the respective heat transfer rates of the two be Q1 & Q2. And
Q = m C dT ------>(3) where
m = mass C = specific heat capacity dT = infinitesimal or small change in temperatureSo when we equate Q1 & Q2, then with the help already known values, one could easily find out Q.
Back to the overall heat transfer coefficient, it takes into account the individual heat transfer coefficients of each stream and the resistance of the pipe material.It is calculate as follows:
$frac {1} {UA} = Sigma frac{1} {hA} + Sigma R$ R = Resistance(s) to heat flow in pipe wall (K/W)But more complex relationships exist, for example when heat transfer takes place by different routes in parallel.And the thermal resistance due to the pipe wall is calculated as follows- $R = frac{x}{k cdot A}$ x = the wall thickness (m)k = the thermal conductivity of the material (W/(m·K))A = the total area of the heat exchanger (m²) The following relationship is often used: $frac{1}{U_{exp}}$ = $frac{1}{U_{pre}}+R_f$
where
Uexp = overall heat transfer coefficient based on experimental data for the heat exchanger in the "fouled" state, $frac{W}{m^2K}$ Upre = overall heat transfer coefficient based on calculated or measured ("clean heat exchanger") data, $frac{W}{m^2K}$ Rf = thermal resistance due to fouling, $frac{m^2K}{W}$ In general, the heat transfer coefficients, h inner and h outer are also taken in consideration for heat exchanger tubes. And it's very important for a chemical engineer to calculate the surface area of heat transfer.

Here is a recommended book on extended heat transfer by D.O.Kern and A.D.Kraus.

And the widely used books, softwares or standards in industries, while dealing with heat exchangers is TEMA which is an acronym for Tubular Exchanger Manufacturers Association on shell and tube heat exchanger mechanical design...

Note: If I had made any mistake, then please inform me. Whatever info I've provided here is based on my today's class, and some internet surfing.

7:04
Daily (?) Pump Trap: 2/5/10 edition
» ‎ Chemjobber

Good morning! From Januaruy 25 to February 4, there have been 87 positions posted on the ACS Careers website. Of these, 32 (37%) are from academia and 2 (2.2%) are from our friends at Kelly Scientific Resources. Lots of industrial positions this time around -- mostly chemical industry-related.

Beer pong cups free: Dart Container ("a leading manufacturer of insulated foam cups and containers") is looking for a M.S./Ph.D. polymer/organic chemist with 5 years experience in paper R&D.

Colloids: Hexion is looking for a M.S./Ph.D. chemist with experience with experience in colloidal and dispersion science.

Interesting?: Bioo Scientific is looking for a M.S./Ph.D. food/analytical chemist with experience in "with strong emphasis on development and optimization of procedures to isolate organic compounds from complex matrices such as food samples." Huh.

Aerogels: Americal Aerogel is looking for a B.S./M.S./Ph.D. formulation chemist for a position in "sol-gel processing of organic aerogel materials." That sounds interesting; don't quite know what it is, though.

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