Tuesday, 25 December 2012

Christmas Greetings : London

Hello folks,

A very merry Christmas and happy New Year to all! As you may be realized, I have not posted in a while. I've been busy with some projects and I also did some travelling. Following that, the festive preparations and celebrations kept me busy and I suspect for some more time. :D

London is a beautiful city with truly friendly and honorable people. At the same time, it is also one of the most expensive cities I've traveled to.

Let me share with you some of the sights and experiences in London while providing some suggestions on what to expect.

Here are some rough guidelines on the kind of expenditure to expect when travelling to London.

Arrival at the airport

  1. Upon arrival at the airport, I suggest taking the subway or the 'tube' to your place of accommodation. It is far more economical than hailing one of the infamous London's Black Cabs which will easily set you back around £40. Comparatively, a subway ride to the city center (Zone 1) would cost about £2-3. Less than 10% of the cost.
  2. If you are travelling in London for more than a day or two, I suggest you get the subway card, also known as the 'Oyster' card. This card allows you to store credits in it so that you can avoid the queues at subway stations. Each Oyster card contains £5 in deposit. So you need to pay £5 on top of the amount you with to 'top-up' into the card.
  3. Most flights fly into London's Heathrow Airport. It has FIVE terminals. Terminals 4 and 5 have individuals have individual stations. If I am not mistaken, Terminals 1,2 and 3 share the same subway station. In any case, I would suggest that you purchase an Oyster card prior to your travel to London. Because the queues to purchase the Oyster card will be long.
  4. You may wish to find more information at the following address : Transport for London
Travelling in London

Travelling in London is very convenient using the subways and buses. In some cases you may need to take the Docklands Light Railway (DLR) for areas that are further away from the city center. Along river Thames, there are ferries that can take you to directly to the opposite bank and save you some time. It is recommended that you pre-plan routes using Google Maps so as to avoid having to wait periods of time for your transport. It is also prudent to verify time opening hours of all attractions.

It would be very useful to have a small map of London and the subways. You can get this for free at the airport or at some tourist attractions. This is particularly important because the subways in London are connected by (1) different colored lines and (2) trains may not stop at the end of the line but in the middle of it so you will need to re-plan routes on the go.

Day Trips

There are numerous websites that offer day tours however I feel that a tour guide is not necessary if sufficient preparatory reading is done early in advance. Friends recommended me The London Pass which can be purchased online. It is not cheap but for the price it is an all inclusive pass for the public transport and selected attractions You can check out the website for more information and I urge you to read the conditions carefully to avoid disappointment.

If you wish for a quick look around London, you may wish to check out the Bus Tours that bring you around the attractions in London and you can 'hop on and hop off' at various stops. I have not tried out these Bus Tours but I have seen plenty of them in London. Some examples would be  The Original Sightseeing Tour and The Big Bus Tours. If you would like a sightseeing cruise along the river Thames, then City Cruises might be suitable for you.

On a side note, most Museums in London are free. They are surprising free for the fact that they are really good. The exhibits are well maintained and very well described. Definitely worth a visit. 

Food in London

In general, I find an average lunch/dinner to cost around £13-15 per person in a restaurant.
This would comprise of a main couse and a non-alcoholic drink.
  • To enjoy the same meal at a cheaper price, I suggest that you request for water straight from the tap (tapwater) and this can save you a few British pounds. 
A cheaper alternative would be to visit the nearby fast food places such as Macdonalds. A meal would still cost you £6 but it is still half the price of eating in a restaurant.

My personal favorite however, is to visit Starbucks or Pret a Manger for a quick sandwich and a coffee/tea. The cheapest coffee/tea would cost around £1-1.50 and a sandwich would range from £2.50-4.50. 
  • It should be noted that prices would be more expensive if you wish to 'eat-in' at the diners so it would be good if you could eat on the go or find a nice spot in the spacious parks in London.

Living expenses

The daily living expenses (without accommodation) would easily comprise of £4-6 for transport, £15 for dinner and £6 for lunch and breakfast. individually. And that would make up to approximately £33 per day on average.

It is undoubtedly not the cheapest city to travel about it but of course, it is nevertheless a city worth visiting.

Pleasant trip to all who wishes to visit London. Hope this provides good information to those who are planning their trip.

More updates will be forthcoming!

Signing off~

Sunday, 18 November 2012

How to get your work published...on high impact journals (Part II)

Heya folks,

In the previous post, we talked the importance of having original content if anyone wants to have a paper published. And its very important indeed. No one would want to read magazines with similar content by different authors page after page.

But .... why are some journals more 'popular' or of 'higher impact' than others? What makes people pay attention to them? 

The answer ... is novelty.


Readers want to see new information that is exciting. Just stating the obvious or paraphrasing common content is not interesting. An example would be our daily newspaper. We will flip through the pages quickly unless we see a headline that catches our attention. Something new, something out of the blue, something unexpected. That's novelty.

Good journal magazines like Nature and Science continue to attract readers because they contain a collection of articles that explains novel ideas with solid evidence. Ideas needs to be backed up with proofs and that's what the referees are for. 

Submitting article to referees

When an article is submitted to a magazine, the editor will sent it to two or more referees who are experts in that particular field to review the write-up. They will give their opinions on the merits of the article based on their experience as well as the evidence provided. Therefore, solid evidence such as characterization, data, trends, graphs and diagrams are of paramount importance.

Novelty ... often gets mixed up with originality!

These referees will also look out for novelty. Being experts in the field, they are experienced enough to know whether your article contains key points that will spearhead new frontiers in the field. It is different from being original. In fact it is an additional requirement to being original. 

Bring original means that you have prepared content that has not been published before. Being novel means your content is revolutionary , capable of helping people make breakthroughs or make people go 'wow, I did not think that's possible!'. Examples of revolutionary would be the article on DNA model by Watson and Crick.

Its not something that is easily described. Rather its more easily identified by 'feel'. I am sure you have read abstracts and said 'that's rubbish'. But have you ever wanted to read on because you wanted to know more? That article that keeps you wanting to know the details has more value.

Students tend to believe that journals will accept all works as long as their work has not been done before but editors are selective. 

So ... how to be novel?

My humble two cents in the next post ...

signing off~

Saturday, 10 November 2012

Where do I find IDEAS for my research proposal?

Heya folks,

To be perfectly honest, there is no easy answer to this question. More experienced researchers have told me they get ideas from their work (experience) as the years goes by and they know intuitively what they would like to study and what is commercially viable. What about the novices ...?

1. Start off by reading

As a professor once said ... there is NEVER too much research. Keep research and reading. Don't stop. There is always something new to stimulate you or something done previously to help guide your initial work.

You may wish to start by reading some articles from Peer Reviewed Journals online. Just google and you can find plenty. After which you might want to dwell further into specific topics by going directly to the website of these Journals (More updates soon!) or search using some tools such as SciFinder and Web of Knowledge that are likely to be offered by your school library or subscribed by your company.

From the reading exercise, have a FEEL of the current status of research in your field of interest. You definitely do not want to perform duplicate work. And try to SPOT research that interests you. That is the topic or type of work you might want to consider focusing upon.

2. Communicate

Talking to peers and seniors who have experience will help you. They may offer advice and opinions on the research route you intend to take or provide some insights on the workings of a reaction if they have done similar work. This will save you LOTS of time and may be even more effective than readings. Sometimes its like striking Jackpot. Really. I would recommend doing this after you've done some fundamental readings so that you have enough base knowledge to initiate a meaningful conversation. But ... try to get to this step as soon as possible.

3. Don't procrastinate!

Seriously, don't! Steps 1 and 2 takes time and there's no guarantee that doing both once will work. Some people take iterations! No matter how intuitive or 'common sense' these pointers sound, they are necessary. Underestimating the importance of preparing solid research proposals is just plainly not worth it. Start early!

Going through these steps have worked for me in general. Computers unfortunately cannot substitute for good and hard work, and I will venture a guess that they are unlikely to be able to do so in the near future...

Well fortunately for us, that the reason why scientists and researches have a Job!

signing off~

Saturday, 3 November 2012

How to get your work published...on high impact journals (Part I)

Heya folks,

This is a question that a budding researcher or (i hope?) a student will eventually ask. How do I get my work published in high visibility journals. To be honest, it can be both easy and difficult at the same time...

I've had the privilege of attending a seminar conducted by @Dr. Joerg Heber, who is a senior editor from Nature materials. Here he provided some interesting advice on how to get published on Nature and I believe they do apply for most other Journals as well. 

As the post may be a little long, it will be done in a couple of parts, each containing a topic and a quick recap for subsequent posts. Here we get started on the topic of originality...


First and foremost, the work must be original. Identical work should not have been done and published previously. It is very important to perform the necessary due diligence to continuously keep up with updates regarding your field of work and look out for similarities to the work you have done. I would suggest performing checks by searching important keywords on Google or Google Scholar. While they are definitely not foolproof, they may provide some assurance.

A more scholarly approach to keep up with the latest updates would be to subscribe to the Journals where you intend to publish your article and the 'popular' Journals such as Angewandte ChemieJournal of the American Chemical SocietyAmerican Chemical Society or Nature Chemistry. The list just goes on and on. There are plenty of good and relevant peer reviewed journals and deserve our attention. However, if and in most circumstances, we do not have the time to read all of them it becomes important to pick and choose those most relevant to us.

Plagiarism Check!

And consider this... we have FINALLY written our article, performed all the necessary formatting changes, editing and we have a Journal in mind to submit to. Should we submit now? Well, you can. But I would suggest a quick check via ithenticate. It is a online service similar to turnitin but more specific to research related and scholarly work. It detects plagiarism and checks for originality against a wide database. Ever wonder if you accidentally adopted a nicely written phase from the 'introduction' of a journal article? This is possibly a tool that locates that for you. Perhaps you might want to try it out.

 *disclaimer: I am in no way affiliated or advertising for ithenticate, I did try out their services recently and thought it might be helpful both new and experienced users.

So .... next on how to get your work published (II)....

signing off~

Tuesday, 30 October 2012

Can we do Science at home... Is it even possible?

Heya folks,

Most people associate research and all things science to the laboratory. And they think the laboratory is the place where all the scientists and research go and use all sorts of expensive, high tech gadgets to conduct studies that possibly impact our lives. Is it really true?

Well, its mostly true. Some experiments have to involve machines that are huge and cannot be easily moved around, such as the Nuclear magnetic resonance machines as well as the infra-red and ultra violet spectrometers.  However, computational based chemistry utilized servers that can be hosted in any part of the world. Which means, anyone can get access to them and start an experiment as long as you have access to the internet. For smaller scale simulations, you can actually do them on your own laptop or desktop computer.

So, yes. You can do scientific research in the comfort of your own home! Its easy to get started if you have the appropriate tools and software license in your college or company. Alternatively you can always find open-sourced programs that are completely free or available for use for educational purposes.

Let me recommend some in the next post!

signing off~

Monday, 29 October 2012

What EXACTLY is computational chemistry simulations ...?

Heya folks,

This is a question that is commonly asked in the minds of aspiring researchers and students when they are introduced into theoretical or computational based chemistry. Is it easy or hard or just too plain crazy to understand?

Well, computational based chemistry does dabble in quantum mechanics and its definitely a complex subject that require one to be comfortable in fundamental college mathematics before diving straight into it. This is something that freshmen college students might want to think about before picking up a class related to the subject. But I digress ...

In my opinion its a difficult subject made easy with the assistance of modern computers. With continuous improvements by Intel and AMD, our computers are now able to process much more complex information more quickly than before. And this involves solving the infamous Schrodinger equation with some caveats (more discussed soon!). By letting computers handle most of the work, we just need to focus on two things:

1. Tell the computer what to do

This sounds simple but it is essentially difficult. Despite the technological advancements, computers cannot help you do your homework, much less do your research for you without you telling it what to do. Here, we have to prepare the appropriate input settings into the software before performing the necessary calculations. These settings have to be carefully determined and in most cases, sampling tests may only need to be performed initially and not throughout a research project. Although most software has a set of default values, I stress the importance of understanding the individual settings and personalize them because EACH and every chemical reaction or study is fundamental different. Speaking from experience, it feels utterly terrible when you realize you need to make some changes after doing a lot of work. It just slows things down and make you look pain ineffective and unproductive.

2. Designing studies and reactions

Now, this is the hard part. Designing novel studies and research proposals is the bread and butter of not only chemists but scientists in general. It is the most fundamental and critical stage of any research and one which I notice students seem to underestimate until much later.

Having a solid research proposal with clear goals on what to focus upon WILL help you a lot because you have a clear picture of what you need to get done even when you get stressed out and tired during the err ... enjoyable and enriching process of research. Less running around in circles means more productivity and it just makes you seem trustworthy because people know you have a PLAN.

So The question is how to get these ideas since they are so important ... ?

More in my next post ...

signing off~

Sunday, 28 October 2012


Heya folks,

The title says it all, this webpage will be somewhat focused and below are some of the items that I will strive to include on a regular basis.

Some of them such as 'tips and tricks' will be posted as and when I pick up any or when I realise something might be useful to the wider audience. Others such as 'computational stuff/examples' will be a more regular feature and a couple of ' new series' on 'Writing' and 'Getting Published' will be  included gradually.

Updates on upcoming items will be updated regularly, so will recaps. If you missed anything, no worries, you can always find it in my recap posts or under the 'archives'.

Things to look forward to:

  1. Research tips and tricks 
  2. Article reviews
  3. (Useful) website reviews
  4. Computational stuff - examples
  5. How to subscribe to journals
  6. Research : How to do it systematically
  7. Writing tips : How to write systematically, minimize distraction 
  8. Reading tips: How sieve out important information quickly
signing off~

Friday, 26 October 2012

Let's get this blog started

Hey guys JohnHDchem here,

I am a (young?) theoretical chemist and I created this blog because I hope to offer come useful tips for follow novice simulations people who have a headache with the settings, option selections and stuff.

I certainly do not claim to be an expert in any way so the content in this blog are mainly my experiences and stuff which I have learnt from tutorials. If there is any discrepancy with the information, leave a comment and we can all have a discussion.

I intend to post some examples along the way and talk about how they are done. Screenshots and pictures are likely to be included, and maybe videos with commentary in the future.

I mainly work on the vienna ab initio simulations package (VASP), dmol and CASTEP, so information would center around these software packages.

Hoping to post some content soon.

Let's get this blog started