Tuesday, January 31, 2012

First announcement: Electronic Structure Theory for Strongly Correlated Systems



In celebration of Per Ake Malmqvist' 60th birthday and his career dedicated to quantum chemistry.

May 30 - June 1, 2012
Palermo, Italy


Important deadlines: 
March 1st, 2012 - early-bird registration 
April 15th, 2012 - deadline for abstract submission  

Registration: http://www.teokem.lu.se/PAM60/registration.html
Note that the number of participants is limited.

For more information please, contact Valera.Veryazov@teokem.lu.se

Sunday, January 29, 2012

Energy transfers to maximize entropy: a lesson from Molecular Driving Forces

This is Figure 3.14 from Dill and Bromberg's Molecular Driving Forces, which is my favorite book on statistical mechanics.  It is a beautiful example from a beautiful book.

If you haven't already, it is a good idea to read Illustrating entropy and Where does the ln come from in S = k ln(W).  Go ahead, I'll wait right here.

System $A$ has an internal energy $U_A=2$ which is distributed among the 10 particles in $$\frac{10!}{8!2!}=45$$different ways.  Similarly, System $B$ has an internal energy $U_B=4$ which is distributed among the 10 particles in 210 different ways.

If the two systems are allowed to exchange energy, what is the most probable distribution of energies?  It is the one for which $$W_{total}=W_AW_B$$ is largest.

Now compute $W_{total}$ for three cases: no energy transfer ($U_A=2,U_B=4$), one where energy is transferred from $A$ to $B$ ($U_A=1,U_B=5$), and one where energy is transferred from $B$ to $A$ ($U_A=3,U_B=3$).  If you don't have a calculator handy, try Wolfram-Alpha.  Which state is the most probable?


Energy transfers to maximize the total entropy, not equalize energies
The most probable state has the largest total entropy since $$S_{total}=k\ln(W_{total})$$In this particular case maximizing the entropy leads to equal energy, but that is only because the two systems have the same number of particles. Consider system $A$ in the figure above in thermal contact with system $B$ with the same energy ($U_B=2$) but only four particles.  What is the most likely state? (Don't guess, compute!)


Maximizing entropy, means equalizing temperatures
It should be clear by now that if you change the internal energy, you change the entropy$$dS=\left(\frac{\partial S}{\partial U}\right)dU$$This is actually just the thermodynamic definition of entropy $dS=dq_{rev}/T$ which means that$$\frac{1}{T}=\left(\frac{\partial S}{\partial U}\right)$$When $S_{total}$ is a maximum the change in total entropy is zero, so $$\begin{aligned}dS_{total}&=dS_A+dS_B\\&=\left(\frac{\partial S_A}{\partial U_A}\right)dU_A+\left(\frac{\partial S_B}{\partial U_B}\right)dU_B\\&=\frac{1}{T_A}dU_A+\frac{1}{T_B}dU_B\\&=\left(\frac{1}{T_A}-\frac{1}{T_B}\right)dU_A\\&=0\end{aligned}$$Here I have made use of the fact that the total internal energy is conserved$$dU_A=-dU_B$$

Thursday, January 19, 2012

That's Classic!

I've very recently had the joy of setting up classical simulations for use in my research developing the next generation of force-fields. Since I've dealt with quantum mechanics and classical mechanics derived from quantum mechanics, my need for classical simulations on proteins and ligands has been void. Until now.

I only know of two tools to actually calculate Molecular Dynamics simulations on entire proteins: The Tinker package and the GROMACS package. I've tinkered(!) around with the first package and kept a good distance to the latter, but times have changed since I needed to include a ligand. GROMACS (and Tinker for that matter) are tuned to either proteins (in solution) or small molecules (in solution)*. If you want another molecule to use for the MD, you must first obtain the force-field parameters somehow. Since the most of us have no time for that, or that the next generation force-field is on its way but not quite there yet, what do you do?

To start from nothing and finish two days later, I did what any (in)sane scientist would do if no-one in the department has apparent experience with a particular piece of software: I Googled and I browsed the GROMACS "guides". The first is good if you know what to look for, and the latter is good to get inspiration, but it does not quite get you there since information always seem to be outdated just a bit.

Here is how I did it:
  1. Find the structure of interest to you on the Protein Data Bank. Build your ligand into that system using your favorite build tool. You should now have a PDB file with a protein and a ligand.
  2. Use SwissParam (more info below) to make a topology file (actually it is a force-field) of your ligand.
  3. Follow the SwissParam Gromacs guide until step 6 (you must include this step!)
  4. Follow the Protein-Ligand Complex guide by Justin Lemkul from the solvation step (it is good to actually read the entire guide). This will get you to make a production run MD of 1 ns of your own system.
  5. Analyze your MD! This is out of scope for this post, but man was I happy when the MD actually successfully finished.
Note on SwissParam
The SwissParam tool takes a small molecule of interest and generates what is know in GROMACS-speak as a topology file, but in regular office-chatter, this is known as a force-field. Here is an exert from the main page of SwissParam

The data are derived from the Merck Molecular ForceField (MMFF). Dihedral angle terms are taken as is, while only the harmonic part of the bond, angle and improper terms are retained. Charges are taken from MMFF. Van der Waals parameters are taken from the closest atom type in CHARMM22.

The paper of SwissParam(doi:10.1002/jcc.21816) has been published so give it a read if you're really feeling geeky.

* I should note that if one chooses the MMFF 94 force field in Tinker, one should potentially be able to use it for everything, but it is a bit messy to actually set up and run not to mention that I found absolutely no way to automate the atom type-setting.

Tuesday, January 10, 2012

Where does the ln come from in S = k ln(W) ?

The relationship between entropy ($S$) and degeneracy ($W$ or $g$ depending on the book) $$S = k\ln(W)$$ is one of the fundamental equations of statistical mechanics.  But where does it come from?  Or more precisely, why $\ln(W)$ and not, say, $\sin(W)$?  And why does $k$ have units of J/K?

I believe it goes back the second law of thermodynamics, i.e. it is based on observation.  The second law can be stated in many ways and one is that heat ($q$) spontaneously flows only from hot ($T_h$) to cold ($T_c$) bodies.

Mathematically this can be stated as $$\frac{q}{T_c}-\frac{q}{T_h}>0$$ or $$\Delta S >0$$ where $S$ is defined* as $$dS=\frac{dq_{rev}}{T}$$ This establishes the units of $S$ and, hence, $k$.

Furthermore, since $q$ (like all energy) is additive, $S$ must be additive: $S_{total}=S_A+S_B$.  However, $W_{total}=W_AW_B$, so $S=kW$ won't work.  However, $S = k\ln(W)$ will.

The final question is now whether the logarithm is the only mathematical function for which $f(xy)=f(x)+f(y)$.  It turns out that it is** if we require the function to be continuous (thanks to Niels Grønbæk for help here), which we do since $S$ as defined by the second law is non-discrete like the energy.

Another important property of $\ln(W)$ is that is has a maximum value when $W$ is largest.  So the most probable state will have the largest entropy.

* This definition begs the question: if heat is transferred, what $T$ do you use, the one before or after the heat transfer?  The answer is that $dq$ has to be so small that $T$ is not affected.  Since $T$ is not affected this is a $rev$ersible process.  Furthermore, notice that this law also introduces the concept of temperature.

** Se also http://www.physicsforums.com/showthread.php?t=566358.  Not that I understand all of it!

Related blog posts
Illustrating entropy
Entropy, volume, and temperature

Monday, January 9, 2012

Extended deadline - PhD scholarship - characterization of hyperthermopilic enzymes - position 1


This PhD scholarship (position 1) is for 3 years in the project "HOT modifications of hyperthermophilic enzymes and their modulation of enzyme properties and structures", starting from March 1, 2012.

Position 1 is for investigating protein posttranslational modification-function relationships of hyperthermopilic enzymes at Archaea Centre.The selected candidate at the Archaea Centre will: (1) perform biochemical characterization of selected hyperthermophilic proteins and (2) study the functional roles of these proteins in the hyperthermophilic host Sulfolobus islandicus. While the biochemical characterization includes site-directed mutagenesis of the hyperthermophilic enzymes and subsequent characterization of the mutant proteins, in vivo functions of these proteins will be revealed by functional genomics studies of gene deletion mutants and/or over-expression strains. By closely interacting with the Protein Structure group, these investigations will lead to novel knowledge of the relationship between protein posttranslational modifications and their functions. Applicants for the Archaea Centre position should hold an MSc degree in biology, biochemistry or a related field, have strong and broad experience in microbiology. Prior experience with archaeal enzymes or archaeal genetics is an advantage.

Applicants should have good interpersonal and communication skills and fluency in spoken and written English. It is also expected that the successful candidate will maintain a close interaction with other members and PhD students in the Structural Biology and NMR Laboratory. The Archaea Centre and the Structural Biology and NMR Laboratory provide an inspiring working atmosphere in state-of-the-art laboratories at Copenhagen Biocenter. The position is open to both Danish and international applicants.

An assessment committee will be appointed to evaluate the applications. The final selection of two successful candidates will be made by the Head of Department, based on the recommendations of the evaluation committee. The successful candidate will then be requested to formally apply for enrolment as PhD student at the PhD school of Science, University of Copenhagen.

Terms of appointment and payment are in accordance with the agreement between the Danish Ministry of Finance and the Danish Federation of Professional Associations (AC). The starting salary for candidates with an MSc degree will be a minimum of DKK 309.179 per year (April 2011 level) plus pension contribution DKK 42.243 and the possibility to negotiate wage.

The University of Copenhagen wishes to reflect the diversity of society and welcomes applications from all qualified candidates regardless of personal background.

Applicants are requested to submit their applications by filling in relevant parts of the form titled ?Application for PhD scholarship and enrolment to the PhD School" available at http://www.science.ku.dk/phd/staff/forms/applying_forms/101025_Application_for_scholarship_and_admission.doc/

The form, together with appendices requested in the form including a motivating cover letter should be e-mailed as a single PDF-file to job2@bio.ku.dk Please include in the subject field ?your name - HOT modifications Project 1". In addition a signed hardcopy of the application must also be sent directly to Associate Professor Qunxin She, Department of Biology, Ole Maaløes Vej 5, 2200 København N, Denmark.

The deadline for applications is Friday, January 20, 2011 at 12:00 noon Danish local time.

Applications received after the deadline, or with insufficient documentation or otherwise not complying with the above requirements, may not be considered. It is expected that the successful candidate will be enrolled at the PhD School of the Faculty of Science starting March 1, 2012.

More information about the PhD program can be found at http://www1.bio.ku.dk/english/education/phd/protein_sciences/. Further information about the position can be obtained via email to Associate Professor Qunxin She, e-mail: qunxin@bio.ku.dk
Københavns Universitet er Danmarks ældste universitet, grundlagt 1479, og hører til blandt de største i Norden og de højest rangerende i Europa. Universitetet består af otte fakulteter, som omfatter biovidenskab, farmaceutisk videnskab, humaniora, jura, naturvidenskab, samfundsvidenskab, sundhedsvidenskab og teologi. www.ku.dk
Frist: 20-01-2012
Arbejdsgiver: Det Naturvidenskabelige Fakultet

Saturday, January 7, 2012

Chemists whose blogs I would love to read

This idea just popped into my head a few hours ago while shopping for groceries, so the list just off the top of my head.  I would love to read about what pops into their heads, what they find interesting at the moment, what annoys them, etc.  Anyway, here is a list with a sentence or two of why I think they might write interesting blog posts. 

Ken Dill.  Because his book Molecular Driving Forces has some really fantastic, simple, examples that beautifully illustrate fundamental concepts in statistical mechanics.

Mark Ratner. Because I heard him give a really well presented Telluride Town Talk once.

Alexander Pines.  Because he gave a a great series of lectures on his work while I was at the University of Iowa.  In some of the talks more than half the time was spent on an overview of the field: you learned a lot, unencumbered by boring details, and understood how his contributions fit into the big picture.

David Baker. Because I think the whole idea behind, and implementation of, the Fold.it program is pure genius.

Donald Hilvert. Because he made a function enzyme from only 4 amino acids and because the 4 amino acids spell IKEA! That's innovative!

Richard Zare. Pretty much completely outside my field but I have never heard him give a dull talk.

But you may say "Jan, just because they did X doesn't mean they'll write interesting blog posts".  But that's easy to refute: I've always found Anthony Nicholls' talks very interesting and when he finally started a blog, his posts turned out to be very interesting as well.  Case closed.

Anyway, who's on your list?

Thursday, January 5, 2012

PhD position: Coupled Electron Transfer Processes in Proteins

Thesis Project in Molecular Simulation 
Institute of Structural Biology 
Grenoble, France

A grant for a thesis project starting in October 2012 and financed by the CEA is available at the Institute of Structurale Biology – Jean-Pierre Ebel in Grenoble, France. Applications must be made on the IRTELIS website (http://www-dsv.cea.fr/PhDtraining ou http://www- dsv.cea.fr/phd-program) before the beginning of March 2012. Interviews of selected candidates will be held later, normally in May.

Thesis supervisor: Martin Field (martin.field@ibs.fr and http://www.pdynamo.org

Coupled Electron Transfer Processes in Proteins

This thesis project will study coupled electron transfer processes (CETPs) in proteins using molecular modeling and simulation techniques. Electron transfer (ET) is an essential element of many biological transformations, but it rarely occurs in isolation and is most often found coupled to additional processes, such as light excitation, proton transfer and other types of chemical reaction. Although ET itself is well understood at a theoretical level, CETPs still present significant challenges. This project aims to investigate CETPs in two classes of system. The first are the fluorescent proteins for which CETPs have been implicated in many of the processes, including blinking, bleaching and radiation damage, that limit their usefulness in molecular biological applications. The second are artificially designed hydrogen-evolving complexes that use light to generate the necessary source of electrons for hydrogen production. The project will require some method development, given the current state-of-the-art, but the core of the project will focus on the applications, in close collaboration with experimental groups.

The Host Group
The thesis will take place in the DYNAMO/DYNAMOP research group at the Institute of Structurale Biology – Jean-Pierre Ebel (http://www.ibs.fr). The IBS is run jointly by the CEA, the CNRS and the Université Joseph Fourier University (Grenoble I) and is part of the Life Sciences Division of the CEA.

The DYNAMO/DYNAMOP group, led by Martin Field, specializes in the development and application of theoretical and computational techniques for studying the structure and function of biological macromolecules and their complexes (http://www.pdynamo.org and http://www.ibs.fr/groups/dynamics-and-kinetics-of-molecular/dynamo-560/?lang=en).


Grenoble is the capital of the French Alps. It possesses a unique mountain setting and is ideally situated for outdoor activities. The Grenoble area is an important centre of industry and science (the second largest in France) and is host to numerous cultural institutions. It is also the third largest student area in France with 60,000 students (including 6,000 foreign students).

Useful iPad apps

iAnnotate: I use this app to read manuscript drafts, reports, theses, you name it.  It has great annotation tools such as highlight and notes.  I don't recall printing out a paper just to read it since I got this app.

Flipboard: I use this app to read Facebook, twitter, and blogs I subscribe to using Google Reader.

Zite: This app collects web posts of possible interest to you under different topics.  You can tell it which posts you like and it will find more like it.  I have found many very interesting things using this app.

Hand writing (using the AluPen Stylus)
Penultimate: I use this app to take notes at meeting, or jot down ideas, or sketch things.  You can mail individual pages or entire note books to others.

ReplayNote: I use this app to make pencasts for teaching (example).

Explain Everything: This is an alternative to ReplayNote that I just found.  I am not sure which one I prefer yet.

SyncPad: I actually don't use this very much, but it is just so cool: what you draw on this app will appear at http://mysyncpad.com/xxx where you specify xxx in the app.  You can use this as an aid when explaining somethings to someone on the phone or Skype.

File transfer
Dropbox: I keep all my ongoing projects on a Dropbox account.  This means I can access all these files on my iPad using the Dropbox app.   Furthermore, iAnnotate can also be set up to transfer papers from/to Dropbox.

Handy iPad tips
Screenshots: press the Power and Home buttons simultaneously.  The screenshot goes into your photo album.  You can import screenshots from the photo album to apps like Penultimate or ReplayNote where you can draw on top of it.   See also the Skitch app, which does this automatically.

Moving between apps: put 4 fingers on the screen and swipe up to get a menu of open apps or swipe left and right to move between apps.

Monday, January 2, 2012

Seminar by Andrea Cavalli: The Resolution and Dynamics of NMR Structures

Andrea Cavalli from the University of Cambridge will be giving a seminar on Monday Jan 16th at 10:00AM entitled

The Resolution and Dynamics of NMR Structures

The seminar will take place in room 1.2.03 at the Biocenter.

Andrea was the first to demonstrate that one can determine structures of proteins from NMR chemical shift data alone. He will talk about this work, as well as more recent work on the structure and dynamics of proteins.

Blog posts, videos and "other publications"

Every year I have to fill out several "what have you accomplished last year?" forms.  I've just send in one of them.  There is a section on "other publications", which, I guess, is intended for non-refereed articles and books.  But there are now many other ways to disseminate information so I added:

http://molecularmodelingbasics.blogspot.com  ca 65,000 page views in 2011
http://proteinsandwavefunctions.blogspot.com ca 7,000 page views in 2011 (group blog with contributions from others)

http://blip.tv/molmodbasics ca 11,000 views in 2011


http://propka.org ca 23,000 page views 2011
http://biofetsim.org ca 1,000 page views 2011

I chose to list views rather than the number of blog posts, videos, or presentations I created in 2011.  I think these numbers are more telling, but I would be happy to hear other suggestions.

It would be interesting to know how many times my papers have been viewed in 2011, but this information is not available for most journals i have published in, and it would be a pain in the neck to collect this data even if it was. (What I do know is that they have been cited 1204 times in 2011 according to Web of Science.)