44th US Japanese Conference on Cholera and Enteric Infections

We have an excellent conference in San Diego on Cholera and other enteric infections. We had a chance to talk to many people in the field and get feedback on our research.

Energy Landscapes

Well I have finished a set of CHARMM preparations for a mapping the transition pathways and the energy landscapes along those trajectories for the activation of LFA-1 I-domain. Now moving the topology files and pdb files to the Atlantis computing cluster.

Check out Graduation

Graduation

Running Dynamics

We have started a new dynamics simulation on another machine because our Itanium2 cluster has been core dumping NAMD. Why, I do not know? The error message is "regcache incompatible with malloc", though I am not sure why we got this message. Also, I have had this message on runs that worked. This new machine is a SGI Altix and we will see if job 3732 runs to completion.

Isotope Filter Pulse Programs

Well I have finished the paper before Thanksgiving so now am expanding the documentation for my thesis. Hoping to get some good graphic program to make diagrams for a presentation I will give. In the past, I have used postscript edited by hand. The spectra for the paper and thesis look great this way! Anyway, I will evaluate any postscript editors I can get my hands on over the Christmas break. (If you have suggestions please comment or email!!)

Thanks

Charmm

We are getting Charmm and NAMD setup with our favorite protein. Actually this was initially done last year but I am getting John to finish the project because I have not had the time. The build, solvation, and first minimization ran today.
JWC

A Modified Nuclear Magnetic Resonse Pulse Program for Our Bruker 800

Well, I have had the chance to get into some pulse programming because a NOESY-HQSC experiment that we need required the 3D program to be modified to a 2D version. The 1H / 13C correlation for this experiment is through a double inept transfer with 13C (and 15N) filter in the F1 dimension. The primary change in the pulse program was to remove the F2PH(ip3, id10) macro call and to change the arguments for the F1PH macro call

original lines:
F1PH(rd10 & rp3 & ip7 & ip13, id0)
F2PH(ip3, id10)

new line:
F1PH(ip7 & ip13, id0)

This effectively removed the increment on id10 and reduced the experiment to two dimensions. In addition the placement of the unblanking of the gradient was moved to just before the initial 90 degree pulse on proton (p1) based on correspondence with Dr. Rainer Kuemmerle at Bruker.


1 ze
d11 pl12:f2
2 d11 do:f2
3 d1 pl1:f1
50u UNBLKGRAD <--- This is the new line
(p1 ph1)
p19:gp4
d16
DELTA2
(p15:sp18 ph1):f2

# ifdef LABEL_CN
DELTA3 pl3:f3
(center (p2 ph2) (p22 ph1):f3 )
# else
DELTA3
(p2 ph2)
# endif /*LABEL_CN*/

DELTA4
p19:gp4
d16 pl2:f2
(p1 ph11)

I am also looking into the spectra that I collected last fall to see what parameters need better optimization.

Cool testing

Darfur

The holocaust museum had a excellent speakercome and talk about Darfur and what common people can do to make a difference in the crisis. As the conflict begins to spill over into Chad and the Central Republic, we need to stay involved in pushing our elected officials to apply pressure on the Sudanese government.

At the University of Houston, we are planning a walk to help raise awareness about the crisis. It is on Sunday, May 4th, and if you are interested in walking come to the campus between 7 - 9 am at the chapel (north side of campus)

you can register at: http://www.savedarfur.org/page/event/detail/4v5xc
or pass on the word.

The president has continued to do a great job is getting the word out and his trip in Africa has hopefully reminded some people of the cost in human lives.

http://www.iht.com/articles/2008/02/19/africa/prexy.php

http://news.yahoo.com/s/ap/20080219/ap_on_re_af/bush_africa

The Welch Conference

I felt that the Welch Conference in October was one of the best I have been to. It was titled Physical Biology – From Atoms to Cells, and it covered many topics including folding, novel amino acids, membranes, and quantum physics. The key note speakers were the Welch awardees, Noel Hush and William Miller. However the conference also featured many Noel Prize winners.

The lecture of William Miller on quantum mechanics and molecular simulation was very fascinating to me because I had just finished a semester of TAing in a class of biophysics. The notion of coherence as a structural feature in the eigen space representation helped to extend my limited perceptions. However the general approach of converting a two point boundary problem to an initial value problem using a closed integral was familiar. How he cast the problem as a diatic needs further investigation, as my use of diatics and tensor mathematics was limited to structures (beam theory). Need to lookup Wigner Functions.