User:Kaihsu/ideas

Scientific ideas waiting for imminent breakthrough; but alas, I have no resources for working on them.

Hybrid elastic network–finite element model
The general idea is to use ‘hybrid particle–finite element’ (or ‘hybrid particle–continuum’) method to link conventional continuum elasticity method (say, finite element) with conventional elastic network model. – Kaihsu Tai (with thanks to Nathan Baker, Ben Hall, Hyunji Kim, and Mark Sansom)

overview
An integrative approach to understanding mechanosensation. Christopher C. Poirier and Pablo A. Iglesias Briefings in Bioinformatics (2007) 8:258 http://dx.doi.org/10.1093/bib/bbm025

finite element
Y.C. Zhou, Michael Holst, J. Andrew McCammon (2007) A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces. Journal of Mathematical Analysis and Applications http://dx.doi.org/10.1016/j.jmaa.2007.07.084

Yuye Tang, Guoxin Cao, Xi Chen, Jejoong Yoo, Arun Yethiraj, Qiang Cui (2006) A Finite Element Framework for Studying the Mechanical Response of Macromolecules: Application to the Gating of the Mechanosensitive Channel MscL. Biophysical Journal 91:1248–1263

Feng Feng, William S. Klug (2006) Finite element modeling of lipid bilayer membranes. Journal of Computational Physics 220(1):394–408

elastic network ad extremum
P. Doruker, R.L. Jernigan and I. Bahar, Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23 (2002), pp. 119–127. http://dx.doi.org/10.1002/jcc.1160

D. Ming, Y. Kong, M.A. Lambert, Z. Huang and J. Ma, How to describe protein motion without amino acid sequence and atomic coordinates. Proc. Natl. Acad. Sci. USA 99 13 (2002), pp. 8620–8625. http://dx.doi.org/10.1073/pnas.082148899

Y. Kong, D. Ming, Y. Wu, J.K. Stoops, Z.H. Zhou and J. Ma, Conformational exibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model. J. Mol. Biol. 330 (2003), pp. 129–135. http://dx.doi.org/10.1016/S0022-2836(03)00555-2

Paul Maragakis, Martin Karplus (2005) Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase. Journal of Molecular Biology 352(4):807–822 http://dx.doi.org/10.1016/j.jmb.2005.07.031

Miyashita, O; Onuchic, JN; Wolynes, PG. 2003. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. PNAS 100 (22): 12570-12575. http://dx.doi.org/10.1073/pnas.2135471100.

Jhih-Wei Chu and Gregory A. Voth (2007) Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model. Biophysical Journal 93:3860-3871 http://dx.doi.org/10.1529/biophysj.107.112060

scooped?
Mark Bathe. A Finite Element framework for computation of protein normal modes and mechanical response. arXiv:0704.0634v1 [q-bio.BM]


 * Now published as Mark Bathe (2008) A finite element framework for computation of protein normal modes and mechanical response Proteins 70(4):1595–1609. – Kaihsu 14:05, 15 December 2008 (UTC)

via Professor Stephen David Bond
Almost scooped. – Kaihsu 16:49, 28 August 2008 (UTC)

Oscar Gonzalez fitting elastic models (2001): http://www.ma.utexas.edu/users/og/publications.html

Frank Brown has something on elasticity of membranes: Grace Brannigan, Frank L. H. Brown (2007) Contributions of Gaussian Curvature and Nonconstant Lipid Volume to Protein Deformation of Lipid Bilayers. [http://dx.doi.org/10.1529/biophysj.106.094953 ''Biophys. J.'' 92(3):864–876].

via Professor Peter Tieleman
Definitely scooped by Qiang Cui now. – Kaihsu 13:09, 9 January 2009 (UTC)

Yuye Tang, Guoxin Cao, Xi Chen, Jejoong Yoo, Arun Yethiraj, Qiang Cui (2006) A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. [http://dx.doi.org/10.1529/biophysj.106.085985 ''Biophys. J.'' 91(4):1248–1263].

Xi Chen, Qiang Cui, Yuye Tang, Jejoong Yoo, Arun Yethiraj (2008) Gating mechanisms of mechanosensitive channels of large conductance, I: a continuum mechanics-based hierarchical framework. [http://dx.doi.org/10.1529/biophysj.107.128488 ''Biophys. J.'' 95(2):563–580].

Yuye Tang, Jejoong Yoo, Arun Yethiraj, Qiang Cui, Xi Chen (2008) Gating mechanisms of mechanosensitive channels of large conductance, II: systematic study of conformational transitions. [http://dx.doi.org/10.1529/biophysj.107.128496''Biophys. J.'' 95(2):581–596]

New vocabulary for systems biology
New vocabulary for systems biology: towards an ‘Oxford Systems-Biology Dictionary’. So far biochemical network notations, such as Kitano (2003) ‘A graphical notation for biochemical networks’ Biosilico 1:169–176, have catalogued alphabets of systems biology: in these schemes, we speak of ‘glyphs’, literally ‘letters’, the ABCs of a language. In reports such as Deckard and Sauro (2004) ‘Preliminary studies on the in silico evolution of biochemical networks’ ChemBioChem 5:1423–1431; Qi and Ge (2006) ‘Modularity and dynamics of cellular networks’ PLoS Comput. Biol. 2(12):e174, we see the beginnings of a vocabulary: we start to speak of modules (swappable units in the network) and/or motifs (recurring patterns embedded in the network). Are we able to catalogue, not just the letters, but whole ‘words’ as well? When someone asks ‘what are the possible modules providing a bifurcating behaviour?’, we shall one day be able to look it up in a ‘dictionary’ and reply, ‘yes, here are the three modules under the heading bifurcation’ (or even ‘look it up yourself!’).

via Professor Chung-chieh Ken Shan
Chung-chieh Ken Shan pointed out: Regarding "New vocabulary for systems biology", perhaps the good talks I went to by Vincent Danos and Walter Fontana at APLAS 2007 and POPL 2008 are relevant.
 * http://www.cs.ucsd.edu/popl/08/popl2008-fontana.pdf
 * http://fontana.med.harvard.edu/www/Documents/WF/Lectures/Signaling/popl08.pdf

Professor Andrew Basden
Also see the discussion about design patterns and languages in Andrew Basden’s recent book Philosophical Frameworks for Understanding Information Systems (ISBN 978-1599040363). – Kaihsu 15:38, 22 May 2008 (UTC)

Dr Mark Poolman
Mark G. Poolman, David A. Fell, Christine A. Raines (2003) Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. European Journal of Biochemistry 270(3):430–439.

CellML crew
Gratifyingly, my idea has been incorporated in the minutes of the Auckland Bioengineering Institute. Thanks!

Archiving by libre-distribution
The saga of Doctor Who missing episodes is good evidence for archiving by distributing material under a libre licence. In case of catastrophe, the material useful to others (and to humanity in general) has a good chance of being retrieved from somewhere (else) in the world.

Cultural escrow
The idea of a cultural escrow.
 * w:Public Domain Day