User:Jih24/sandbox

I'm planning on adding a simulations section

Johns Hopkins University The goal of molecular biophysics is to explain biological phenomena in terms of the physical and chemical properties of participating ions and molecules.

This rapidly evolving field draws from the rich interactions that have developed among the traditional areas of chemistry, biology, physics, genetics, computer science, and others.

The Program in Molecular Biophysics is for students who are interested in the integration of diverse disciplines toward greater understanding of living matter.

Researchers in the program combine the power of modern spectroscopic methods and computational approaches to unravel the determinants of self-assembly in biological systems.

Others use the tools of chemistry and structural biology to probe the physical bases for molecular recognition and guide the design of new and better drugs to treat debilitating diseases.

Still others focus on fundamental aspects of solution thermodynamics and refine the description of biological macromolecules in their cellular environment.

What criteria have to be met in order to be considered molecular biophysics? (answer this question) Has to integrate math, physics, specific instrumentation with interactions.

Criteria: Derivative calculus, integral calculus, matrix algebra, statistics, differential equations, relate to the biological field. Math can be used for analysis as well as for predictive properties for what will happen in the future.

molecular biophysics - structural biologists look at the structure. Physical chemistry cell- signalling cell trafficking Translation transcription Enzyme metabolism (catalysis) Electrophysiology

Looking at the functionality (or interaction between 2 specific objects) specifically makes it biophysics. Myosin light chain kinase Sphincter is constricting Determining the macroscopic function, by looking at the constituent parts. Differs from engineering, because biophysics is more analysis, whereas engineering is more inventive.

Need to examine the dynamics in order to determine the function.

Difference between structure and dynamics. Can use biochemical analysis which focuses on the diachotamus relationship of whether something is there or not Gel analysis is a specific test used to determine the presence or absence of a certain substance.

Molecular Structure (single molecules) Structural Organization (Supramolecular structures) Dynamic Bahavior (Viruses/small living systems)

Molecular Simulations

Because we have quantum mechanical models of atoms, we can perform simulations via programs such as CHARMM and NAMD which will enable us to see how the constituents in molecular systems will interact with each other.

[insert picture with simulation which was made by the user]

References

Sources

• Perutz MF (1962). Proteins and Nucleic Acids: Structure and Function. Amsterdam: Elsevier. ASIN B000TS8P4G.
• Perutz MF (1969). "The haemoglobin molecule". Proceedings of the Royal Society of London. Series B. 173 (31): 113–40. Bibcode:1969RSPSB.173..113P. doi:10.1098/rspb.1969.0043. PMID 4389425.
• Dogonadze RR, Urushadze ZD (1971). "Semi-Classical Method of Calculation of Rates of Chemical Reactions Proceeding in Polar Liquids". J Electroanal Chem. 32 (2): 235–245. doi:10.1016/S0022-0728(71)80189-4.
• Volkenshtein M.V., Dogonadze R.R., Madumarov A.K., Urushadze Z.D. and Kharkats Yu.I. Theory of Enzyme Catalysis.- Molekuliarnaya Biologia (Moscow), 6, 1972, pp. 431–439 (In Russian, English summary. Available translations in Italian, Spanish, English, French)
• Rodney M. J. Cotterill (2002). Biophysics : An Introduction. Wiley. ISBN 978-0-471-48538-4.
• Sneppen K, Zocchi G (2005-10-17). Physics in Molecular Biology (1 ed.). Cambridge University Press. ISBN 0-521-84419-3.
• Glaser, Roland (2004-11-23). Biophysics: An Introduction (Corrected ed.). Springer. ISBN 3-540-67088-2.
• Hobbie RK, Roth BJ (2006). Intermediate Physics for Medicine and Biology (4th ed.). Springer. ISBN 978-0-387-30942-2.
• Cooper WG (2009). "Evidence for transcriptase quantum processing implies entanglement and decoherence of superposition proton states". BioSystems. 97 (2): 73–89. doi:10.1016/j.biosystems.2009.04.010. PMID 19427355.
• Cooper WG (2009). "Necessity of quantum coherence to account for the spectrum of time-dependent mutations exhibited by bacteriophage T4". Biochem. Genet. 47 (11–12): 892–910. doi:10.1007/s10528-009-9293-8. PMID 19882244.
• Goldfarb, Daniel (2010). Biophysics Demystified. McGraw-Hill. ISBN 0-07-163365-0.

External links

• Biophysical Society
• Journal of Physiology: 2012 virtual issue Biophysics and Beyond
• bio-physics-wiki
• Link archive of learning resources for students: biophysika.de (60% English, 40% German)
• Journal of Medicine, Physiology and Biophysics,(IISTE), USA. Chief Editor of the journal is Ignat Ignatov. Chief editor of all IISTE journals is Alexander Decker.

Category:Applied and interdisciplinary physics

Where are you doing your edits on your page? I am looking to do my peer review. Trb9 (talk) 22:04, 5 November 2016 (UTC)

Notes

Sources for adding to my article on molecular dynamics

Invented the Ramachandran plot.

Vijayan, M.; Johnson, L. N. (2005). "Gopalasamudram Narayana Ramachandran. 8 October 1922 - 7 April 2001: Elected FRS 1977". Biographical Memoirs of Fellows of the Royal Society. 51: 367. doi:10.1098/rsbm.2005.0024.

Molecular Forcefields

Lennard-Jones, J. E. (1924), "On the Determination of Molecular Fields", Proc. R. Soc. Lond. A, 106 (738): 463–477, Bibcode:1924RSPSA.106..463J, doi:10.1098/rspa.1924.0082

High resolution carbon rings

Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki (2015). "Chemical structure imaging of a single molecule by atomic force microscopy at room temperature". Nature Communications. 6: 7766. Bibcode:2015NatCo...6E7766I. doi:10.1038/ncomms8766. PMC 4518281free to read. PMID 26178193.

First mathmatic description of a chemical bond.

Laidler, K. J. (1993). The World of Physical Chemistry. Oxford University Press. p. 346. ISBN 0-19-855919-4.