Biophysics

Reynolds C, King P M and Richards W G 1992 Free energy calculations in molecular biophysics Mol. Phys. 76 251... 

Pratt L R and Hummer G (eds) 1999 Simulation and theory of electrostatic interactions in solution computational chemistry, biophysics and aqueous solutions AlP Conf. Proc. (Sante Fe, NM, 1999) vol 492 (New York American Institute of Physics)... 

Katchalsky A and Curran P F 1965 Nonequilibrium Thermodynamics in Biophysics (Cambridge, MA ITarvard University Press)... 

One of the well known advantages of resonance Raman spectroscopy is that samples dissolved in water can be studied since water is transparent in the visible region. Furthennore, many molecules of biophysical interest assume their native state in water. For this reason, resonance Raman spectroscopy has been particularly strongly embraced in the biophysical connnunity. 

Asher S A 1993 UV resonance Raman-spectroscopy for analytical, physical and biophysical chemistry 2 Anal. Chem. 

Cantor C R and Schimmel P R 1980 Biophysical Chemistry, Part II Techniques for the Study of Biological Structure and Function (San Francisco Freeman)... 

Knoll G and Plattner H 1989 Ultrastructural analysis of biological membrane fusion and a tentative correlation with biochemical and biophysical aspects Electron Microscopy of Subcellular Dynamics ed H Plattner (London CRC) pp 95-117... 

Jimenez R and Fleming G R 1996 Ultrafast spectroscopy of photosynthetic systems Biophysical Techniques In Photosynthesis ed J Amesz and A J Hoff (Dordrecht Kluwer) pp 63-73... 

Classical biophysical chemistry has concentrated heavily on tlie elucidation of tlie stmctures of bioniolecules and... 

Circular dicliroism has been a useful servant to tire biophysical chemist since it allows tire non-invasive detennination of secondary stmcture (a-helices and P-sheets) in dissolved biopolymers. Due to tire dissymmetry of tliese stmctures (containing chiral centres) tliey are biaxial and show circular birefringence. Circular dicliroism is tlie Kramers-Kronig transfonnation of tlie resulting optical rotatory dispersion. The spectral window useful for distinguishing between a-helices and so on lies in tlie region 200-250 nm and hence is masked by certain salts. The metliod as usually applied is only semi-quantitative, since tlie measured optical rotations also depend on tlie exact amino acid sequence. 

From the viewpoint of biophysical chemistry, the main problems to be solved are (i) what is the submolecular basis of... 

It has become fashionable to prefix the names of disciplines with bio , as in biophysics, bioinfonnatics and so on, giving the impression that in order to deal with biological systems, a different kind of physics, or infonnation science, is needed. But there is no imperative for this necessity. Biological systems are often very complex and compartmentalized, and their scaling laws may be different from those familiar in inanimate systems, but this merely means that different emphases from those useful in dealing with large unifonn systems are required, not that a separate branch of knowledge should necessarily be developed. 

BIOSON Research Institute and Dept of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands... 

Chair of Molecular and Applied Biophysics, Kharkov State University, Svobody Sq. 4, Kharkov 310077, Ukraine... 

Biophysics Division, Institute of Radiophysics and Electronics, Nat. Acad. Sci. of Ukraine, Akad. Proskura Str. 12, Kharkov 310085, Ukraine... 

Lahajnar, G., Zupancic, L, Rupprecht, A. Proton NMR relaxation and diffusion study of water sorbed in oriented DNA and hyaluronic acid samples. In Biophysics of Water (Franks, F., Mathias, S., eds) Wiley, New York (1982) 231-234... 

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA current address Department of PharmaceuticaJ Chemistry, UCSF, San Francisco, CA, USA... 

Department of Biophysics, University of Warsaw, 02-089 Warsaw, Poland Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0365, USA... 

Nevertheless, the technique suffers from a severe time scale problem -the trajectories are computed for (at most) a few nanoseconds. This is far too short compared to times required for many processes in biophysics. For example, the ii to T conformational transition in hemoglobin lasts tens of microseconds [1], and the typical time for ion migration through the gramicidin channel is hundreds of nanoseconds. This limits (of course) our ability to make a meaningful comparison to experiments, using MD. 

Extending time scales of Molecular Dynamics simulations is therefore one of the prime challenges of computational biophysics and attracted considerable attention [2-5]. Most efforts focus on improving algorithms for solving the initial value differential equations, which are in many cases, the Newton s equations of motion. 

C. G. Lambert, Multipole-based Algorithms in Molecular Biophysics and Non-parametric Statistics, Ph.D. Dissertation, Duke University Department of Computer Science, 1997. 

Theoretical Biophysics Group, University of Illinois and Beckman Institute,... 

Richards F M 1977. Areas, Volumes, Packing and Protein Structure. Annual Review in Biophysics ana Bioengineering 6 151-176. 

C. Giessner-Prettre, B. Pullman, Quarterly Reviews of Biophysics 20, 113 (1987). 

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