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Mechanical forces are generated in the cell during processes as diverse as chromosomal segregation, replication, transcription, translation, translocation of proteins across membranes, cell locomotion, and catalyzed protein and nucleic acid folding and unfolding, among others as protein folding, DNA elasticity, the protein-induced bending of DNA and the induced catalysis of enzymes. Our objetive is to understand the role of mechanical force in biochemistry.
We thought about implementing a full functionality Mechanochemistry Simulator with the possibility to extend and add new features in the future. Our work is based on the research of peruvian scientist Carlos Bustamante .
Most biological systems, including molecular machines and cells, are nonequilibrium steady states. For small systems, the equation of state and the spectrum of fluctuations are fully determined by so-called control parameters. Nonnequilibrium systems are characterized by irreversible heat losses between the system and its environment, typically a thermal bath. Mechanochemistry is a fertile ground where physics, chemistry, and biology converge.
- Chemla, Y.R., Moffitt, J.R., and C. Bustamante, Exact Solutions for Kinetic Models of Macromolecular Dynamics. J. Phys. Chem. B 112(19), 6025 -6044 (2008)
- Bustamante C, Liphardt J, Ritort F. The nonequilibrium thermodynamics of small systems. Physics Today 58 (7): 43-48 JUL (2005).
- Bustamante C, Chemla YR, Forde NR & Izhaky D . Mechanical processes in biochemistry. Annual Review of Biochemistry (2004) 73: 705-748.
- Bustamante C, Bryant Z, Smith SB. Ten years of tension: single-molecule DNA mechanics. Nature (2003) 421: 423 - 427