Chemical reactions biomolecular

A reasonable approach for achieving long timesteps is to use implicit schemes [38]. These methods are designed specifically for problems with disparate timescales where explicit methods do not usually perform well, such as chemical reactions [39]. The integration formulas of implicit methods are designed to increase the range of stability for the difference equation. The experience with implicit methods in the context of biomolecular dynamics has not been extensive and rather disappointing (e.g., [40, 41]), for reasons discussed below. 

Finally, in Sect. 7.6, we have discussed how various free energy calculation methods can be applied to determine free energies of ensembles of pathways rather than ensembles of trajectories. In the transition path sampling framework such path free energies are related to the time correlation function from which rate constants can be extracted. Thus, free energy methods can be used to study the kinetics of rare transitions between stable states such as chemical reactions, phase transitions of condensed materials or biomolecular isomerizations. 

Onuchic J. N. and Wolynes P. G. Energy landscapes, glass transitions, and chemical-reaction dynamics in biomolecular or solvent environment. J. Chem. Phys. (1993) 98(3) 2218-2224. 

The electrical properties of devices constructed with biomaterials follow the same physical laws as do conventional microelectronic devices and thus equivalent-circuit analysis can be used as a design tool for bioelectronics. What sets biomolecular (and synthetic molecular) electronic devices apart from conventional electronic devices is the exploitation of the vast repertoire of organic and biological chemical reactions and the fact that molecular devices can be constructed with a dimension in the nanometer scale (nanotechnology and nanobiology). 

Because quartz crystal microbalances are compact and sensitive, a large literature has developed on their use as sensors of both chemical and biomolecular reactions and processes at surfaces. A current review of this literature, with 176 references, is by Marx [44]. To quote from the abstract of this review The technique possesses a wide detection range. At the low mass end, it can detect monolayer surface coverage by small molecules or polymer films. At the upper end, it is capable of detecting. ..complex arrays of biopolymers and biomacromolecules, even whole cells. Another important and unique feature of the technique is the ability to... 

Ley, D., Gerbig, D., Schreiner, P. R. (2012). Tunnelling control of chemical reactions - the organic chemist s perspective. Organic, Biomolecular Chemistry, i0(19), 3781-3790. 

Finally, we should note that the success of the KPS work in describing gas-phase chemical reaction dynamics has stimulated continuing research aimed at using first-principles methods to describe reaction dynamics in gas-surface scattering, in biomolecular processes, and in other processes taking place in condensed phases [17]. 

DSC measures heat as a function of changing temperature. It is typically used to discern a wide range of thermal transitions in biological systems and the thermodynamic parameters associated with these changes. ITC is typically used for monitoring a chemical reaction initiated by the addition of a binding component and has become the method of choice for characterizing biomolecular interactions. 

Hu H, Yang W (2008) Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem 59 573-601 Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed 48 1198-1229... 

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