Computer simulations energy landscapes

Atomic level studies of complex peptide and protein energy landscapes have become more detailed as computers have become faster, allowing for longer sampling simulations... 

In what follows, we use simple mean-field theories to predict polymer phase diagrams and then use numerical simulations to study the kinetics of polymer crystallization behaviors and the morphologies of the resulting polymer crystals. More specifically, in the molecular driving forces for the crystallization of statistical copolymers, the distinction of comonomer sequences from monomer sequences can be represented by the absence (presence) of parallel attractions. We also devote considerable attention to the study of the free-energy landscape of single-chain homopolymer crystallites. For readers interested in the computational techniques that we used, we provide a detailed description in the Appendix. ... 

K., Larson, V., Luty, B. A., Rose, P W., Verkhivker, G. M. (1999) Computer simulations of ligand-protein binding with ensembles of protein conformations a Monte Carlo study of HIV-1 protease binding energy landscapes. Inti J Quantum Chem 72, 73-84. 

Computer simulation using lattice models and energy landscape theory using abstract models predict that the fastest folding of small proteins should occur without intermediates and by an extended nucleation process. Stable intermediates slow... 

The information about the existence of the multiple intermediate conformational states involving the enzymatic active complex formation and a detailed characterization of the energy landscape (Fig. 24.7) of the complex formation process cannot be obtained either by only an ensemble-averaged experiment, only a single-molecule experiment, or a solely computational approach. The combined approach demonstrated here is essential to achieve the potential of both single-molecule spectroscopy and MD simulations for studies of slow enzymatic reactions and protein conformational change dynamics. 

Crystallization usually involves very long time scales (at least when compared to time scales of routine calculations) and complicated potential energy landscapes. Computer simulations of this process are, therefore, considered to be difficult in general. In a series of papers, Haymet and coworkers investigated the structure and dynamics of the ice/water interface. In their approach, the pre-built patches of water and ice were put together to create the interface. The necessity to simulate the highly improbable creation of the crystallization nucleus was thus avoided. Similar setup was used by other groups to assess various properties of the ice/water interface. ... 

The hyperdynamics method teaches us that by redefining the energy landscape in such a way that the relative rates of different competing processes are unchanged, the simulation can be run in a sped up form, and the net simulation time can be computed (statistically) after the fact. Ultimately, the size of this boost factor is determined by the lowest energy barrier in the system since evidently we require that AF > 0. 

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