ABSTRACT
Metadynamics is a powerful computational tool to obtain the free-energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus to gain an ever-increasing understanding on the general principles underlying the mechanism of protein folding. We show that it is possible to couple metadynamics and Monte Carlo algorithms to obtain the free energy of model proteins in a way which is computationally very economical.
Subject(s)
Algorithms , Models, Molecular , Monte Carlo Method , Proteins/chemistry , Proteins/genetics , Surface Properties , ThermodynamicsABSTRACT
In performing protein-denaturation experiments, it is common to employ different kinds of denaturants interchangeably. We make use of molecular dynamics simulations of Protein L in water, in urea, and in guanidinium chloride (GdmCl) to ascertain if there are any structural differences in the associated unfolding processes. The simulation of proteins in solutions of GdmCl is complicated by the large number of charges involved, making it difficult to set up a realistic force field. Furthermore, at high concentrations of this denaturant, the motion of the solvent slows considerably. The simulations show that the unfolding mechanism depends on the denaturing agent: in urea the beta-sheet is destabilized first, whereas in GdmCl, it is the alpha-helix. Moreover, whereas urea interacts with the protein accumulating in the first solvation shell, GdmCl displays a longer-range electrostatic effect that does not perturb the structure of the solvent close to the protein.
Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/ultrastructure , Guanidine/chemistry , Models, Chemical , Models, Molecular , Urea/chemistry , Binding Sites , Computer Simulation , Protein Binding , Protein Conformation , Protein DenaturationABSTRACT
We present a generalization of the self-consistent analysis of carbon nanotube (CNT) field effect transistors (FETs) to the case of multi-wall/multi-band coherent carrier transport. The contribution to charge diffusion, due to different walls and sub-bands of a multi-wall (mw) CNT is shown to be non-negligible, especially for high applied external voltages and 'large' diameters. The transmission line formalism is used in order to solve the Schrödinger equation for carrier propagation, coupled to the Poisson equation describing the spatial voltage distribution throughout the device. We provide detailed numerical results for semiconducting mw-nanotubes of different diameters and lengths, such as current-voltage characteristics and frequency responses.
