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Register a new userUnbiased sampling of globular lattice proteins in three dimensions
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Added by
Jesper Lykke Jacobsen
Publication date
2007
fields
Physics
and research's language is
English
Authors
Jesper Lykke Jacobsen
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We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64^3 = 262144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system.
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Monte Carlo simulations using Wang-Landau sampling are performed to study three-dimensional chains of homopolymers on a lattice. We confirm the accuracy of the method by calculating the thermodynamic properties of this system. Our results are in good agreement with those obtained using Metropolis importance sampling. This algorithm enables one to accurately simulate the usually hardly accessible low-temperature regions since it determines the density of states in a single simulation.
We consider the phase diagram of self-avoiding walks (SAW) on the simple cubic lattice subject to surface and bulk interactions, modeling an adsorbing surface and variable solvent quality for a polymer in dilute solution, respectively. We simulate SAWs at specific interaction strengths to focus on locating certain transitions and their critical behavior. By collating these new results with previous results we sketch the complete phase diagram and show how the adsorption transition is affected by changing the bulk interaction strength. This expands on recent work considering how adsorption is affected by solvent quality. We demonstrate that changes in the adsorption crossover exponent coincide with phase boundaries.
We have investigated the relaxational dynamics for a protein model at various temperatures. Theoretical analysis of this model in conjunction with numerical simulations suggests several relaxation regimes, including a single exponential, a power law and a logarithmic time dependence. Even though a stretched exponential form gives a good fit to the simulation results in the crossover regime between a single exponential and a power law decay, we have not been able to directly deduce this form from the theoretical analysis.
We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of interacting elastic lattice polymers and allows a sufficiently good sampling of long and compact configurations, an essential prerequisite to study the scaling behaviour of free energies. By simulating interacting self-avoiding rings at several temperatures in the collapsed phase, we estimate both the bulk and the surface free energy. Moreover from the corresponding estimate of the entropic exponent $alpha-2$ we provide evidence that, unlike for swollen and $Theta$-point rings, the hyperscaling relation is not satisfied for globular rings.
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely unsolved, key problem in structural biology. Here, we introduce a general model and use computer simulations to study the equilibrium properties and the folding kinetics of a $C_{alpha}$-based two helix bundle fragment (comprised of 66 amino-acids) of Bacteriorhodopsin. Various intermediates are identified and their free energy are calculated toghether with the free energy barrier between them. In 40% of folding trajectories, the folding rate is considerably increased by the presence of non-obligatory intermediates acting as traps. In all cases, a substantial portion of the helices is rapidly formed. This initial stage is followed by a long period of consolidation of the helices accompanied by their correct packing within the membrane. Our results provide the framework for understanding the variety of folding pathways of helical transmembrane proteins.
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