相关论文: Solvation Effects on Free Energy Surface of Polyal…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
Helix-coil transitions in poly-alanine molecules of length 10 are studied by multicanonical Monte Carlo simulations. The solvation effects are included by either a distance-dependent dielectric permittivity or by a term that is proportional…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…
A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods…
We have investigated the potential energy surface for neutral and charged alanine and glycine chains consisting of up to 6 amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
We use energy landscape methods to investigate the response of a supercooled liquid to random pinning. We classify the structural similarity of different energy minima using a measure of overlap. This analysis reveals a correspondence…
Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the…
We study the free energy landscape of the small peptide Met-enkephalin. Our data were obtained from a generalized-ensemble Monte Carlo simulation taking the interactions among all atoms into account. We show that the free energy landscape…
Na is known to deliver very low energy capacity for sodium intercalation compared to Lithium. In this study, we use quantum mechanics based metadynamics simulations to obtain the free energy landscape for sodium ion intercalation from…
Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…
We perform, with the help of cloud computing resources, extensive Langevin simulations which provide free energy estimates for unbiased three dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to…
We study helix-coil transitions in an all-atom model of polyalanine. Molecules of up to length 30 residues are investigated by multicanonical simulations. Results from two implicit solvent models are compared with each other and with that…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
A simple, efficient, and accurate method is proposed to map multi-dimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [Maragliano & Vanden-Eijnden, Chem. Phys. Lett. 426,…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for…
We present results of molecular simulations of a model protein whose hydrophobic collapse proceeds as a cascade of downhill transitions between distinct intermediate states. Different intermediates are stabilized by means of appropriate…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
We present a simple model system with four hard disks moving in a circular region for which free energy landscapes can be directly calculated and visualized in two and three dimensions. We construct several energy landscapes for our system…