相关论文: Energy landscapes and dynamics of xylo-nucleic aci…
Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the…
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The…
We describe a numerical study of the potential energy landscape for the two-dimensional XY model (with no disorder), considering up to 100 spins and CPU and GPU implementations of local optimization, focusing on minima and saddles of index…
The complexity and unpredictability of postbuckling responses in even simple thin shells have raised great challenges to emerging technologies exploiting buckling transitions. Here we comprehensively survey the buckling landscapes to show…
Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular…
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to…
We apply energy landscape methods to digital alchemy, defining a system in which the parameters of the potential are treated as degrees of freedom. Using geometrical optimisation, we locate minima and transition states on the landscape for…
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…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
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 show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We…
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
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…
Neural network models have been used to construct energy landscapes for modeling biological phenomena, in which the minima of the landscape correspond to memory patterns stored by the network. Here, we show that dynamic properties of those…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
In experiments and in simulations, the free energy of a state of a system can be determined from the probability that the state is occupied. However, it is often necessary to impose a biasing potential on the system so that high energy…
In the free energy landscape picture of glassy systems, the slow dynamics characteristic of these systems is believed to be due to the existence of a complicated free-energy landscape with many local minima. We show here that for a…
We present studies of the potential energy landscape of selected binary Lennard-Jones thirteen atom clusters. The effect of adding selected impurity atoms to a homogeneous cluster is explored. We analyze the energy landscapes of the studied…