相关论文: Construction of a pathway map on a complicated ene…
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 describe a robust and efficient chain-of-states method for computing Minimum Energy Paths~(MEPs) associated to barrier-crossing events in poly-atomic systems. The path is parametrized in terms of a continuous variable $t \in [0,1]$ that…
Many problems in physics, material sciences, chemistry and biology can be abstractly formulated as a system that navigates over a complex energy landscape of high or infinite dimensions. Well-known examples include phase transitions of…
The planar bistable device [Tsakonas \textit{et al., Appl. Phys. Lett.}, 2007, {\textbf{90}}, 111913] is known to have two distinct classes of stable equilibria: the diagonal and rotated solutions. We model this device within the…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
The minimum energy path (MEP) is the most probable transition path that connects two equilibrium states of a potential energy landscape. It has been widely used to study transition mechanisms as well as transition rates in the fields of…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
The low-temperature driven or thermally activated motion of several condensed matter systems is often modeled by the dynamics of interfaces (co-dimension-1 elastic manifolds) subject to a random potential. Two characteristic quantitative…
We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion…
The phase transition in the number partitioning problem (NPP), i.e., the transition from a region in the space of control parameters in which almost all instances have many solutions to a region in which almost all instances have no…
A novel and powerful method is presented for the study of rare switching events in complex systems with multiscale energy landscapes. The method performs an umbrella sampling of the equilibrium distribution of the system in hyperplanes…
We investigate the energy landscape of two- and three-dimensional XY models with nearest-neighbor interactions by analytically constructing several classes of stationary points of the Hamiltonian. These classes are analyzed, in particular…
Physical systems evolve from one state to another along paths of least energy barrier. Without a priori knowledge of the energy landscape, multidimensional search methods aim to find such minimum energy pathways between the initial and…
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…
Pathway idea is a switching mechanism by which one can go from one functional form to another, and to yet another. It is shown that through a parameter $\alpha$, called the pathway parameter, one can connect generalized type-1 beta family…
In order to better understand the occurrence of phase transitions, we adopt an approach based on the study of energy landscapes: The relation between stationary points of the potential energy landscape of a classical many-particle system…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Many physical and chemical processes, such as folding of biopolymers, are best described as dynamics on large combinatorial energy landscapes. A concise approximate description of dynamics is obtained by partitioning the micro-states of the…
Given a multidimensional free-energy or potential-energy landscape, finding reaction paths that connect an initial (or reactant) state and a final (or product) state is important for biophysics and materials science. The likelihood of a…