Related papers: Visualizing Free Energy Landscapes for Four Hard D…
Understanding and simulating how a quantum system interacts and exchanges information or energy with its surroundings is a ubiquitous problem, one which must be carefully addressed in order to establish a coherent framework to describe the…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We study the global geometry of the energy landscape of a simple model of a self-gravitating system, the self-gravitating ring (SGR). This is done by endowing the configuration space with a metric such that the dynamical trajectories are…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
The stationary points of the potential energy function V are studied for the \phi^4 model on a two-dimensional square lattice with nearest-neighbor interactions. On the basis of analytical and numerical results, we explore the relation of…
Stability landscapes are useful for understanding the properties of dynamical systems. These landscapes can be calculated from the system's dynamical equations using the physical concept of scalar potential. Unfortunately, for most…
An extended use of renewable energies and a trend towards increasing energy consumption lead to challenges such as temporal and spatial decoupling of energy generation and consumption. This work evaluates the possible applications and…
The tempo and mode of an adaptive process is strongly determined by the structure of the fitness landscape that underlies it. In order to be able to predict evolutionary outcomes (even on the short term), we must know more about the nature…
The full theoretical analysis of the kinetics of multicomponent nucleation is presented. The relief of the free energy with surface excesses was analyzed, the valleys and ridges were described, their mutual interaction was studied. The new…
With the help of metadynamics it is possible to calculate efficiently the free energy of systems displaying high energy barriers as a function of few selected "collective variables". In doing this, the contribution of all the other degrees…
Disconnectivity graphs are used to visualize the minima and the lowest energy barriers between the minima of complex systems. They give an easy and intuitive understanding of the underlying energy landscape and, as such, are excellent tools…
We study the potential energy landscape explored during a compression-decompression cycle for the SPC/E (extended simple point charge) model of water. During the cycle, the system changes from low density amorphous ice (LDA) to high density…
We study the 3-spin spherical model with mean-field interactions and Gaussian random couplings. For moderate system sizes of up to 20 spins, we obtain all stationary points of the energy landscape by means of the numerical polynomial…
We use molecular dynamics simulations to investigate dynamic heterogeneities and the potential energy landscape of the Gaussian core model (GCM). Despite the nearly Gaussian statistics of particles' displacements, the GCM exhibits giant…
Complex energy landscapes often arise in biological systems, e.g. for protein folding, biochemical reactions or intracellular transport processes. Their physical effects are often reflected in the first-passage times arising from these…
Diffusive operations, which mix the populations of different elements of phase space, can irreversibly transform a given initial state into any of a spectrum of different states from which no further energy can be extracted through…
We introduce a mean-field model for the potential energy landscape of a thin fluid film confined between parallel substrates. The model predicts how the number of accessible basins on the energy landscape and, consequently, the film's ideal…
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…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Cloud platforms' growing energy demand and carbon emissions are raising concern about their environmental sustainability. The current approach to enabling sustainable clouds focuses on improving energy-efficiency and purchasing carbon…