Related papers: Energy landscapes and rare events
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
A model of holographic dark energy with an interaction with matter fields has been investigated. Choosing the future event horizon as an IR cutoff, we have shown that the ratio of energy densities can vary with time. With the interaction…
Hierarchical tree structures are common in many real-world systems, from tree roots and branches to neuronal dendrites and biologically inspired artificial neural networks, as well as in technological networks for organizing and searching…
Encoding the complex features of an energy landscape is a challenging task, and often chemists pursue the most salient features (minima and barriers) along a highly reduced space, i.e. 2- or 3-dimensions. Even though disconnectivity graphs…
Complex systems throughout Nature display structures and functions that are built and maintained, at least in part, by optimal energies flowing through them--not specific, ideal values, rather ranges in energy rate density below which…
We investigate the multi-valley energy landscape of a 3-D on-lattice network model for covalent glasses, numerically determining the shape of the valleys, the local density of states, the density of minima and the local connectivity. We…
A complete understanding of the precipitous onset of slow dynamics in systems such as supercooled liquids requires making direct connections between dynamics and the underlying potential energy landscape. With the aid of a switch in…
We propose a method for the simulation of particle fragmentation based on the calculation of the energy landscape inside the particle. The landscape of strain energy is calculated in terms of internal stress using the principles of damage…
We investigate the relation between the entanglement properties of a quantum state and its energy for macroscopic spin models. To this aim, we develop a general method to compute energy bounds for states without certain forms of…
Turbulent flows in a thin layer can develop an inverse energy cascade leading to spectral condensation of energy when the layer height is smaller than a certain threshold. These spectral condensates take the form of large-scale vortices in…
I review the issue of string and compactification scales in the weak-coupling regimes of string theory. I explain how in the Brane World scenario a (effectively) two-dimensional transverse space that is hierarchically larger than the string…
With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space…
Dynamical energy analysis was recently introduced as a new method for determining the distribution of mechanical and acoustic wave energy in complex built up structures. The technique interpolates between standard statistical energy…
The Voronoi model is a popular tool for studying confluent living tissues. It exhibits an anomalous glassy behavior even at very low temperatures or weak active self-propulsion, and at zero temperature the model exhibits a disordered solid…
Energy landscape analysis is a data-driven method to analyze multidimensional time series, including functional magnetic resonance imaging (fMRI) data. It has been shown to be a useful characterization of fMRI data in health and disease. It…
Energy landscape models characterize neural dynamics by assigning energy values to each brain state that reflect their stability or probability of occurrence. The conventional energy landscape models rely on binary brain state…
Rare transitions in stochastic processes can often be rigorously described via an underlying large deviation principle. Recent breakthroughs in the classification of reversible stochastic processes as gradient flows have led to a connection…
The concept of fragility provides a possibility to rank different supercooled liquids on the basis of the temperature dependence of dynamic and/or thermodynamic quantities. We recall here the definitions of kinetic and thermodynamic…
We briefly review some of the scientific challenges and epistemological issues related to climate science. We discuss the formulation and testing of theories and numerical models, which, given the presence of unavoidable uncertainties in…
Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system's…