Related papers: Energy landscapes and rare events
Recent studies of concentrated solid solutions have highlighted the role of varied solute interactions in the determination of a wide variety of mesoscale properties. These solute interactions emerge as spatial fluctuations in potential…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus,…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
Systems with a complex dynamics like glasses or models of biological evolution are often pictured in terms of complex landscapes, with a large number of possible collective states. We show on the example of a stochastic spin model with…
We introduce a class of $n$-dimensional (possibly inhomogeneous) spin-like lattice systems presenting modulated phases with possibly different textures. Such systems can be parameterized according to the number of ground states, and can be…
A phenomenological free energy model is proposed to describe the behavior of smectic liquid crystals, an intermediate phase that exhibits orientational order and layering at the molecular scale. Advantageous properties render the functional…
The gap in statistics between multi-variate and time-series analysis can be bridged by using entropy statistics and recent developments in multi-dimensional scaling. For explaining the evolution of the sciences as non-linear dynamics, the…
Global climate change, extreme climate events, earthquakes and their accompanying natural disasters pose significant risks to humanity. Yet due to the nonlinear feedbacks, strategic interactions and complex structure of the Earth system,…
In the field of quantum chaos, the study of energy levels plays an important role. The aim of this review paper is to critically discuss some of the main contributions regarding the connection between classical dynamics, semi-classical…
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…
Many systems in biology, physics and engineering can be described by systems of ordinary differential equation containing many parameters. When studying the dynamic behavior of these large, nonlinear systems, it is useful to identify and…
Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems…
With increased access to data and the advent of computers, the use of statistical tools and numerical simulations is becoming commonplace for ecologists. These approaches help improve our understanding of ecological phenomena and their…
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…
To analyze high-dimensional systems, many fields in science and engineering rely on high-level descriptions, sometimes called "macrostates," "coarse-grainings," or "effective theories". Examples of such descriptions include the…
Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure -- a barrier tree -- the leaves and internal nodes of which represent, respectively, the local minima and the…
Scientific research in many fields routinely requires the analysis of large datasets, and scientists often employ workflow systems to leverage clusters of computers for their data analysis. However, due to their size and scale, these…
In years to come, we shall see substantial progress in our understanding of nuclear structure - a rich and many-faceted field. An important element in this task will be to extend the study of nuclei into new domains. The journey to 'the…
Depth, number, and shape of the basins of the potential energy landscape are the key ingredients of the inherent structure thermodynamic formalism introduced by Stillinger and Weber [F. H. Stillinger and T. A. Weber, Phys. Rev. A 25, 978…