Related papers: Visualizing Free Energy Landscapes for Four Hard D…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
The application of numerical techniques to the study of energy landscapes of large systems relies on sufficient sampling of the stationary points. Since the number of stationary points is believed to grow exponentially with system size, we…
On the basis of the density functional theory, we give a clear definition of the free energy landscape. To show the usefulness of the definition, we construct the free energy landscape for rearrangement of atoms in an FCC crystal of hard…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
We present the study of the landscape structure of athermal soft spheres both as a function of the packing fraction and of the energy. We find that, on approaching the jamming transition, the number of different configurations available to…
We describe a reverse integration approach for the exploration of low-dimensional effective potential landscapes. Coarse reverse integration initialized on a ring of coarse states enables efficient "navigation" on the landscape terrain:…
Random matrix theory yields valuable insights into the universal features of quantum many-body chaotic systems. Although all-to-all interactions are traditionally studied, many interesting dynamical questions, such as transport of a…
Energy landscapes provide a conceptual framework for structure prediction, and a detailed understanding of their topological features is necessary to develop efficient methods for their exploration. The ability to visualise these surfaces…
Machine learning techniques are being increasingly used as flexible non-linear fitting and prediction tools in the physical sciences. Fitting functions that exhibit multiple solutions as local minima can be analysed in terms of the…
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 that the thermodynamics and the kinetics of the phase transition between wormhole and two black hole described by the two coupled SYK model can be investigated in terms of the stochastic dynamics on the underlying free energy…
Using the inherent structure formalism originally proposed by Stillinger and Weber [Phys. Rev. A 25, 978 (1982)], we generalize the thermodynamics of an energy landscape that has an ideal glass transition and derive the consequences for its…
We propose a way to analyze the landscape geometry explored by a glassy system after a quench solely based on time series of energy values recorded during a simulation. Entry and exit times for landscape `valleys' are defined operationally…
We discuss the problem of partitioning a macroscopic system into a collection of independent subsystems. The partitioning of a system into replica-like subsystems is nowadays a subject of major interest in several field of theoretical and…
Glasses are amorphous solids whose constituent particles are caged by their neighbors and thus cannot flow. This sluggishness is often ascribed to the free energy landscape containing multiple minima (basins) separated by high barriers.…
We present a three-dimensional lattice-gas model with trivial thermodynamics, but nontrivial dynamics. The model is characterized by each particle having its own random energy landscape. The equilibrium dynamics of the model were…
This letter propose a new model for characterizing traffic dynamics in scale-free networks. With a replotted road map of cities with roads mapped to vertices and intersections to edges, and introducing the road capacity L and its handling…
Many biological processes involve numerous coupled degrees of freedom, yet free-energy estimation is often restricted to one-dimensional profiles to mitigate the high computational cost of multidimensional sampling. In this work, we extend…
We consider a dynamical system consisting of subsystems indexed by a lattice. Each subsystem has one conserved degree of freedom ("energy") the rest being uniformly hyperbolic. The subsystems are weakly coupled together so that the sum of…
Recently, the stochastic dynamical model based on the free energy landscape was proposed to quantify the kinetics of the black hole phase transition. An essential concept is the generalized free energy of the fluctuating black hole, which…