相关论文: Visualizing Free Energy Landscapes for Four Hard D…

Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…

The past few years have seen great strides in our ability to build synthetic microscopic machines. However, the function of such machines is often controlled directly by externally applied fields that deterministically specify the…

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…

We present a simple mathematical model of glassy dynamics seen as a random walk in a directed, weighted network of minima taken as a representation of the energy landscape. Our approach gives a broader perspective to previous studies…

Translating the complex, multi-dimensional data from simulations of biomolecules to intuitive knowledge is a major challenge in computational chemistry and biology. The so-called "free energy landscape" is amongst the most fundamental…

We apply two independent data analysis methodologies to locate stable climate states in an intermediate complexity climate model and analyze their interplay. First, drawing from the theory of quasipotentials, and viewing the state space as…

Dynamical connectivity graphs, which describe dynamical transition rates between local energy minima of a system, can be displayed against the background of a disconnectivity graph which represents the energy landscape of the system. The…

The thermodynamic and kinetic anomalies of supercooled liquids are analyzed from the perspective of energy landscapes. A mean field model, a generalized random energy model of liquids is developed, which exhibits a dynamical transition of…

The techniques which allow the numerical evaluation of the statistical properties of the potential energy landscape for models of simple liquids are reviewed and critically discussed. Expressions for the liquid free energy and its…

Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…

For a system consisting of active soft spheres in three dimensions, we study the transition from a fluid where overlaps between particles can only occur for a short time after a collision to a state where clusters of overlapping particles…

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…

Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…

The surface free energy is the difference between the free energies for a system with open boundary conditions and the same system with periodic boundary conditions. We use the quantum transfer matrix formalism to express the surface free…

An oft-used concept in modeling macromolecules is the free energy landscape, obtained by coarse-graining a vast number of microstates into a low-dimensional mesh of mesostates. If the landscape contains two or more local minima…

Maximizing the amount of work harvested from an environment is important for a wide variety of biological and technological processes, from energy-harvesting processes such as photosynthesisto energy storage systems such as fuels and…

A simulation is performed aiming at checking the existence of a well defined stationary state for a two dimensional system of driven hard disks when energy dissipation takes place at the system boundaries and no bulk impurities are present

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…

We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…

The aging dynamics of a simple model glass is numerically investigated observing how it takes place in the potential energy landscape $V$. Partitioning the landscape in basins of minima of $|\nabla V|^2$, we are able to elucidate some…