相关论文: Visualizing Free Energy Landscapes for Four Hard D…
A fluctuation relation, which is an extended form of the Jarzynski equality, is introduced and discussed. We show how to apply this relation in order to evaluate the free energy landscape of simple systems. These systems are manipulated by…
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…
In this work, the effects of excluded volume are studied in the "one to five hard disks in a box" system. For one and two disks in different types of cages, the attractive and repulsive forces are calculated analytically. Attractive forces…
We investigate the kinetics and the free energy landscape of the crystallization of hard spheres from a supersaturated metastable liquid though direct simulations and forward flux sampling. In this first paper, we describe and test two…
Energy landscapes are high-dimensional surfaces representing the dependence of system energy on variable configurations, which determine crucially the system's emergent behavior but are difficult to be analyzed due to their high-dimensional…
Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means…
We consider several multiscale-in-time kinetic Monte Carlo models, in which some variables evolve on a fast time scale, while the others evolve on a slow time scale. In the first two models we consider, a particle evolves in a…
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram…
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their stationary probabilities or free energies. Often, these…
We apply a recently proposed criterion for the existence of phase transitions, which is based on the properties of the saddles of the energy landscape, to a simplified model of a system with gravitational interactions, referred to as the…
A novel method for glassy landscape exploration is presented which utilizes a time series of energy values collected during an isothermal relaxation after a thermal quench. A sub-series of increasingly rare events, or quakes, which are…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
A `polydisperse' system has an infinite number of conserved densities. We give a rational procedure for projecting its infinite-dimensional free energy surface onto a subspace comprising a finite number of linear combinations of densities…
We consider a simple model to describe the widths of the mode locked intervals for the critical circle map. Using two different partitions of the rational numbers, based on Farey series and Farey tree levels respectively, we calculate the…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
We describe a numerical study of the potential energy landscape for the two-dimensional XY model (with no disorder), considering up to 100 spins and CPU and GPU implementations of local optimization, focusing on minima and saddles of index…
In this paper we expose the results of our recent work on the dynamical TAP approach to mean field glassy systems. Our aim is to clarify the connection between free energy landscape and out of equilibrium dynamics in solvable models.…
Smartphones, laptops, and data centers are CMOS-based technologies that ushered our world into the information age of the 21st century. Despite their advantages for scalable computing, their implementations come with surprisingly large…
We apply energy landscape methods to digital alchemy, defining a system in which the parameters of the potential are treated as degrees of freedom. Using geometrical optimisation, we locate minima and transition states on the landscape for…
An interesting class of physical systems, including those associated with life, demonstrates the ability to hold thermalization at bay and perpetuate states of high free-energy compared to a local environment. In this work, we study quantum…