Related papers: Structural relaxation in Morse clusters: Energy la…
We generalize the small scale dynamics of the universe by taking into account models with an equation of state which evolves with time, and provide a complete formulation of the cluster virialization attempting to address the nonlinear…
For particles confined to two dimensions, any curvature of the surface affects the structural, kinetic and thermodynamic properties of the system. If the curvature is non-uniform, an even richer range of behaviours can emerge. Using a…
We examine the structure and dynamics of small isolated $N$-particle clusters interacting via short-ranged Morse potentials. "Ideally preprared ensembles" obtained via exact enumeration studies of sticky hard sphere packings serve as…
A database of minima and transition states corresponds to a network where the minima represent nodes and the transition states correspond to edges between the pairs of minima they connect via steepest-descent paths. Here we construct…
The Earth's surface is composed of a staggering diversity of particulate-fluid mixtures: dry to wet, dilute to dense, colloidal to granular, and attractive to repulsive particles. This material variety is matched by the range of relevant…
We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
Global optimization of atomistic structure rely on the generation of new candidate structures in order to drive the exploration of the potential energy surface (PES) in search for the global minimum energy (GM) structure. In this work, we…
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…
We perform molecular-dynamics simulations of a molecular system in supercooled states for different values of inertia parameters to provide evidence that the long-time dynamics depends only on the equilibrium structure. This observation is…
Neural network models have been used to construct energy landscapes for modeling biological phenomena, in which the minima of the landscape correspond to memory patterns stored by the network. Here, we show that dynamic properties of those…
We have exactly solved the relaxational dynamics of a model protein which possesses a kinetically perfect funnel-like energy landscape. We find that the dependence of the relaxation time, $\tau$, on the density of states (DOS) and the…
Semiflexible polymers in poor solvents exhibit a rich variety of collapsed morphologies, including globules, toroids, and rodlike bundles, arising from the competition between attractive interactions and chain stiffness. Computer…
Simulations of a stochastic fixed-energy sandpile in one and two dimensions reveal slow relaxation of the order parameter, even far from the critical point. The decay of the activity is best described by a stretched-exponential form. The…
Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel" that is concisely defined in terms of energy minima and…
Properties of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form are investigated numerically. A considerable number of glassy local…
In this paper, we analyse the phase space structure of the roaming dynamics in a two degree of freedom potential energy surface consisting of two identical planar Morse potentials separated by a distance. This potential energy surface was…
Morse complexes are gradient-based topological descriptors with close connections to Morse theory. They are widely applicable in scientific visualization as they serve as important abstractions for gaining insights into the topology of…
Accounting for the triaxial shapes of galaxy clusters will become important in the context of upcoming cosmological surveys. We show that, compared to the gas density distribution, the cluster gravitational potential can be better…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…