Related papers: Energy Landscapes for Digital Alchemy
Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion…
We present the advantages of a multiscale modelling strategy for the understanding of systems with charged interfaces. On the one hand, one can simulate a complex system at different levels, depending on the relevant length and time scales…
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…
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 complex physics of glass forming systems is controlled by the structure of the low energy portions of their potential energy landscapes. Here, we report that a modified metadynamics algorithm efficiently explores and samples low energy…
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…
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…
The broad success of optimally controlling quantum systems with external fields has been attributed to the favorable topology of the underlying control landscape, where the landscape is the physical observable as a function of the controls.…
The physical regions (domains or basins) within the molecular structure are open systems that exchange charge between them and consequently house a fractional number of electrons (net charge). The natural framework describing the quantum…
We investigate ground state configurations of atomic systems in two dimensions interacting via short range pair potentials. As the number of particles tends to infinity, we show that low-energy configurations converge to a macroscopic…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
We investigate the formation of polycrystalline structures in a class of particle systems. The atomistic energy is modeled as a sum of particle energies that favor atoms being locally isometric to a reference lattice. The discrete frame…
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.…
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…
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,…
Canyon landscapes in high dimension can be described as manifolds of small, but extensive dimension, immersed in a higher dimensional ambient space and characterized by a zero potential energy on the manifold. Here we consider the problem…
Disconnectivity graphs are used to characterize the potential energy surfaces of Lennard-Jones clusters containing 13, 19, 31, 38, 55 and 75 atoms. This set includes members which exhibit either one or two `funnels' whose low-energy regions…
A diffuse interface (phase field) model for an electrochemical system is developed. We describe the minimal set of components needed to model an electrochemical interface and present a variational derivation of the governing equations. With…
For decades, it was unknown how electron bifurcating systems in Nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron bifurcating molecular machines could not be designed and built.…
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…