Related papers: Energy landscapes for the self-assembly of supramo…
The maximum-weight matching problem and the behavior of its energy landscape is numerically investigated. We apply a perturbation method adapted from the analysis of spin glasses. This gives inside into the complexity of the energy…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
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…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
The concept of potential energy landscapes is applied in many areas of science. We experimentally realize a random potential energy landscape (rPEL) to which colloids are exposed. This is achieved exploiting the interaction of matter with…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
We study the global geometry of the energy landscape of a simple model of a self-gravitating system, the self-gravitating ring (SGR). This is done by endowing the configuration space with a metric such that the dynamical trajectories are…
In principle, all of the dynamical complexities of many-body systems are encapsulated in the potential energy landscapes on which the atoms move - an observation that suggests that the essentials of the dynamics ought to be determined by…
We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity…
Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome,…
We investigate the energy landscape of two dimensional network models for covalent glasses by means of the lid algorithm. For three different particle densities and for a range of network sizes, we exhaustively analyse many configuration…
The paper describes combinatorial framework for planning of geological exploration for oil-gas fields. The suggested scheme of the geological exploration involves the following stages: (1) building of special 4-layer tree-like model (layer…
We propose a computationally lean, two-stage approach that reliably predicts self-assembly behavior of complex charged molecules on a metallic surfaces under electrochemical conditions. Stage one uses ab initio simulations to provide…
Describing the complex landscape of infinite-dimensional free energy is generally a challenging problem. This difficulty arises from the existence of numerous minimizers and, consequently, a vast number of saddle points. These factors make…
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,…
Recent breakthroughs in the study of scattering amplitudes have uncovered profound and unexpected connections with combinatorial geometry. These connections range from classical structures -- such as polytopes, matroids, and Grassmannians…
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…
According to the mean-field glass theory, the (free) energy landscape of disordered systems is hierarchical and ultrametric if they belong to the full-replica-symmetry-breaking universality class. However, examining this theoretical picture…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
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…