Related papers: Recognizing Local and Global Structural Motifs at …
We investigate associative-memory behavior in a reconfigurable particle packing programmed by purely local cyclic driving. The system is a two-dimensional bidisperse Lennard--Jones particle assembly with periodic boundaries evolved under…
Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs---a combination of local network features. One technique to…
Defects dictate the properties of many functional materials. To understand the behaviour of defects and their impact on physical properties, it is necessary to identify the most stable defect geometries. However, global structure searching…
The development of interatomic potentials that can accurately capture a wide range of physical phenomena and diverse environments is of significant interest, but it presents a formidable challenge. This challenge arises from the numerous…
Accurate structural analysis is essential to gain physical knowledge and understanding of atomic-scale processes in materials from atomistic simulations. However, traditional analysis methods often reach their limits when applied to…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
Understanding the spatial arrangements of atom-centered coordination octahedra is crucial for relating structures to properties for many materials families. Traditional case-by-case inspection becomes a prohibitive task for discovering…
The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
Amphiphilic molecules spontaneously form self-assembly structures based on physical conditions such as molecular structure, concentration, and temperature. These structures exhibit various useful functions according to their morphology. The…
Many algorithms for processing probabilistic networks are dependent on the topological properties of the problem's structure. Such algorithms (e.g., clustering, conditioning) are effective only if the problem has a sparse graph captured by…
Monads govern computational side-effects in programming semantics. They can be combined in a ''bottom-up'' way to handle several instances of such effects. Indexed monads and graded monads do this in a modular way. Here, instead, we equip…
One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists…
Amphiphilic molecules spontaneously form self-assembled structures of various shapes depending on their molecular structures, the temperature, and other physical conditions. The functionalities of these structures are dictated by their…
Due to the subtle balance of intermolecular interactions that govern structure-property relations, predicting the stability of crystal structures formed from molecular building blocks is a highly non-trivial scientific problem. A…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
Network representations have been effectively employed to analyze complex systems across various areas and applications, leading to the development of network science as a core tool to study systems with multiple components and complex…
Paradigmatic model systems, which are used to study the mechanical response of matter, are random networks of point-atoms, random sphere packings, or simple crystal lattices, all of these models assume central-force interactions between…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
We present a new theoretical framework for modelling the cluster growing process. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing…