Related papers: Topological potentials guiding protein self-assemb…

Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current…

Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…

Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the…

Equilibrium self-assembly and conventional materials processing techniques fall far short of mimicking dynamic self-actuating processes that are commonplace throughout biology. To bridge the gap between living and synthetic matter, we study…

Porous and heterogeneous materials are found in many applications from composites, membranes, chemical reactors, and other engineered materials to biological matter and natural subsurface structures. In this work we propose an integrated…

We introduce three stochastic cooperative models for particle deposition and evaporation relevant to ionic self-assembly of nanoparticles with applications in surface fabrication and nanomedicine. We present a method for mapping a…

The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…

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…

High-tech equipment critically relies on flexures for precise manipulation and measurement. Through elastic deformation, flexures offer extreme position repeatability within a limited range of motion in their degrees of freedom, while…

A binary mixture of particles interacting with spherically-symmetric potentials leading to microsegregation is studied by theory and molecular dynamics (MD) simulations. We consider spherical particles with equal diameters and volume…

Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…

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…

Peptide self-assembly prediction offers a powerful bottom-up strategy for designing biocompatible, low-toxicity materials for large-scale synthesis in a broad range of biomedical and energy applications. However, screening the vast sequence…

We develop an empirical potential for silicon which represents a considerable improvement over existing models in describing local bonding for bulk defects and disordered phases. The model consists of two- and three-body interactions with…

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…

In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…

Molecular dynamics (MD) simulations involving reactive potentials can be used to model material failure. The empirical potentials which are used in such simulations are able to adapt to the atomic environment, at the expense of a…

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…

We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…

We prove that by successively combining subassemblies, we can achieve sublinear construction times for "staged" assembly of micro-scale objects from a large number of tiny particles, for vast classes of shapes; this is a significant advance…