Related papers: Mechanical prions: Self-assembling microstructures

Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…

Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…

A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…

Prion diseases caused by the conversion from a soluble normal cellular prion protein into insoluble abnormally folded infectious prions, are invariably fatal and highly infectious degenerative diseases that affect a wide variety of…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

The automatic design of robots has existed for 30 years but has been constricted by serial non-differentiable design evaluations, premature convergence to simple bodies or clumsy behaviors, and a lack of sim2real transfer to physical…

Bone remodeling involves the coordinated removal of bone by osteoclasts and addition of bone by osteoblasts, a process that is modulated by the prevailing mechanical environment. In this paper a fully coupled model of bone remodeling is…

Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…

The vision of Organic Computing addresses challenges that arise in the design of future information systems that are comprised of numerous, heterogeneous, resource-constrained and error-prone components or devices. Here, the notion organic…

We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…

We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new…

Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…

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…

Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

Technical systems have evolved over time into large and complex Interwoven Systems consisting of several to a huge number of (possibly heterogeneous) subsystems that have interdependencies. The resultant mutual influences among subsystems…

The ability to control Poisson's ratio of functional materials has been one of the main objectives of researchers attempting to develop structures efficient from the perspective of protective, biomedical and soundproofing devices. This task…

Biological membranes are host to proteins and molecules which may form domain-like structures resulting in spatially-varying material properties. Vesicles with such heterogeneous membranes can exhibit intricate shapes at equilibrium and…

The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…

Biological materials exhibit complex structure-property relationships which are only beginning to be elucidated. Understanding the underlying physical mechanisms of the structure-property relationships is the key to designing bioinspired…