Related papers: Frustration in Biomolecules
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
Many problems in physics, material sciences, chemistry and biology can be abstractly formulated as a system that navigates over a complex energy landscape of high or infinite dimensions. Well-known examples include phase transitions of…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
Energy landscape theory describes how a full-length protein can attain its native fold after sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the…
The frustration index is a key measure for analysing signed networks, which has been underused due to its computational complexity. We use an exact optimisation-based method to analyse frustration as a global structural property of signed…
Geometric frustration arises when lattice structure prevents simultaneous minimization of local interactions. It leads to highly degenerate ground states and, subsequently, complex phases of matter such as water ice, spin ice and frustrated…
The idea of charge frustration is applied to describe the properties of such diverse physical systems as oil-water-surfactant mixtures and metal-ammonia solutions. The minimalist charge-frustrated model possesses one energy scale and two…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
Solutes added to solutions often dramatically impact molecular processes ranging from the suspension or precipitation of colloids to biomolecular associations and protein folding. Here we revisit the origins of the effective attractive…
Dense systems of active matter exhibit highly dynamic collective motion characterized by intermingled vortices, referred to as active turbulence. The interaction between these vortices is key to controlling turbulent dynamics, and a…
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…
Definition of frustration is expressed by transitivity of binary entanglement relation in considered complex system. Extending this definition into n-ary relation a hierarchy of frustrations is derived. As a complex system the U.S.…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Frustration, that is, the impossibility of satisfying the energetic preferences between all spin pairs simultaneously, underlies the complexity of many fundamental properties in spin systems, including the computational difficulty in…
Aligning human-interpretable concepts with the internal representations learned by modern machine learning systems remains a central challenge for interpretable AI. We introduce a geometric framework for comparing supervised human concepts…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Biofilms are complex, self-organized consortia of microorganisms that produce a functional, protective matrix of biomolecules. Physically, the structure of a biofilm can be described as an entangled polymer network which grows and changes…