Related papers: Frustration in Biomolecules
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
In geometrically frustrated assemblies local inter-subunit misfits propagate to intra-assembly strain gradients, giving rise to anomalous self-limiting assembly thermodynamics. Here, we use theory and coarse-grained simulation to study a…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
Predicting the 3D structure of a macromolecule, such as a protein or an RNA molecule, is ranked top among the most difficult and attractive problems in bioinformatics and computational biology. Its importance comes from the relationship…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
Geometrical frustration in thin sheets is ubiquitous across scales in biology and becomes increasingly relevant in technology. Previous research identified the origin of the frustration as the violation of Gauss's \emph{Theorema Egregium}.…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Frustration is an important phenomenon in condensed matter physics because it can introduce a new order parameter such as chirality. Towards understanding a mechanism of the frustration in strongly correlated systems, we study a holographic…
Geometric frustration is known to completely damage kinetic processes of some of the orbitals (and their associated quantum coherence) as to produce flat bands in the non-interacting systems. The impact of introducing additional interaction…
Bundles of filaments are subject to geometric frustration: certain deformations (e.g. bending while twisted) require longitudinal variations in spacing between filaments. While bundles are common -- from protein fibers to yarns -- the…
Plants solve complex problems without centralized control, relying instead on growth-driven dynamics to sense, navigate, and optimize resource acquisition. This review presents a unified physical framework for understanding plant behavior…
Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
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…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…