Related papers: Frustration, dynamics and catalysis
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…
As Phil Anderson noted long ago, frustration can be generally defined by measuring the fluctuations in the coupling energy across a plane boundary between two large blocks of material. Since that time, a number of groups have studied the…
The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
The motility of a fish keratocyte on a flat substrate exhibits two distinct regimes: the non-migrating and the migrating one. In both configurations the shape is fixed in time and, when the cell is moving, the velocity is constant in…
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…
Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…
The existence of definite orders in frustrated quantum systems is related rigorously to the occurrence of fully factorized ground states below a threshold value of the frustration. Ground-state separability thus provides a natural measure…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is…
Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their contents via the lysosomal pathway. In cases of mild stress,…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Cell polarization underlies many cellular processes, such as differentiation, migration, and budding. Many living cells, such as budding yeast and fission yeast, use cytoskeletal structures to actively transport proteins to one location on…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
Proteins are aminoacid chains that diffusively fold or unfold depending on the thermal and chemical environmental conditions. While sophisticated models account for detailed aspects of real proteins, finding traits that unify protein…
Local stresses in a tissue, a collective property, regulate cell division and apoptosis. In turn, cell growth and division induce active stresses in the tissue. As a consequence, there is a feedback between cell growth and local stresses.…