相关论文: Gauge symmetries and structure of proteins
It's been said that "mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better". Here we aim for something even better. We try to combine mathematical physics and biology into a picoscope of…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
The Higgs mechanism gives mass to Yang-Mills gauge bosons. According to the conventional wisdom, this happens through the spontaneous breaking of gauge symmetry. Yet, gauge symmetries merely reflect a redundancy in the state description and…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
We analyze models of electroweak symmetry breaking in warped 5-dimensional space with gauge bosons and fermions in the bulk. The Higgs boson is identified with the 5th component of a gauge field. We dynamically generate the Higgs potential…
An earlier suggestion that scalar fields in gauge theory may be introduced as frame vectors or vielbeins in internal symmetry space, and so endowed with geometric significance, is here sharpened and refined. Applied to a $u(1) \times su(2)$…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
We combine the principle of gauge invariance with extrinsic string geometry to develop a lattice model that can be employed to theoretically describe properties of chiral, unbranched homopolymers. We find that in its low temperature phase…
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…
In this paper we discuss a one-dimensional Abelian Higgs model with Chern-Simons interaction as an effective theory of one-dimensional curves embedded in three-dimensional space. We demonstrate how this effective model is compatible with…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
We present a non-perturbative model of Gauge-Higgs Unification. We consider a five-dimensional pure SU(2) gauge theory with orbifold boundary conditions along the fifth dimension, such that the symmetry is reduced to U(1) at the fixed…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We consider classical gauge theory with spontaneous symmetry breaking on a principal bundle $P\to X$ whose structure group $G$ is reducible to a closed subgroup $H$, and sections of the quotient bundle $P/H\to X$ are treated as classical…
In this article, we review gauge-Higgs unification models based on gauge theories defined on six-dimensional spacetime with $S^2/Z_2$ topology in the extra spatial dimensions. On the extra $S^2/Z_2$ space, non-trivial boundary conditions…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…