Origin of Scaling Behavior of Protein Packing Density: A Sequential Monte Carlo Study of Compact Long Chain Polymers

Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find that the radius of gyration provides poor description of protein packing but the alpha contact number we introduce here characterize proteins well. We further demonstrate that protein-like scaling relationship between packing density and chain length is observed in off-lattice self-avoiding walks. A key problem in studying compact chain polymer is the attrition problem: It is difficult to generate independent samples of compact long self-avoiding walks. We develop an algorithm based on the framework of sequential Monte Carlo and succeed in generating populations of compact long chain off-lattice polymers up to length $N=2,000$. Results based on analysis of these chain polymers suggest that maintaining high packing density is only characteristic of short chain proteins. We found that the scaling behavior of packing density with chain length of proteins is a generic feature of random polymers satisfying loose constraint in compactness. We conclude that proteins are not optimized by evolution to eliminate packing voids.Comment: 9 pages, 10 figures. Accepted by J. Chem. Phy

Space from Hilbert Space: Recovering Geometry from Bulk Entanglement

We examine how to construct a spatial manifold and its geometry from the entanglement structure of an abstract quantum state in Hilbert space. Given a decomposition of Hilbert space $\mathcal{H}$ into a tensor product of factors, we consider a class of "redundancy-constrained states" in $\mathcal{H}$ that generalize the area-law behavior for entanglement entropy usually found in condensed-matter systems with gapped local Hamiltonians. Using mutual information to define a distance measure on the graph, we employ classical multidimensional scaling to extract the best-fit spatial dimensionality of the emergent geometry. We then show that entanglement perturbations on such emergent geometries naturally give rise to local modifications of spatial curvature which obey a (spatial) analog of Einstein's equation. The Hilbert space corresponding to a region of flat space is finite-dimensional and scales as the volume, though the entropy (and the maximum change thereof) scales like the area of the boundary. A version of the ER=EPR conjecture is recovered, in that perturbations that entangle distant parts of the emergent geometry generate a configuration that may be considered as a highly quantum wormhole.Comment: 37 pages, 5 figures. Updated notation, references, and acknowledgemen