Related papers: Self-Organized Criticality: A Guide to Water-Prote…
Examining locomotion has improved our basic understanding of motor control and aided in treating motor impairment. Mice and rats are the model system of choice for basic neuroscience studies of human disease. High frame rates are needed to…
Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
The goal of this paper is to present a new efficient image segmentation method based on evolutionary computation which is a model inspired from human behavior. Based on this model, a four layer process for image segmentation is proposed…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
We report on the direct measurement of the correlation times of the protein backbone carbons and proximal waters of hydration in mechanically strained elastin by nuclear magnetic resonance methods. The experimental data indicate a decrease…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Coherent filaments at the ocean surface often appear to be transient watermass boundaries, where currents converge, surfactants accumulate, and frontal structure at depth can possibly delineate enhanced biological activity in the upper…
Intelligence is often discussed in terms of neural networks in the cerebral cortex, whose evolution has presumably been influenced by Darwinian selection. Here we present molecular evidence that one of the many kinesin motors, Kif14, has…
Zebrafish pretectal neurons exhibit specificities for large-field optic flow patterns associated with rotatory or translatory body motion. We investigate the hypothesis that these specificities reflect the input statistics of natural optic…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
Hyperpolarized water can be a valuable aid in protein NMR, leading to amide group 1H polarizations that are orders of magnitude larger than their thermal counterparts. Suitable procedures can exploit this to deliver 2D 1H-15N correlations…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
We used single-molecule tracking to probe the local rheology of interfacial water. Fluorescent rhodamine molecules were tracked on silica surfaces as a function of ambient relative humidity, which controlled the thickness of condensed water…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
Rivers exhibit fractal-like properties that are associated with scaling laws linking geometry and size. The optimal channel network (OCN) model, which is a mathematically tractable representation of river networks often used in theoretical…
Making sense of Wasserstein distances between discrete measures in high-dimensional settings remains a challenge. Recent work has advocated a two-step approach to improve robustness and facilitate the computation of optimal transport, using…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Polymer association at liquid-liquid interfaces is a promising way to spontaneously obtain soft self-healing membranes. In the case of reversible bonding between two polymers, the macromolecules are mobile everywhere within the membrane and…
Motivation: Protein sequence world is discrete as 20 amino acids (AA) while its structure world is continuous, though can be discretized into structural alphabets (SA). In order to reveal the relationship between sequence and structure, it…