Related papers: Protein container disassembly pathways depend on g…
How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has…
A general method is described for detecting and analysing galaxy systems. The multivariate geometrical structure of the sample is studied by using an extension of the method which we introduced in a previous paper. The method is based on an…
Insight in the crumpling or compaction of one-dimensional objects is of great importance for understanding biopolymer packaging and designing innovative technological devices. By compacting various types of wires in rigid confinements and…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
The structure and stresses of static granular packs in cylindrical containers are studied using large-scale discrete element molecular dynamics simulations in three dimensions. We generate packings by both pouring and sedimentation and…
The cosmic web consists of a complex configuration of voids, walls, filaments, and clusters, which formed under the gravitational collapse of Gaussian fluctuations. Understanding under what conditions these different structures emerge from…
We study the fragment size distributions after crushing of single and many particles under uniaxial compression inside a cylindrical container by means of numerical simulations. Under the assumption that breaking goes through the bulk of…
This paper deals with the relations among structural, topological, and chemical properties of the E.Coli proteome from the vantage point of the solubility/aggregation propensity of proteins. Each E.Coli protein is initially represented…
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with $12$ corresponding packaging signals in three affinity bands. This whole…
From tumour invasion to cell sorting and animal territoriality, many biological systems rely on nonlocal interactions that drive complex spatial organisation. Partial differential equations (PDEs) with nonlocal advection are increasingly…
Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
Self-assembly of proteins into amyloid aggregates is an important biological phenomenon associated with human diseases such as Alzheimer's disease. Amyloid fibrils also have potential applications in nano-engineering of biomaterials. The…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit…
This survey for mathematicians summarizes several works by the author on protein geometry and protein function with applications to viral glycoproteins in general and the spike glycoprotein of the SARS-CoV-2 virus in particular. Background…
A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Viral capsids are usually spherical, and for a significant number of viruses exhibit overall…