arXiv subjects

S. Tesoro

Publications and source records attributed to S. Tesoro.

4 recordsLinked to original sources

arXiv2018

The determinism and boundedness of self-assembling structures

Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the determinism and boundedness of the self-assembly. The former tells us whether the same set of building blocks always generates the same structure, and the latter whether it grows indefinitely. These properties are highly relevant in the context of protein structures, as the difference between deterministic protein self-assembly and nondeterministic protein aggregation is central to a number of diseases. Here we introduce a graph theoretical approach that can determine the determinism and boundedness for several geometries and dimensionalities of self-assembly more accurately and quickly than conventional methods. We apply this methodology to a previously studied lattice self-assembly model and discuss generalizations to a wide range of other self-assembling systems

cond-mat.soft↗

arXiv2016

Non-deterministic self-assembly with asymmetric interactions

We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter can lead to self-limiting cluster growth. Furthermore, by adjusting the relative abundance of self-assembly particles in a two-particle mixture, we are able to tune the final sizes of these clusters. We show that this is a fundamental property of asymmetric interactions, which has potential applications in bioengineering, and provides new insights into the study of diseases caused by protein aggregation.

cond-mat.soft↗

arXiv2016

Non-deterministic self-assembly of two tile types on a lattice

Self-assembly is ubiquitous in nature, particularly in biology, where it underlies the formation of protein quaternary structure and protein aggregation. Quaternary structure assembles deterministically and performs a wide range of important functions in the cell, whereas protein aggregation is the hallmark of a number of diseases and represents a non-deterministic self-assembly process. Here we build on previous work on a lattice model of deterministic self-assembly to investigate non-deterministic self-assembly of single lattice tiles and mixtures of two tiles at varying relative concentrations. Despite limiting the simplicity of the model to two interface types, which results in 13 topologically distinct single tiles and 106 topologically distinct sets of two tiles, we observe a wide variety of concentration-dependent behaviours. Several two-tile sets display critical behaviours in form of a sharp transition from bound to unbound structures as the relative concentration of one tile to another increases. Other sets exhibit gradual monotonic changes in structural density, or non-monotonic changes, while again others show no concentration dependence at all. We catalogue this extensive range of behaviours and present a model that provides a reasonably good estimate of the critical concentrations for a subset of the critical transitions. In addition we show that the structures resulting from these tile sets are fractal, with one of two different fractal dimensions.

cs.ET↗

arXiv2016

A 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNA

The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string structure. In this work we present a 1 dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We focus on the case of genomic sheep DNA, and we start from effective potentials valid at infinite dilution and determined from high resolution in vitro salt dialysis experiments. We study positioning within a polynucleosome chain, and compare the results for genomic DNA to that obtained in the simplest case of homogeneous DNA, where the problem can be mapped to a Tonks gas. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on experimentally observable quantities in experiments on polynucleosome chromatin fibres reconstituted in vitro.

physics.bio-ph↗