13 papers · ranked by Valyu relevance
Matthew Bailey, Mark Wilson
One of the critical tools of persistent homology is the persistence diagram. We demonstrate the applicability of a persistence diagram showing the existence of topological features (here rings in a 2D network) generated over time instead of space as a tool to analyse trajectories of biological networks. We show how the…
Authors not listed
Active assembly of matter is a defining trait of living systems, enabling the creation of far-from-equilibrium materials essential for the functionality of life. This is achieved through energy-dissipative, multi-step processes facilitated by various biomolecular agents for chemical and mechanical assembly of matter.…
Amit Kahana, Lior Segev, Doron Lancet
The origin of life must have involved an unlikely transition from chaotic chemistry to reproducing supramolecular structures. Previous quantitative analyses of reproducing mutually catalytic networks made of simple molecules have led to increasing popularity of this pre-RNA scenario for life’s origin. Here, we…
Matthew H. J. Bailey, Mark Wilson
Networks of biopolymers occur often in nature, and are vulnerable to damage over time. In this work, a coarse grained model of collagen IV molecules is applied in a 2D hexagonal network and the mechanisms by which these networks can rupture are explored. The networks are stretched linearly in order to study their…
Harry Gray
Developed in this article is the electron transfer network, a graph structure whose adjacent nodes are reversibly coupled chemically reactive species whose forward and reverse rate constants are calculated by semiclassical electron transfer theory. These ET networks resemble electric circuits containing branches…
Authors not listed
The structural complexities of polymer networks, i.e., multiple functional groups, diverse connection sites, and various defects, make it difficult to accurately describe their microstructure using theoretical models and traditional metrics such as cross-link density (XLD). This study uses multi-scale molecular…
harry gray
The matrix exponential method as implemented in MATLAB is demonstrated as a facile tool for solving the time-dependent concentrations of an arbitrary chemically reactive network modelled as a coupled linear system of first-order differential equations. The method is used to verify a 10 species network incorporating…
Dariia Yehorova, Rory Crean, Peter Kasson, Shina Caroline Lynn Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction…
Stephen Goldup, Ivan Aprahamian
All chemists are familiar with the idea that, at equilibrium steady state, the relative concentrations of species present in a system are predicted by the corresponding equilibrium constants, which are in turn related to the relative free energy difference of the system components. There is also no net flux between…
Authors not listed
We present a chemical framework in which adaptive organization is achieved by tuning a gated quantum resonator (adaptive genomic resonator) {driven quantum oscillator} across a driven, dissipative reaction manifold (fitness landscape) {Hamiltonian potential surface}. In this view, catalytic elements set gain and phase…
Benjamin Ries, Richard J Gowers, James RB Eastwood, Irfan Alibay + 4 more
Alchemical free energy campaigns can be planned using graph theory by building up networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce Konnektor, an open-source Python package, for systematically planning, modifying, and analyzing free energy…
Murari Singh, Zachary M. Sherman, Delia J. Milliron, Thomas M. Truskett
Gel assemblies of functional nanoparticles, reversibly associated into percolating networks using bifunctional linking molecules, offer promise as versatile materials platforms. Molecular linkers can be customized to template interparticle spacing and modify colloidal network attributes, enabling design for…
James Swift, Matthew Arran Turner, James Christopher Reynolds
A rapid headspace analysis method for the authenticity testing of whiskies of different brands and years was developed for a low cost, deployable atmospheric pressure ionisation mass spectrometer, which required minimal sample preparation. Principal component analysis was applied to the time-averaged mass spectra, the…