Related papers: Synthesis and materialization of a reaction-diffus…
In the reaction-diffusion process $A+B \to \varnothing$ on random scale-free (SF) networks with the degree exponent $\gamma$, the particle density decays with time in a power law with an exponent $\alpha$ when initial densities of each…
This computational study introduces a theoretical framework for practical, electrochemical fuel generation displaying exponential product yields as functions of time. Exponential reaction scaling is simulated through an autocatalytic cycle…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
We present an approach to synthesizing new graph structures from empirically specified distributions. The generative model is an auto-decoder that learns to synthesize graphs from latent codes. The graph synthesis model is learned jointly…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
Many protein design applications, such as binder or enzyme design, require scaffolding a structural motif with high precision. Generative modelling paradigms based on denoising diffusion processes emerged as a leading candidate to address…
Piebaldism usually manifests as white areas of fur, hair or skin due to the absence of pigment-producing cells in those regions. The distribution of the white and colored zones does not follow the classical Turing patterns. Here we present…
Assembly theory predicts that a distinguishing signature of life is its ability to produce complex molecules in abundance, opening new possibilities for life detection. Experimental validation of this approach has so far relied on abiotic…
Non-uniform product (color) distribution in colorimetric paper-based sensors affects the accuracy and reliability of measurements. The underlying mechanisms responsible for this are still unclear. The coffee ring effect explains the…
In this article we propose a unified framework in order to study reaction-diffusion systems containing self- and cross-diffusion using a free energy approach. This framework naturally leads to the formulation of an energy law, and to a…
Control over the physical properties of materials is ubiquitously required in many fields. One means by which this can be achieved is controlling the internal structure of multi-component materials with an eye to enhancing mechanical…
Retrosynthesis is essential for designing synthetic pathways for complex molecules and can be revolutionized by AI to automate and accelerate chemical synthesis planning for drug discovery and materials science. Here, we propose a…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
Nature offers remarkable examples of complex photonic architectures such as those responsible for the iridescent colors of butterfly wings that emerge spontaneously during growth, well before any centralized control takes place. Arising…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
It has been pointed out that if an autocatalytic cycle produces primitive membrane chemicals, it can compose a self-maintaining proto cell. Moreover, it is known that a proto cell can divide itself spontaneously as it grows. An unsolved…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…