Related papers: Synthesis and materialization of a reaction-diffus…
When thin films are grown on a substrate by chemical vapor deposition, the evolution of the first deposited layers may be described, on mesoscopic scales, by dynamical models of the reaction-diffusion type. For monoatomic layers, such…
Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…
Most binary superlattices created using DNA functionalization or other approaches rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
The discovery of inorganic crystal structures with targeted properties is a significant challenge in materials science. Generative models, especially state-of-the-art diffusion models, offer the promise of modeling complex data…
Fractal-like nanopatterned DNA thin films have been fabricated on mica substrate by Langmuir-Blodgett (LB) technique. Structures and components of DNA nanopatterns were investigated using atomic force microscopy (AFM) and X-ray…
Photonic crystals -- a class of materials whose optical properties derive from their structure in addition to their composition -- can be created by self-assembling particles whose sizes are comparable to the wavelengths of visible light.…
Active networks made of biopolymers and motor proteins are valuable bioinspired systems that have been used in the last decades to study the cytoskeleton and its self-organization under mechanical stimulation. Different techniques are…
The amoeboid organism, the plasmodium of Physarum polycephalum, behaves on the basis of spatio-temporal pattern formation by local contraction-oscillators. This biological system can be regarded as a reaction-diffusion system which has…
Three-dimensional molecular generators based on diffusion models can now reach near-crystallographic accuracy, yet they remain fragmented across tasks. SMILES-only inputs, two-stage pretrain-finetune pipelines, and one-task-one-model…
We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential…
Antibodies are versatile proteins that bind to pathogens like viruses and stimulate the adaptive immune system. The specificity of antibody binding is determined by complementarity-determining regions (CDRs) at the tips of these Y-shaped…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations:…
Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…
Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery.…
This paper concentrates on relationships of formal systems with biology. The paper is based on previous papers by the author. We have freely used texts of those papers where the formulations are of use, and we have extended the concepts and…
Reaction diffusion systems are often used to study pattern formation in biological systems. However, most methods for understanding their behavior are challenging and can rarely be applied to complex systems common in biological…
Deterministic reaction networks (RNs) are tools to model diverse biological phenomena characterized by particle systems, when there are abundant number of particles. Examples include but are not limited to biochemistry, molecular biology,…
Retrosynthesis poses a key challenge in biopharmaceuticals, aiding chemists in finding appropriate reactant molecules for given product molecules. With reactants and products represented as 2D graphs, retrosynthesis constitutes a…