Related papers: Optimality in self-organized molecular sorting
Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion…
Optimal prediction approximates the average solution of a large system of ordinary differential equations by a smaller system. We present how optimal prediction can be applied to a typical problem in the field of molecular dynamics, in…
How condensed-matter simulations depend on the number of molecules being simulated ($N$) is sometimes itself a valuable piece of information. Liquid crystals provide a case in point. Light scattering and $2d$-IR experiments on…
Diffusion trajectory distillation accelerates sampling by training a student model to approximate the multi-step denoising trajectories of a pretrained teacher model using far fewer steps. Despite strong empirical results, the trade-off…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
The conceptual landscape of convection has two simple gateways: optimal function and random form. Optimal convection adjusts toward a univariate ideal called neutrality. Convection form involves elements (parcels, bubbles, drafts) whose…
Most recent advances in machine learning and analytics for process control pose the question of how to naturally integrate new data-driven methods with classical process models and control. We propose a process modeling framework enabling…
This paper provides an elementary, self-contained analysis of diffusion-based sampling methods for generative modeling. In contrast to existing approaches that rely on continuous-time processes and then discretize, our treatment works…
In this work we study the stochastic process of two-species coagulation. This process consists in the aggregation dynamics taking place in a ring. Particles and clusters of particles are set in this ring and they can move either clockwise…
We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for…
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…
We propose a computationally lean, two-stage approach that reliably predicts self-assembly behavior of complex charged molecules on a metallic surfaces under electrochemical conditions. Stage one uses ab initio simulations to provide…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…
Recent advances in classical density functional theory are combined with stochastic process theory and rare event techniques to formulate a theoretical description of nucleation, including crystallization, that can predict nonclassical…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…
In this paper we consider a statistical estimation problem known as atomic deconvolution. Introduced in reliability, this model has a direct application when considering biological data produced by flow cytometers. In these experiments,…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
Theories of protein crystallization based on spheres that form close-packed crystals predict optimal assembly within a `slot' of second virial coefficients and enhanced assembly near the metastable liquid-vapor critical point. However, most…
The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…