Related papers: Regional compartmentalization in multienzyme-relat…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
Self-assembly processes in biological and synthetic biomolecular systems are often governed by the spatial separation of biochemical processes. While previous work has focused on optimizing self-assembly through fine-tuned reaction…
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as…
Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…
A biomolecular system representing the first realization of associative memory based on enzymatic reactions in vitro has been designed. The system demonstrated "training" and "forgetting" features characteristic of memory in biological…
Due to the intrinsic complexity and nonlinearity of chemical reactions, direct applications of traditional machine learning algorithms may face with many difficulties. In this study, through two concrete examples with biological background,…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
Phase-separated liquid condensates can spatially organize and thereby regulate chemical processes. However, the physicochemical mechanisms underlying such regulation remain elusive as the intramolecular interactions responsible for phase…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
The practical description of disordered chemical reactions, where reactions involve multiple species at multiple sites, is presently challenge using correlated electronic structure methods. Here we describe the gradient theory of…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
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…
Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…
One of the primary challenges in quantum chemistry is the accurate modeling of strong electron correlation. While multireference methods effectively capture such correlation, their steep scaling with system size prohibits their application…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
An accurate description of strong correlation is quintessential for the exploration of emerging chemical phenomena. While near-term variational quantum algorithms provide a theoretically scalable framework for quantum chemical problems, the…
Catalysis lies at the heart of chemical reactivity, yet its foundational principles remain fragmented across the distinct domains of homogeneous, heterogeneous, and enzymatic systems Here, we propose a unifying theoretical model that…