Related papers: Precision and Stability Issues in VBL, the Virtual…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against cancer. The experiments are…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a models' dynamics over a large parameter space…
Bistability is considered wide-spread among bacteria and eukaryotic cells, useful e.g. for enzyme induction, bet hedging, and epigenetic switching. However, this phenomenon has mostly been described with deterministic dynamic or well-mixed…
The rapid development of AI highlights the pressing need for sustainable energy, a critical global challenge for decades. Nuclear fusion, generally seen as an ultimate solution, has been the focus of intensive research for nearly a century,…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
The influence of the internal structure of a biological cell (e.g., a leukocyte) on its dynamics and rheology is not yet fully understood. By using 2D numerical simulations of a bilamellar vesicle (BLV) consisting of two vesicles as a cell…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
With the advancement of computational network science, its research scope has significantly expanded beyond static graphs to encompass more complex structures. The introduction of streaming, temporal, multilayer, and hypernetwork approaches…
Electrochemistry workflows utilize various instruments and computing systems to execute workflows consisting of electrocatalyst synthesis, testing and evaluation tasks. The heterogeneity of the software and hardware of these ecosystems…
Electrochemistry ecosystems are promising for accelerating the design and discovery of electrochemical systems for energy storage and conversion, by automating significant parts of workflows that combine synthesis and characterization…
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of…
The reproduction of a living cell requires a repeatable set of chemical events to be properly coordinated. Such events define a replication cycle, coupling the growth and shape change of the cell membrane with internal metabolic reactions.…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
We have considered the complexity and asymptotic stability in the process of biochemical substance exchange in a coupled ring of cells. We have used coupled maps to model this process. It includes the coupling parameter, cell affinity and…
The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the…
Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and…
One of many important features of the tumour microenvironment is that it is a place of active Darwinian selection where different tumour clones become adapted to the variety of ecological niches that make up the microenvironment. These…
The computational treatment of many-electron systems capable of exchanging {electrons and nuclei} with the environment represents one of the outermost frontiers in simulation methodology. The exchanging process occurs in a large variety of…