Related papers: Modeling and Modifying Response of Biochemical Pro…
We review the recent advances reported in the field of integrated photonic waveguide meshes, both from the theoretical as well as from the experimental point of view. We show how these devices can be programmed to implement both traditional…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Protein design has the potential to revolutionize biotechnology and medicine. While most efforts have focused on proteins with well-defined structures, increased recognition of the functional significance of intrinsically disordered…
Biomolecular logic systems processing biochemical input signals and producing "digital" outputs in the form of YES/NO were developed for analysis of physiological conditions characteristic of liver injury, soft tissue injury and abdominal…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
To facilitate a rapid response to pandemic threats, this paper focuses on developing a mechanistic simulation model for in vitro transcription (IVT) process, a crucial step in mRNA vaccine manufacturing. To enhance production and support…
Chemical reaction prediction remains a fundamental challenge in organic chemistry, where existing machine learning models face two critical limitations: sensitivity to input permutations (molecule/atom orderings) and inadequate modeling of…
Simplified stochastic models are widely used in the study of frequency-resolved noise propagation in biochemical reaction networks, a common measure being the coherence between random fluctuations in molecule number trajectories. Such…
Efficient execution of parameter sensitivity analysis (SA) is critical to allow for its routinely use. The pathology image processing application investigated in this work processes high-resolution whole-slide cancer tissue images from…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Membrane systems are a biologically-inspired computational model based on the structure of biological cells and the way chemicals interact and traverse their membranes. Although their dynamics are described by rules, encoding membrane…
We briefly review simulation schemes for the investigation of rare transitions and we resume the recently introduced Transition Interface Sampling, a method in which the computation of rate constants is recast into the computation of fluxes…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
The scope of the paper is the analysis of the possibility of increasing conversion in different types of systems based on continuous stirred tank reactors. A numerical model of the cascade with constant direction of material flow is tested,…
Finite element model updating utilizing frequency response functions as inputs is an important procedure in structural analysis, design and control. This paper presents a highly efficient framework that is built upon Gaussian process…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…