Related papers: Improvements in continuum modeling for biomolecula…
The intensity matching approach for tractable performance evaluation and optimization of cellular networks is introduced. It assumes that the base stations are modeled as points of a Poisson point process and leverages stochastic geometry…
Identifying a coupled dynamical system out of many plausible candidates, each of which could serve as the underlying generator of some observed measurements, is a profoundly ill posed problem that commonly arises when modelling real world…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
In ionic solutions, there are multi-species charged particles (ions) with different properties like mass, charge etc. Macroscopic continuum models like the Poisson-Nernst-Planck (PNP) systems have been extensively used to describe the…
The ability to represent intracellular biochemical dynamics via deterministic and stochastic modelling is one of the crucial components to move biological sciences in the observe-predict-control-design knowledge ladder. Compared to the…
Continuum solvation models are becoming increasingly relevant in condensed matter simulations, allowing to characterize materials interfaces in the presence of wet electrified environments at a reduced computational cost with respect to all…
We propose a new approach to model composition, based on reducing several models to the same level of complexity and subsequent combining them together. Firstly, we suggest a set of model reduction tools that can be systematically applied…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…
In a mathematical model of interacting biological organisms, where external interventions may alter behavior over time, traditional models that assume fixed parameters usually do not capture the evolving dynamics. In oncology, this is…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Efforts toward a comprehensive description of behavior have indeed facilitated the development of representation-based approaches that utilize deep learning to capture behavioral information. As behavior complexity increases, the expressive…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
Nonlinear dynamic models are widely used for characterizing functional forms of processes that govern complex biological pathway systems. Over the past decade, validation and further development of these models became possible due to data…
Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…
Control of nonlinear distributed parameter systems (DPS) under uncertainty is a meaningful task for many industrial processes. However, both intrinsic uncertainty and high dimensionality of DPS require intensive computations, while…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…