Related papers: Integrative modelling of biomolecular dynamics
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
The majority of solid tumours arise in epithelia and therefore much research effort has gone into investigating the growth, renewal and regulation of these tissues. Here we review different mathematical and computational approaches that…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
We propose a mathematical kinetic framework to investigate interactions between tumor cells and the immune system, focusing on the spatial dynamics of tumor progression and immune responses. We develop two kinetic models: one describes a…
Urban systems are intrinsically complex, involving different dimensions and scales, and consequently various approaches and scientific disciplines. In that context, urban simulation models have been coined as essential for the construction…
Kinetically constrained models have been widely studied in the context of glass formers and non-equilibrium statistical mechanics. Although their simple local rules often result in structureless static properties, their dynamics exhibit…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
A dynamical quantum model assigns an eigenstate to a specified observable even when no measurement is made, and gives a stochastic evolution rule for that eigenstate. Such a model yields a distribution over classical histories of a quantum…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
Thanks to novel, powerful brain activity recording techniques, we can create data-driven models from thousands of recording channels and large portions of the cortex, which can improve our understanding of brain-states neuromodulation and…
Molecular Dynamics (MD) simulation is widely used to analyze the properties of molecules and materials. Most practical applications, such as comparison with experimental measurements, designing drug molecules, or optimizing materials, rely…
Dynamic models are widely used to mathematically describe biological phenomena that evolve over time. One important area of application is leukaemia research, where leukaemia cells are genetically modified in preclinical studies to explore…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Recent advances at the intersection of control theory, neuroscience, and machine learning have revealed novel mechanisms by which dynamical systems perform computation. These advances encompass a wide range of conceptual, mathematical, and…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…