Related papers: Simulating Organogenesis in COMSOL
The mechanical properties of vertebrate bone are largely determined by a process which involves the complex interplay of three different cell types. This process is called {\it bone remodeling}, and occurs asynchronously at multiple sites…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
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…
Multiphysics simulations play an essential role in accurately modeling complex interactions across diverse scientific and engineering domains Although neural operators especially the Fourier Neural Operator FNO have significantly improved…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
The study of thrombosis is crucial to understand and develop new therapies for diseases like deep vein thrombosis, diabetes related strokes, pulmonary embolism etc. The last two decades have seen an exponential growth in studies related to…
How cells regulate the number of organelles is a fundamental question in cell biology. While decades of experimental work have uncovered four fundamental processes that regulate organelle biogenesis, namely, de novo synthesis, fission,…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Simulation of a multicomponent lipid bilayer having a fixed percentage of cholesterol is done to study phase transition leading to domain formation. The concept of random lattice has been used in simulation to account for the coupling…
In the field of optics and nanophotonics, simulation of electromagnetic scattering plays a major role in the study of complex nanostructures and optical devices. The numerical analysis of scattering spectra, even for nanocavities with…