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Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo(More)
Morphogenesis implies the controlled spatial organization of cells that gives rise to tissues and organs in early embryonic development. While morphogenesis is under strict genetic control, the formation of specialized biological structures of specific shape hinges on physical processes. Tissue engineering (TE) aims at reproducing morphogenesis in the(More)
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Genes and molecules set up the conditions for the physical processes to act, in particular to shape the embryo. As development continues the changes brought about by the physical processes lead to changes in gene expression.(More)
We demonstrate how the surrogate process approximation (SPA) method can be used to compute both the potential of mean force along a reaction coordinate and the associated diffusion coefficient using a relatively small number (10-20) of bidirectional nonequilibrium trajectories coming from a complex system. Our method provides confidence bands which take the(More)
The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with an approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of light-harvesting (LH) complexes was performed on an 87 055 atom system comprised of a(More)
With the widespread availability of high performance computer clusters and effi cient parallel molecular modeling software, molecular dynamics (MD) simulations became an indispensable tool for the study of the structure-function relationship in proteins with known crystal structures. However, understanding at atomic level the functioning of membrane bound(More)