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Biological cells are able to generate intricate structures and respond to external stimuli, sculpting their membrane from within. Simplified biomimetic systems can aid in understanding the principles which govern these shape changes and…
Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
We investigate micro-to-macroscopic derivations in two models of living cells, in presence to cell-cell adhesive interactions. We rigorously address two PDE-based models, one featuring non-local terms and another purely local, as a a result…
I show the assumed Bilayer structure of cell membranes is Topologically falsified by known aminophospholipid dynamics in metabolically-active, Far from Equilibrium cells. The sensitivity of lipid and cytoplasmic flows to temperature,…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Doxorubicin (DOX) is one of the most efficient antitumor drugs employed in numerous cancer therapies. Its incorporation into lipid-based nanocarriers, such as liposomes, improves the drug targeting into tumor cells and reduces drug side…
Engineering simple, artificial models of living cells allows synthetic biologists to study cellular functions under well-controlled conditions. Reconstituting multicellular behaviors with synthetic cell-mimics is still a challenge because…
We are interested in exploring interacting particle systems that can be seen as microscopic models for a particular structure of coupled transport flux arising when different populations are jointly evolving. The scenarios we have in mind…
picFoam is a fully kinetic electrostatic Particle-in-Cell(PIC) solver, including Monte Carlo Collisions(MCC), for non-equilibrium plasma research in the open-source framework of OpenFOAM. The solver's modular design, based on the same…
We investigate with computer simulations the critical radius of pores in a lipid bilayer membrane. Ilton et al. (2016) recently showed that nucleated pores in a homopolymer film can increase or decrease in size, depending on whether they…
In this article we propose and investigate a hierarchy of mathematical models based on partial differential equations (PDE) and ordinary differential equations (ODE) for the simulation of the biophysical phenomena occurring in the…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
A biochemical network can be simulated by a set of ordinary differential equations (ODE) under well stirred reactor conditions, for large numbers of molecules, and frequent reactions. This is no longer a robust representation when some…