Related papers: Towards Experimental P-systems using multivesicula…
This work presents a simply methodology for coating small unilamellar liposomes bearing different degrees of positive charge with polyelectrolyte multilayers using the sequential Layer-by-Layer (LbL) deposition method. The liposomes were…
Molecular docking is a critical computational strategy in drug design and discovery, but the complex diversity of biomolecular structures and flexible binding conformations create an enormous search space that challenges conventional…
Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
Understanding dynamic and complex interaction of biological membranes with extracellular matrices plays a crucial role in controlling a variety of cell behavior and functions, from cell adhesion and growth to signaling and differentiation.…
We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
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…
We investigate the influence of a non-ionic surfactant like polymer on phospholipid vesicles. Our results from cryogenic transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), small angle neutron and X-ray scattering…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
The industrial implementation of biofuel production from lignocellulosic biomass faces a number of economic obstacles. One of these is the cost of enzymes, typically used for cellulose hydrolysis. Nature provides some hints towards the…
Membrane computing and P systems are a paradigm of massively parallel natural computing introduced by Gheorghe P\u{a}un in 1999, inspired by the structure of the living cell and by its biochemical reactions. In spite of this explicit…
A Boolean network is a discrete dynamical system operating on vectors of Boolean variables. The action of a Boolean network can be conveniently expressed as a system of Boolean update functions, computing the new values for each component…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
P systems are computing conceptual computing devices that are at least as powerful as Turing machines. However, until recently it was not known how one can encode any recursive function as a P~system. Here we propose a new encoding of…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We develop a theory of percolation with plasticity systems (PWPs) rendering properties of interest for neuromorphic computing. Unlike the standard percolation between two large electrodes, they have multiple ($N\gg 1$) interfaces and…
Biological membranes are known to form various structural motifs, from lipid bilayers to tubular filaments and networks facilitating e.g. adhesion and cell-cell communication. To understand the biophysical processes underpinning lipid-lipid…
Phosphatidylinositol phosphates (PIPs) are membrane phospholipids that play crucial roles in a wide range of cellular functions. However, there is a dearth of experimental data in the literature on PIPs because their investigations are not…