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Whether live cell membranes show miscibility phase transitions (MPTs), and if so, how they fluctuate near the transitions remain outstanding unresolved issues in physics and biology alike. Motivated by these questions we construct a generic…
Biological tissue integrity is actively maintained by cells. It is essential to comprehend how cells accomplish this in order to stage tissue diseases. However, addressing the complexity of a cell's system of interrelated mechanisms poses a…
We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We map molecular dynamics simulations of fluid-fluid interfaces onto mesoscale continuum theories for partially miscible fluids. Unlike most previous work, we examine not only the interface order parameter and density profiles, but also the…
We present a new class of models for assessing the cell dynamics characterising muscular dystrophies. The proposed approach comprises a system of integro-differential equations for the statistical distributions, over a large patient cohort,…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Collective cell migration plays a central role in tissue development, morphogenesis, wound repair and cancer progression. With the growing realization that physical forces mediate cell motility in development and physiology, a key…
A physical scenario accounting for the existence of size-limited submicrometric domains in cell membranes is proposed. It is based on the numerical investigation of the counterpart, in lipidic membranes where proteins are diffusing, of the…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Known as one of the hallmarks of cancer [30], cancer cell invasion of human body tissue is a complicated spatio-temporal multiscale process which enables a localised solid tumour to transform into a systemic, metastatic and fatal disease.…
With the growth of artificial intelligence (AI), there has been an increase in the adoption of computer vision and deep learning (DL) techniques for the evaluation of microscopy images and movies. This adoption has not only addressed…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of…
All simulation approaches eventually face limits in computational scalability when applied to large spatiotemporal domains. This challenge becomes especially apparent in molecular-level particle simulations, where high spatial and temporal…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
The friction and adhesion between elastic bodies are strongly influenced by the roughness of the surfaces in contact. Here we develop a multiscale molecular dynamics approach to contact mechanics, which can be used also when the surfaces…
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…
The dynamical properties of classical fluids at pico-liter scale attract experimentally and theoretically much attention in the soft-matter and biophysics communities, due to the appearance of the microfluidics, also called 'lab-on-a-chip',…