Related papers: Improvements in continuum modeling for biomolecula…
We study equilibrium properties of polymer films and droplets on a solid substrate employing particle-based simulation techniques (Molecular Dynamics) and a continuum description. Parameter-passing techniques are explored that facilitate a…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
Particle-in-Cell (PIC) simulation codes have wide applicability to first-principles modeling of multidimensional nonlinear plasma phenomena, including wake-field accelerators. This review addresses both finite difference and pseudo-spectral…
Electrochemical cells serve as a building block for producing and storing electrical energy from chemical reactions. The analysis of ion transport in these systems forms the foundation for understanding more complex electrochemical systems…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Difficulties in founding microscopically the Vlasov equation for Coulomb-interacting particles are recalled for both the statistical approach (BBGKY hierarchy and Liouville equation on phase space) and the dynamical approach (single…
Long-term biomolecular dynamics are critical for understanding key evolutionary transformations in molecular systems. However, capturing these processes requires extended simulation timescales that often exceed the practical limits of…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
In this article we address the study of ion charge transport in the biological channels separating the intra and extracellular regions of a cell. The focus of the investigation is devoted to including thermal driving forces in the…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Human blood flow is a multi-scale problem: in first approximation, blood is a dense suspension of plasma and deformable red cells. Physiological vessel diameters range from about one to thousands of cell radii. Current computational models…
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…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…