Related papers: Dynamic Density Functional Theory of Multicomponen…
We present Monte Carlo simulations of an ultra coarse-grained lipid bilayer with different number of lipids on both leaflets. In the simulations, we employ a new method for measuring the elastic parameters of the membrane, including the…
The development of traction-force microscopy, in the past two decades, has created the unprecedented opportunity of performing direct mechanical measurements on living cells as they adhere or crawl on uniform or micro-patterned substrates.…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
Probability density models based on deep networks have achieved remarkable success in modeling complex high-dimensional datasets. However, unlike kernel density estimators, modern neural models do not yield marginals or conditionals in…
Dynamical systems are ubiquitous within science and engineering, from turbulent flow across aircraft wings to structural variability of proteins. Although some systems are well understood and simulated, scientific imaging often confronts…
Capsules as well as dynamic routing between them are most recently proposed structures for deep neural networks. A capsule groups data into vectors or matrices as poses rather than conventional scalars to represent specific properties of…
Intraoperative observation of tissue internal structure is often difficult. Hence, real-time soft tissue deformation is essential for the localization of tumor and other internal structures. We propose a method to simulate the internal…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
This work aims to describe a mathematical model and a numerical method to simulate a thin anisotropic composite membrane moving and deforming in 3D space under a dynamic load of an arbitrary time and space profile. The model and the method…
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
The mechanical behaviour of solid biological tissues has long been described using models based on classical continuum mechanics. However, the classical continuum theories of elasticity and viscoelasticity cannot easily capture the…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
We present a theoretical model for the description of the adsorption kinetics of globular proteins onto charged core-shell microgel particles based on Dynamic Density Functional Theory (DDFT). This model builds on a previous description of…
For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
We propose a simple mathematical model to describe the mechanical relaxation of cells within a curved epithelial tissue layer represented by an arbitrary curve in two-dimensional space. This model generalises previous one-dimensional models…
Density functional theory (DFT) is a powerful theoretical tool widely used in such diverse fields as computational condensed matter physics, atomic physics, and quantum chemistry. DFT establishes that a system of $N$ interacting electrons…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…