Related papers: Modeling compartmentalization within intracellular…
Fluid flow through layered materials with different wetting behavior is observed in a wide range of applications in biological, environmental and technical systems. Therefore, it is necessary to understand the occuring transport mechanisms…
A simulation methodology for predicting the time-course of enzymatic digestions is described. The model is based solely on the enzyme's subsite architecture and concomitant binding energies. This allows subsite binding energies to be used…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
The prominent collective character of long-range interacting quantum systems makes them promising candidates for quantum technological applications. Yet, lack of additivity overthrows the traditional picture for entanglement scaling and…
Generation of molecules with desired chemical and biological properties such as high drug-likeness, high binding affinity to target proteins, is critical for drug discovery. In this paper, we propose a probabilistic generative model to…
In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles,…
Finite Element Modeling (FEM) has been widely used to model the electric field distribution, to study the interaction between stimulation electrodes and neural tissue. However, due to the insufficient computational capability to represent…
The particle-in-cell numerical method of plasma physics balances a trade-off between computational cost and intrinsic noise. Inference on data produced by these simulations generally consists of binning the data to recover the particle…
Sampling the phase space of molecular systems -- and, more generally, of complex systems effectively modeled by stochastic differential equations -- is a crucial modeling step in many fields, from protein folding to materials discovery.…
We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…
The Ribosome Flow Model (RFM) describes the unidirectional movement of interacting particles along a one-dimensional chain of sites. As a site becomes fuller, the effective entry rate into this site decreases. The RFM has been used to model…
Cell migration is a fundamental process underlying the survival and function of both unicellular and multicellular organisms. Crawling motility in eukaryotic cells arises from cyclic protrusion and retraction driven by the cytoskeleton,…
Resonant Energy Transfer (RET) from an optically excited donor molecule (D) to a non-excited acceptor molecule (A) residing nearby is widely used to detect molecular interactions in living cells. Stoichiometric information, such as the…
Understanding sub-cellular protein localisation is an essential component to analyse context specific protein function. Recent advances in quantitative mass-spectrometry (MS) have led to high resolution mapping of thousands of proteins to…
The brain is composed of billions of neurons with virtually endless morphologies and ion channel compositions, resulting in unique extracellular waveforms. Nevertheless, almost all neuronal morphologies can be reduced to a simple…
We present the standard electromagnetic Particle-in-Cell method, starting from the discrete approximation of derivatives on a uniform grid. The application to second-order, centered, finite-difference discretization of the equations of…