Related papers: Excluded volume effects in on- and off-lattice rea…
Brownian diffusion of rod-like polymers in the presence of randomly distributed spherical obstacles is studied using molecular dynamics (MD) simulations. It is observed that dependence of the reduced diffusion coefficient of these…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
The modelling of human crowd behaviors offers many challenging questions to science in general. Specifically, the social human behavior consists of many physiological and psychological processes which are still largely unknown. To model…
The Vicsek model (Vicsek et al. 1995) is a very popular minimalist model to study active matter with a number of applications to biological systems at different length scales. With its off-lattice implementation and periodic boundary…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion…
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to…
The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes…
Diffusion-limited reactions (DLR) are usually described within the Smoluchowski theory, which neglects interactions between the diffusing components. We propose a first extension of such frame- work that incorporates excluded-volume…
Generative modeling within constrained sets is essential for scientific and engineering applications involving physical, geometric, or safety requirements (e.g., molecular generation, robotics). We present a unified framework for…
The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate…
By discretising space into compartments and letting system dynamics be governed by the reaction-diffusion master equation, it is possible to derive and simulate a stochastic model of reaction and diffusion on an arbitrary domain. However,…
The formation of clusters in nuclear matter is investigated, which occurs e.g. in low energy heavy ion collisions or core-collapse supernovae. In astrophysical applications, the excluded volume concept is commonly used for the description…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In…
Recently proposed generative models for discrete data, such as Masked Diffusion Models (MDMs), exploit conditional independence approximations to reduce the computational cost of popular Auto-Regressive Models (ARMs), at the price of some…
The excluded volume effects of randomly branched polymers are investigated. To approach this problem we assume the Gaussian distribution of segments around the center of gravity. Once this approximation is introduced, we can make use of the…
Microfluidics provides a powerful and versatile technology to accurately control spatial and temporal conditions for cell culturing and can therefore be used to study cellular responses to gradients. Here we use Lattice Boltzmann methods…
Recent advancements in diffusion models have notably improved the perceptual quality of generated images in text-to-image synthesis tasks. However, diffusion models often struggle to produce images that accurately reflect the intended…