Related papers: Markov models of coarsening in two-dimensional foa…
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a non-equilibrium steady state. We apply this method to study the globule-stretch transition of a single…
We conduct experiments on a class of two-dimensional semiwet foams generated through compressing a three-dimensional soap foam between two glass plates. To induce a spatially uniform rupturing process on foam boundaries, an additional plate…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
We propose generalizations of a number of standard network models, including the classic random graph, the configuration model, and the stochastic block model, to the case of time-varying networks. We assume that the presence and absence of…
In this work, we present a general method to establish properties of multi-dimensional continuous-time Markov chains representing stochastic reaction networks. This method consists of grouping states together (via a partition of the state…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
We introduce a model with diffusive and evaporation/condensation processes, depending on 3 parameters obeying some inequalities. The model can be solved in the sense that all correlation functions can be computed exactly without the use of…
A mean-field theory is developed for the scale-invariant length distributions observed during the coarsening of one-dimensional faceted surfaces. This theory closely follows the Lifshitz-Slyozov-Wagner theory of Ostwald ripening in…
We propose an extension of the Contextual Graph Markov Model, a deep and probabilistic machine learning model for graphs, to model the distribution of edge features. Our approach is architectural, as we introduce an additional Bayesian…
In a recent series of papers [1--3], a statistical model that accounts for correlations between topological and geometrical properties of a two-dimensional shuffled foam has been proposed and compared with experimental and numerical data.…
Image acquisition techniques such as micro-computed tomography are nowadays widely available. Quantitative analysis of the resulting 3D image data enables geometric characterization of the micro-structure of materials. Stochastic geometry…
In the early days of gene expression data, researchers have focused on gene-level analysis, and particularly on finding differentially expressed genes. This usually involved making a simplifying assumption that genes are independent, which…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
Formation of a molecular network from multifunctional precursors is modelled with a random graph process. The random graph model favours reactivity for monomers that are positioned close in the network topology, and disfavours reactivity…
This study presents a novel algorithm based on machine learning (ML) for the precise segmentation and measurement of detonation cells from soot foil images, addressing the limitations of manual and primitive edge detection methods prevalent…
For dry foams, the transport of gas from small high-pressure bubbles to large low-pressure bubbles is dominated by diffusion across the thin soap films separating neighboring bubbles. For wetter foams, the film areas become smaller as the…
We utilize total-internal reflection to isolate the two-dimensional `surface foam' formed at the planar boundary of a three-dimensional sample. The resulting images of surface Plateau borders are consistent with Plateau's laws for a truly…
A Markov state model of the dynamics of a protein-like chain immersed in an implicit hard sphere solvent is derived from first principles for a system of monomers that interact via discontinuous potentials designed to account for local…
We develop numerical methods to simulate the fluid-mechanical erosion of many bodies in two-dimensional Stokes flow. The broad aim is to simulate the erosion of a porous medium (e.g. groundwater flow) with grain-scale resolution. Our fluid…
Molecular simulations provide a powerful means to unravel the complex relationships between network architecture and the mechanical response of polymer networks, with a particular emphasis on rupture and fracture phenomena. Although…