Related papers: Pathway Histogram Analysis of Trajectories: A gene…
Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman…
Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differences) depend on the relative populations of different…
Experiments, in particular on biological systems, typically probe lower-dimensional observables which are projections of high-dimensional dynamics. In order to infer consistent models capturing the relevant dynamics of the system, it is…
Numerical simulations of plasma flows are crucial for advancing our understanding of microscopic processes that drive the global plasma dynamics in fusion devices, space, and astrophysical systems. Identifying and classifying particle…
Stochastic models of diffusion are routinely used to study dispersal of populations, including populations of animals, plants, seeds and cells. Advances in imaging and field measurement technologies mean that data are often collected across…
The recent availability of routine medical data, especially in a university-clinical context, may enable the discovery of typical healthcare pathways, i.e., typical temporal sequences of clinical interventions or hospital readmissions.…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
Drivers' heterogeneity and the broad range of vehicle characteristics on public roads are primarily responsible for the stochasticity observed in road traffic dynamics. Understanding the behavioural differences in drivers (human or…
The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…
Pathway idea is a switching mechanism by which one can go from one functional form to another, and to yet another. It is shown that through a parameter $\alpha$, called the pathway parameter, one can connect generalized type-1 beta family…
Understanding the dynamics of an environment, such as the movement of humans and vehicles, is crucial for agents to achieve long-term autonomy in urban environments. This requires the development of methods to capture the multi-modal and…
Trajectory prediction in a cluttered environment is key to many important robotics tasks such as autonomous navigation. However, there are an infinite number of possible trajectories to consider. To simplify the space of trajectories under…
After collecting data from observations or experiments, the next step is to build an appropriate mathematical or stochastic model to describe the data so that further studies can be done with the help of the models. In this article, the…
Single-particle tracking (SPT) has become a popular tool to study the intracellular transport of molecules in living cells. Inferring the character of their dynamics is important, because it determines the organization and functions of the…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
A quantum trajectory describes the evolution of a quantum system undergoing indirect measurement. In the discrete-time setting, the state of the system is updated by applying Kraus operators according to the measurement results. From an…
We present a general mathematical framework for trajectory stratification for simulating rare events. Trajectory stratification involves decomposing trajectories of the underlying process into fragments limited to restricted regions of…
Continuous-time random walks (CTRWs) on discrete state spaces, ranging from regular lattices to complex networks, are ubiquitous across physics, chemistry, and biology. Models with coarse-grained states, for example those employed in…
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. Our study investigated both the biophysics of conformational transitions as well as the possibility of increasing…
Understanding the mechanisms underlying crystal formation is crucial. For most systems, crystallization typically goes through a nucleation process that involves dynamics that happen at short time and length scales. Due to this, molecular…