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DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Single-molecule fluorescence spectroscopy is a powerful method that avoids ensemble averaging, but its temporal resolution is limited by the fluorescence lifetime to nanoseconds at most. At the ensemble level, two-dimensional spectroscopy…
We introduce the Frustrated Distance Matrix (FDM) model, a dynamic extension of the static distance-matrix ensemble on S^2 analyzed by Bogomolny, Bohigas, and Schmit (BBS). Its entries are pairwise geodesic distances between N Brownian…
There is much interest in the Hierarchical Dirichlet Process Hidden Markov Model (HDP-HMM) as a natural Bayesian nonparametric extension of the ubiquitous Hidden Markov Model for learning from sequential and time-series data. However, in…
Statistical clustering in dynamic networks aims to identify groups of nodes with similar or distinct internal connectivity patterns as the network evolves over time. While early research primarily focused on static Stochastic Block Models…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
The hidden Markov model (HMM) provides a powerful framework for inference in time-varying environments, where the underlying state evolves according to a Markov chain. To address the optimal filtering problem in general dynamic settings, we…
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…
A multi-relaxation-time discrete Boltzmann model (DBM) with split collision is proposed for both subsonic and supersonic compressible reacting flows, where chemical reactions take place among various components. The physical model is based…
Harmonic instability occurs frequently in the power electronic converter system. This paper leverages multi-resolution dynamic mode decomposition (MR-DMD) as a data-driven diagnostic tool for the system stability of power electronic…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model…
Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
In medicine, comorbidities refer to the presence of multiple, co-occurring diseases. Due to their co-occurring nature, the course of one comorbidity is often highly dependent on the course of the other disease and, hence, treatments can…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly. Current grading systems based on imaging biomarkers only coarsely group disease stages into broad categories and are unable to predict future disease…
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…
Oscillatory combustion in aero engines and modern gas turbines often has significant adverse effects on their operation, and accurately recognizing various oscillation modes is the prerequisite for understanding and controlling combustion…
Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…