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This article considers the generative modeling of the (mixed) states of quantum systems, and an approach based on denoising diffusion model is proposed. The key contribution is an algorithmic innovation that respects the physical nature of…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
It has been recently shown that a state generated by a one-dimensional noisy quantum computer is well approximated by a matrix product operator with a finite bond dimension independent of the number of qubits. We show that full quantum…
Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
We review recent progress made in quantum information processing (QIP) which can be applied in the simulation of quantum systems and chemical phenomena. The review is focused on quantum algorithms which are useful for quantum simulation of…
In this article, we use the theory of quantum channels and open quantum systems to provide an efficient unitary characterization of a class of stochastic generators known as quantum hidden Markov models (QHMMs). By utilizing the unitary…
Stochastic chemical reaction networks (CRNs) are complex systems which combine the features of concurrent transformation of multiple variables in each elementary reaction event, and nonlinear relations between states and their rates of…
Biomolecular processes are typically modeled using chemical reaction networks coupled to infinitely large chemical reservoirs. A difference in chemical potential between these reservoirs can drive the system into a non-equilibrium steady…
Matthew Fisher recently postulated a mechanism by which quantum phenomena could influence cognition: Phosphorus nuclear spins may resist decoherence for long times, especially when in Posner molecules. The spins would serve as biological…
Generative quantum machine learning has gained significant attention for its ability to produce quantum states with desired distributions. Among various quantum generative models, quantum denoising diffusion probabilistic models (QuDDPMs)…
This paper presents Timed Quorum System (TQS), a new quorum system especially suited for large-scale and dynamic systems. TQS requires that two quorums intersect with high probability if they are used in the same small period of time. It…
Quorum sensing is the mechanism by which bacteria communicate and synchronize group behaviors. Quantitative information on parameters such as the copy number of particular quorum-sensing proteins should contribute strongly to understanding…
Many important phenomena in biochemistry and biology exploit dynamical features such as multi-stability, oscillations, and chaos. Construction of novel chemical systems with such rich dynamics is a challenging problem central to the fields…
We present SMILES-embeddings derived from the internal encoder state of a Transformer [1] model trained to canonize SMILES as a Seq2Seq problem. Using a CharNN [2] architecture upon the embeddings results in higher quality interpretable…
Quantitative susceptibility mapping (QSM) is an MRI phase-based post-processing method that quantifies tissue magnetic susceptibility distributions. However, QSM acquisitions are relatively slow, even with parallel imaging. Incoherent…
Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible…
Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via "quorum sensing". Elucidating the mechanisms that control autoinducer production is,…
Markov state models (MSMs) are a widely used method for approximating the eigenspectrum of the molecular dynamics propagator, yielding insight into the long-timescale statistical kinetics and slow dynamical modes of biomolecular systems.…
Clustering of molecules on biological membranes is a widely observed phenomenon. In some cases, such as the clustering of Ras proteins on the membranes of mammalian cells, proper cell signaling is critically dependent on the maintenance of…