Related papers: Modelling ion channels with a view towards identif…
Most epidemic processes on networks can be modelled by a compartmental model, that specifies the spread of a disease in a population. The corresponding compartmental graph describes how the viral state of the nodes (individuals) changes…
We consider the problem of simultaneous estimation of a sequence of dependent parameters that are generated from a hidden Markov model. Based on observing a noise contaminated vector of observations from such a sequence model, we consider…
Characterization of non-Markovian open quantum dynamics is both of theoretical and practical relevance. In a seminal work [Phys. Rev. Lett. 120, 040405 (2018)], a necessary and sufficient quantum Markov condition is proposed, with a clear…
To be fully useful for public health practice, models for epidemic response must be able to do more than predict -- it is also important to incorporate the mechanisms underlying transmission dynamics to enable policymakers and practitioners…
We consider the filtering of continuous-time finite-state hidden Markov models, where the rate and observation matrices depend on unknown time-dependent parameters, for which no prior or stochastic model is available. We quantify and…
The main subject of the thesis is the study of stationary nonequilibrium states trough the use of microscopic stochastic models that encode the physical interaction in the rules of Markovian dynamics for particles configurations. These…
The purpose of this paper is to set out the problems of modeling quantum communication and signal processing where the communication between systems via a non-Markovian channel. This is a general feature of quantum transmission lines. Our…
Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental observables of complex molecules from large amounts of…
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…
Autoregressive generative models -- including Transformers, recurrent neural networks, classical Kalman filters, state space models, and Mamba -- all generate sequences by sampling each output from a deterministic summary of the past,…
We investigate what a snapshot of a quantum evolution - a quantum channel reflecting open system dynamics - reveals about the underlying continuous time evolution. Remarkably, from such a snapshot, and without imposing additional…
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…
A universal definition of non-Markovianity for open systems dynamics is proposed. It is extended from the classical definition to the quantum realm by showing that a `transition' from the Markov to the non-Markov regime occurs when the…
Continuous-time Markov chains are used to model stochastic systems where transitions can occur at irregular times, e.g., birth-death processes, chemical reaction networks, population dynamics, and gene regulatory networks. We develop a…
The deterministic dynamics of randomly connected neural networks are studied, where a state of binary neurons evolves according to a discreet-time synchronous update rule. We give a theoretical support that the overlap of systems' states…
We prove that under certain mild assumptions, the entropy rate of a hidden Markov chain, observed when passing a finite-state stationary Markov chain through a discrete-time continuous-output channel, is jointly analytic as a function of…
A sequence of controlled collisions between a quantum system and its environment (composed of a set of quantum objects) naturally simulates (with arbitrary precision) any Markovian quantum dynamics of the system under consideration. In this…
We study multiple ionization in proton collisions with water, methane, and ammonia molecules using an independent-atom model. Previous work on total (net) capture and ionization cross sections is extended to treat the multiple ionization…
A quantized physical framework, called the five-anchor model, is developed for a general understanding of the working mechanism of ion channels. According to the hypotheses of this model, the following two basic physical principles are…
Exposure to air pollution is associated with increased morbidity and mortality. Recent technological advancements permit the collection of time-resolved personal exposure data. Such data are often incomplete with missing observations and…