Related papers: Expanding the Temporal Analysis in Single-Molecule…
Many studies of biomedical time series signals aim to measure the association between frequency-domain properties of time series and clinical and behavioral covariates. However, the time-varying dynamics of these associations are largely…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Single-molecule experimental techniques track the real-time dynamics of molecules by recording a small number of experimental observables. Following these observables provides a coarse-grained, low-dimensional representation of the…
Parameterizing mathematical models of biological systems often requires fitting to stable periodic data. In cardiac electrophysiology this typically requires converging to a stable action potential through long simulations. We explore this…
For over 30 years, mode-coupling theory (MCT) has been the de facto theoretic description of dense fluids and the liquid-glass transition. MCT, however, is limited by its ad hoc construction and lacks a mechanism to institute corrections.…
The long-time behavior of the velocity autocorrelation function (VACF) is investigated by the molecular dynamics simulation of a two-dimensional system which has both a many-body interaction and a random potential. With strengthening the…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis…
From flocks of birds to biomolecular assemblies, systems in which many individual components independently consume energy to perform mechanical work exhibit a wide array of striking behaviors. Methods to quantify the dynamics of these so…
We present a general and flexible framework for detecting regime changes in complex, non-stationary data across multi-trial experiments. Traditional change point detection methods focus on identifying abrupt changes within a single time…
We investigate the lifetimes of complexes formed in ultracold molecule collisions. Employing both transition-state-theory and an optical model approach we examine processes that can extend the lifetime of complexes beyond that predicted by…
Much of interesting complex biological behaviour arises from collective properties. Important information about collective behaviour lies in the time and space structure of fluctuations around average properties, and two-point correlation…
We present here a general iterative formula which gives a (formal) series expansion for the time autocorrelation of smooth dynamical variables, for all Hamiltonian systems endowed with an invariant measure. We add some criteria, theoretical…
We study a system of diffusing point particles in which any triplet of particles reacts and is removed from the system when the relative proximity of the constituent particles satisfies a predefined condition. Proximity-based reaction…
We develop a broadly-applicable computational method for the automatic exploration of the bimolecular multi-reaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Many biological and medical questions can be modeled using time-to-event data in finite-state Markov chains, with the phase-type distribution describing intervals between events. We solve the inverse problem: given a phase-type…
New advances in nano sciences open the door for scientists to study biological processes on a microscopic molecule-by-molecule basis. Recent single-molecule biophysical experiments on enzyme systems, in particular, reveal that enzyme…
Self-consistent N-body simulations are efficient tools to study galactic dynamics. However, using them to study individual trajectories (or ensembles) in detail can be challenging. Such orbital studies are important to shed light on global…
We propose a simple method to estimate the parameters of a continuously measured quantum system, by fitting correlation functions of the measured signal. We demonstrate the approach in simulation, both on toy examples and on a recent…