Related papers: Exploring Conformational Landscapes Along Anharmon…
Spontaneous synchronisation is a collective phenomenon that can occur in both dynamical classical and quantum systems. Here, we analyse the spontaneous synchronisation dynamics of vibrations assisting energy transfer in a bio-inspired…
The numerical simulation of weakly nonlinear ultrasound is important in treatment planning for focused ultrasound (FUS) therapies. However, the large domain sizes and generation of higher harmonics at the focus make these problems extremely…
Hagedorn wavepacket dynamics yields exact single vibronic level (SVL) fluorescence spectra in global harmonic models. To partially describe the effects of anharmonicity, important in the spectra of real molecules, we describe a combination…
Modeling the evolution of high-dimensional systems from limited snapshot observations at irregular time points poses a significant challenge in quantitative biology and related fields. Traditional approaches often rely on dimensionality…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
Studying the jamming transition of granular and colloidal systems, has lead to a proliferation of theoretical and numerical results formulated in the language of the eigenspectrum of the dynamical matrix for these disordered system. Only…
Chirping Alfv\'{e}n modes are considered as potentially harmful in burning Tokamak plasmas. In this paper, the nonlinear evolution of a single-toroidal-number chirping mode is analysed by numerical particle simulation. This analysis can be…
Fluorescence microscopy is widely used for the study of biological specimens. Deconvolution can significantly improve the resolution and contrast of images produced using fluorescence microscopy; in particular, Bayesian-based methods have…
The entrainment between weakly-coupled nonlinear oscillators, as well as between complex signals such as those representing physiological activity, is frequently assessed in terms of whether a stable relationship is detectable between the…
FRET measurements can provide dynamic spatial information on length scales smaller than the diffraction limit of light. Several methods exist to measure FRET between fluorophores, including Fluorescence Lifetime Imaging Microscopy (FLIM),…
The time evolution of anharmonic molecular wave packets is investigated under the influence of the environment consisting of harmonic oscillators. These oscillators represent photon or phonon modes and assumed to be in thermal equilibrium.…
Employing both Bayesian statistics and the theory of nonlinear dynamics, we present a practically efficient method to extract a phase description of weakly coupled limit-cycle oscillators directly from time series observed in a rhythmic…
Cosmological experiments often employ Bayesian workflows to derive constraints on cosmological and astrophysical parameters from their data. It has been shown that these constraints can be combined across different probes such as Planck and…
The natural vibrational frequencies of biological particles such as viruses and bacteria encode critical information about their mechanical and biological states as they interact with their local environment and undergo structural…
Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a…
Fragmentation methods applied to multireference wave functions constitute a road towards the application of highly accurate ab initio wave function calculations to large molecules and solids. However, it is important for reproducibility and…
The problem of acquiring elastic properties of a composite material from the data of the vibrational testing is considered. The specimen is considered to abide by the linear elasticity laws and subject to viscoelastic damping. The BVP for…
The atomistic resolution recently achieved by ultrafast spectroscopies demands corresponding theoretical advances. Real-time time-dependent density-functional theory (RT-TDDFT) with Ehrenfest dynamics offers an optimal trade-off between…
The increasing penetration of renewable energy sources, characterised by low inertia and intermittent disturbances, presents substantial challenges to power system stability. As critical indicators of system stability, frequency dynamics…
In this paper, we propose a variable time-step linear relaxation scheme for time-fractional phase-field equations with a free energy density in general polynomial form. The $L1^{+}$-CN formula is used to discretize the fractional…