Related papers: Nonlinear Dynamic Force Spectroscopy
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
In many mechanical, electrical, and general physical systems evolving over time or space, spectral analysis methods as Fast Fourier Transform (FFT), Short Term Fourier Transform (STFT), Power Spectrum Density (PSD) plays a very important…
Dynamic Mode Decomposition (DMD) is a data-driven and model-free decomposition technique. It is suitable for revealing spatio-temporal features of both numerically and experimentally acquired data. Conceptually, DMD performs a…
Forced desorption of a semiflexible polymer chain on a solid substrate is theoretically investigated. The pulling force versus displacement is studied for different adsorption energy and persistence length P. It is found that the…
Directional area scattering factor (DASF) is a critical canopy structural parameter for vegetation monitoring. It provides an efficient tool for decoupling of canopy structure and leaf optics from canopy reflectance. Current standard…
Single-molecule force spectroscopy has proven to be a powerful tool for studying the kinetic behavior of biomolecules. Through application of an external force, conformational states with small or transient populations can be stabilized,…
In this paper, a dual estimation methodology is developed for both time-varying parameters and states of a nonlinear stochastic system based on the Particle Filtering (PF) scheme. Our developed methodology is based on a concurrent…
Substances such as chemical compounds are invisible to human eyes, they are usually captured by sensing equipments with their spectral fingerprints. Though spectra of pure chemicals can be identified by visual inspection, the spectra of…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
We propose a new method of calculating electronically excited states that combines a density functional theory (DFT) based ground state calculation with a linear response treatment that employs approximations used in the time-dependent…
Diffusing-Wave Spectroscopy (DWS) treats the transport of photons through turbid samples as a diffusion process, thereby making it possible to extract the dynamics of scatterers from measured correlation functions. The analysis of DWS data…
Polymer stretching in random smooth flows is investigated within the framework of the FENE dumbbell model. The advecting flow is Gaussian and short-correlated in time. The stationary probability density function of polymer extension is…
We present a theory for the elasticity of cross-linked stiff polymer networks. Stiff polymers, unlike their flexible counterparts, are highly anisotropic elastic objects. Similar to mechanical beams stiff polymers easily deform in bending,…
We describe experiments that probe the response to a point force of 2D granular systems under a variety of conditions. Using photoelastic particles to determine forces at the grain scale, we experimentally show that disorder, packing…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
Vibrational sum- and difference-frequency generation (SFG and DFG) spectroscopy probes the nonlinear response of interfaces at mid-infrared (MIR) wavelengths while detecting upconverted signals in the visible. Recent work has moved from…
We study the spin-crossover molecule Fe(phen)$_2$(NCS)$_2$ using density functional theory (DFT) plus dynamical mean-field theory, which allows access to observables not attainable with traditional quantum chemical or electronic structure…
A system of partial differential equations (PDEs) is derived to compute the full-field stress from an observed kinematic field when the flow rule governing the plastic deformation is unknown. These equations generalize previously proposed…
Density Functional Tight Binding (DFTB) is an attractive method for accelerated quantum simulations of condensed matter due to its enhanced computational efficiency over standard Density Functional Theory approaches. However, DFTB models…