Related papers: Exploring Conformational Landscapes Along Anharmon…
Accurate force fields are essential for reliable molecular simulations. These models are refined against quantum mechanical calculations and experimental measurements, which are subject to random and systematic errors. Bayesian Inference of…
Recent advances in ultrashort laser pulse techniques have opened up a wide variety of applications in both fundamental physics and industrial fields. In this work, $ab$ $initio$ molecular dynamics simulations based on time-dependent density…
We report a computational study of the anharmonicity of the vibrational modes of various individual fullerenes using the "moments method" [Y. Gao and M. Daw, Modelling Simul. Mater. Sci. Eng. 23 045002 (2015)] with a Tersoff-style potential…
This paper develops a harmonic-domain framework for systems with variable fundamental frequency. A variable-frequency sliding Fourier decomposition is introduced in the phase domain, together with necessary and sufficient conditions for…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
Biological macromolecules have complex and non-trivial energy landscapes, endowing them a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is…
In many real-world applications, functional data exhibit considerable variability in both amplitude and phase. This is especially true in biomechanical data such as the knee flexion angle dataset motivating our work, where timing…
In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy…
Autoresonance is a phenomenon of physical interest that may take place when a nonlinear oscillator is forced at a frequency that varies slowly. The stroboscopic averaging method (SAM), which provides an efficient numerical technique for the…
The stretching and bending vibrations of methane are studied in a local anharmonic model of molecular vibrations. The use of symmetry-adapted operators reduces the eigenvalue problem to block diagonal form. For the 44 observed energies we…
A comparative study of the properties of the anelastic and subseismic approximations is presented. The anelastic approximation is commonly used in astrophysics in compressible convection studies whereas the subseismic approximation comes…
Classical tools of nonlinear dynamics are used to study the highly excited vibrations of small molecules. For effective Hamiltonians with one polyad number (approximate constant of motion), previously developed methods locate new anharmonic…
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…
A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian…
A recent proposal for practical calculation of vibrational mode lifetimes is tested on simple, low-dimensional anharmonic models. The proposed scheme approximates the mode lifetime in terms of ensemble averages of specific functions in…
Nanoscale biosensors are devices designed to detect analytes by combining biological components and physicochemical detectors. One of the well known methods of constructing these sensors is by using nanocantilevers. These microscopic…
Many processes of scientific and technological interest are characterized by time scales that render their simulation impossible if one uses present day simulation capabilities. To overcome this challenge a variety of enhanced simulation…
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethora of enhanced sampling methods has been developed. One…
Many modern engineering structures exhibit nonlinear vibration. Characterizing such vibrations efficiently is critical to optimizing designs for reliability and performance. For linear systems, steady-state vibration occurs only at the…
For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate…