Related papers: Ab initio Molecular Dynamics in Adaptive Coordinat…
Adaptive precision molecular dynamics simulations have developed along energy- and force-coupling approaches, which allow for a continuous transition between different particle descriptions or interaction potentials. Most approaches…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
Analytic first and second derivatives of the energy are developed for the fragment molecular orbital method interfaced with molecular mechanics in the electrostatic embedding scheme at the level of Hartree-Fock and density functional…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration…
Here, we propose a new modified quantum mechanics and its new algorithms of atomic fine-structure,asymmetric variational method based on hydrogen-like atom orbit. In addition, as we all know, the ab initio calculation of atomic…
We introduce an improved semiclassical dynamics approach to quantum vibrational spectroscopy. In this method, a harmonic-based phase space sampling is preliminarily driven toward non-harmonic quantization by slowly switching on the actual…
First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing…
In parallel with the evolution of femtosecond and attosecond laser as well as free-electron laser technology, a variety of theoretical methods have been developed to describe the behavior of atoms, molecules, clusters, and solids under the…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
We formulate a method for incorporating quantum fluctuations into molecular- dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous…
We measure molecular vibrations with femtometer precision using time-resolved x-ray absorption spectroscopy. For a demonstration, a Raman process excites the A$_{1g}$ mode in gas-phase SF$_6$ molecules with an amplitude of $\approx50$ fm,…
We propose and computationally study a method for simultaneously orienting the angular momentum of asymmetric top molecules along: 1) a laboratory-fixed direction; 2) the molecular intermediate moment of inertia axis; 3) the laser field…
We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest…
Quantum computing has the potential to reduce the computational cost required for quantum dynamics simulations. However, existing quantum algorithms for coupled electron-nuclear dynamics simulation either require fault-tolerant devices, or…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
We study the contributions of off-resonant transitions to the dynamics of a system of N multilevel atoms sharing one excitation and interacting with the quantized vector electromagnetic field. The Rotating Wave Approximation significantly…