Related papers: High-Throughput Computation of Anharmonic Low-Freq…
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
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…
Phonon anharmonicity is ubiquitous in real materials and is crucial for understanding thermal properties and phase stability. In this work, we show that anharmonic phonon modes can be obtained by maximizing their vibration stability during…
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…
We investigate anharmonically coupled high- and low-frequency excitations in a planar lattice of adsorbed molecules interacting with phonons of a crystal. Dephasing of high-frequency local vibrations by low-frequency resonance modes is…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…
While the vibrational thermodynamics of materials with small anharmonicity at low temperatures has been understood well based on the harmonic phonons approximation; at high temperatures, this understanding must accommodate how phonons…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
Accurate prediction of molecular vibrational frequencies is important to identify spectroscopic signatures and reaction thermodynamics. In this work, we develop a method to quantify uncertainty associated with density functional theory…
We compare the harmonic and anharmonic properties of the vibrational modes in 3-dimensional jammed packings of frictionless spheres interacting via repulsive, finite range potentials. A crossover frequency is apparent in the density of…
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…
Anharmonicities provide a wealth of information about the vibrational dynamics, mode coupling and energy transfer within a polyatomic system. In this contribution we show how driven molecular dynamics trajectories can be used to extract…
Understanding the vibrational and thermal properties of amorphous solids is one of the most discussed and long-standing issues in condensed matter physics. Recent works have made significant steps towards understanding harmonic vibrational…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
Vibrations of damaged bearings are manifested as modulations in the amplitude of the generated vibration signal, making envelope analysis an effective approach for discriminating between healthy and abnormal vibration patterns. Motivated by…
The thermoelectric properties of a molecular junction model, appropriate for large molecules such as fullerenes, are studied within a non-equilibrium adiabatic approach in the linear regime at room temperature. A self-consistent calculation…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…
Harnessing the power of low-dimensional materials in thermal applications calls for a solid understanding of the anomalous thermal properties of such systems. We analyze thermal conduction in one-dimensional systems by determining the…