Related papers: A Rational Approach to Ring Flexibility in Interna…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
The size of rings (also called cyclic polymers) in bidisperse blends of chemically identical rings is analyzed by computer simulations. Data of entangled ring blends and blends of interpenetrating rings are compared and it is shown that the…
By means of computer simulations and solution of the equations of the Mode Coupling Theory (MCT), we investigate the role of the intramolecular barriers on several dynamic aspects of non-entangled polymers. The investigated dynamic range…
Among the current challenges in Space Weather, one of the main ones is to forecast the internal magnetic configuration within Interplanetary Coronal Mass Ejections (ICMEs). Currently, a monotonic and coherent magnetic configuration observed…
Transport of rodlike particles in confinement environments of macromolecular networks plays crucial roles in many important biological processes and technological applications. The relevant understanding has been limited to thin rods with…
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
Convergence with respect to imaginary-time discretization is an essential part of any path-integral-based calculation. However, an unfortunate property of existing non-preconditioned numerical integration schemes for path-integral molecular…
In the isochronous mass spectrometry (IMS) performed at storage rings, masses of short-lived nuclides are determined through precision measurements of their mean revolution times. However, the distribution of revolution times could be…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
Two-dimensional Raman and hybrid terahertz/Raman spectroscopic techniques provide invaluable insight into molecular structure and dynamics of condensed-phase systems. However, corroborating experimental results with theory is difficult due…
We have earlier reported the MOLSDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the MOLS method, developed in our laboratory. In this paper we report iMOLSDOCK, the 'flexible receptor' extension we have…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying…
Developing new methods for the accurate and efficient calculations of real-time quantum correlation functions is deemed one of the most challenging problems of modern condensed matter theory. Many popular methods, such as centroid molecular…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
Mean-Field Ring Polymer Molecular Dynamics (MF-RPMD) is a powerful, efficient, and accurate method for approximate quantum dynamic simulations of multi-level system dynamics. Initial efforts to compute nonadiabatic reaction rates using…