Related papers: Molecular hyperdynamics coupled with the nonorthog…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
Photo-induced processes are fundamental in nature, but accurate simulations are seriously limited by the cost of the underlying quantum chemical calculations, hampering their application for long time scales. Here we introduce a method…
The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…
A roughly constant temperature over a wide range of densities is maintained in molecular clouds through radiative heating and cooling. An isothermal equation of state is therefore frequently employed in molecular cloud simulations. However,…
Starting with the exact factorization of the molecular wavefunction, this paper presents the results from the numerical implementation in nonadiabatic molecular dynamics of the recently proposed bohmion method. Within the context of quantum…
Atomic scale simulations at finite temperature are an ideal approach to study the thermodynamic properties of magnetic transition metals. However, the development of interatomic potentials explicitly taking into account magnetic variables…
We present a method for total energy minimizations and molecular dynamics simulations based either on tight-binding or on Kohn-Sham hamiltonians. The method leads to an algorithm whose computational cost scales linearly with the system…
The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…
We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…
We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions. We start by introducing the formalism of the new…
Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
We present a detailed description of semi-quantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian…
Non-Hermitian quantum systems have recently attracted considerable attention due to their exotic properties. Though many experimental realizations of non-Hermitian systems have been reported, the non-Hermiticity usually resorts to the…
A transferable tight-binding potential has been constructed for heteroatomic systems containing carbon and hydrogen. The electronic degree of freedom is treated explicitly in this potential using a small set of transferable parameters which…
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…