Related papers: Fast method for quantum mechanical molecular dynam…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…
Constrained molecular dynamics(CoMD) model, previously introduced for nuclear dynamics, has been extended to the atomic structure and collision calculations. Quantum effects corresponding to the Pauli and Heisenberg principle are enforced…
Standard molecular dynamics (MD) and Monte Carlo (MC) simulation deals with spherical particles. Extending these standard simulation methodologies to the non-spherical cases is non-trivial. To circumvent this problem, non-spherical bodies…
Quantum particle simulations have largely been based on time-independent, split-operator schemes in which kinetic and potential operators are interwoven to provide accurate approximations to system dynamics. These simulations can be very…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
Simulating spontaneous structural rearrangements in macromolecules with classical Molecular Dynamics (MD) is an outstanding challenge. Conventional supercomputers can access time intervals up to tens of $\mu$s, while many key events occur…
A cardinal obstacle to performing quantum-mechanical simulations of strongly-correlated matter is that, with the theoretical tools presently available, sufficiently-accurate computations are often too expensive to be ever feasible. Here we…
Quantum transport and other phenomena are typically modeled by coupling the system of interest to an environment, or bath, held at thermal equilibrium. Realistic bath models are at least as challenging to construct as models for the quantum…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
How well can quantum computers simulate classical dynamical systems? There is increasing effort in developing quantum algorithms to efficiently simulate dynamics beyond Hamiltonian simulation, but so far exact resource estimates are not…
By exploiting the complexity intrinsic to quantum dynamics, quantum technologies promise a whole host of computational advantages. One such advantage lies in the field of stochastic modelling, where it has been shown that quantum stochastic…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…
We developed a general theoretical approach and a user-ready computer code that permit to study the dynamics of collisional energy transfer and ro-vibrational energy exchange in complex molecule-molecule collisions. The method is a mixture…
Two types of approaches to modeling molecular systems have demonstrated high practical efficiency. Density functional theory (DFT), the most widely used quantum chemical method, is a physical approach predicting energies and electron…
We present an efficient method to mix well converged ab initio forces with simpler and faster ones in molecular dynamics. While the cheap forces are evaluated every time step, the converged ones correct the trajectory only every n time…