Related papers: Conservative adaptive-precision interatomic potent…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
A new method is proposed for integrating the equations of motion of an elastic filament. In the standard finite-difference and finite-element formulations the continuum equations of motion are discretized in space and time, but it is then…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
Many important physical systems can be described as the evolution of a Hamiltonian system, which has the important property of being conservative, that is, energy is conserved throughout the evolution. Physics Informed Neural Networks and…
A new approach for describing the effective electronic states of "atoms in compounds" to study the properties of molecules and condensed matter which are circumscribed by the operators heavily concentrated in atomic cores is proposed. Among…
In this paper we present a procedure to integrate, up to quadratures, the matching conditions of the energy shaping method. We do that in the context of underactuated Hamiltonian systems defined by simple Hamiltonian functions. For such…
We have investigated plasma-surface interactions with molecular dynamics (MD) simulations. It, however, is high cost computation and is limited to simulations for materials of nanometer order. In order to overcome the limitation, a…
Conformal prediction is an uncertainty quantification method that constructs a prediction set for a previously unseen datum, ensuring the true label is included with a predetermined coverage probability. Adaptive conformal prediction has…
Understanding protein conformational dynamics is essential for elucidating biological function but remains challenging due to the wide range of timescales and the complexity of collective motions. Enhanced sampling methods overcome…
A new and intuitive perturbative approach to time-dependent quantum mechanics problems is presented, which is useful in situations where the evolution of the Hamiltonian is slow. The state of a system which starts in an instantaneous…
While it is known that Hamiltonian systems may undergo a phenomenon of condensation akin to Bose-Einstein condensation, not all the manifestations of this phenomenon have been uncovered yet. In this work we present a novel form of…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
The traditional explicit electrostatic momentum-conserving Particle-in-cell algorithm requires strict resolution of the electron Debye length to deliver numerical accuracy. The explicit electrostatic energy-conserving Particle-in-Cell…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
Electric fields, applied to insulators, cause transitions between valence and conduction bands, giving rise to current. Adjustments of the Hamiltonian can perfect the quality of the insulator, shutting down transitions whilst fully…
The aim of hybrid methods in simulations is to communicate regions with disparate time and length scales. Here, a fluid described at the atomistic level within an inner region P is coupled to an outer region C described by continuum fluid…
Many optimally scaling quantum simulation algorithms employ controlled time evolution of the Hamiltonian, which is typically the major bottleneck for their efficient implementation. This work establishes a compression protocol for encoding…
In this work, we developed an interatomic potential for saturated hydrocarbons using the modified embedded-atom method (MEAM), a reactive semi-empirical many-body potential based on density functional theory and pair potentials. We…
Partial differential equations (PDEs) are central to computational electromagnetics (CEM) and photonic design, but classical solvers face high costs for large or complex structures. Quantum Hamiltonian simulation provides a framework to…