Related papers: Adaptive Resolution Molecular Dynamics Technique: …
This work continues the parametric investigation on the sampling nuances of the Dynamic Mode Decomposition (DMD) under the Koopman analysis. Through turbulent wakes, the investigation corroborated the generality of the universal convergence…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
In this study some properties of the methanol-water mixture such as diffusivity, density, viscosity, and hydrogen bonding were calculated at different temperatures and atmospheric pressure using molecular dynamics simulations (MDS). The…
We propose a time-adaptive predictor/multi-corrector method to solve hyperbolic partial differential equations, based on the generalized-$\alpha$ scheme that provides user-control on the numerical dissipation and second-order accuracy in…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
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…
In conventional glassformers at sufficiently short times and low enough temperatures, molecules are mutually caged by the intermolecular potential. The fluctuation and dissipation from motion of caged molecules when observed by elastic…
We consider the thermodynamic consistency of the charge response function in the (extended) Hubbard model. In DMFT, thermodynamic consistency is preserved. We prove that the static, homogeneous DMFT susceptibility is consistent as long as…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
Dynamic mode decomposition (DMD) has become a powerful data-driven method for analyzing the spatiotemporal dynamics of complex, high-dimensional systems. However, conventional DMD methods are limited to matrix-based formulations, which…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
Demand response (DR) programs aim to engage distributed demand-side resources in providing ancillary services for electric power systems. Previously, aggregated thermostatically controlled loads (TCLs) have been demonstrated as a…
Value functions arise as a component of algorithms as well as performance metrics in statistics and engineering applications. Computation of the associated Bellman equations is numerically challenging in all but a few special cases. A…
The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular…
We study the role of active coupling on the transport properties of homogeneously charged macromolecules in an infinitely dilute solution. An enzyme becomes actively bound to a segment of the macromolecule, exerting an electrostatic force…
Quantum-mechanical methods are widely used for understanding molecular interactions throughout biology, chemistry, and materials science. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple…
A new solver featuring time-space adaptation and error control has been recently introduced to tackle the numerical solution of stiff reaction-diffusion systems. Based on operator splitting, finite volume adaptive multiresolution and high…
Molecular Dynamics method is based on solution of Newtonian differential equations of motion. A new very accurate and efficient time-reversible explicit integrator was derived on the basis of second order Tailor expansion of force. There is…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…