Related papers: Interactions between Large Molecules: Puzzle for R…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
Quantitative prediction of thermodynamic properties in solution is essential for translating atomistic simulations into reliable chemical insight. As an exemplar system, the behaviour of CaCO$_3$ in water has been widely studied to…
In this work we investigate the ground state and the dissipative quantum dynamics of interacting charged particles in an external potential at finite temperature. The recently devised time-dependent quantum Monte Carlo (TDQMC) method allows…
We present a new method to couple the Direct Simulation Monte Carlo (DSMC) algorithm with molecular dynamics (MD). The coupling approach generalizes prior coupling methods using a cell-based decision. The approach is supported by a lifting…
This study evaluates the uncertainty in nanodosimetric calculations caused by variations in interaction cross sections within Monte Carlo Track Structure (MCTS) simulation codes. Nanodosimetry relies on accurately simulating particle…
Correlations between electrons and the effective dimensionality are crucial factors that shape the properties of an interacting electron system. For example, the onsite Coulomb repulsion, U, may inhibit, or completely block the intersite…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to…
A general polarizable embedded (PE) quantum mechanics/molecular mechanics scheme for periodic systems is presented, describing mutual polarization of the two subsystems. The QM system, described with density functional theory (DFT), is…
We study beryllium dihydride (BeH$_2$) and acetylene (C$_2$H$_2$) molecules using real-space diffusion Monte Carlo (DMC) method. The molecules serve as perhaps the simplest prototypes that illustrate the difficulties with biases in the…
We report a scalable Fortran implementation of the phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) and demonstrate its excellent performance and beneficial scaling with respect to system size. Furthermore, we investigate…
Atomic nuclei are composite systems, and they may be dynamically excited during nuclear reactions. Such excitations are not only relevant to inelastic scattering but they also affect other reaction processes such as elastic scattering and…
The density matrix quantum Monte Carlo (DMQMC) set of methods stochastically samples the exact $N$-body density matrix for interacting electrons at finite temperature. We introduce a simple modification to the interaction picture DMQMC…
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…
Many approaches to three-dimensional constrained macromolecular chains at thermal equilibrium, at about room temperatures, are based upon constrained Classical Hamiltonian Dynamics (cCHDa). Quantum-mechanical approaches (QMa) have also been…
Ambiguity in the contact between laboratory instruments and equations of quantum mechanics is formulated in terms of responses of the instruments to commands transmitted to them by a Classical digital Process-control Computer (CPC); in this…
Multipole moments are the first order responses of the energy to spatial derivatives of the electric field strength. The quality of density functional theory (DFT) prediction of molecular multipole moments thus characterizes errors in…
Diffusive molecular communication (DMC) is one of the most promising approaches for realizing nano-scale communications in biological environments for healthcare applications. In this paper, a DMC system in biological cylindrical…
In this paper, we address the symbol synchronization issue in molecular communication via diffusion (MCvD). Symbol synchronization among chemical sensors and nanomachines is one of the critical challenges to manage complex tasks in the…