Related papers: Solvent-aware Interfaces in Continuum Solvation
In the given paper the algorithm describing original and universal principles of a triangulation of a smooth molecular surface: solvent excluding solvent (SES), received by primary and secondary rolling, and solvent accessible surface (SAS)…
Estimating the effects of continuous-valued interventions from observational data is a critically important task for climate science, healthcare, and economics. Recent work focuses on designing neural network architectures and…
Quantum computing with discrete variable (DV, qubit) hardware is approaching the large scales necessary for computations beyond the reach of classical computers. However, important use cases such as quantum simulations of physical models…
Multi-solid systems are foundational to a wide range of real-world applications, yet modeling their complex interactions remains challenging. Existing deep learning methods predominantly rely on implicit modeling, where the factors…
We show how the dispersive regime of the Jaynes-Cummings model may serve as a valuable tool to the study of open quantum systems. We employ it in a bottom-up approach to build an environment that preserves qubit energy and induces varied…
This article presents a multi-physics methodology for the numerical simulation of physical systems that involve the non-linear interaction of multi-phase reactive fluids and elastoplastic solids, inducing high strain-rates and high…
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…
Molecular dynamics simulations are indispensable for exploring the behavior of atoms and molecules. Grounded in quantum mechanical principles, quantum molecular dynamics provides high predictive power but its computational cost is dominated…
We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…
Simplifying composite open quantum systems through model reduction is central to enable their analytical and numerical understanding. In this work, we introduce a self-consistent approach to eliminate the cavity degrees of freedom of cavity…
Multiphysics incompressible fluid dynamics simulations play a crucial role in understanding intricate behaviors of many complex engineering systems that involve interactions between solids, fluids, and various phases like liquid and gas.…
In this work, we present a computational formulation based on continuum mechanics to study the interaction of fluid membranes embedded with semiflexible filaments. This is motivated by systems in membrane biology, such as cytoskeletal…
Employing a classical density-functional description of liquid environments, we introduce a rigorous method for the diffusion quantum Monte Carlo calculation of free energies and thermodynamic averages of solvated systems that requires…
The primary objective of research in modern sensor technologies is to develop innovative detection methods for the rapid analysis of complex molecular systems. The present work demonstrates that the quantum mechanism of selective detection,…
The shrinking core model describes the reaction of a spherical solid particle with a surrounding fluid. In this work, we revisit the SCM by deriving it from the underlying physical processes and performing a careful non-dimensionalisation,…
Further advancement of quantum computing (QC) is contingent on enabling many-body models that avoid deep circuits and excessive use of CNOT gates. To this end, we develop a QC approach employing finite-order connected moment expansions…
In quantum/classical (QM/CM) partitioning methods for multi-scale modeling, one is often forced to introduce uncontrolled phenomenological effects of the environment (CM) in the quantum (QM) domain as ab initio quantum calculations are…
The rapid development of quantum computers has enabled demonstrations of quantum advantages on various tasks. However, real quantum systems are always dissipative due to their inevitable interaction with the environment, and the resulting…
We discuss in detail a recently proposed hybrid particle-continuum scheme for complex fluids and evaluate it at the example of a confined homopolymer solution in slit geometry. The hybrid scheme treats polymer chains near the impenetrable…
Simulation of the interaction of light with matter, including at the few-photon level, is important for understanding the optical and optoelectronic properties of materials, and for modeling next-generation non-linear spectroscopies that…