Interactive physically-based structural modeling of hydrocarbon systems

Abstract

Hydrocarbon systems have been intensively studied via numerical methods, including electronic structure computations, molecular dynamics and Monte Carlo simulations. Typically, these methods require an initial structural model (atomic positions and types, topology, etc.) that may be produced using scripts and/or modeling tools. For many systems, however, these building methods may be ineffective, as the user may have to specify the positions of numerous atoms while maintaining structural plausibility.In this paper, we present an interactive physically-based modeling tool to construct structural models of hydrocarbon systems. As the user edits the geometry of the system, atomic positions are also influenced by the Brenner potential, a well-known bond-order reactive potential. In order to be able to interactively edit systems containing numerous atoms, we introduce a new adaptive simulation algorithm, as well as a novel algorithm to incrementally update the forces and the total potential energy based on the list of updated is decoupled from the number of atoms in the system. We show that our approach may be used to effectively build realistic models of hydrocarbon structures that would be difficult or impossible to produce using other tools.

Real-time feedback from iterative electronic structure calculations

“…We extended our real‐time quantum chemistry framework within the SAMSON molecular editor to reactivity studies based on iterative electronic structure methods. As SCF methods, we implemented the semiempirical Parametrized Method 6 (PM6) and self‐consistent DFTB variants .…”

Block‐adaptive quantum mechanics: An adaptive divide‐and‐conquer approach to interactive quantum chemistry

“…One possible adaptive approach to control the computational cost of each time step consists in reducing the number of nucleus degrees of freedom, to reduce the cost of updating the potential energy. [16, 32] In our ASED‐MO D&C method,[4] the matrices H i and S i involved in the eigenproblem (7) corresponding to subsystem ${\cal S}_i$ are constant when all atoms in the extended subsystem ${\cal S}_i^*$ are frozen in space.…”

“…To take advantage of this fact, we extend the approach that we previously introduced for adaptive Cartesian mechanics coordinates. [16] Precisely, we freeze and unfreeze groups of atoms, according to the applied atomic forces and the system's decomposition into overlapping subsystems. We call this first component block‐adaptive Cartesian mechanics.…”

Novel use of a disposable digital pressure transducer to increase the safety of pericardiocentesis

“…A force‐feedback device as in HQC is also utilized in the interactive molecular dynamics framework,9 which implements a classical treatment of the forces in molecular systems. Another example is the recently presented semi‐empirical interactive implementation for optimizing molecular structures of hydrocarbons during editing the structures 10, 11…”