Beyond direct simulation Monte Carlo (DSMC) modelling of collision environments

Direct simulation Monte Carlo (DSMC) models have been successfully adopted and adapted to describe gas flows in a wide range of environments since the method was first introduced by Bird in the 1960s. We propose a new approach to modelling collisions between gas-phase particles in this work - operating in a similar way to the DSMC model, but with one key difference. Particles move in a mean field, generated by all previously propagated particles, which removes the requirement that all particles be propagated simultaneously. This yields a significant reduction in computation effort and lends itself to applications for which DSMC becomes intractable, such as when a species of interest is only a minor component of a large gas mixture

A circuit topology approach to categorizing changes in biomolecular structure

The biological world is composed of folded linear molecules of bewildering topological complexity and diversity. The topology of folded biomolecules such as proteins and ribonucleic acids is often subject to change during biological processes. Despite intense research, we lack a solid mathematical framework that summarizes these operations in a principled manner. Circuit topology, which formalizes the arrangements of intramolecular contacts, serves as a general mathematical framework to analyze the topological characteristics of folded linear molecules. In this work, we translate familiar molecular operations in biology, such as duplication, permutation, and elimination of contacts, into the language of circuit topology. We show that for such operations there are corresponding matrix representations as well as basic rules that serve as a foundation for understanding these operations within the context of a coherent algebraic framework. We present several biological examples and provide a simple computational framework for creating and analyzing the circuit diagrams of proteins and nucleic acids. We expect our study and future developments in this direction to facilitate a deeper understanding of natural molecular processes and to provide guidance to engineers for generating complex polymeric materials

Beyond direct simulation Monte Carlo (DSMC) modelling of collision environments

Direct simulation Monte Carlo (DSMC) models have been successfully adopted and adapted to describe gas flows in a wide range of environments since the method was first introduced by Bird in the 1960s. We propose a new approach to modelling collisions between gas-phase particles in this work – operating in a similar way to the DSMC model, but with one key difference. Particles move in a mean field, generated by all previously propagated particles, which removes the requirement that all particles be propagated simultaneously. This yields a significant reduction in computation effort and lends itself to applications for which DSMC becomes intractable, such as when a species of interest is only a minor component of a large gas mixture

A variable time step self-consistent mean field DSMC model for three-dimensional environments.

A self-consistent mean field direct simulation Monte Carlo (SCMFD) algorithm was recently proposed for simulating collision environments for a range of one-dimensional model systems. This work extends the one-dimensional SCMFD approach to three dimensions and introduces a variable time step (3D-vt-SCMFD), enabling the modeling of a considerably wider range of different collision environments. We demonstrate the performance of the augmented method by modeling a varied set of test systems: ideal gas mixtures, Poiseuille flow of argon, and expansion of gas into high vacuum. For the gas mixtures, the 3D-vt-SCMFD method reproduces the properties (mean free path, mean free time, collision frequency, and temperature) in excellent agreement with theoretical predictions. From the Poiseuille flow simulations, we extract flow profiles that agree with the solution to the Navier-Stokes equations in the high-density limit and resemble free molecular flow at low densities, as expected. The measured viscosity from 3D-vt-SCMF is ∼15% lower than the theoretical prediction from Chapman-Enskog theory. The expansion of gas into vacuum is examined in the effusive regime and at the hydrodynamic limit. In both cases, 3D-vt-SCMDF simulations produce gas beam density, velocity, and temperature profiles in excellent agreement with analytical models. In summary, our tests show that 3D-vt-SCMFD is robust and computationally efficient, while also illustrating the diversity of systems the SCMFD model can be successfully applied to

Simulation of inelastic collisions and rotational cooling of ammonia in a 4 K helium buffer gas cell

info:eu-repo/semantics/nonPublishe

Simulating rotationally inelastic collisions using a Direct Simulation Monte Carlo method

A new approach to simulating rotational cooling using a direct simulation Monte Carlo (DSMC) method is described and applied to the rotational cooling of ammonia seeded into a helium supersonic jet. The method makes use of ab initio rotational state changing cross sections calculated as a function of collision energy. Each particle in the DSMC simulations is labelled with a vector of rotational populations that evolves with time. Transfer of energy into translation is calculated from the mean energy transfer for this population at the specified collision energy. The simulations are compared with a continuum model for the on-axis density, temperature and velocity; rotational temperature as a function of distance from the nozzle is in accord with expectations from experimental measurements. The method could be applied to other types of gas mixture dynamics under non-uniform conditions, such as buffer gas cooling of NH$_3$ by He

Using a direct simulation Monte Carlo approach to model collisions in a buffer gas cell

A direct simulation Monte Carlo (DSMC) method is applied to model collisions between He buffer gas atoms and ammonia molecules within a buffer gas cell. State-tostate cross sections, calculated as a function of collision energy, enable the inelastic collisions between He and NH3 to be considered explicitly. The inclusion of rotationalstate-changing collisions affects the translational temperature of the beam, indicating that elastic and inelastic processes should not be considered in isolation. The properties of the cold molecular beam exiting the cell are examined as a function of the cell parameters and operating conditions; the rotational and translational energy distributions and are in accord with experimental measurements. The DSMC calculations show that thermalisation occurs well within the typical 10-20 mm length of many buffer gas cells, suggesting that shorter cells could be employed in many instances – yielding a higher flux of cold molecules