Speed and accuracy tradeoffs in molecular electrostatic computation

textIn this study, we consider electrostatics contributed from the molecules in the ionic solution. It plays a significant role in determining the binding affinity of molecules and drugs. We develop the overall framework of computing electrostatic properties for three-dimensional molecular structures, including potential, energy, and forces. These properties are derived from Poisson-Boltzmann equation, a partial differential equation that describes the electrostatic behavior of molecules in ionic solutions. In order to compute these properties, we derived new boundary integral equations and designed a boundary element algorithm based on the linear time fast multipole method for solving the linearized Poisson-Boltzmann equation. Meanwhile, a higher-order parametric formulation called algebraic spline model is used for accurate approximation of the unknown solution of the linearized Poisson-Boltzmann equation. Based on algebraic spline model, we represent the normal derivative of electrostatic potential by surrounding electrostatic potential. This representation guarantees the consistent relation between electrostatic potential and its normal derivative. In addition, accurate numerical solution and fast computation for electrostatic energy and forces are also discussed. In addition, we described our hierarchical modeling and parameter optimization of molecular structures. Based on this technique, we can control the scalability of molecular models for electrostatic computation. The numerical test and experimental results show that the proposed techniques offer an efficient and accurate solution for solving the electrostatic problem of molecules.Computer Science

LAURA Users Manual: 5.6

This users manual provides in-depth information concerning installation and execution of Laura, version 5. Laura is a structured, multiblock, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 Laura code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent recompilations, providing more intuitive distribution of functionality, and simplifying inter- faces required for multi-physics coupling. As a result, Laura now shares gas-physics modules, MPI modules, and other low-level modules with the Fun3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flow field radiation

Shape dynamics, lipid hydrodynamics, and the complex viscoelasticity of bilayer membranes

Biological membranes are continuously brought out of equilibrium, as they shape organelles, package and transport cargo, or respond to external actions. Even the dynamics of plain lipid membranes in experimental model systems are very complex due to the tight interplay between the bilayer architecture, the shape dynamics, and the rearrangement of the lipid molecules. We formulate and numerically implement a continuum model of the shape dynamics and lipid hydrodynamics, which describes the bilayer by its midsurface and by a lipid density field for each monolayer. The viscoelastic response of bilayers is determined by the stretching and curvature elasticity, and by the inter-monolayer friction and the membrane interfacial shear viscosity. While the bilayer equilibria are well understood theoretically, dynamical calculations have relied on simplified continuum approaches of uncertain transferability, or on molecular simulations reaching very limited length and time scales. Our approach incorporates the main physics, is fully nonlinear, does not assume predefined shapes, and can access a wide range of time and length scales. We validate it with the well understood tether extension. We investigate the tubular lipid transport between cells, the dynamics of bud absorption by a planar membrane, and the fate of a localized lipid density asymmetry in vesicles. These axisymmetric examples bear biological relevance and highlight the diversity of dynamical regimes that bilayers can experience

Critical issues for predicting worker exposure to gaseous contaminants in a wind tunnel

In this study, three dimensional computational fluid dynamics (CFD) simulations are used to investigate the distribution and level of contaminant concentrations in the breathing zone of a worker when airborne contaminants are released within an arm\u27s-length in front of the worker who has his back to the airflow. The main goals were to numerically evaluate the effect of different factors on the worker exposure and to recommend a turbulence model preferable for this type of simulation. These factors include the body shape, the heat flux from the body, the ventilation intensity, the free stream turbulence, and the unsteadiness. The comparison between the numerical results and the experimental data has shown good agreement.;An extensive case study with FLUENT concluded with the following observations: (1) The heat flux from the body significantly affects the flow field and the subsequent contaminant concentration field at low Reynolds numbers; (2) The free stream turbulence plays an important role in the variation of exposure measurements at low Reynolds numbers; (3) Results calculated with the Large Eddy Simulation (LES) illustrate the turbulence structure in the wake of the manikin and indicate that the flow unsteadiness plays an important role in the variation of exposure measurements; (4) Calculations with various body shapes suggests that oversimplified body shapes may lead to inaccurate predictions in worker exposure assessment; (5) The concentrations measured at the lapel could be very different than the concentrations measured near the mouth.;To further improve the predictability of turbulence models for the present study, a non-linear (cubic) low-Re turbulence model has been selected, modified and implemented in the DREAM code which was developed at West Virginia University. Benchmark tests on turbulent channel flow, backward facing step flow and flow around a square cylinder have shown that this model is remarkably superior to linear eddy-viscosity models, and the results are even comparable to others\u27 predictions with LES, which is much more computationally expensive. So it could be a good alternative as a reliable and accurate turbulence model in simulating turbulent flow past a bluff body

The finite element method in low speed aerodynamics

The finite element procedure is shown to be of significant impact in design of the 'computational wind tunnel' for low speed aerodynamics. The uniformity of the mathematical differential equation description, for viscous and/or inviscid, multi-dimensional subsonic flows about practical aerodynamic system configurations, is utilized to establish the general form of the finite element algorithm. Numerical results for inviscid flow analysis, as well as viscous boundary layer, parabolic, and full Navier Stokes flow descriptions verify the capabilities and overall versatility of the fundamental algorithm for aerodynamics. The proven mathematical basis, coupled with the distinct user-orientation features of the computer program embodiment, indicate near-term evolution of a highly useful analytical design tool to support computational configuration studies in low speed aerodynamics

Investigating the Dynamics and Fragmentation of Nitroaromatic Radical Cations Through Femtosecond Time-Resolved Mass Spectrometry and Computational Chemistry

Chemists have sought to control molecular dissociation with lasers for decades. Effective control of unimolecular dissociation was only achieved with the development of high-intensity ultrashort pulsed lasers and coherent control techniques that operate on timescales faster than vibrational energy redistribution. In view of this, our lab has specialized in the study of polyatomic radical cations using femtosecond time-resolved mass spectrometry (FTRMS). The interest in radical cations stems from the fact that they are highly reactive species that contribute to many physical, chemical, and biological processes. For instance, radical cations participate in shock initiation of detonated energetic materials used as explosives and propellants. In this regard, we have studied some nitroaromatic radical cations commonly used as models for energetic materials. We discuss some results involving the dynamics of vibrational wave packets and rearrangement/fragmentation pathways. Concerning vibrational wave packet dynamics, we employed computational chemistry to predict the most efficient probe wavelength for our experimental measurements on nitrobenzene cation demonstrating the feasibility and convenience of this approach. We also investigated pump-probe control schemes to manipulate fragmentation product yields in p-nitrotoluene (PNT) cation. Finally, we investigated the dissociation dynamics and fragmentation pathways of o-nitroaniline, a model compound for the military explosive 2,4,6-triamino-1,3,5-trinitrobenzene (TATB). This model seems to capture the hydrogen bonding features that lead to energetically unfavorable rearrangement/fragmentation pathways in TATB. We expect that our experimental and computational results provide insights into the inherent stability of this molecule that explains the low sensitivity (and therefore relatively high safety) of TATB as an explosive

SOLID-SHELL FINITE ELEMENT MODELS FOR EXPLICIT SIMULATIONS OF CRACK PROPAGATION IN THIN STRUCTURES

Crack propagation in thin shell structures due to cutting is conveniently simulated using explicit finite element approaches, in view of the high nonlinearity of the problem. Solidshell elements are usually preferred for the discretization in the presence of complex material behavior and degradation phenomena such as delamination, since they allow for a correct representation of the thickness geometry. However, in solid-shell elements the small thickness leads to a very high maximum eigenfrequency, which imply very small stable time-steps. A new selective mass scaling technique is proposed to increase the time-step size without affecting accuracy. New ”directional” cohesive interface elements are used in conjunction with selective mass scaling to account for the interaction with a sharp blade in cutting processes of thin ductile shells