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Documents published in Scipedia

• Mechanistic studies on the self-assembly of PLGA patchy particles and their potential applications in biomedical imaging

  C. Salvador-Morales, B. Brahmbhatt, V. Márquez-Miranda, I. Araya-Dura, J. Canan, F. González-Nilo, C. Vilos, J. Cebral, F. Mut, R. Lohner, B. Leong, G. Sundaresan, J. Zweit

  Langmuir (2016). Vol. 32 (31), pp. 7929-7949

  
  

  Abstract

  Currently, several challenges prevent poly(lactic-co-glycolic acid) (PLGA) particles from reaching clinical settings. Among these is a lack of understanding of the molecular mechanisms involved in the formation of these particles. We have been studying in depth the formation of patchy polymeric particles. These particles are made of PLGA and lipid–polymer functional groups. They have unique patch–core–shell structural features: hollow or solid hydrophobic cores and a patchy surface. Previously, we identified the shear stress as the most important parameter in a patchy particle’s formation. Here, we investigated in detail the role of shear stress in the patchy particle’s internal and external structure using an integrative experimental and computational approach. By cross-sectioning the multipatch particles, we found lipid-based structures embedded in the entire PLGA matrix, which represents a unique finding in the PLGA field. By developing novel computational fluid dynamics and molecular dynamics simulations, we found that the shear stress determines the internal structure of the patchy particles. Equally important, we discovered that these particles emit a photoacoustic (PA) signal in the optical clinical imaging window. Our results show that particles with multiple patches emit a higher PA signal than single-patch particles. This phenomenon most likely is due to the fact that multipatchy particles absorb more heat than single-patchy particles as shown by differential scanning calorimetry analysis. Furthermore, we demonstrated the use of patchy polymeric particles as photoacoustic molecular probes both in vitro and in vivo studies. The fundamental studies described here will help us to design more effective PLGA carriers for a number of medical applications as well as to accelerate their medical translation.

  Abstract
  Currently, several challenges prevent poly(lactic-co-glycolic acid) (PLGA) particles from reaching clinical settings. Among these is a lack of understanding of the [...]

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• Running large‐scale CFD applications on Intel‐KNL–based clusters

  A. Tiwari, A. Cauble-Chantrenne, A. Jundt, J. Peraza, R. Lohner, J. Baum, L. Carrington

  Int. J. Numer. Meth. Fluids (2018). Vol. 86 (11), pp. 699-716

  
  

  Abstract

  Intel's latest Xeon Phi processor, Knights Landing (KNL), has the potential to provide over 2.6 TFLOPS. However, to obtain maximum performance on the KNL, significant refactoring and optimization of application codes are still required to exploit key architectural innovations that KNL features—wide vector units, many‐core node design, and deep memory hierarchy. The experience and insights gained in porting and running FEFLO (a typical edge‐based finite element code for the solution of compressible and incompressible flows) on the KNL platform are described in this paper. In particular, optimizations used to extract on‐node parallelism via vectorization and multithreading and improve internode communication are considered. These optimizations resulted in a 2.3× performance gain on a 16 node runs of FEFLO, with the potential for larger performance gains as the code is scaled beyond 16 nodes. The impact of the different configurations of KNL's on‐package MCDRAM (Multi‐Channel DRAM) memory on FEFLO's performance is also explored. Finally, the performance of the optimized versions of FEFLO for KNL and Haswell (Intel Xeon) is compared.    

  Abstract
  Intel's latest Xeon Phi processor, Knights Landing (KNL), has the potential to provide over 2.6 TFLOPS. However, to obtain maximum performance [...]

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• Load balancing for chemically reacting flows

  R. Lohner, F. Fogashi, J. Baum

  Int. J. Numer. Meth. Heat and Fluid Flows (2017). Vol. 27 (12), pp. 2768-2774

  
  

  Abstract

  Purpose A common observation made when computing chemically reacting flows is how CPU intensive these are in comparison to cold flow cases. The update of tens or hundreds of species with hundreds or thousands of reactions can easily consume more then 95\% of the total CPU time. In many cases the region where reactions (combustion) are actually taking place comprises only a very small percentage of the volume. Typical examples are flame fronts propagating through a domain. In such cases only a small fraction of points/cells needs a full chemistry update. This leads to extreme load imbalances on parallel machines. Design/methodology/approach Points that require a full chemistry update are identified, gathered, and distributed across the network so that work is evenly distributed. Once the chemistry has been updated, the unknowns are gathered back. Findings The procedure has been found to work extremely well, leading to optimal load balance with insignificant communication overheads. Research limitations/implications In many production runs, the procedure leads to a reduction in CPU requirements of more than an order of magnitude. This allows much larger and longer runs, improving accuracy and statistics. Practical implications The procedure has allowed the calculation of chemically reacting flow cases that were hitherto not possible. Originality/value As far as we know, this type of load balancing has not been published before.

  Abstract
  Purpose A common observation made when computing chemically reacting flows is how CPU intensive these are in comparison to cold flow cases. The update of tens or hundreds [...]

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• Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research

  A. Erdemir, P. Hunter, G. Holzapfel, L. Loew, J. Middleton, C. Jacobs, P. Nithiarasu, R. Lohner, G. Wei, B. Winkelstein, V. Barocas, F. Guilak, J. Ku, J. Hicks, S. Delp, M. Sacks, J. Weiss, G. Ateshian, S. Mass, A. McCulloch, G. Peng

  Journal of Biomechanics Engineering (2018). Vol. 140 (2), pp. 1-11

  
  

  Abstract

  The role of computational modeling for biomechanics will be increasingly prominent. In computational biomechanics, model sharing can facilitate assessment of reproducibility, and can provide an opportunity for repurposing and reuse, and a venue for medical training. The community's desire to investigate biological and biomechanical phenomena crossing multiple systems, scales, and physical domains, also motivates sharing of modeling resources as blending of models developed by domain experts is anticipated. The goal of this article is to understand current perspectives in the biomechanics community for the sharing of computational models and related resources. Opinions on opportunities, challenges, and pathways to model sharing, particularly as part of the scholarly publishing workflow, were sought. A synthesis of these opinion pieces indicates that the community recognizes the necessity and usefulness of model sharing. There is a strong will to facilitate model sharing and there are corresponding initiatives by the scientific journals. Outside the publishing enterprise, infrastructure to facilitate model sharing in biomechanics exists and simulation software developers are interested in accommodating the community's needs for sharing of modeling resources. Encouragement for the use of standardized markups, concerns related to quality assurance, acknowledgement of increased burden, and importance of stewardship of resources are noted. In the short-term, it is advisable that the community builds upon recent strategies and experiments with new pathways for continued demonstration of model sharing, its promotion, and its utility. Nonetheless, the need for a long term strategy to unify approaches in sharing computational models and related resources is acknowledged.

  Abstract
  The role of computational modeling for biomechanics will be increasingly prominent. In computational biomechanics, model sharing can facilitate assessment of reproducibility, [...]

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• Fundamental Diagrams for Specific Very High Density Crowds

  R. Lohner, B. Muhamad, P. Dambalmath, E. Haug

  Collective Dynamics (2017). Vol. 2 (A13), pp.1-15

  
  

  Abstract

  An experimental campaign was undertaken to measure the pedestrian flow in the region close to the Kaaba during the Hajj pilgrimages of 2014 and 2015. High resolution video and photographs were used. The space was divided into areas of 10 sqm. The pedestrians were counted, and the velocity measured from video clips. The results were surprising: the velocity in the very high density region increases, which implies also an increase of the flux. The flux in this region (with more than 8 p/sqm) reaches values that exceed 3.5 p/m/sec, much higher than previously recorded under more `standard conditions' in corridors and passages.

  Abstract
  An experimental campaign was undertaken to measure the pedestrian flow in the region close to the Kaaba during the Hajj pilgrimages of 2014 and 2015. High resolution video [...]

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• Practical applicability of optimizations and performance models to complex stencil-based loop kernels in CFD

  K. Wichmann, M. Kronbichler, R. Lohner, W. Wall

  International Journal of High Performance Computing Applications (2018). Vol. 33 (4), pp. 602-618

  
  

  Abstract

  This work investigates the application and interaction of optimization techniques and performance models in a computational fluid dynamics (CFD) approach employing an OpenMP parallelized, explicit, weakly compressible, finite difference–based solver for the incompressible Navier–Stokes equations using a five-point wide stencil. The presented loop and stencil optimizations lead to a 6.8× increase in per core throughput. In order to verify optimal CPU utilization, performance models are applied to the tuned code. Three different performance models are considered: a roofline-based model, utilizing purely theoretical figures, one which is enhanced by measurements, and the execution cache memory model. It is shown that the models provide reliable estimates for simple benchmarks, such as seven-point stencils for scalar Laplacians, but the estimate quality is significantly worse for the complex and tuned stencil. While it is possible to include even more details in the model, it eventually leads to a state in which it purely reproduces the benchmarks from which it was derived. Thus, the applied general-purpose performance models are found to inaccurately predict the actual performance. They overestimate the achievable performance by more than about 97% for highly tuned code. Through further code tuning, 66% of the predicted performance could be achieved.

  Abstract
  This work investigates the application and interaction of optimization techniques and performance models in a computational fluid dynamics (CFD) approach employing an OpenMP [...]

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• Post processing-based interpolation schemes for nested Cartesian finite difference grids of different size

  A. Figueroa, R. Lohner

  Int. J. Numer. Meth. Fluids (2018). Vol. 89 (6), pp. 196-215

  
  

  Abstract

  Nested Cartesian grid systems by design require interpolation of solution fields from coarser to finer grid systems. While several choices are available, preserving accuracy, stability, and efficiency at the same time require careful design of the interpolation schemes. Given this context, a series of interpolation algorithms based on postprocessing halo information on nested Cartesian finite difference grids of different size were developed and tested. The results obtained indicate that most of these do not yield the expected improvement, and some even tend to make the solver unstable. However, some third‐ and fourth‐order interpolation functions do yield considerable accuracy improvement, are stable, and are worth implementing.

  Abstract
  Nested Cartesian grid systems by design require interpolation of solution fields from coarser to finer grid systems. While several choices are available, preserving accuracy, [...]

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• Using ensemble Kalman filter to determine parameters for computational crowd dynamics simulations

  F. Togashi, T. Misaka, R. Lohner, S. Obayashi

  Engineering Computations (2018). Vol. 35 (7), pp. 2612-2628

  
  

  Abstract

  It is of paramount importance to ensure safe and fast evacuation routes in cities in case of natural disasters, environmental accidents or acts of terrorism. The same applies to large-scale events such as concerts, sport events and religious pilgrimages as airports and to traffic hubs such as airports and train stations. The prediction of pedestrian is notoriously difficult because it varies depending on circumstances (age group, cultural characteristics, etc.). In this study, the Ensemble Kalman Filter (EnKF) data assimilation technique, which uses the updated observation data to improve the accuracy of the simulation, was applied to improve the accuracy of numerical simulations of pedestrian flow.

  Abstract
  It is of paramount importance to ensure safe and fast evacuation routes in cities in case of natural disasters, environmental accidents or acts of terrorism. The same applies [...]

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• Detailed simulation of viral propagation in the built environment (preprint)

  R. Lohner, H. Antil, S. Idelsohn, E. Oñate

  Computational Mechanics (2020). 10.1007/s00466-020-01881-7

  
  

  Abstract

  A summary is given of the mechanical characteristics of virus contaminants and the transmission via droplets and aerosols. The ordinary and partial differential equations describing the physics of these processes with high fidelity are presented, as well as appropriate numerical schemes to solve them. Several examples taken from recent evaluations of the built environment are shown, as well as the optimal placement of sensors.

  Abstract
  A summary is given of the mechanical characteristics of virus contaminants and the transmission via droplets and aerosols. The ordinary and partial differential equations [...]

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• An Investigation of Stationary and Moving Cased Charge Detonations in Stone Lined Pipes

  J. Baum, O. Soto, F. Togashi, R. Lohner, M. Giltrud, J. Bell

  (2019). 31st International Symposium on Shock Waves 1. ISSW 2017. Springer, Cham

  
  

  Abstract

  This paper describes the application of a coupled CFD and CSD methodology to the simulation of a thick-cased explosive-filled cylinder placed inside a pipe composed of either steel or various strength stones. The objective is to better understand the energy exchange mechanisms between the impacting case debris produced by either stationary or moving charges on the surrounding pipe material and its affect on the energy propagation in the pipe.  

  Abstract
  This paper describes the application of a coupled CFD and CSD methodology to the simulation of a thick-cased explosive-filled cylinder placed inside a pipe composed of either [...]

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