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20/06/2019

Sim4Life Major Release V5.0

Sim4Life Major Release V5.0

With Sim4Life V5.0, we are introducing to our customers a new and very powerful feature: our new suite of low-frequency electromagnetic solvers! These new solvers are finite element method (FEM) based, high-performance-computing (HPC) enabled, and operate on unstructured meshes, powering a substantial increase in speed and accuracy in multi-scale applications where devices with small structural details are integrated in a larger, human-sized environment. Compared to other platforms available on the market, the new FEM solvers provide a number of important benefits, including unique semi-insulating layers, anisotropic tensorial inhomogeneous electrical conductivity distributions (e.g., image-based), new boundary conditions, as well as specialized visualization and analysis tools. In addition, a large number of meshing tools has been developed to support the new solvers, including a tetrahedral volume mesher based on the powerful Visual Kinematics (VKI) engine. The meshing tools are ideally suited to handle relevant features of computer-aided-design (CAD) based structures, e.g., of medical implants or other complex geometries.

Special emphasis has been placed on boosting graphical user interface (GUI) performance, in particular for handling huge amounts of modeling/simulation entities. In V5.0, simulations with thousands of neurons can be performed more than one order of magnitude faster compared to previous versions, making the simulation of complex neurostimulation applications an everyday task in Sim4Life.

Researchers in computational life sciences thus benefit from a one-of-a-kind integrated modeling package that allows creation of image-based models, optimal simulation of the electromagnetic exposure of nerves, support for the anisotropic nature of neural tissues, and the combination of the first neuro-functionalized Virtual Population (ViP) model Yoon-sun V4.0 – all within the same platform.

In response to user requests, Sim4Life V5.0 also features various improvements that boost modeling productivity and further push the boundaries of real-world simulation complexity. Highlights include new features for our 5G Toolkit (beamforming, cumulative distribution function (CDF), far-field figures of merit), increased usability of the GUI/Simulation Trees (secondary view, list, grouping, filtering), HPC/GPU extensions, various data analysis/post-processing enhancements, and new functionalized Korean ViP V3.1 and V4.0 models for more complex and detailed simulations.  

Encompassing many additional features, improvements and bug fixes, the new release makes your everyday even more fun and more effective. Feedback, as always, is greatly welcome!

Unstructured LF FEM Solvers

NOVEL SUITE OF UNSTRUCTURED FEM SOLVERS

  • Sim4Life V5.0 includes a wide range of validated HPC-enabled FEM solvers - designed to complement the established Sim4Life solver suite.
  • The new solvers support message passing interface (MPI) parallelization based on a combination of the widely applied PETSc library for numerical matrix operations, powerful preconditioners (e.g., algebraic-multigrid method from HYPRE) and in-house developments. They support unstructured, mixed elements (tetrahedral, prismatic, shell, etc.).
  • The new solvers add a wide range of specific benefits inherent to simulations that support unstructured meshes (e.g., support for localized refinement, or conformal adaptivity) or that are particular to the specific solver that was implemented (ohmic-current-dominated electrostatic, electroquasistatic, magnetostatic, magnetoquasistatic, thermal).
  • All new solvers come with a dedicated Python API that allows power-users to further automatize processes or perform advanced analyses. Furthermore, the post-processor has been extended to support handling and visualization of unstructured result fields and inhomogeneous and/or anisotropic material property distributions.

NEW EXTENSIVE MESHING SUITE

  • To support the novel unstructured FEM solvers in Sim4Life V5.0, a large number of meshing tools has been developed, including a new tetrahedral volume mesher based on the powerful VKI engine, capable of providing meshes from highly complex geometries and CAD structures (e.g., of medical implants).
  • The Sim4Life V5.0 volume mesher is complemented with import tools for users who intend to use third-party meshes (e.g., VTK vtu, EXODUS, NASTRAN). In addition, a 2D mesher allows the creation of surface meshes of complex structures, such as nerve cross-sections.
  • In V5.0, advanced mesh processing tools capable of dealing with very complex meshes, such as from CAD-derived solids or from anatomical models, are readily available. These include (i) a local remeshing tool (locally adapts surface or volume meshes to improve mesh quality); (ii) a mesh refinement tool (refines the overall mesh or a sub-volume); (iii) a mesh extrusion tool (extrudes 2D meshes along a trajectory into prismatic/hexahedral based elongated structures); (iv) a thin layer insertion tool (inserts thin layers at interfaces between meshed regions).
  • Meshes can be visualized in a newly created mesh viewer, which also offers functionalities for quantification of mesh quality by means of a wide range of metrics and rapid visualization of low-quality element locations requiring further processing.

Unstructured meshing and FEM simulation in Sim4Life V5.0: Modeling the neuroelectric response of complex nerves (e.g., the Vagus Nerve) to electrostimulation by electroceuticals has never been so easy, precise and realistic. 2.5D extruded neurostimulation models can be created by extruding nerve cross section images, populated with arbitrary number of myelinated and unmyelinated fibers. The new solvers permit to model the anisotropy of nerve tissues and the thin membranes surrounding the fascicles (perineurium), e.g., to test the nerve responses to neurostimulation from different electrodes, pulse waveforms, and to optimize stimulation parameters.

Neuronal Dynamics Simulation

NEURO SIMULATION ENHANCEMENTS & PERFORMANCE BOOSTS

  • The specialized functionality of some of Sim4Life V5.0’s new solvers has been aligned with the safety assessment and therapy needs of the neuromodulation community. This includes support for semi-insulating thin layers and inhomogeneous, anisotropic electrical conductivity distributions.
  • Dedicated tools to allow image-based assignment of inhomogeneous conductivity tensors (e.g., based on diffusion-tensor imaging data) have also been implemented.
  • A C-fiber model based on the work of Sundt (Sundt et. al., JNP, 2015) is now available.
  • In V5.0, support for exposure and neuromodulation simulations involving the highly detailed and neuro-functionalized Yoon-sun V4.0 model has been improved. Sensory- and motor-neuron nerve fiber models are automatically assigned to the different trajectories, and nerve tissue padding can be added.
  • The new release includes the possibility to link T-NEURO simulations to post-processing analysis results and allows neurostimulation investigations based on arbitrary field distributions as electromagnetic sources.
  • In Sim4Life V5.0, the performance of simulation workflows involving a large number of neurons has been drastically improved, which is particularly important for simulation of whole-body peripheral nervous system exposure, or nerve models with a large statistical collection of neurons.
  • Speedup of more than one order of magnitude has been achieved for a complex scenario (whole-body Yoon-sun V4.0, peripheral nerve stimulation in MRI, thousands of fibers discretized at 16 µm).

Extended ViP & Neuro-Functionalization

NEURO-FUNCTIONALIZED ANATOMICAL MODELS

  • Sim4Life V5.0 users are provided with two new human anatomical ViP models: the Korean female Yoon-sun V4.0 (26 y, 1.52 m, 55 kg, released December 2018), and the Korean male Jeduk V3.1 (33 y, 1.62 m, 64.5 kg, released April 2019). Jeduk V3.1 has the same tissues identified as other V3.x ViP models.
  • Both Yoon-sun and Jeduk are posable and have tissue material parameters pre-assigned from the IT’IS tissues properties database. Yoon-sun V4.0 is the first next-generation ViP model to be functionalized for more complex and detailed simulations. Nerves, muscles, veins, and arteries have been separated into individual functional tissues. Nerve trajectories have been generated with properties pre-assigned for T-NEURO investigations.

Introducing the new Korean male ViP model Jeduk cV3.1: Watch the movie here.

Unrivaled 5G Simulation Toolbox: Important New Features

BEAMFORMING & CDF

  • Owing to the versatility of both the Parameterization Engine and the data analysis pipeline, Sim4Life V5.0 can now be used to quantitatively determine how a device might operate under different operating conditions.
  • The existing parameterized Sweep function allows the new Aggregate algorithm to gather figures of merit of phased-array antennas (e.g., gain or polarization) across a user-defined range of configurations. This ensures evaluation of the maximum gain that can be achieved in any spatial direction when sweeping through the entire codebook of available phase/amplitude configurations.
  • In V5.0, a CDF algorithm has been added for any dataset expressed in spherical coordinates, such as far-field quantities, which can be used, for example, to evaluate the coverage capability of an antenna array.

FAR-FIELD FIGURES OF MERIT

  • Of particular importance for antenna design engineers, the Radiation Evaluator for antenna simulations in V5.0 now computes two additional figures of merit: the front/back ratio and the side lobe level.

UI Enhancements & Performance Boosts

SIGNIFICANT GUI PERFORMANCE IMPROVEMENTS & RESPONSIVENESS

  • Huge efforts have been made to refactor parts of the UI code in V5.0 to drastically increase performance of the model and simulation trees when handling hundreds of thousands of entities (solids, objects).
  • UI responsiveness could thus be reduced from several minutes to a fraction of a second for tree buildup and handling (scrolling, multi-selection, etc.), ribbon and context population, and tab switching (independent of the number of selected items).
  • V5.0 now also provides a new ultrafast, asynchronous search and filter algorithm for trees.

INTUITIVE SECONDARY TREE VIEW IN EXPLORER TREE 

  • To further increase usability, the simulation outline view in Sim4Life V5.0 has been enhanced and now offers a brand-new secondary tree view in the explorer tree.
  • The secondary tree view allows the user to intuitively build, monitor, and manage complex simulation trees with lots of components, thanks to a clever way of splitting the view based on a dedicated grouping and visualization of objects that share the same settings.

HPC & Post-Processing/Analysis

ENHANCED GPU COMPUTING

  • In combination with the latest AXE GPU, HPC library, Sim4Life V5.0 provides support for the NVIDIA Turing generation GPU architecture (enabling GPUs like the GeForce RTX 2080), resulting in a significant performance boost over previous architectures.

MAXIMUM INTENSITY PROJECTION 

  • Sim4Life V5.0 now includes a Maximum Intensity Projection viewer, which allows visualization at a glance of a 3D field distribution projected onto a 2D plane. The method is essential, e.g., for analysis of field distributions and to track local hotspots in terms of specific absorption rate (SAR), temperature, etc.
  • Generic interpolation and conversion to cell and point data (commonly used in analysis workflows) is faster by a factor of at least 50.

AVAILABILITY OF PYTHON 3 IN FUTURE RELEASES

  • The end of life (EOL) date for Python 2.7, which is currently included in Sim4Life, has been announced for 2020. In addition, there is a growing demand from our users for implementation of the latest Python 3 framework. To accommodate this need, we are happy to announce that Python 3 will be made available in Sim4Life by the end of 2019. We are working tirelessly on different updating strategies to make sure that our users will experience a smooth transition to the higher Python version.

A more comprehensive list of improvements, fixes, and new features is included in the Release Notes.

To experience the power and elegance of Sim4Life V5.0 or for further information, please contact us by email at s4l-sales@zmt.swiss or by phone at +41 44 245 9765.

The relevant Sim4Life installers for Win7/Win8/8.1/Win10 64-bit platforms can be downloaded here. Existing customers with an up-to-date annual maintenance and support plan, will receive individually all pertinent information regarding the software installer download and updated licenses.

At ZMT we are committed to supporting our customers with the most innovative software solutions, testing equipment, and service.

The Sim4Life Team

Advanced neurostimulation investigations in Sim4Life V5.0: creation of personalized nerve structures featuring arbitrary distributions of electrophysiological models of myelinated and unmyelinated axons, within Yoon-sun V4.0. Nerve models can be derived from histological cross section images that can be meshed to generate 3D unstructured meshes. Anisotropic tissue conductivities can be assigned e.g. to the endoneurium, and the perineurium can be modeled as a thin virtual insulating layer.

 

MRI safety investigations in V5.0: Peripheral Nerve Stimulation (PNS) by MRI gradients switching using 950 individual nerve trajectories within the posable Yoon-sun V4.0 neuro-functionalized anatomical body model. Prediction of thresholds and sites for PNS (arbitrary body position and posture) applying EM-neuronal simulations using electrophysiological sensory and motor fibers, custom gradient coil hardware models and gradient waveforms. Gradient coil optimization to reduce the risk of PNS is also possible in combination with the Gradient Coil Builder.

 

Unstructured LF

Tetrahedral mesh for unstructured FEM simulation of a wireless power transfer (WPT) transmit coil in Sim4Life V5.0: Local refinement under constrained quality bounds was used to enforce high resolution of the conformal mesh near the wire while maintaining good conditioning of all elements. A corresponding movie performed in Sim4Life's sub-package, SEMCAD X Matterhorn V18.0 is available here.

 

Unstructured LF Analysis

Analysis/post-processing in Sim4Life V5.0: Low-frequency magnetic field generated by a transmit/receive WPT coil system in use for charging an electric vehicle. The unstructured FEM solvers also compute the electric field induced inside a person who is crouching beside the front wheel. The visualization shows the SAR at the surface of the skin.

 

Jeduk V3.1

Korean male ViP model Jeduk V3.1: Illustration of detailed muscles, internal organs, the peripheral nervous system, and circulatory system trees (from left to right). The model includes the same tissues as all adult male ViP V3.x models.

 

Posed Jeduk

Posing in Sim4Life V5.0: Use of the biomechanical FEM Poser Tool in Jeduk V3.1 to account for different real-life postures. In line with Korean female ViP model Yoon-sun V3.1, the neck joints between skull and C1, and between C1 and C2, have been made posable, including forward/backwards flexion and extension, lateral bending, and rotation.

 

5G Toolkit

Extended 5G Toolkit in Sim4Life V5.0: Radiation pattern and electric near-field of a steerable 5G customer premises equipment (CPE) base station operating at 25 GHz. All eight independent ports were simulated within minutes on a recent GPU - GeForce RTX 2080.

 

UI Secondary Tree Toolkit

UI enhancements in Sim4Life V5.0: The new secondary tree view in the explorer tree allows the user to easily and intuitively build, monitor, and manage complex simulation trees with hundreds of thousands of components.

 

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