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Biomedical Engineering and Bioengineering Commons™
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Articles 1 - 6 of 6
Full-Text Articles in Biomedical Engineering and Bioengineering
Computing Spatiotemporal Heat Maps Of Lipid Electropore Formation: A Statistical Approach, Willy Wriggers, Frederica Castellani, Julio A. Kovacs, P. Thomas Vernier
Computing Spatiotemporal Heat Maps Of Lipid Electropore Formation: A Statistical Approach, Willy Wriggers, Frederica Castellani, Julio A. Kovacs, P. Thomas Vernier
Mechanical & Aerospace Engineering Faculty Publications
We extend the multiscale spatiotemporal heat map strategies originally developed for interpreting molecular dynamics simulations of well-structured proteins to liquids such as lipid bilayers and solvents. Our analysis informs the experimental and theoretical investigation of electroporation, that is, the externally imposed breaching of the cell membrane under the influence of an electric field of sufficient magnitude. To understand the nanoscale architecture of electroporation, we transform time domain data of the coarse-grained interaction networks of lipids and solvents into spatial heat maps of the most relevant constituent molecules. The application takes advantage of our earlier graph-based activity functions by accounting for …
A Balanced Approach To Adaptive Probability Density Estimation, Julio Kovacs, Cailee Helmick, Willy Wriggers
A Balanced Approach To Adaptive Probability Density Estimation, Julio Kovacs, Cailee Helmick, Willy Wriggers
Mechanical & Aerospace Engineering Faculty Publications
Our development of a Fast (Mutual) Information Matching (FIM) of molecular dynamics time series data led us to the general problem of how to accurately estimate the probability density function of a random variable, especially in cases of very uneven samples. Here, we propose a novel Balanced Adaptive Density Estimation (BADE) method that effectively optimizes the amount of smoothing at each point. To do this, BADE relies on an efficient nearest-neighbor search which results in good scaling for large data sizes. Our tests on simulated data show that BADE exhibits equal or better accuracy than existing methods, and visual tests …
Biophysical Tools To Study Cellular Mechanotransduction, Ismeel Muhamed, Farhan Chowdhury, Venkat Maruthamuthu
Biophysical Tools To Study Cellular Mechanotransduction, Ismeel Muhamed, Farhan Chowdhury, Venkat Maruthamuthu
Mechanical & Aerospace Engineering Faculty Publications
The cell membrane is the interface that volumetrically isolates cellular components from the cell's environment. Proteins embedded within and on the membrane have varied biological functions: reception of external biochemical signals, as membrane channels, amplification and regulation of chemical signals through secondary messenger molecules, controlled exocytosis, endocytosis, phagocytosis, organized recruitment and sequestration of cytosolic complex proteins, cell division processes, organization of the cytoskeleton and more. The membrane's bioelectrical role is enabled by the physiologically controlled release and accumulation of electrochemical potential modulating molecules across the membrane through specialized ion channels (e.g., Na⁺, Ca2+, K⁺ channels). …
Computational Assessment Of Neural Probe And Brain Tissue Interface Under Transient Motion, Michael Polanco, Sebastian Bawab, Hangsoon Yoon
Computational Assessment Of Neural Probe And Brain Tissue Interface Under Transient Motion, Michael Polanco, Sebastian Bawab, Hangsoon Yoon
Mechanical & Aerospace Engineering Faculty Publications
The functional longevity of a neural probe is dependent upon its ability to minimize injury risk during the insertion and recording period in vivo, which could be related to motion-related strain between the probe and surrounding tissue. A series of finite element analyses was conducted to study the extent of the strain induced within the brain in an area around a neural probe. This study focuses on the transient behavior of neural probe and brain tissue interface with a viscoelastic model. Different stages of the interface from initial insertion of neural probe to full bonding of the probe by astro-glial …
Multi-Scale Visualization Of Molecular Architecture Using Real-Time Ambient Occlusion In Sculptor, Manuel Wahle, Willy Wriggers
Multi-Scale Visualization Of Molecular Architecture Using Real-Time Ambient Occlusion In Sculptor, Manuel Wahle, Willy Wriggers
Mechanical & Aerospace Engineering Faculty Publications
The modeling of large biomolecular assemblies relies on an efficient rendering of their hierarchical architecture across a wide range of spatial level of detail. We describe a paradigm shift currently under way in computer graphics towards the use of more realistic global illumination models, and we apply the so-called ambient occlusion approach to our opensource multi-scale modeling program, Sculptor. While there are many other higher quality global illumination approaches going all the way up to full GPU-accelerated ray tracing, they do not provide size-specificity of the features they shade. Ambient occlusion is an aspect of global lighting that offers great …
Distal Placement Of An End-To-Side Bypass Graft Anastomosis: A 3d Computational Study, John Di Cicco, Ayodeji Demuren
Distal Placement Of An End-To-Side Bypass Graft Anastomosis: A 3d Computational Study, John Di Cicco, Ayodeji Demuren
Mechanical & Aerospace Engineering Faculty Publications
A three-dimensional (3D) computational fluid dynamics study of shear rates around distal end-to-side anastomoses has been conducted. Three 51% and three 75% cross-sectional area-reduced 6 mm cylinders were modeled each with a bypass cylinder attached at a 30-degree angle at different placements distal to the constriction. Steady, incompressible, Newtonian blood flow was assumed, and the full Reynolds-averaged Navier-Stokes equations, turbulent kinetic energy, and specific dissipation rate equations were solved on a locally structured multiblock mesh with hexahedral elements. Consequently, distal placement of an end-to-side bypass graft anastomosis was found to have an influence on the shear rate magnitudes. For the …