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Multiscale Multicellular Modeling of Tissue Function and Disease using CompuCell3D
03 Jun 2020 | | Contributor(s):: James A Glazier, Juliano Ferrari Gianlupi
Multiscale multicellular models combine representations of subcellular biological networks, cell behaviors, tissue level effects and whole body effects to describe tissue outcomes during development, homeostasis and disease. I will briefly introduce these simulation methodologies, the CompuCell3D...
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Nanosphere Electrostatics Lab Tutorial
11 Nov 2019 | | Contributor(s):: Jayanath Chamindu Sandanuwan Kadupitiya Kadupitige, Ballard, Joshua Brendan
Accurate knowledge of ionic structure & dynamics is critical to study nanoparticle dynamics. Nanoparticles are polarized in most solvents. Simulating the dynamics of ions near polarizable nanoparticles is challenging: Need to solve Poisson equation at every timestep....
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Nanoscale Simulations & Engineering Applications: Applications - Self-Assembly in Nanoconfinement
04 Feb 2019 | | Contributor(s):: Vikram Jadhao
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[Illinois] Nanopore Sequencing of DNA
04 Oct 2013 | | Contributor(s):: Aleksei Aksimentiev
The idea of using a nanopore to sequence DNA continues to generate excitement among scientists and entrepreneurs. The spectacular progress in using biological enzymes to enable nanopore sequencing indicates the imminent arrival of nanopores in practical biomedical applications. Even more exciting...
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[illinois] BioMEMS and Bionanotechnology: Integration of Life Sciences and Engineering at the Micro and Nanoscale
10 Jul 2013 | | Contributor(s):: Rashid Bashir
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Optical BioMEMS Microfluidic Technologies for Hand-Held, Point-of-Care, Medical Devices
23 Nov 2009 | | Contributor(s):: James Leary
Portable, point-of-care, medical diagnostic devices could provide an important new component in more cost-effective healthcare delivery. Rapid measurements of blood samples during an examination within a doctor’s office or in the field, could allow immediate appropriate treatment of medical...
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Illinois Center for Nanoscale Science and Technology and Nano-CEMMS: A Hard Day in the Life of a Soft Cell
12 May 2009 | | Contributor(s):: Jeffrey Fredberg
AHard Day in the Life of a Soft CellWith every beat of the heart, inflation of the lung, or peristalsis of the gut, cell types of diverse function are subjected to substantial stretch. But what physical laws govern the abilities of the cytoskeleton to deform, contract, and remodel at the...
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Illinois MATSE 280 Introduction to Engineering Materials, Lecture 3 Part 4: Structures via Diffusion
28 Sep 2008 | | Contributor(s):: Duane Douglas Johnson, Omar N Sobh
Structures via DiffractionGoals Define basic ideas of diffraction (using x-ray, electrons, or neutrons, which, although they are particles, they can behave as waves) and show how to determine: Crystal Structure Miller Index Planes and Determine the Structure Identify cell symmetry Learning...
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Illinois MATSE 280 Introduction to Engineering Materials, Lecture 3 Part 3: Crystallographic Points, Directions, and Planes
22 Sep 2008 | | Contributor(s):: Duane Douglas Johnson, Omar N Sobh
Crystallographic Points, Directions, and PlanesIssues to Address...How to define points, directions, planes, as well aslinear, planar, and volume densitiesDefine basic terms and give examples of each: Points (atomic positions) Vectors (defines a particular direction - plane normal) Miller Indices...
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Illinois MATSE 280 Introduction to Engineering Materials, Lecture 3 Part 2: Structure of Ceramics
21 Sep 2008 | | Contributor(s):: Duane Douglas Johnson, Omar N Sobh
Structure of CeramicsIssues to Address...Structures of ceramic materials: How do they differ from that of metals?Define basic terms and give examples of each: Lattice Basis Atoms (Decorations or Motifs) Crystal Structure Unit Cell Coordination Numbers Describe hard-sphere packing and identify...
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Illinois MATSE 280 Introduction to Engineering Materials, Lecture 3 Part 1: Structure of Metals and Ceramics
19 Sep 2008 | | Contributor(s):: Duane Douglas Johnson, Omar N Sobh
Structures of Metals and CeramicsGoals Define basic terms and give examples of each: Lattice Basis Atoms (Decorations or Motifs) Crystal Structure Unit Cell Coordination Numbers Describe hard-sphere packing and identify cell symmetry Crystals density: the mass per volume (e.g. g/cm3) Linear...
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Illinois MatSE 280 Introduction to Engineering Materials, Lecture 2: Atomic Structure and Interatomic Bonding
18 Aug 2008 | | Contributor(s):: Duane Douglas Johnson, Omar N Sobh
Refortify your chemistry - Atomic scale structuresGoals Define basic concepts: Filling of Atomic Energy Levels: Pauli Exclusion Principle Atomic Orbitals (s-, p-, d-, and f- type electrons) Types of Bonding between Atoms The Periodic Table (and solid state structures)...
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Multiscale Methods to Simulate and Predict Membrane Organization: atomistic molecular dynamics to mean field Langevin dynamics
08 Aug 2008 | | Contributor(s):: Larry H. Scott, Omar N Sobh
There is considerable interest in the lateral organization of biological membranes. While membrane proteins obviously influence on the localized properties of membranes, the lipids themselves also can self-organize within the bilayer. Computational models can complement the growing body of...
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Hierarchy of Simulation Approaches for Charge Transport Simulation
01 Aug 2008 | | Contributor(s):: Omar N Sobh, Umberto Ravaioli
General considerations Model simulation hierarchy Continuum model Particle Transport Monte Carlo model Examples of simulations Umberto Ravaioli - University of Illinois, Urbana-ChampaignNCN@Purdue Student Leadership Team Network for Computational Nanotechnology The Institute for Nanoelectronics...
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Nanocomposite-Modified Electrodes for Sensing Biological Analytes
30 Jul 2008 | | Contributor(s):: V. Yegnaraman
Electrochemical sensing of analytes is mostly enabled by transducers based on potentiometry and amperometry. In this, design of sensing (working) electrode is of utmost importance since it only decides the sensitivity and selectivity features of the sensor. Chemical modification of the electrode...
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Strategies for Preparation and Manufacture of Polymer-based Nanoparticulate Formulations
21 Jul 2008 | | Contributor(s):: Stephen R. Byrn
Nanoparticles hold great promise for drug delivery applications. Several polymer-based formulations containing nanoparticles are in late phase development or on the market. In fact, polymer dispersions provide one of the best methods to prepare nanoparticles of small-molecule organic drugs....
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Lecture 24: The 4 Molecules of life
29 Apr 2008 | | Contributor(s):: Paul R Selvin
Atoms, Molecules, Macromolecules, you!Amino Acids, Sugars used as signals, Fatty Acids/Lipids
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Molecular modeling of lipid bilayer edge and hybrid-MCMD method: Implementation and application
29 Apr 2008 | | Contributor(s):: Yong Jiang
Introduction to mixed lipid systems, Hybrid Monte Carlo and MD (atomistic) algorithm for mixed lipid systems
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Lecture 18: Magnetotaxis
28 Apr 2008 | | Contributor(s):: Klaus Schulten, Paul R Selvin
Biochemical Mechanisms for Magnetic Orientation in Animals, guest lecture Klaus Schulten.
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Lecture 2: Central Dogma of Biology; Partition Function
28 Apr 2008 | | Contributor(s):: Paul R Selvin
Nucleic Acids, DNA,RNA, Cell size, Nucleotides, Boltzman factor, Partition function