Group Meetings


All listed group meetings/seminars are 1:15-2:30pm in ACES 4.304, unless otherwise noted.

Date Speaker Title
2012/10/17 Deukhyun Cha Poisson Boltzmann Solver for Solvation Energy
2012/10/10 Tomoyuki Nishita Particle-based Simulation for Computer Graphics
2012/9/26 Chandrajit Bajaj Big Data Analytics for Molecular/Cellular Bioinformatics
2012/9/19 Chandrajit Bajaj The Forward Problem in Medical Imaging and Microscopy II
2012/9/12 Niklas Elmqvist It’s About Time: Analyzing, Forecasting, and Reasoning with Temporal Data
2012/9/5 Chandrajit Bajaj The Forward Problem in Medical Imaging and Microscopy I
2012/8/29 Chandrajit Bajaj Introduction to Multi-modal Biomedical Imaging
2012/8/22 Chandrajit Bajaj From Voxel Maps to Analysis Ready 3D Meshed Models
2012/8/15 Qin Zhang and Deukhyun Cha Multi-Domain Quality Meshing for Volumetric Data
2012/8/8 Radhakrishna Bettadapura Flexible fitting in 3D EM II
2012/8/1 John Edwards Surface segmentation for improved remeshing
2012/7/25 Radhakrishna Bettadapura Flexible fitting in 3D EM I
2012/7/18 Eric Daniel Image Processing Techniques: Theory and Practice
2012/7/11 Radhakrishna Bettadapura MHDFFit: Hierarchical Domain-Based Flexible Fitting
2012/6/27 Muhibur Rasheed Multi-resolution smooth molecular surfaces using octrees
2012/6/20 Deukhyun Cha Abstract Cost Model for Parallelizing Molecular Energetics using CUDA
2012/6/13 Qin Zhang Macromolecular Modeling from Cryo-EM Density Map and Sequences
2012/6/6 Radhakrishna Bettadapura and Muhibur Rasheed Modeling SIV spike protein interactions with F2Dock
2012/5/30 Itamar Gal Orientation Determination by Categorical Optimization
2012/5/23 Alex Rand TBA
2012/5/16 Muhibur Rasheed Analysis of viral capsid protein interactions
2012/5/9 Deukhyun Cha Enhancing visualization of molecular structure in multiple resolution
2012/5/2 Qiming Yuan A comparison of machine learning techniques for protein docking prediction
2012/4/25 Radhakrishna Bettadapura Flexible refinement of crystal structures into density maps
2012/4/18 Chandrajit Bajaj (1) Automating the Visualization of Biological Machines and (2) A-periodic Tilings and Icosahedral Viral Capsid Protein Assemblies
2012/4/11 Zhang Qin The Contrast Transfer Function in Transmission Electron Microscopy
2012/4/4 Maysam Moussalem Cancer Therapeutics: A Case Study in Lead Optimization in Computational Drug Design
2012/3/28 Francesco Bonaldi TBA
2012/3/21 Maysam Moussalem Cancer Therapeutics: A Case Study in Lead Optimization in Computational Drug Design
2012/3/7 Muhibur Rasheed Dynamic Computation of Smooth Molecular Surfaces
2012/2/29 Alex Rand Quadratic Serendipity Finite Elements on Polygons Using Generalized Barycentric Coordinates
2012/2/22 Eric Daniel Determination of Particle Orientation from 2d Cyro-EM Projections.
2012/2/15 Radhakrishna Bettadapura Part 1: Fast Rigid-Body Correlations using Selectively Uniform SO(3) Fourier transforms / Part 2: A Flexibility Model for Flexible Fitting
2012/2/1 Paolo Podio-Guidugli The atomistic content of the notion of stress: from Irving&Kirkwood to Parrinello&Rahman, with the help of Noll
2012/1/31 Paolo Cermelli Applications of the theory of crystallographic phase transitions to the study of conformational changes in viral capsids. (ICES Seminar: 3:30pm, ACE 6.304)
2012/1/25 Michael Holst Theory and Numerical Treatment of the Einstein Constraint Equations
2012/1/24 Yunrong Zhu Design and Analysis of Adaptive Finite Element Methods for Nonlinear PDE (Special Time/Place: 11:00am, ACE 4.304)
2012/1/18 Francesco Bonaldi Mechanical Modeling of Viral Capsids


Date Speaker Title
2011/12/15 Michael Holst Geometric PDE, Adaptive Methods, Finite Element Exterior Calculus, and Applications in Relativity (Joint ICES Seminar: 3:30 pm, ACES 6.304)
2011/12/14 Andrew Gillette Finite Element Exterior Calculus for Evolution Problems (Special Time: 3:30 pm, ACES 6.304)
2011/12/14 Mohamed Ebeida Random Unstructured Meshes via Maximal Poisson-disk Sampling (Special Time: 3:00 pm, ACES 4.304)
2011/12/14 Scott Mitchell Geometry of distance functions for probability distributions (Special Time: 2:00 pm, ACES 4.304)
2011/12/8 Muhibur Rasheed and John Edwards Thesis Proposal Preparation (Special Time: 1:30 pm, ACES 2.404B)
2011/11/12 Wenping Wang Free-form Shape Modeling Using Cyclides Splines (Special Time: 11 am)
2011/11/11 Deukhyun Cha and Zhang Qin TBA
2011/11/11 Muhibur Rasheed and Qiming Yuan Training F2Dock
2011/11/11 Deukhyun Cha and Alexander Rand Surfaces for Molecular Electrostatics
2011/10/28 Philippe Block Geometry in Compression Structures, (11am)
2011/10/26 None —-
2011/10/19 Maysam Moussalem A Reduced Flexibility Model for Macromolecules
2011/10/12 Radhakrishna Bettadapura Understanding Shear in Proteins
2011/10/5 Muhibur Rasheed Multi-protein docking for viral capsids
2011/9/28 Zhang Qin Ribosomal Protein Modeling for Trypanosoma Brucei from a 5.16A EM Density Map
2011/9/21 Eric Greg Daniel Classification of Heterogeneous Particles in Cryo-EM Reconstructions
2011/9/14 Qiming Yuan Learning Parameters in F2Dock
2011/9/7 John Edwards Polyhedron Separation
2011/8/31 Deukhyun Cha Parallelizing molecular energy and force calculations using cilk++ and CUDA
2011/8/24 Alex Rand Code Review: TexMol and VolRover
2011/6/2 Radhakrishna Bettadapura Flexible Fitting of Crystal Structures into Density Maps
2011/6/1 Maysam Moussalem A Reduced Flexibility Model and Improved Scoring Scheme For Lead Optimization In Computational Drug Design
2011/5/11 Dima Kozakov Sampling macromolecular recognition landscapes using Fast Fourier Transforms based approaches and their generalizations
2011/5/4 Wenping Wang Centroidal Voronoi Tessellation vs. Optimal Delaunay Triangulation
2011/4/27 Andrew Gillette Stability of Dual Discretization Methods for PDEs
2011/4/20 Maysam Moussalem Lead Optimization in Computational Drug Design: An Iterative Approach to Structural and Chemical Refinement
2011/4/13 Md Muhibur Rasheed Multi protein docking
2011/4/6 Radhakrishna Bettadapura Flexible fitting of subunit assemblies into cryo-EM density maps
2011/3/30 Deukhyun Cha Survey of GPU-accelerated Molecular Dynamics
2011/3/25 John Edwards Analysis-ready 3D reconstructions of complex objects from planar cross-sectional slices
2011/3/23 Michael Holst Convergence of Adaptive Finite Element Methods for Nonlinear Geometric PDE
2011/3/16 [ No Meeting - Spring Break ]
2011/3/9 Maysam Moussalem Molecular docking: current approaches and remaining challenges
2011/3/2 Anil Hirani Optimal (Co)homologous (Co)chains
2011/2/23 Ajay Gopinath Statistical regularization method for electron tomography reconstruction
2011/2/16 Ozan Oktem Computational Anatomy – An approach to incorporate a priori shape information into 3D electron microscopy
2011/2/9 Ozan Oktem Simulation of Transmission Electron Microscope Images of Biological Specimens
2011/2/2 Alexander Rand A Closer Look at the Poisson-Boltzmann Model (pdf)
2011/1/26 Zhang Qin Molecular Surfaces: Area, Volume, and Atomic Derivatives
2011/1/19 Andrew Gillette Conforming Vector Interpolation Functions for Polyhedral Meshes


Date Speaker Title
2010/11/22 Pradeep Sen Applications of Compressed Sensing in Computer Graphics and Imaging
2010/11/17 Gema Quintana Rational Curves from Rotation-Minimizing Frames
2010/11/10 Andrew Gillette Compatibility Conditions for Dual Discretization Methods
2010/11/03 Deukhyun Cha GPU-assisted Photo Realistic Rendering(Particle-based Participating Media Rendering)
2010/10/27 John Edwards The Connectome: Challenges and Approaches
2010/10/20 Ventaka Dintyala High Quality Docking Procedures
2010/10/13 Md Muhibur Rasheed Docking and configurational entropy
2010/10/06 Zhang Qin Evolution based skeletonization for 3D image and its applications
2010/09/29 Radhakrishna Bettadapura Fast Fourier Fitting
2010/09/22 Antje Vollrath The Nonequispaced Fast SO(3) Fourier Transform, and its Applications
2010/09/15 Maysam Moussalem Molecular Docking: Flexibility Models, Search and Scoring
2010/09/08 Ajay Gopinath Tomographic Reconstruction Using Statistical Regularization
2010/09/01 Alexander Rand A Boundary Element Solver for Poisson-Boltzmann Based Molecular Electrostatics
2010/08/25 Various Speakers SPM Practice Talks
2010/05/05 Radhakrishna Bettadapura Protein Flexibility Models
2010/04/28 Zhang Qin EnDock: A Novel Variational Energy Based Enhancement to Protein-Protein Docking
2010/04/21 Bharadwaj Subramanian Quasi-continuum Method: Coupling Atomistic and Continuum Scales
2010/04/14 Itamar Gal Solubility by Radicals and Monodromy of Riemann Surfaces
2010/04/07 Chandrajit Bajaj Modeling Electrical Field Coupling in Neurons
2010/03/31 Rezaul Chowdhury Multithreaded Programming with Cilk++
2010/03/24 Andrew Gillette New Model Stability Criteria for Mixed Finite Elements
2010/03/17 n/a [no meeting - spring break]
2010/03/10 12:45:00 US/Central Maysam Moussalem Comparative Study of Three Reranking Methods for Protein-Protein Docking
2010/03/03 Rezaul Chowdhury F2Dock and Other Stories
2010/02/24 Yufei Li and Bharadwaj Subramanian Non-linear Continuum Elasticity Modeling of Viral Capsids
2010/02/17 Md Muhibur Rasheed Dynamic and Adaptive Coarse-graining of Molecular Models
2010/02/10 John Edwards Topologically correct reconstruction of tortuous contour forests
2010/02/03 Cliff Rumsey Constructing and Simulating Reduced Models of the Neuropil
2010/01/27 Alex Rand and Radhakrishna Bettadapura WEB-Spline Finite Element Methods
2010/01/20 Ajay Gopinath On Statistical Regularization of Electron Tomography Reconstruction


Date Speaker Title
2009/12/02 Radhakrishna Bettadapura Electron Tomography Molecular Modeling: Fitting and Docking
2009/11/25 10:00:00 US/Central Bharadwaj Subramanian and Albert Chen TBA (Room = ACES 2.404B)
2009/11/18 Qin Zhang On the Computation of Area, Volume and Their Derivatives with Respect to Atomic Centers for Molecular Surfaces
2009/11/11 Radhakrishna Bettadapura and Ajay Gopinath (Click for titles and abstracts)
2009/11/04 Albert Chen Framework of Electrostatic Computation of Molecular Models
2009/10/28 Maysam Moussalem Hydrogen Bonding in Protein-Protein Docking
2009/10/21 Md Muhibur Rasheed Viral Capsid Self-Assembly
2009/10/14 Andrew Gillette and Alexander Rand Neuronal Modeling Topics (see abstract for titles)
2009/10/07 Ajay Gopinath and Bharadwaj Subramanian Electron Tomography and Viral Capsids
2009/09/30 Rezaul, Zhang, Albert, Andrew SIAM/ACM Conference Talks Practice
2009/09/23 Various Speakers TexMol and VolRover Status Reports
2009/09/16 Various Speakers VolRover Functionality Report
2009/09/09 Fahad Chowdhury and John Edwards Neuronal Modeling Topics (see abstract for titles)
2009/09/02 13:30:00 GMT-5 Alexander Rand Finite Element Interpolation on Poor Quality Simplicial Meshes
2009/08/26 13:30:00 GMT-5 Cliff Rumsey and Fahad Chowdhury Electrical and Diffusion Modeling of Extracellular Space
2009/08/25 09:30:00 GMT-5 Dr. Paolo Podio-Guidugli Atomistic/Continuum Methods
2009/08/24 09:30:00 GMT-5 Dr. Paolo Podio-Guidugli The Molecular Dynamics Approach II
2009/08/19 09:30:00 GMT-5 Dr. Paolo Podio-Guidugli The Molecular Dynamics Approach I
2009/08/18 09:30:00 GMT-5 Dr. Paolo Podio-Guidugli Phase Transformations by Atomic Rearrangement II
2009/08/17 09:30:00 GMT-5 Dr. Paolo Podio-Guidugli Phase Transformations by Atomic Rearrangement I
2009/08/12 Maysam Moussalem Simulated Docking: Scoring and Re-ranking
2009/08/07 10:30:00 GMT-5 Radhakrishna Bettadapura Protein Structural Dynamics
2009/08/05 Ajay Gopinath Non-rigid alignment methods for statistical image processing
2009/07/29 Md Muhibur Rasheed An overview of viral capsid self assembly
2009/07/22 Albert Chen Force Fields in Molecular Dynamics
2009/07/15 Wenqi Zhao Computer simulation in molecular modeling
2009/07/10 Bharadwaj Subramanian LBIE Mesher – A Status Report
2009/07/08 Qin Zhang Selected Topics Related to Morse Theory (Part II)
2009/07/01 Rezaul Chowdhury Fast Summations for F2Dock
2009/06/24 Alex Mollere Solving Poisson’s Equation with the WEB Spline FEM
2009/06/17 Andrew Gillette Automated Neuronal Reconstruction: Current Challenges and Proposed Quantification
2009/06/10 Cliff Rumsey Electrophysiology Models Derived from EM Reconstructions
2009/05/06 Soumojit Sarkar Parallelization scheme for F2Dock
2009/04/29 Maysam Moussalem A Comparative Study of Protein-Protein Docking Programs and their Scoring Programs — Part II
2009/04/22 Md Muhibur Rasheed On reassembling fractured objects by geometric matching
2009/04/15 Radhakrishna Bettadapura Fitting Crystal Structures Into Density Maps: What Lies Ahead
2009/04/08 Qin Zhang Selected Topics Related To Morse Theory (Part I)
2009/04/01 [CoLab Workshop] CoLab Workshop:
2009/03/25 Cliff Rumsey Generating Reduced Models of Dendrites
2009/03/18 n/a [no meeting - spring break]
2009/03/11 Rezaul Chowdhury The Current State of the In-House Docking Software
2009/03/04 Ajay Gopinath Born Approximation in Electron Microscopy
2009/02/25 Ojaswa Sharma Level Set Based Segmentation on CUDA
2009/02/18 Bharadwaj Muralidharan Quality Improvement of Meshes
2009/02/11 Albert Chen Discrete Regularization Methods for Dirac Delta Function in Level Set Methods
2009/02/04 Andrew Gillette Geometric Discretization of Stress and Elasticity
2009/01/28 E. Alex Mollere A Model for 3-D Signal Propagation in Passive Dendrites
2009/01/21 Ozan Öktem Electron tomography: Current approaches and a view towards the future


Date Speaker Title
2008/12/12 Ajay Gopinath Structure elucidation in electron tomography, part II
2008/12/08 Radhakrishna Bettadapura Structure-elucidation pipeline
2008/12/03 Md Muhibur Rasheed Implementation of PG and how it uses CGAL to produce 3D arrangements
2008/12/03 Bharadwaj Muralidharan Quality Improvement of Octree-Dual contouring based Adaptive Hexahedral meshes
2008/11/24 Maysam Moussalem Adaptive Search in F2Dock
2008/11/19 Andrew Gillette Applications of the Hodge Decomposition to Biological Structure and Function Modeling
2008/11/19 Wenqi Zhao Fast and Accurate Macromolecular Solvation Energy and Force Computations
2008/11/17 Albert Chen Poisson-Boltzmann Electrostatic Computation using Fast Multiple Boundary Element Method: Theory, Implementation and Application
2008/11/12 Alex Mollere Finite Element Methods with WEB Splines
2008/11/05 Jose Rivera CVC Software Status
2008/10/29 Ajay Gopinath Structure elucidation in electron tomography
2008/10/22 Radhakrishna Bettadapura Secondary structure elucidation from density maps
2008/10/15 Wenqi Zhao NFFT-based polarization energy and force computation in the GB model
2008/10/10 10:30:00 GMT-5 Albert Chen Preliminary Report of Iterative Solution Methods for Linearized Poisson-Boltzmann boundary Integral Equations
2008/10/08 Andrew Gillette Quality Meshing of a Forest of Branching Structures
2008/10/01 Chandrajit Bajaj Skeletonization and Reduced Finite Element Models
2008/09/24 Cliff Rumsey Electrophysiological models of dendritic properties derived from reconstructed dendrites
2008/09/10 Rezaul Chowdhury Protein Side-Chain Packing Using Network Flows
2008/09/03 Qin Zhang Geometric Partial Differential Equations Methods in Geometric Design and Modeling
2008/08/26 10:30:00 GMT-5 Zeyun Yu Multiscale Geometric Modeling of Biomedical Systems: Bridging the Gap between Imaging and Simulation
2008/08/22 10:30:00 GMT-5 Wenqi Zhao Electrostatic solvation energy with coarse-grained models
2008/08/20 Maysam Moussalem Simulated Docking Search and Affinity Scoring
2008/08/19 15:30:00 GMT-5 Carlos Óscar Sánchez Sorzano Mathematical and computational challenges for visual proteomics and genomics
2008/08/15 09:30:00 GMT-5 Andrew Gillette Topology-controlled Stable Function Modeling for Biology
2008/08/13 Aditi Saha 3D arrangement of spheres for Packing Grids
2008/08/12 15:30:00 GMT-5 Yoel Shkolnisky Reference Free Cryo-EM Structure Determination through Eigenvectors of Sparse Matrices
2008/08/08 09:30:00 GMT-5 Albert Chen Modeling Electrostatics and Flow Dynamics of 3D Deformable Interfaces in Biology
2008/08/06 Jesse Sweet Volume Tranformations and Mesh Visualizations
2008/07/23 Jose Rivera Status Update on CVC Computing Resources And Suggestions For Streamlining CVC Software Development
2008/07/16 Ajay Gopinath Generating Models from Tomographic Electron Microscopy
2008/07/09 Radhakrishna Bettadapura Protein side-chain packing using network flow — implementations and experimentation
2008/07/02 Lei Na Constructing Weight Functions by A-Splines
2008/06/25 Cliff Rumsey Modeling dendrites in three dimensions from reconstructed EM data
2008/06/18 Rezaul Chowdhury Protein Side-chain Repacking using Network Flows
2008/06/11 Wenqi Zhao Hierarchical coarse-grained modeling
2008/06/04 Albert Chen New Fast Multipole Approach for Protein Implicit Solvation Electrostatic Boundary Element Solver
2008/05/21 Aditi Saha Multiresolution Data Structures in Molecular Bioinformatics and Docking
2008/05/19 Vijay Srinivasan Theory of Dimensioning and Parameterizing Geometric Models
2008/05/14 Ravikant D V S An efficient coarse grained potential for unbound protein-protein docking
2008/04/23 Radhakrishna Bettadapura Normal Mode Analysis with Applications to Molecular Fitting
2008/04/16 Lei Na High Order Cubature for A-splines and A-patches
2008/04/09 Albert Chen Coarse Grained PB Potential and Forces
2008/04/02 Wenqi Zhao Coarse Grained GB Energetcs and Forces
2008/03/26 Inkulu Spatially Realistic Local Circuits of the Hippocampus from ssEM
2008/03/19 Rezaul Chowdhury Flexible Docking
2008/03/05 Maysam Moussalem Virtual Drug Screening using AutoDock 4
2008/02/27 06:00:00 US/Central Chandrajit Bajaj Quantitative Visualization of Multiscale Bio-Imaging
2008/02/20 Ajay Gopinath Tomographic Electron Microscopy
2008/02/13 Jesse Sweet Quality Finite Element Meshes
2008/02/06 06:00:00 US/Central Chandra Bajaj Interrogative Visualization from Algebraic Finite Elements
2008/01/30 Andrew Gillette The State of Affairs in Protein Modeling
2008/01/23 Chandra Bajaj Molecular Microscopy to Biophysical Modeling