Journal paper in Mathematics for Computation

Journal paper accepted for publication in Mathematics for Computation, 2013

A. Rand; A. Gillette; C. Bajaj
Quadratic Serendipity Finite Elememts on Polygons using Genralized Barycentric Coordinates
Mathematics for Computation, Accepted for Publication, 2013.

Abstract:
We introduce a nite element construction for use on the class of convex, planar polygons and show it obtains a quadratic error convergence estimate. On a convex . . . → Read More: Journal paper in Mathematics for Computation

Journal paper in Nature

Jouranl paper published in Nature, Feb, 2013

Y. Hashem , A. Georges , J. Fu , S. Buss , F. Jossinet , A. Jobe , Q. Zhang , H. Liao , R. Grassucci , C. Bajaj , E. Westhof , S. Madison-Antenucci, J. Frank
High-resolution cryo-EM structure of the unique Trypanosoma brucei 80S ribosome
Nature, Feb. 2013, doi:10.1038/nature11872

Abstract:
Ribosomes, the . . . → Read More: Journal paper in Nature

Training F2Dock

CVC Seminar Wed Nov 9 1:15-2:30pm ACES 4.304

Speakers: Muhibur Rasheed and Qiming Yuan

Title: Training F2Dock

F2Dock is a rigid body docking software which has a FFT based on-the-fly scoring scheme involving shape complementarity, electrostatics, simple charge complementarity and interface propensity, followed by a rescoring and reranking phase using proximity clustering, clash filter, Lennard-Jones filter, antibody filter, enzyme . . . → Read More: Training F2Dock

A Reduced Flexibility Model for Macromolecules

CVC Seminar Wed Oct 19 1:15-2:30pm ACES 4.304

Speaker: Maysam Moussalem

Title: A Reduced Flexibility Model for Macromolecules

Abstract: One of the biggest challenges in computational drug design is the need for accurate and efficient modeling and exploration of macromolecules’ large number of degrees of freedom, which would result in better pose prediction in lead optimization. In this talk, . . . → Read More: A Reduced Flexibility Model for Macromolecules

Understanding shear in proteins

CVC Seminar Wed Oct 12 1:15-2:30pm ACES 4.304

Speaker: Radhakrishna Bettadapura

Title: Understanding shear in proteins

Abstract: Shear is lateral motion between a pair of protein interfaces. Though there are tens of proteins—and hundreds of accompanying interfaces— which are known to undergo shear, little is known about the shearing mechanism itself. Do a given pair of protein interfaces . . . → Read More: Understanding shear in proteins

Special Seminar: Geometry in Compression Structures

Special Seminar: 11 am, October 28, 2011, ACES 4.304:

Geometry in Compression Structures

Philippe Block, PhD
Assistant Professor in Building Structure
Institute of Technology in Architecture, ETH Zurich
http://block.arch.ethz.ch

This lecture will present a new computational form finding method for exploring three-dimensional equilibrium networks, based on (re-)discovered understanding of the stability of the spectacular vaults from the Gothic. Through the use of intuitive . . . → Read More: Special Seminar: Geometry in Compression Structures

Multi-protein docking for viral capsids

CVC Seminar Wed Oct 5 1:15-2:30pm ACES 4.304

Speaker: Muhibur Rasheed

Title: Multi-protein docking for viral capsids

Abstract:
Many biological functions are carried out by macromolecules or complexes composed of multiple proteins and nucleic acids. For example, the ribosome in E. Coli has 56 proteins, and viral capsids can be formed by hundreds of proteins. In this talk, we introduce . . . → Read More: Multi-protein docking for viral capsids

CVC Seminar Wed Sept 14 1:15-2:30pm ACES 4.304

Speaker: Qiming Yuan

Title: Learning Parameters in F2Dock

Abstract: Choosing parameters for a scoring function plays an important role in protein-protein docking prediction. Some previous approaches only rely on empirical statistics, positive examples or average negative examples. We formulate a learning framework for deriving parameters for scoring function based on observed . . . → Read More:

Parallelizing molecular energy and force calculations using cilk++ and CUDA

CVC Seminar Wed Aug 31 1:15-2:30pm ACES 4.304

Deukhyun Cha

Parallelizing molecular energy and force calculations using cilk++ and CUDA

Parallelization is an obvious tool for accelerating serial algorithms, but effective results often require a further treatment of the algorithm. Many commodity PCs provide high performance multi-threading environment including multi-core CPUs and programmable GPUs. In this talk, I will . . . → Read More: Parallelizing molecular energy and force calculations using cilk++ and CUDA

Code Review: TexMol and VolRover

CVC Seminar: Wednesday, August 24 1:15-2:30pm Room TBA

Alex Rand

Code Review: TexMol and VolRover

In our first seminar of the semester, we will review the current status of our primary graphical user applications, TexMol and VolRover. We will discuss currently implemented features, work in progress and give a short tutorial on how to quickly add new features to . . . → Read More: Code Review: TexMol and VolRover