Current Research

Sub-Cellular elements (SCE).

My recent work involves modeling multi-cellular systems using sub-cellular elements (SCEM). In contrast to the Cellular Potts models (CPM), a dynamical system is developed that defines cellular shape and elasticity, by emulating the cytoskeleton, and uses the Lennard-Jones potential, to mimic cellular adhesion, giving more realistic simulations. The current methods use harmonic restraints between the sub-cellular elements (SCE) to give the correct shape and elasticity, extensions of the model to cell division allows the restraint to be removed beyond a given distance.

Cells colliding

The Figure above is an example of a Newtonian Mechanics (NM) representation of cell collision using Protomol. These tests illustrate elasticity and adhesion of cells and we have proposed methods of coupling the flow and NM codes.

Normal Mode Langevin (NML).

The NML coarse grained method utilizes a normal mode decomposition of the dynamical space to achieve large numerical step size. Our first paper 'Normal Mode Partitioning of Langevin Dynamics for Biomolecules' authored by Christopher R. Sweet, Paula Petrone, Vijay S. Pande and Jesús A. Izaguirre was published in the Journal of Chemical Physics. It established the basic principles and theory of the method, and the corresponding informational website can be found here. To implement an efficient realization has required further work on Hessian diagonalization and Langevin methods for large step size. Further information can be found by using the 'NML' top menu item. The graphic depicts the block structure of the Hessian that is used to allow an efficient diagonalization method.

Block Hessian relationship to Protein

GPU code.

Implementing Molecular Dynamics (MD) code on GPUs is a current hot topic! It is especially attractive to our NML method as it utilizes many linear algebra routines from Lapack, which is available to new GPU development kits. One of the problems with GPU calculations is that they are generally single precision arithmetic, which can lead to large force field errors if not implemented correctly.

In conjunction with our GPU code implementation we are developing Shadow Hamiltonian methods to test the numerics. More details can be found by using the 'GPU' top menu item.

OpenMM group

Recent work with the OpenMM group at Stanford University has yielded a GPU implementation of our coarse grained Normal Mode Langevin method. 


We have produced a Java Molecular Viewer using the JOGL OpenGL bindings. This allows us to observe simulations that are running remotely, and can be seen in action on the NML website. It is also used in the Grid Heating effort at the Greenhouse conservatory in South Bend to show the scientific efforts being used to heat the conservatory.

Viewer rolling platelet

The viewer has now been extended to viewing Blood Clot simulations, Fibrin networks, Social Network data and Microtubule simulations. More information on the top menu OpenGL item.


Open source Protomol embodies the new NML method in addition to standard MD methods. We have issued version 3 as part of our Folding@Home project in conjunction with the Pande group. More information using the top menu Protomol item.