White J.K. – TechConnect Briefs

A Nyström-Like Approach to Integral Equations with Singular Kernels

Kuo S.-H., White J.K., Massachusetts Institute of Technology, US

When boundary element methods are used to solve Laplace or Helmholtz problmes associated with complicated three-dimensional geometries, the associated integral equation is typically discretized using a piecewise constant basis, and a system of equations is [...]

A Robust Approach for Estimating Diffusion Constants from Concentration Data in Microchannel Mixers

Coelho C.P., Desai S., Freeman D., White J.K., Massachusetts Institute of Technology, US

In this paper we present a robust and geometry independent method for the estimation of diffusion coeffients of solutes from image data. Our diffusion coefficient estimation algorithm works in two steps. First, given the device [...]

A Curved Panel Integration Technique for Molecular Surfaces

Bardhan J.P., Altman M.D., Lippow S.M., Tidor B., White J.K., Massachusetts Institute of Technology, US

A key step in computational drug design is the calculation of binding free energies between drug candidates and their target; one important component of these binding free energies is the van der Waals interactions that [...]

A pFFT Accelerated Linear Strength BEM Potential Solver

Willis D.J., White J.K., Peraire J., Massachusetts Institute of Technology, US

A linear strength, Galerkin Boundary Element Meth- od (BEM) for the solution of the three dimensional, direct potential boundary integral equation is presented. The method incorporates node based linear shape functions of the single and [...]

Perturbation Analysis of TBR Model Reduction in Application to Trajectory-Piecewise Linear Algorithm for MEMS Structures

Vasilyev D., Rewienski M., White J.K., Massachusetts Institute of Technology, US

MEMS devices generate challenging test cases for nonlinear model order reduction methods, due to their strongly nonlinear behavior. One of the model order reduction methods which can handle this nonlinear behavior is a Trajectory-Piecewise linear [...]

Dealing with Stiffness in Time-Domain Stokes Flow Simulation

Coelho C.P., White J.K., Silveira L.M., MIT - RLE, US

As microfluidic devices become more common and more elaborate, it becomes necessary to develop simulation tools that allow the efficient and yet accurate three dimensional time-domain analysis of the behavior of these devices. Detailed time [...]

Biomolecule Electrostatic Optimization with an Implicit Hessian

Bardhan J.P., Lee J-H., Altman M.D., Leyffer S., Benson S., Tidor B., White J.K., Massachusetts Institute of Technology, US

Computational rational drug design is the application of computer simulation techniques to improve screening processes for new drugs or to design them de novo. The goal is to identify molecules that have high affinity and [...]

Fast Methods for Biomolecule Charge Optimization

Bardhan J.P., Lee J-H., Kuo S.S., Altman M.D., Tidor B., White J.K., Massachusetts Institute of Technology, US

We report a Hessian-implicit optimization method for linearly constrained quadratic programs. Our research focuses on the energetics of protein-protein interactions, and this method was developed to quickly solve the charge optimization problem: given a ligand [...]

Efficiency Improvements in Fast Stokes Solvers

De S., Wang X., White J.K., Massachusetts Institute of Technology, US

In this paper we present several techniques to improve the efficiency and accuracy of the precorrected FFT accelerated Fast Stokes solver based on a boundary element discretization of the integral form of the incompressible Stokes [...]

Improving Trajectory Piecewise-Linear Approach to Nonlinear Model Order Reduction for Microm䁡chined Devices Using an Aggregated Projection Basis

Rewienski M., White J.K., Massachusetts Institute of Technology, US

In this paper we present an improved algorithm for nonlinear model order reduction (MOR) based on the trajectory piecewise-linear method proposed in [6] which, as shown before, provides an e ective and eÆcient strategy for [...]