Eric Darve

Professor Darve has a joint position with the Institute for Computational and Mathematical Engineering at Stanford.

Research Centers

Professor Darve is involved in two Research Centers at Stanford: the Advanced Simulation and Computing Center and the Army High-Performance Computing and Research Center.

Research

Darve's research is focused on the development of numerical methods for large scale scientific computing with applications in bio molecular simulations, acoustics, electrodynamics and microfluidics. In these applications, the computational expense of simulating large and complex systems is very significant and in many instances beyond current computer capabilities. Professor Darve is developing innovative numerical techniques to reduce this computational expense and enable the simulation of industrial size systems over realistic time scales. Examples of numerical techniques are new formulations of the Fast Multipole Method applicable to simulations of biological macro-molecules and to acoustic/electromagnetic scattering. Professor Darve has also an activity in computer science in which he uses processors with novel architectures (such as GPU, Cell) for scientific computing.

Bio-molecular Modeling

Professor Darve has developed several numerical methods to study mechanical properties of proteins. This includes a new approach to compute free energy called the adaptive biasing force, new time integrators with multiple time steps (e.g. Asynchronous Variational Integrators) and novel techniques to compute electrostatic forces on parallel computers called the fast plane wave algorithm.

In collaboration with the NASA Ames Research Center, Darve modeled the insertion of an amphipathic peptide in a membrane. This is a precursor step in forming an ion channel through the membrane.

Amphipathic helix inserted in a mimetic membrane

Molecular modeling can also be applied to understanding the mechanical properties of bundles of microtubules found in sensory neurons of nematodes. This is in collaboration with M. Goodman (School of Medicine, Stanford). These microtubules are responsible for amplifying mechanical forces applied to the surface of the neuron.

Dimer forming the basic building block of microtubules

Streaming Computing

A new generation of processors with a few or many cores, e.g. multi-core Intel, GPU, Cell, is about to revolutionize the way scientific computing is done. These processors can perform operations 10 to 100 times faster than a conventional single core processor. However these processors are very difficult to program. New algorithms and programming environments are therefore needed.

Simulation of the compressible Euler equations performed on a GPU. Hypersonic vehicle.

Microfluidics

Charged particles such as DNA flowing in micro or nano size channels have a complex dynamics due to electrophoretic and electro-osmosis flows. In particle particle will have strong hydrodynamic and electrostatic interactions with nearby particles or walls. Several electrokinetic phenomena were studied such as the Induced Charge Electrophoresis which was shown to stabilize sedimenting systems.

Sedimentation of polarizable rods. An applied electric field and the resulting Induced Charge Electrophoresis was shown to stabilize the sedimentation velocity. The figure on the left has no electric field while the figures on the right have an applied vertical electric field of increasing strength.

Main Publications