NanoBioScience Institute 

NBEC - Major Research Groups

Biomolecular Dynamics & Modeling
[Group Leaders: Dr. A. Benderskii (Dynamics) & Dr. Charles Manke (Modeling)].

Femtobiology is an emerging interdisciplinary field that aims to gain molecular-level insight into the biological function using recent advances in ultrafast laser spectroscopy.  The ability to monitor the molecular motions as they unfold in femtosecond and picosecond timescales has tremendously advanced our insight into the molecular interactions and mechanisms involved in such processes as photosynthesis, electron transfer and photoisomerization.  Femtosecond time-domain measurements are keys to establishing the fundamental relations between molecular structure, relaxation properties, chemical reactivity and biological function.  These structure-function relations will allow further advances in our understanding of biological systems and intelligent design of bioengineering applications involving ground-up molecular architecture and predictive-level computer modeling.  Our Center is equipped with a unique ultrafast surface spectroscopy setup that combines surface selectivity, ability to obtain spectra in the fingerprint IR and visible regions, and femtosecond time resolution.  Numerous emerging biotechnologies inspired by the biological function, e.g. protein-based biosensors and energy conversion devices, utilize surfaces in the form of artificial biomimetic structures such as self-assembled monolayers and supported lipid bilayers.

Molecular dynamics (MD) simulation is a powerful tool to the elucidation of events at short time scales and at the microscopic level.  Recent advances in algorithms and computational speed has allowed the investigation of complex systems in fully atomistic detail, including transmembrane proteins in lipid bilayers with explicit treatment of water and counter-ions.  Simulations provide valuable atomic-level insight that is not available experimentally.  Furthermore, the nature of simulation allows for the study of systems at extreme conditions (high temperature and pressure) that would otherwise remain inaccessible.  Current technological applications of simulation by our group include the development of novel surfactants for pressurized metered dose inhalers (da Rocha), sensing of chemical and biological agents with templated molecular recognition materials (Potoff) and the transport of bio-molecules in confined geometries (Manke).  Our group is well prepared to undertake this effort.  The da Rocha and Potoff research groups maintain dedicated Linux clusters of 18 and 56 CPUs, respectively for molecular simulation research.  Our group has extensive experience in molecular dynamics and the study of interfacial phenomena (da Rocha), code and algorithm development, force fields and ab initio calculations (Potoff), transport phenomena and dissipative particle dynamics (Manke).  The simulation group will utilize their expertise to support the center in three major areas:

 This collaboration complements the femtosecond spectroscopy data acquisition and analysis, and can also help in the assignment of the molecular modes and relaxation mechanisms.  For example, calculated MD trajectories will be analyzed to extract the H-bonding statistics (average number of H-bonds per water molecule), as a function of distance from the bilayer interface, in order to deconvolute frequency domain spectra of the OH-stretch band.  The ultrafast relaxation timescales will be modeled to elucidate the underlying molecular motions and how they are affected by the membrane surface and the chemical nature and concentration of the electrolyte.  Large-scale atomistic simulations also provide the necessary resolution to develop improved mean field potentials for the evaluation of mesoscopic phenomena that cannot be investigated currently by MD, and also to refine models for membrane proteins that constitute a large fraction of the human genome.  Thus the power and scope of nano and femto biosciences combined, in the study of cellular and molecular processes is profound, allowing for new discoveries in biology, and in the design and development of new nano and femto technologies.

Updated: 04/23/2008