Seminar on Nanoscale Theory, Modeling, and Simulation


Schedule: Spring 2010

Place:  Sumwalt 102


  • 1/27/10: Prof. Bill Poirier, Texas Tech U.
  • 2/3/10: Prof. Xiaoming Wang, Florida State University.
  • 2/24/10: Prof. Lishi Luo, Department of Mathematics, Old Dominion University.
  • 3/24/10: Prof. S. K. Saikin, Department of Chemistry and Chemical Biology, Harvard University
  • 3/31/10: Prof. Huanxiang Zhou, Department of Physics, Florida State University.
  • 4/14/10: Prof. Weitao Yang, Duke University.

******************************* Title and Abstract **********************************************

NTMS Seminar Sum 102, 3:30-4:30 pm on 4/14/2010.

Free energies and mechanisms of chemical reactions in enzymes and in
solution with QM/MM minimum free energy path

Prof. Weitao Yang, Duke University

Combined QM/MM methods provide an accurate and efficient energetic
description of complex chemical and biological systems, leading to
significant advances in the understanding of chemical reactions in solution
and in enzymes.  Ab initio QM/MM methods capitalize on the accuracy and
reliability of the associated quantum mechanical approaches, however at a
much higher computational cost compared with semiempirical quantum
mechanical approaches. Thus reaction path and activation free energy
calculations encounter unique challenges in simulation timescales and phase
space sampling.  Recent developments of the QM/MM minimum free energy path
method overcome these challenges and enable accurate free energy
determination for reaction processes in solution and enzymes.  The key is
the sequential sampling and optimization on the potential of mean force
surface. Applications to several enzymes will be featured.

H. Hu, Z. Y. Lu, and W. T. Yang, "Qm/mm minimum free-energy path:
Methodology and application to triosephosphate isomerase," Journal of
Chemical Theory and Computation, vol. 3, pp. 390-406, 2007.

H. Hu, Z. Y. Lu, J. M. Parks, S. K. Burger, and W. T. Yang, "Quantum
mechanics/molecular mechanics minimum free-energy path for accurate reaction
energetics in solution and enzymes: Sequential sampling and optimization on
the potential of mean force surface," Journal of Chemical Physics, vol. 128,
p. 034105, 2008.

H. Hu, A. Boone, and W. T. Yang, "Mechanism of OMP decarboxylation in
orotidine 5 '-monophosphate decarboxylase," Journal of the American Chemical
Society, vol. 130, pp. 14493-14503, 2008.

H. Hu and W. T. Yang, "Free energies of chemical reactions in solution and
in enzymes with ab initio quantum mechanics/molecular mechanics methods,"
Annual Review of Physical Chemistry, vol. 59, pp. 573-601, 2008.

X. C. Zeng, H. Hu, X. Q. Hu, and W. T. Yang, "Calculating solution redox
free energies with ab initio quantum mechanical/molecular mechanical minimum
free energy path method," Journal of Chemical
Physics, vol. 130, no. 16, p. 164111, 2009.


NTMS Seminar, SUM 102, 3:30-4:30 pm, 3/31/2010

Modeling Crowding Effects of Cellular Environments

Prof. Huan-Xiang Zhou, Physics Department, Florida State University


Inside cells proteins and other macromolecules are present at a very

high total concentration.  Such macromolecular crowding can

significantly change the biophysical and biochemical properties of

proteins.  In particular, crowding significantly shortens the lag times

of protein aggregation and protein polymerization.  In this talk I will

first give an overview of crowding effects.  I'll then present our

ongoing studies using in vitro experiments and atomistic simulations to

model crowding.


NTMS Seminar at SUM 102 on 3/24/2010

Electronic origin of surface-enhanced Raman scattering (SERS)

Dr. S. K. Saikin
Department of Chemistry and Chemical Biology, Harvard University

Raman scattering from molecules adsorbed on a rough noble metal surface is strongly enhanced as compared to neat samples. The achievable substrate-averaged enhancement is in the range of 10^7-10^9 times for non-resonantly probed analytes. This phenomenon, discovered about 30 years ago, can provide a high sensitivity and an extended selectivity to the design of novel chemical sensors.
There are two characteristic length scales associated with the signal enhancement. On a nanometer scale plasmonic excitations in the metal substrate concentrate optical fields. This process can be controlled experimentally by the design of the substrates and can be described theoretically by solving Maxwell equations for electromagnetic fields in a medium with a frequency-dependent dielectric constant. More controversial and less reproducible “chemical effects” appear on the atomic length scale and are associated with the molecule-surface binding.
I will discuss the role of chemical binding in the enhancement and distortion of Raman spectra using results of our recent computational studies of Raman response from metal-molecular structures. Also, I will try to introduce a theoretical approach to SERS that unifies both plasmonic and chemical contributions.


NTMS Seminar 2/24/10 at Sumwalt 102, 3:30 PM

Speaker: Prof. Lishi Luo

Department of Mathematics and Statistics, Center for Computational Sciences

Old Dominion University

This presentation will provide an introduction of the mathematical background of the lattice Boltzmann equation (LBE). I will first show the derivation of the LBE from the linearized Boltzmann equation. This allows us to understand the nature and the limitations of the lattice Boltzmann method for applications in computational  fluid dynamics (CFD). I will discuss a detailed comparison of the lattice Boltzmann (LB) and the pseudo-spectral (PS) methods for direct numerical simulations (DNS) of the decaying turbulence in a three dimensional periodic cube. Our results show that LBE is an explicit second-order scheme with relatively low numerical dissipation and dispersion. To demonstrate the versatility and efficacy of the LB method, I will also show some other applications using the LB method, such as particulate suspensions in fluids, multi-component fluids through porous media, and free-surface flows.


NTMS Seminar 1/27/10 at Sumwalt 102, 3:30 PM

Speaker: Prof. Bill Poirier
Dept of Chemistry & Biochemistry
Texas Tech University

Title: Quantum Dynamics of Hydrogen Interacting Exohedrally with
Single-Walled Carbon Nanotubes
Abstract: This work investigates the fundamental dynamical interactions of hydrogen
with single-walled carbon nanotubes, addressing possible ramifications
for hydrogen storage via the catalytic spillover mechanism. In the first
study, a single H atom is employed; spin-polarized density functional
theory (DFT) calculations are performed for a single hydrogen atom
interacting exohedrally with a (5,5) single-walled carbon nanotube (SWNT),
and also full 3D quantum dynamics calculations to compute all H atom bound
rovibrational states. The system exhibits a chemisorptive well-depth of
755 meV, which is unfavorably high for spillover; however, an unexpected
coherent quantum migration mechanism is revealed, which may account for
the experimentally observed reversibility of the adsorption/desorption
kinetics,  and enhancement at low temperatures and pressures. A subsequent DFT and
quantum dynamics study, performed under more realistic conditions of full
H-atom coverage, was also performed; the latter is characterized
by a similar quantum migration effect, but also overall energetics that
are much more favorable to spillover than the single H-atom case.


NTMS Seminar 2/3/10 at Sumwalt 102, 3:30 PM

Title:  Approximating Long Time Statistical Properties in Dissipative

Speaker: Xiaoming Wang

Affiliation: Florida State University

Abstract: It is well-known that physical laws for large chaotic systems
are revealed statistically. We consider temporal approximations of long
time statistical properties of dissipative chaotic systems. We demonstrate
that appropriately designed time discretizations are able to capture
asymptotically the long time statistical properties of the underlying
continuous dynamical systems. Applications to the infinite Prandtl number
model for convection will be discussed.



Schedule: Spring 2009

Place:  Sumwalt 102
Time:  3:00-4:00pm
  • 3/18/09: Jack Wells, ORNL.
  • 3/19/09: Weinan E, Princeton (IMI distinguished lecture; Location: LC 412).
  • 3/25/09: Jay Walton, Texas A&M.
  • 4/1/09: Alejandro Rey, McGill.
  • 4/3/09: Yanzhao Cao, Auburn U.
  • 4/15/09: Chun Liu, IMA/UMN/PSU.
  • 4/16/09: Stephen Irle.
  • 4/22/09: Adri  Duin, Penn St.
  • 4/29/09: Di Ventra, UCSD.