### Seminar on Nanoscale Theory, Modeling, and Simulation

#### Schedule: Spring 2010

**Place:**

**Sumwalt 102**

Time:

Time:

**3:30-4:30pm**

**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

#### Abstract:

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.

References

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**

**Abstract:**

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
Systems
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.**

*******************************************************************************

#### Archive:

#### 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.