Volume 6 Issue 1 June 2007

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https://doi.org/10.33697/ajur.2007.006

Guest Opinion: Undergraduate Research at the University of Northern Iowa

https://doi.org/10.33697/ajur.2007.007

Author(s):

Joel K. Haack

Affiliation:

College of Natural Sciences, University of Northern Iowa, Cedar Falls, Iowa 50614-0181 USA


Identification, Optimization and Preliminary X-ray Diffraction of a New Crystal Form of the
N-terminal Domain of the HIV-1 CA Protein

https://doi.org/10.33697/ajur.2007.008

Author(s):

Ryan Van Woerkom, Andrew Dixon, Rob Oslund and Bruce R. Howard

Affiliation:

Department of Physical Science, Southern Utah University, Cedar City, Utah 84720 USA

ABSTRACT:

In an effort to better understand the detailed intersubunit interactions of the N-terminal Domain of the CA (capsid) protein from HIV-1 within the conical core of the mature virus, we have identified a novel crystal form of this domain and have optimized conditions to grow single protein crystals suitable for x-ray analysis. These high quality crystals diffract to better than 1.8 Å resolution on a rotating anode generator.


Particle Beam Waist Location in Plasma Wakefield Acceleration: Methods, Data and Discussion

https://doi.org/10.33697/ajur.2007.009

Author(s):

Adrian Down

Affiliation:

Department of Physics, University of California, Berkeley, California 94720-7300 USA

ABSTRACT:

The role of beam waist location in interactions between a plasma and a particle beam is not yet fully understood. Nonlinear effects with the plasma make an analysis of such interactions difficult. Five simulations are presented in this report, with the waist location of a beam of ultra-relativistic electrons propagating through one meter of self-ionized lithium plasma. The simulation parameters are chosen to model the recent experiment 167 at the Stanford Linear Accelerator, relevant to the design of future plasma wakefield accelerating afterburners. It is found that beams focused near the point of entry into the plasma propagate further into the plasma and accelerate witness particles to a greater maximum energy before disintegrating. These results could indicate that ion channel formation is dependent on the drive beam waist location and that the plasma accelerating medium can have an observable effect on the focusing of the drive beam.


Molecular Dynamics Simulations of Hexane Deposited onto Graphite: An Explicit–Hydrogen Model at ρ = 1 

https://doi.org/10.33697/ajur.2007.010

Authors and Affiliations:

M.J. Connolly and M.W. Roth
Department of Physics, University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

Carlos Wexler
Department of Physics and Astronomy, University of Missouri – Columbia, Columbia, Missouri 65211 USA

Paul A. Gray
Department of Computer Science, University of Northern Iowa, Cedar Falls, Iowa 50614-0507 USA

ABSTRACT:

We present the results of parallel Molecular Dynamics computer simulations of hexane (C6H14) adlayers physisorbed onto a graphite substrate in the density range 0.5 ≤ ρ ≤1 in units of monolayers, with emphasis on monolayer completion (ρ = 1). The hexane molecules are modeled to explicitly include hydrogens and the graphite is modeled as a six – layer all atom structure. In the explicit hydrogen simulations, the herringbone solid loses its orientational order at T1 = 140 °K, fairly consistent with results of UA simulations. However there is almost no nematic meso-phase or negative energy change at the loss of herringbone order. The explicit hydrogen melting temperature is T2 = 160 °K—somewhat lower than seen in experiment and in UA simulations. Generally, results for the all–atom model agree well with experiment, as the molecules remain overall flat on the substrate in the solid phase. At densities below about ρ = 0.875 the system supports a connected network which stabilizes it against thermal fluctuations and yields much more reasonable sub-monolayer- melting behavior. The united atom picture, on the other hand, departs significantly from experiment at most sub-monolayer- densities and gives melting temperatures several decades below what is experimentally observed. The purpose of this work is to compare the results of UA and explicit hydrogen MD simulations of hexane on graphite mainly at ρ = 1, to discuss cursory explorations at sub-monolayer- densities and mention open questions related to the system that are worth pursuing. Various structural and thermodynamic order parameters and distributions are presented in order to outline such differences.