Robinson Group Monte Carlo Simulation Code
Legacy version, 05/16/12
Many of our simulations are run using an in-house Monte Carlo code designed for simulating ordering of polar molecules. We have released the code used for five of our papers published between 2010 and 2015 (DOIs: 10.1021/jp1010605, 10.1021/jp1022423, 10.1021/jp107995t, 10.1021/jp507736r, and 10.1021/acs.jpcb.5b00009) under the NCSA open source license, and it is available for download here (link to the right). The package contains brief documentation and usage examples. This code is configured for one or two-component systems of dipolar spheroids and should be usable on any system with a C++ compiler and standard C++ library. It has since been superseded an improved version developed by Andreas Tillack, which is designed for general molecular systems and automated fitting of coarse-grained parameters; this code is not yet available for public release.
High Dipole Moment Organic MaterialsHow can organic chromophores be processed on a large scale to produce highly efficient semi-conducting materials?
Organic chromophores, which have high dipole moments, are becoming increasingly important in electro-optic
applications. These materials may soon replace many of the metal oxides currently used in the semiconductor
industry. Their efficiency is limited however, by the inability of materials designers to fully orient large
arrays of such chromophores, as outlined in this
paper in Science,
As part of the NSF-funded Science and Technology Center
to develop materials for information technology, we are investigating the origin of the difficulty of alignment of
these materials using Monte Carlo methods of statistical mechanics. We have theoretically explained the experimental
observation that the large dipole moments make chromophore alignment at high concentrations impossible using current
strategies. The theoretical work parallels the experimental work, as we investigate the possible improvements in
performance by embedding chromophores into dendritic materials, or attaching them to polymeric backbones. We are
currently investigating methods to overcome the dipolar interactions that make alignment a problem. We are building
EPR-active analogs of the high dipole moments chromophores to directly measure the order of these large arrays.
Membrane Binding Proteins
What are the general principles used by signaling-proteins to recognize membrane surfaces?
We have used the "Spin Relaxant EPR" method to determine the orientations of several membrane-binding proteins
to the varied membrane surfaces. We have studied bee venom Phospholipase A2 (bvPLA2), and clearly determined that
the primary attachment site is near the active site of the enzyme. This provides a physical basis for the model of
bvPLA2 action - called the "scooting model" - which states that the enzyme remains attached but moves among sites
to cut the phospholipids.
We are looking at a variety of different proteins and mutants of those proteins to determine the motifs used by
signaling-proteins to recognize membrane surfaces. The systems being examined include the distress signaling
proteins Cytosolic Phospholipase A2 (cPLA2) (signaling production of eicosinoids and prostaglandins),
Phospholipase-C (the delta-1 isoform) (signaling calcium uptake and release), and Factor VIIIa (signaling
release of thrombin). Please see our
Docking Orientation of Bee Venom Phospholipase A2 as Determined by the Interaction of EPR
Spin Labels (Red/Blue Groups) with a Gradient of Ionic Spin Relaxants (not shown) Above the Membrane Surface.
Nucleic Acid Structures and Dynamics
What features of the structures of DNA are important in protein recognition?
In particular, the internal motions of DNA play a significant role in the energetics of DNA binding and protein
recognition. We study the modes of motion of DNA to determine the types of dynamics accessible to DNA. We have
developed a dynamic-sensitive probe that is sensitive to Electron Paramagnetic Resonance (EPR) Spectroscopy. The
probe is covalently linked to a base pair and may be incorporated into an oligomer of DNA at will. These probes
have been used to test the theories on elasticity, and determine the dependence of DNA flexibility on base
composition and sequence. To read more about how we determine the fundamental dynamic properties, please read our
from April, 2002.
We are using EPR and the spin labels to probe the structures of RNA, such as the TAR binding site, at a variety
of spin labeled sites and comparing the relative changes in dynamics of the spin probes when binding, by proteins
such as the TAT protein. See the articles in JACS, 2001, and 2002.
Single turn of duplex DNA wherein the base pairs have differntial flexibility dependening on
where a modification has been made in which a phosphate group (carrying a -1 charge) has been replaced by a
methylphosponate group which is uncharged.