The static structure factor of amorphous silicon and vitreous silica (2009)
Liquids are in thermal equilibrium and have a non-zero static structure factor S(Q->0) = [-^2]/ = rho*k_B*T*Chi_T where rho is the number density, T is the temperature, Q is the scattering vector and...
Modeling Correlated Main-Chain Motions in Proteins for Flexible Molecular Recognition (2008)
Maria I. Zavodszky, Ming Lei, M. F. Thorpe, Anthony R. Day, Leslie A. Kuhn
ABSTRACT We describe a new method for modeling protein and ligand main-chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational...
Constraint Theory applied to Proteins (2008)
Mykyta Chubynsky, On Hespenheide, Donald J. Jacobs, Leslie A. Kuhn, Ming Lei, A. J. Rader, ...
In this article we review how constraint theory can be applied to proteins to give useful information about the rigid and flexible regions. This approach includes all the constraints in a biomolecule...
Flexibly Screening For Molecules Interacting With Proteins (2007)
M. F. Thorpe, Volker Schnecke, Leslie A. Kuhn
INTRODUCTION Flexibility in Proteins and Their Interactions The flexibility of proteins and their ligands (molecules specifically bound by proteins) has a major influence on the ways they interact....
Hierarchical Rigidity from Pair Distance Fluctuations (2007)
Menor, Scott, Kilfoil, Maria, Thorpe, M. F.
Often, experiments, observations or simulations generate large numbers of snapshots of the configurations of complex many-particle systems. It is important to find methods of extracting useful...
Algorithms for 3D rigidity analysis and a first order percolation transition (2007)
Chubynsky, M. V., Thorpe, M. F.
A fast computer algorithm, the pebble game, has been used successfully to study rigidity percolation on 2D elastic networks, as well as on a special class of 3D networks, the bond-bending networks....
Running title: Coarse Graining for Biomolecular Motion (2006)
This un-edited manuscript has been accepted for publication in Biophysical Journal and is freely available on BioFast at
Self-Organization and the Physics of Glassy Networks (2005)
Boolchand, P., Lucovsky, G., Phillips, J. C., Thorpe, M. F.
Network glasses are the physical prototype for many self-organized systems, ranging from proteins to computer science. Conventional theories of gases, liquids, and crystals do not account for the...
Elliott,R. J., Timmesfeld,K-H., Thorpe,M. F.
Three rather separate projects related to the properties of defects in crystals have been pursued during the year. (1) The effect of defects on the thermal expansion of crystals. It has been shown...
Constrained Geometric Simulation of Diffusive Motion in Proteins (2005)
Stephen Wells, Scott Menor, On Hespenheide, M F Thorpe
We describe a new computational method, FRODA (framework rigidity optimized dynamic algorithm), for exploring the internal mobility of proteins. The rigid regions in the protein are first determined,...
Sampling protein conformations and pathways (2004)
Ming Lei, Maria I. Zavodszky, Leslie A. Kuhn, M. F. Thorpe
Protein flexibility and rigidity can be analyzed using constraint theory, which views proteins as 3D networks of constraints involving covalent bonds and also including hydrophobic inter-actions and...
Protein flexibility and folding / edited by Leslie A. Kuhn and Michael F. Thorpe (2001)
Papers from the Workshop on protein flexibility and folding, Traverse City, Mich. August 13-17, 2000
Petkov, V., Jeong, I-K., Chung, J. S., Thorpe, M. F., Kycia, S., Billinge, S. J. L.
High real-space resolution atomic pair distribution functions (PDF)s from the alloy series Ga_1-xIn_xAs have been obtained using high-energy x-ray diffraction. The first peak in the PDF is resolved...
PREDICTING THE ELASTIC PROPERTIES OF COMPOSITE MATERIALS. (1998)
Davis, L. C., Chen, J., Thorpe, M. F.
Proceedings of the 7th Technical Conference of the American Society for Composites; Held at University Park, Pennsylvania, Oct 1992; Technomic Publishing Company : Lancaster, Pennsylvania
Floppy modes and the free energy: Rigidity and connectivity percolation on Bethe Lattices (1998)
Duxbury, P. M., Jacobs, D. J., Thorpe, M. F., Moukarzel, Cristian F.
We show that negative of the number of floppy modes behaves as a free energy for both connectivity and rigidity percolation, and we illustrate this result using Bethe lattices. The rigidity...
North-Holland VIBRATIONAL THRESHOLDS IN COVALENT NETWORKS (1990)
P. Boolchand, R. N. Enzweiler, Y. Cai, M. F. Thorpe
Vibrational thresholds in covalent networks predicted theoretically have been observed in chalcogenide glasses. The experi-ments have included M6ssbauer-Debye-Waller factors, inelastic neutron...
Excitations in disordered systems / edited by M. F. Thorpe (1982)
Proceedings of a NATO Advanced Study Institute on Excitations in Disordered Systems, held August 23-September 4, 1981 at the Kellogg Center, Michigan State University, East Lansing. Michigan"
Static properties of a random one-dimensional magnet (1975)
The thermodynamic properties of a random classical Heisenberg chain with two kinds of atoms are calculated exactly. The wave vector dependent susceptibility is also obtained. Detailed numerical...
Static properties of a random one-dimensional magnet (1975)
The thermodynamic properties of a random classical Heisenberg chain with two kinds of atoms are calculated exactly. The wave vector dependent susceptibility is also obtained. Detailed numerical...
Static properties of a random one-dimensional magnet (1975)
The thermodynamic properties of a random classical Heisenberg chain with two kinds of atoms are calculated exactly. The wave vector dependent susceptibility is also obtained. Detailed numerical...
Protein unfolding: Rigidity lost
Rader, A. J., Hespenheide, Brandon M., Kuhn, Leslie A., Thorpe, M. F.
We relate the unfolding of a protein to its loss of structural stability or rigidity. Rigidity and flexibility are well defined concepts in mathematics and physics, with a body of theorems and...
Protein unfolding: Rigidity lost
Rader, A. J., Hespenheide, Brandon M., Kuhn, Leslie A., Thorpe, M. F.
We relate the unfolding of a protein to its loss of structural stability or rigidity. Rigidity and flexibility are well defined concepts in mathematics and physics, with a body of theorems and...
A Natural Coarse Graining for Simulating Large Biomolecular Motion
Various coarse graining schemes have been proposed to speed up computer simulations of the motion within large biomolecules, which can contain hundreds of thousands of atoms. We point out here that...
Fitting Low-Resolution Cryo-EM Maps of Proteins Using Constrained Geometric Simulations
Jolley, Craig C., Wells, Stephen A., Fromme, Petra, Thorpe, M. F.
Recent experimental advances in producing density maps from cryo-electron microscopy (cryo-EM) have challenged theorists to develop improved techniques to provide structural models that are...