Modeling shape and dynamics of polymers and biomolecules

Theory and computer simulations.

Our research interests cover all aspects of computer simulation of molecular shape and dynamics, from applications to methodology. The research goal is to understand dynamics and interactions for flexible molecules in various physico-chemical environments. Our methods combine quantum, classical, and statistical mechanics with novel ideas from molecular geometry and topology. These tools are applied to tackle fundamental issues in applications ranging from computer-aided molecular design to protein structure and dynamics.

Changes in chain entanglement show the onset of olding-unfolding transitions in cytochrome c. We have found that refolding is still possible in anhydrous proteins diffusing in a thermal bath with t-relaxation.

Current research projects are aimed at:

(1) Protein folding and polymer dynamics: Understanding the formation (and stability) of large-scale structural features in polymers. Our recent work deals with folding-unfolding transitions for proteins in vacuo and gas phase. Other projects deal with the simulation of phenomena such as polymer melting, polymer grafting and confinement in nanopores. In addition, we continue to develop the mathematical theory to produce efficient global descriptors of macromolecular shape. Emphasis is made on geometrical and knot-theoretical descriptors of biomolecular topology.

(2) Protein structure: Recognizing protein topologies, homologies in tertiary structure, and hydrogen-bonding architectures, and power-law scaling behaviour in protein shapes.

(3) Molecular similarity: Assessing the shape complementarity between small drug molecules and enzymatic receptor sites. Molecular lipo-philicity, flexibility, and electrostatics are used to model the pharmacological activity of a desired ligand. As well, we study the role of solvation and temperature on conformational flexibility and active site recognition.

Recent publications

G.A. Arteca, J.P. Rank and O. Tapia
Simulating trends in reaction path geometry as a function of external fields.  A generalized electronic diabatic model for two-dimensional energy surfaces. 
Int .J. Quantum Chem., 108: 1810-1820. (2008) [PDF] 

G.A. Arteca, J.P. Rank, and O. Tapia
Generalized electronic diabatic approach to structural similarity in two-dimensional potential energy surfaces of various topologies.
Int .J. Quantum Chem., 108: 651-666. (2008)

G.A. Arteca
Externally-steered relaxation of tight polyethylene tangles with various knot topologies
Theor. Chem. Accounts,  118 549-556. (2007)

G.A. Arteca and O. Tapia
A generalized electronic diabatic approach to structural similarity and the Hammond postulate.
Int. J. Quantum. Chem. 107 383-395. (2007)

G.A. Arteca
Folding complexity in a random-walk copolymer model.  (Book Chapter)
Physical and Numerical Methods in Knot Theory, Including Applications to the Life Sciences, J.A. Calvo, K.C. Milett, E.J.  Rawdon and A. Stasiak (eds.)
Series Knots and Everything, vol. 36: 233-256, World Scientific, River Edge, NJ (2005)

J.M. Kneller, C. Elvingson and G.A. Arteca
Shape transitions induced by mechanical external stretching of grafted self-attractive wormlike chains.
Chem. Phys. Lett., 407: 384-390. (2005)

Z. Li and G.A. Arteca
Simulated force-induced unfolding of α-helices: Dependence of stretching stability on primary sequence.
Phys. Chem. Chem. Phys, 7:2018-2026. (2005)

G.A. Arteca
Stress-induced shape transitions in grafted polymers with transient knotted loops.
Phys. Chem. Chem. Phys., 6 (2004) 3500-3507. [Pdf]

G.A. Arteca and O. Tapia
Comparison between a generalized electronic diabatic approach and the Born-Oppenheimer separation scheme in inertial frames
J. Math. Chem., 35 (2004) 1-19. [Abstract]

G.A. Arteca and O. Tapia
On the nature of the unfolded state: Competing mechanisms in the unfolding of anhydrous protein ions
Chem. Phys. Lett., 383 (2004) 462-468. [Pdf]

O. Tapia and G.A. Arteca
Generalized electronic diabatic theory and chemical topology: Conformational changes as a transition in electronic state.
Internet Electr. J. Molecular Design., 2 (2003) 454-474. [Pdf]

G.A. Arteca
A measure of folding complexity for D-dimensional polymers.
J. Chem. Inf. Comput. Sci., 43: 63-67. (2003) [Pdf]

T. Edvinsson, G.A. Arteca, & C. Elvingson 
Path-space ratio as a molecular shape descriptor of polymer conformation.
J. Chem. Inf. Comput. Sci., 43: 126-133. (2003) [Pdf]

G.A. Arteca, K. Veluri, and O. Tapia
Pathways for folding and re-unfolding transitions in denatured conformations of anhydrous proteins.
Chem. Phys. Lett., 350 (2003) 555-562. [Pdf]

G.A. Arteca and O. Tapia
Protein denaturation in vacuo. Intrinsic unfolding pathways associated with the native tertiary structure of lysozyme.
Mol. Phys., 101 (2003) 2743-2753. [Abstract]

G.A. Arteca
Analysis of shape transitions using molecular size descriptors associated with inner and outer regions of a polymer chain.
J. Mol. Struct.-Theochem, 630 (2003) 113-123. [Abstract]

G.A. Arteca
Stress-induced shape transitions in polymers using a new approach to steered molecular dynamics.
Phys. Chem. Chem. Phys., 5 (2003) 407-414. [Pdf]