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 ?-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.
Some
recent representative publications:
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, (2003) “A measure of folding
complexity for D-dimensional polymers.”
J. Chem. Inf. Comput. Sci., 43: 63-67.[Pdf]
T.
Edvinsson, G.A. Arteca, & C. Elvingson
(2003) “Path-space ratio as a molecular
shape descriptor of polymer conformation.”
J. Chem. Inf. Comput. Sci., 43: 126-133.[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]
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