Dmitrii
E. Makarov
Some of the recent topics that we have worked on are listed below
Quantum dynamics of single molecules
- D.E. Makarov and H. Metiu, Control, with a rf field, of photon emission times by a single molecule and its connection to laser-induced localization of an electron in a double well, J. Chem. Phys. 115 (2001) 5989. link to the article text
- D.E.
Makarov, Observation of single molecule transport at surfaces via
scanning microscopies:
- Z.S. Wang and D.E. Makarov, Nanosecond dynamics of single polypeptide molecules revealed by photoemission statistics of fluorescence resonance energy transfer: A theoretical study, J. Phys. Chem. B 107 (2003) 5617-5622. Link to text
Protein dynamics and folding
- D.E.
Makarov and H. Metiu, A model for the kinetics of protein folding:
Kinetic
- Z. S. Wang and D. E. Makarov, Rate of intramolecular contact formation in peptides: The loop length dependence, J. Chem. Phys. 117 (2002) 4591 link to text
- D.E. Makarov and G.J. Rodin, Configurational entropy and mechanical properties of cross-linked polymer chains, Implications for protein and RNA folding, Phys. Rev. E 66 (2002) 011908 link to text
- D.E. Makarov and K.W. Plaxco, The Topomer Search Model: A simple, quantitative theory of two-state protein folding kinetics, Protein Science 12 (2003) 17-26 link
- Serdal Krimizialtin, Venkat Ganesan, and Dmitrii E. Makarov, Translocation of a b-hairpin-forming peptide through a cylindrical tunnel, J. Chem. Phys. 121 (2004) 10268. link
- Z.S.
Wang, Kevin W. Plaxco and Dmitrii E. Makarov, Influence of local, residual structure on the scaling behavior and
dimensions of unfolded proteins, Biopolymers 86 (2007)
321-328 link
- Christina
L. Ting and Dmitrii E. Makarov, Two-dimensional
fluorescence resonance energy transfer as a probe for protein folding: A
theoretical study, J. Chem. Phys. 128 (2008) 115102
link
- Reza
Soheilifard, Dmitrii E. Makarov, and Gregory J. Rodin, Critical evaluation of simple network
models of protein dynamics and their comparison with crystallographic
B-factors, Physical Biology. 5 (2008) 026008. link
Single protein molecules
- D.E.
Makarov, P.K. Hansma, and H. Metiu,
Kinetic
- D.E.
Makarov, Z. Wang, J. Thompson, H.G. Hansma, On the interpretation of
force extension curves of single protein molecules, J. Chem. Phys. 116
(2002) 7760. Link
- D.E.
Makarov and G.J. Rodin, Configurational entropy and mechanical
properties of cross-linked polymer chains, Implications for protein and
RNA folding, Phys. Rev. E 66
(2002) 011908 link
to text
- Nathan Becker, Emin Oroudjev, Stephanie
Mutz, Jason Cleveland, Paul K. Hansma, Cheryl Y. Hayashi, Dmitrii E.
Makarov, and Helen Hansma, Molecular Nanosprings in Spider Capture-Silk
Threads, Nature Materials 2 (2003) 278
- Kilho
Eom, Pai-Chi Li, Dmitrii E. Makarov, and Gregory J. Rodin, Relationship
between the mechanical properties and topology of cross-linked polymer
molecules: Parallel strands maximize
the strength of model polymers and protein domains, J. Phys. Chem. B 107
(2003) 8730. Link
to text published online
- Pai-Chi
Li and Dmitrii E. Makarov, Theoretical studies of the mechanical
unfolding of the muscle protein titin: Bridging the time-scale gap between
simulation and experiment, J.
Chem. Phys 119 (2003) 9260. link
to text
- Pai-Chi
Li and Dmitrii E. Makarov, Ubiquitin-like protein domains show high
resistance to mechanical unfolding similar to that of the I27 domain in
titin: Evidence from simulations, J. Phys. Chem. B. 108 (2004)
745-749. link
- Pai-Chi
Li and Dmitrii E. Makarov, Simulation
of the mechanical unfolding of ubiquitin: Probing different unfolding
reaction coordinates by changing the pulling geometry, J. Chem. Phys. 121 (2004) 4826. link
- Kilho
Eom, Dmitrii E. Makarov, and Gregory J. Rodin, Theoretical studies of the kinetics of mechanical unfolding of
cross-linked polymer chains and their implications for single molecule
pulling experiments, Phys.
Rev. E 71, 021904 (2005).link
- Serdal Kirmizialtin, Lei Huang, and Dmitrii E.
Makarov, Topography of the free energy landscape probed via mechanical
unfolding of proteins, J. Chem. Phys. 122 (2005) 234915 link
- Pai-Chi
Li, Lei Huang, and Dmitrii E.
Makarov, Mechanical unfolding of
segment-swapped protein G dimer: Results from replica exchange molecular
dynamics simulations., J. Phys. Chem B. 110 (2006) 14469-14474 link
- Dmitrii
E. Makarov, New and Notable: unraveling
individual molecules by mechanical forces: Theory meets experiment,
Biophysical Journal, 92 (2007) 4135-4136 link (This is a commentary on this
paper)
- Dmitrii
E. Makarov, A theoretical model for
the mechanical unfolding of repeat proteins, accepted for publication
in Biophysical Journal. preprint
Protein translocation
- Serdal Krimizialtin, Venkat Ganesan, and Dmitrii E. Makarov, Translocation of a b-hairpin-forming peptide through a cylindrical tunnel, J. Chem. Phys. 121 (2004) 10268. link
- Lei Huang, Serdal Kirmizialtin, and Dmitrii E. Makarov, Computer simulations of the translocation and unfolding of a protein pulled mechanically through a pore, J. Chem. Phys. 123 (2005) 124903 link
- Serdal Kirmizialtin, Lei Huang, and
Dmitrii E. Makarov, Computer
simulations of protein translocation, Physica Status Solidi (b) 243 (2006) 2038-2047 link
- Carl P. Goodrich, Serdal
Kirmizialtin, Beatrice M. Huyghues-Despointes, Aiping Zhu, J.
Martin Scholtz, Dmitrii E. Makarov and Liviu Movileanu, Single-molecule
Electrophoresis of b-Hairpin-forming Peptides by
Electrical Recordings and Langevin Dynamics Simulations, 111 (2007) 3332-3335 link
- Lei Huang and Dmitrii E. Makarov, The rate constant of polymer reversal
inside a pore, J. Chem. Phys. 128 (2008) 114903 link
- Lei Huang
and Dmitrii E. Makarov, Translocation
of a knotted polypeptide through a pore, J. Chem. Phys. 129 (2008),
121107. link
- Dmitrii E. Makarov, Computer simulations and theory of protein translocation,
accepted for publication in Accounts of Chemical Research preprint
Translocation of a b-hairpin through the b-barrel part of the a-HL pore – simulations by Serdal
Kirmizialtin:
Dynamics of molecular knots
·
Serdal Kirmizialtin and Dmitrii E. Makarov, Simulations of the untying of molecular friction
knots between individual polymer strands, J. Chem. Phys. 128 (2008)
094901 link
- Lei
Huang and Dmitrii E. Makarov, Langevin
dynamics simulations of the diffusion of molecular knots in tensioned
polymer chains, J. Phys. Chem. A 111(2007) 10338-10344 link
Untying a square knot
between two polymer strands – simulation by Serdal Kirmizialtin
Untying a granny knot between two polymer strands
– simulation by Serdal Kirmizialtin
·
Diffusion
of a knot in a tensioned polymer chain, a simulation by Lei Huang
·
Translocation of knotted
and unknotted peptides through a pore –simulations by Lei Huang.
Absolute free energies from molecular dynamics
or Monte Carlo data
- Lei Huang and Dmitrii E. Makarov, On the calculation of absolute free energies from molecular dynamics or Monte Carlo data, J. Chem. Phys. 124, 064108 (2006). link
Quantum transition state theory
- V.A.
Benderskii, D.E. Makarov, and
- G.
Mills, G.K. Schenter, D.E. Makarov, and H. Jonsson, RAW quantum transition state theory, in ``Classical and
Quantum Dynamics in Condensed Phase Simulations'', ed. B. J. Berne, G.
Ciccotti and D. F. Coker (World Scientific, 1998).
Uses of genetic programming in physics and chemistry
- D.E. Makarov and H. Metiu, Fitting potential energy surfaces: a search in the function space by directed genetic programming, J. Chem. Phys. 108 590 (1998). link to the article text
- D.E. Makarov and H. Metiu, Using Genetic Programming To Solve the Schrödinger Equation, The Journal of Physical Chemistry A 104 (2000) 8540-8545. link to the article text