Lash Miller Chemical Laboratories
80 St. George St.
University of Toronto
Toronto, Ontario, Canada M5S 1A1
Phone: (416)-978-4376
Fax: (416)-978-8775
Office: Lash Miller, Room 239
E-mail: jmschofi@chem.utoronto.ca
The first project focuses mainly on the role of charge and aquation state in the determination of macromolecular structure in biological systems. There has been very little theoretical work on how the conformation of an isolated macromolecule depends on the number of excess charges bound to it, in spite of the fact that many protein and polypeptide molecules contain ions and are present in a variety of charge states at biological pH conditions. We are working on new molecular dynamics and Monte-Carlo simulation methods which are designed to reproduce the correct statics and dynamics of charged polypeptides and other molecules in which proton transfer is important. The goal of the work is to probe how the transitions between folded and extended conformers depend on temperature, aqueous solvation and charge state of the molecule.
Another area of interest is the nature of dynamics of systems with a rough energy landscape. Non-exponential relaxation, experimentally observed in the dynamics of dense glassy fluids and proteins, is a common feature of systems possessing a complex potential energy surface. From a kinetic perspective, such systems typically show significant departures from Arrhenius behavior. It is therefore interesting to try to understand which generic features of the potential energy surface lead to such complicated behavior. In particular, it is appealing to try to establish connections between gross topological features of the potential energy surface, such as funnels, and important dynamical events leading to structural relaxation. We have been working at establishing rigorous theoretical methods to elucidate the complex nature of dynamics in systems with rough energy landscape. In particular, recent work has focused on utilizing mode-coupling theory to provide a microscopic framework for examining dynamic heterogeneity in supercooled systems. Concurrently, we are conducting computer simulation studies to formulate good measures of various aspects of the dynamics.
S. Jalili, L. Karami and J. Schofield, Study of base pair mutations in proline-rich homeodomain (PRH)–DNA complexes using molecular dynamics, Eur. Biophys. J. 42, (2013)
S. Jalili, M. Akhavan and J. Schofield, Study of titanium adsorption on perfect and defected BC3 nanotubes using density function theory", Mol. Phys. 111, (2013)
R. Raghu and J. Schofield, "Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics", J. Chem. Phys. 137, 014901 (2012)
S. Jalili, M. Akhavan and J. Schofield, "Electronic and structural properties of BC3 nanotubes with defects ", J. Phys. Chem. C 116, 13225-13230 (2012)
H. Bayat Movahed, R. van Zon and J. Schofield, "Free energy landscape of protein-like chains with discontinuous potentials" , J. Chem. Phys. 136, 245103 (2012) (13 pages)
J. Schofield, P. Inder, and R. Kapral, "Modeling of solvent flow effects in enzyme catalysis under physiological conditions" , J. Chem. Phys. 136, 205101 (2012), (14 pages)
S. Jalili, C. Mochani, M. Akhavan and J. Schofield, "Molecular dynamics simulation of a graphite-supported copper nanocluster: thermodynamic properties and gas adsorption", Mol. Phys. 110, 267-276 (2012).
A. Kelly, R. van Zon, J. Schofield, and R. Kapral, "Mapping quantum-classical Liouville equation: Projectors and trajectories" , J. Chem. Phys. 136, 084101 (2012), (14 pages)
R. Raghu and J. Schofield, "Simulation of Pressure-Driven Flows in Nanochannels Using Multiparticle Collision Dynamics", J. Phys. Chem. C 114, 20659 - 20671 (2010)
R. van Zon and J. Schofield, "Constructing smooth potentials of mean force, radial distribution functions, and probability densities from sampled data" , J. Chem. Phys. 132, 154110 (2010), (13 pages)
R. van Zon, L. Hernandez de la Pena, G. Peslherbe and J. Schofield, "Quantum free energy differences from non-equilibrium path integrals. I. Methods and numerical application" , Phys. Rev. E 78, 041103 (2008), (11 pages)
R. van Zon, L. Hernandez de la Pena, G. Peslherbe and J. Schofield, "Quantum free energy differences from non-equilibrium path integrals. II. Convergence properties for the harmonic oscillator" , Phys. Rev. E 78, 041104 (2008), (14 pages)
R. van Zon and J. Schofield, "Event-driven dynamics of rigid bodies interacting via discretized potentials" , J. Chem. Phys. 128, 154119 (2008), (9 pages)
R. van Zon, I.P. Omelyan and J. Schofield, "Efficient algorithms for rigid body integration using optimized splitting methods and exact free rotational motion" , J. Chem. Phys. 128, 136102 (2008), (2 pages)
R. van Zon and J. Schofield, "Symplectic algorithms for simulations of rigid body systems using the exact solution of free motion" , Phys. Rev. E 75, 056701 (2007), (5 pages)
R. van Zon and J. Schofield, "Numerical implementation of the exact dynamics of free rigid bodies" , J. Comp. Phys. 225, 145-164 (2007)
L. Hernandez de la Pena, R. van Zon, J. Schofield and S. Opps, "Discontinuous molecular dynamics for semi-flexible and rigid bodies" , J. Chem. Phys. 126, 074105 (2007), (13 pages)
L. Hernandez de la Pena, R. van Zon, J. Schofield and S. Opps, "Discontinuous molecular dynamics for rigid bodies: Applications" , J. Chem. Phys. 126, 074106 (2007), (12 pages)
J. Schofield, "Quantum effects in ab-initio calculations of rate constants for chemical reactions occuring in the condensed phase" , Theor. Chem. Acc. 116, 18-30 (2006)
R. van Zon and J. Schofield, "Mode-Coupling Theory for Multiple-Time Correlation Functions of Tagged Particle Densities and Dynamical Filters Designed for Glassy Systems" , J. Phys. Chem. B 109, 21425 - 21436 (2005)
R. van Zon and J. Schofield, "Glassy dynamics and domains: Explicit results for the East model" , J. Chem. Phys. 122, 194502 (2005), (15 pages)
A. Plyukhin and J. Schofield, "Langevin equation for the extended Rayleigh model with an asymmetric bath", Phys. Rev. E 69, 021112 (2004), (7 pages)
A. Plyukhin and J. Schofield, "On the Langevin equation for the Rayleigh model with finite-ranged interactions", Phys. Rev. E 68, 041107 (2003), (15 pages)
R. Iftimie, D. Salahub and J. Schofield, "An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution" , J. Chem. Phys. 119 , 11285 - 11297 (2003)
R. Iftimie and J. Schofield, "The separation of quantum and classical behavior in proton transfer reactions: Implications from studies of secondary kinetic isotope effects", Int. Journal of Quantum Chemistry 91 , 404-413 (2003)
A. Plyukhin and J. Schofield, "Trapping, reflection and fragmentation in a classical model of atom-lattice collisions", Phys. Rev. E 65 , 026603 (2002), (8 pages)
S. Opps and J. Schofield, "Monte Carlo methods designed for parallel computation", To appear in the conference proceedings of High Performance Computer Systems and Applications, Kluwer Academic Press, 2002
C. C. Wan and J. Schofield, "Solutions of mixed quantum-classical dynamics in multiple dimensions using classical trajectories", J. Chem. Phys. 116, 494-506 (2002)
R. van Zon and J. Schofield, "A mode-coupling theory of multi-point and multi-time correlation functions", Phys. Rev. E 65 , 01106 (2002) (17 pages)
R. van Zon and J. Schofield, "Multiple-point and multiple-time correlation functions in a hard sphere liquid" , Phys. Rev. E 65 , 01107 (2002) (12 pages)
A. Plyukhin and J. Schofield, "Stochastic dynamics with a mesoscopic bath", Phys. Rev. E 64 , (2001) 041103 (10 pages)
R. Iftimie and J. Schofield, "Reaction mechanism and isotope effects derived from centroid transition state theory in intra-molecular proton transfer reactions", J. Chem. Phys. 115, (2001) 5891-5902
A. Plyukhin and J. Schofield, "A stochastic model related to the Klein-Gordon equation", Phys. Rev. E 64, (2001) 037101 (3 pages)
S. Opps and J. Schofield, "Extended state space Monte-Carlo methods", Phys. Rev. E 63, (2001) 56701-56712
R. Iftimie and J. Schofield, "Efficient ab initio sampling methods in rate constant calculations for proton-transfer reactions" J. Chem. Phys.114, (2001) 6763-6773
R. Iftimie, D. Salahub, D. Wei and J. Schofield, "Using a classical potential as an efficient importance function for sampling an ab-initio potential", J. Chem. Phys. 113, (2000) 4852-4862
C. C. Wan and J. Schofield, "Mixed quantum-classical molecular dynamics: Aspects of the multithreads algorithm", J. Chem. Phys. 113, (2000) 7047-7054
C. C. Wan and J. Schofield, "Exact and asymptotic solutions of the mixed quantum-classical Liouville equation", J. Chem. Phys. 112, (2000) 4447-4459
A. H. Marcus, J. Schofield and S. A. Rice, "Experimental Observations of Non-Gaussian Behavior and Stringlike Cooperative Dynamics in Concentrated Quasi-Two-Dimensional Colloidal Liquids", Phys. Rev. E. 60 ,5725-5736, 1999
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