**Publications by Research Area**

### Active Systems

- M.-J. Huang,
**J. Schofield**and R. Kapral, "Chemotactic and hydrodynamic effects on collective dynamics of self-diffusiophoretic Janus motors" ,*New J. Phys.*,**19**125003 (2017) - M.-J. Huang,
**J. Schofield**and R. Kapral, "Transport in active systems crowded by obstacles" ,*J. Phys. A: Math. Theor.***50**074001 (2017) (9 pages) - S.Y. Reigh, M.-J. Huang,
**J. Schofield**and R. Kapral, "Microscopic and continuum descriptions of Janus motor fluid flow fields" ,*Phil. Trans. R. Soc. A***374**, 20160140 (2016) (12 pages) - M.-J. Huang,
**J. Schofield**and R. Kapral, "A microscopic model for chemically-powered Janus motors" ,*Soft Matter***141**, 5581 (2016) (9 pages)

### Biophysics

- S. Jalili, A. Maleki, M. Akhavan, B. Najafi and
**J. Schofield,**"Free energy simulations of amylin I26P mutation in a lipid bilayer" ,*Eur. Biophys. J.***44**, 37 - 47 (2015) **J. Schofield**and H. Bayat, "Derivation of a Markov state model of the dynamics of a protein-like chain immersed in an implicit solvent" ,*J. Chem. Phys.***141**, 095101 (2014) (19 pages)- 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) - 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)

### Computational Methodology

**J. Schofield**, "Optimization and Automation of the Construction of Smooth Free Energy Profiles" ,*J. Phys. Chem. B*, (2017) (13 pages)- S.K. Burger, P.W. Ayers and
**J. Schofield**, "Efficient Parameterization of Torsional Terms for Force Fields" ,*J. Comp. Chem.***35**, 1438-1445 (2014) - S.K. Burger, P.W. Ayers and
**J. Schofield**, "Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting" ,*J. Phys. Chem. B***117**, 14960-14966 (2013) - R. Raghu and
**J. Schofield,**"Simulation of tethered oligomers in nanochannels using multi-particle collision dynamics",*J. Chem. Phys.***137**, 014901 (2012) - 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) - S. Opps and
**J. Schofield,**"Monte Carlo methods designed for parallel computation",*5th Ann. Symp. on High Performance Computing Systems and Applications, Kluwer Academic Press*, 2003 - 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,**"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 - S. Opps and
**J. Schofield,**"Extended state space Monte-Carlo methods",*Phys. Rev. E***63**, (2001) 56701-56712 **J. Schofield**and M. Ratner, "Monte-Carlo Methods For Short Polypeptides",*J. Chem. Phys.***109,**(1998) 9177-9191

### Nanomaterials

- S. Jalili, E. M. Goliaei, and
**J. Schofield,**, "Silver cluster supported on nitrogen-doped graphene as an electrocatalyst with high activity and stability for oxygen reduction reaction",*International J. of Hydrogen Energy***21**, 14522-14533 (2017). - S. Jalili, E. Moharramzadeh Goliaei, and
**J. Schofield,**, "K1.33Mn8O16 as an electrocatalyst and a cathode",*J. Solid State Chem.***246**, 388-398 (2017). - S. Jalili, M Akhavan, and
**J. Schofield,**"Effect of point defects on the properties of silicene-like BSi3 sheets from first-principles" ,*J. Phys. and Chem. of Solids***95**, 106-113 (2016)

- F. Molani , S. Jalili, and
**J. Schofield,**"A novel candidate for hydrogen storage: Ca-decorated zigzag C3N nanotube" ,*Int. J. Hydrogen Energy***41**, 7431 - 7437 (2016)

- M Akhavan, S. Jalili, and
**J. Schofield,**"Effect of diameter and chirality on the structure and electronic properties of BC2N nanotubes" ,*Chem. Phys.***455**, 88-93 (2015)

- F. Molani, S. Jalili, and
**J. Schofield,**"Computational study of interaction of alkali metals with C3N nanotubes" ,*J. Mol. Model***21**, 20 (2015) (7 pages)

- F. Molani, S. Jalili, and
**J. Schofield,**"A computational study of platinum adsorption on defective and non-defective silicon carbide nanotubes" ,*Monatsh. Chem.***146**, 883-890 (2015)

- S. Jalili, F. Houshmand, and
**J. Schofield,**"Study of carrier mobility of tubular and planar graphdiyne" ,*Appl. Phys. A***119**, 571-579 (2015)

- S. Jalili, F. Molani, M. Akhavan, and
**J. Schofield,**"Role of Defects on structural and electronic properties of zigzag C3N nanotubes: A first-principle study"*Physica E***56**, 54 (2014)

- S. Jalili, E. Hosseinzadeh and
**J. Schofield,**"Study of atomic and molecular oxygen chemisorption on BC3 nanotubes with Stone-Wales defects using density functional theory",*Chem. Phys.***438**, 16-22 (2014) - 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) - S. Jalili, M. Akhavan and
**J. Schofield,**"Electronic and structural properties of BC3 nanotubes with defects ",*J. Phys. Chem. C***116**, 13225-13230 (2012)

- 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).

- R. Raghu and
**J. Schofield,**"Simulation of Pressure-Driven Flows in Nanochannels Using Multiparticle Collision Dynamics",*J. Phys. Chem. C***114**, 20659 - 20671 (2010)

**J. Schofield**and S.A. Rice, "Backbone Ordering in Amphiphile Monolayers",*J. Chem. Phys*.**103**, (1995) 5792-5801.

### Mixed quantum-classical dynamics

- C.-Yu Hsieh,
**J. Schofield,**and R. Kapral, Forward-Backward solution of quantum-classical Liouville equation in the adiabatic mapping basis,*Mol. Phys.***111**, 3546-3554 (2013)

- 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)

**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. 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) - 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 - 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) - 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

### Glassy and frustrated systems

- 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)

- 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)

- 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)

- A. Plyukhin and
**J. Schofield,**"A stochastic model related to the Klein-Gordon equation",*Phys. Rev. E***64**, (2001) 037101 (3 pages) - 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

**J. Schofield**, A.H. Marcus and S.A. Rice, "The Dynamics of Quasi Two Dimensional Colloidal Suspensions",*J. Phys. Chem*.**100**, (1996) 18950-18961.**J. Schofield**and I. Oppenheim, "Mode Coupling in Nonequilibrium Granular Flow Systems",,*Physica***A 204**, (1994) 555-605**J. Schofield**and I. Oppenheim, "The hydrodynamics of inelastic granular systems"*Physica***A 196**, (1993) 209-240**J. Schofield**and I. Oppenheim, "Mode Coupling and tagged particle correlation functions: the Stokes-Einstein law",*Physica***A 187**, (1992) 210-242**J. Schofield**and I. Oppenheim, "Mode Coupling and generalized hydrodynamics",*Physica***A 181**, (1992) 89-135

This page is maintained by

*jmschofi@chem.utoronto.ca*

Created September 15, 1997. Last updated September, 2016.