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Publication list by area

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List by Research Areas/Themes 


A. On crystals, liquid crystals, and colloids


A30. Y. Sun, P. Padmanabhan, M. Misra, and F.A. Escobedo, “Molecular dynamics simulation of thermotropic bolaamphiphiles with a swallow-tail lateral chain: formation of cubic network phases” Soft Matter 13, 8542-8555 (2017) . DOI:10.1039/C7SM01819C.

A29. C. Avendano and F. A. Escobedo, “Packing and self-assembly of non-convex colloidal particles: a simulation perspective”, Current Opinion in Colloid & Interface Sci30, 62-69 (2017).

A28. F.A. Escobedo, “Optimizing the formation of colloidal compounds with components of different shape”, J. Chem. Phys. 147, 214501 (2017).

A27. F.A. Escobedo, “Optimizing the formation of solid solutions with components of different shapes”, J. Chem. Phys. 146, 134508 (2017). DOI: 10.1063/1.4979091.

A26. C. Avendano, G. Jackson, E.A. Muller, and F.A. Escobedo, "Assembly of highly open smectic structures formed from interlocking high-symmetry planar nanorings", Proc. Natl. Acad. Sci., USA 113, 9699-9703 (2016).  DOI:10.1073/pnas.1604717113

A25. F.A. Escobedo, "Effect of inter-species selective interactions on the thermodynamics and nucleation free-energy barriers of a tessellating polyhedral compound", J. Chem. Phys. 145, 1211903 (2016). Highlighted as JCP Editors' pick. DOI: 10.1063/1.4953862 

A24. M. Khadilkar and F.A. Escobedo, "Phase behavior of polyhedral nanoparticles in parallel plate confinement", Soft Matter 12, 1506 (2016). [Published online, Dec. 2015]. DOI:10.1039/c5sm02570b 

A23. V. Thapar, T. Hanrath, and F. A. Escobedo, "Entropic self-assembly of freely rotating polyhedral particles confined to a flat interface", Soft Matter11, 1481 (2015).

A22. K. Muangnapoh, C. Avendano, F.A. Escobedo, and C. Liddell-Watson "Degenerate crystals from colloidal dimers under confinement", Soft Matter10, 9729-38 (2014). 

A21. V. Thapar and F.A. Escobedo, "Extensions of the interfacial pinning method and application to hard core systems", J. Chem. Phys. 141, 124117 (2014).

A20. M. Khadilkar and F.A. Escobedo, "Heuristic rule of binary superlattice co-assembly: Mixed plastic mesophases of hard polyhedral nanoparticles", Phys. Rev. Lett. 113, 165504 (2014). DOI: 

A19. V. Thapar and F.A. Escobedo, "Localized orientational order chaperones the nucleation of Rotator phases in hard polyhedral particles",Phys. Rev. Lett.112, 048301 (2014).

A.18 N. Y. C. Lin, S. Goyal, X. Cheng, R.N. Zia, F.A. Escobedo, and I. Cohen, "Far-from-equilibrium sheared colloidal liquids: Disentangling relaxation, advection, and shear-induced diffusion", Phys. Rev. E 88, 062309 (2013). 

A17. M. Khadilkar, U. Agarwal, and F.A. Escobedo, "Phase behavior of binary mixtures of hard convex polyhedra", Soft Matter 9, 11557 (2013).

A16.  C. Avendano, C.M. Liddell Watson, and F.A. Escobedo, "Directed self-assembly of spherical caps via confinement", Soft Matter 9, 9153-66 (2013).

A15.  M. Khadilkar and F.A. Escobedo, "Self-assembly of binary space-tessellating compounds", J. Chem. Phys. 137, 194907 (2012).

A14.  U. Agarwal and F.A. Escobedo, "Effect of quenched size polydispersity on the ordering transitions of hard polyhedral particles", J. Chem. Phys. 137, 024905 (2012).

A13.  U. Agarwal and F.A. Escobedo, "Yielding and shear induced melting of 2D mixed crystals of spheres and dimers", Soft Matter 8, 5916 (2012).

A12.  C. Avendaño and F.A. Escobedo, "Phase behavior of rounded hard squares", Soft Matter 8, 4675 (2012).

A11.  U. Agarwal and F.A. Escobedo, "Mesophase behavior of polyhedral particles", Nature Materials 10, 230 (2011).

A10.  S. J. Gerbode, U. Agarwal, D.C. Ong, C.M. Liddell, F.A. Escobedo and I. Cohen, "Glassy dislocation dynamics in colloidal dimer crystals", Phys. Rev. Lett. 105, 078301 (2010).

A9.  A.J. Crane, F.J. Martinez-Veracoechea, F.A. Escobedo and E.A. Muller "Molecular dynamics simulation of the mesophase behaviour of a model bolaamphiphilic liquid crystal with a lateral flexible chain", Soft Matter 4, 1820 (2008).

A8.  I.D. Hosein, B.S. John, S.H. Lee, F.A. Escobedo and C.M. Liddell, "Rotator and crystalline films via self-assembly of short-bond length colloidal dimers", J. Mat.Chem. 19, 344 (2009).

A7.  S.H. Lee, S.J. Gerbode, B.S. John, A.K. Wolfang, I. Cohen, F.A. Escobedo and C.M. Liddell, "Synthesis and assembly of nonspherical hollow silica colloids under confinement", J. Mater. Chem. 18, 4912 (2008).

A6.  B.S. John, C. Juhlin and F.A. Escobedo, "Phase behavior of colloidal hard perfect tetragonal parallelepides", J. Chem. Phys. 128, 044909 (2008).

A5.  B. John and F.A. Escobedo "Phase behavior of hard colloidal tetragonal prisms - A Monte Carlo simulation study", J. Phys. Chem. B 109, 23008 (2005).

A4.  F.A. Escobedo and Z. Chen, "Liquid crystalline behavior of a semifluorinated oligomer", J. Chem. Phys. 121, 11463 (2004).

A3.  B. John, A. Stroock and F.A. Escobedo, "Cubatic Liquid crystalline behavior in a system of hard cuboids", J. Chem. Phys. 120, 9383 (2004).

A2.  F.A. Escobedo, "Lyotropic isotropic-nematic transitions in polydisperse chain systems; A simulation study", J. Chem. Phys. 118, 10262 (2003).

A1. F.A. Escobedo and J.J. de Pablo, "Monte Carlo Simulation of Athermal Mesogenic Chains. Pure Systems, Mixtures, and Constrained Environments", J. Chem. Phys. 106, 9858 (1997).


C. On block copolymers


C10. P. Padmanabhan, F. Martinez-Veracoechea, and F.A. Escobedo, "Computation of free-energies of cubic bicontinuous phases for blends of diblock copolymer and selective homopolymer", Macromolecules 49, 5232-5243 (2016). DOI: 10.1021/acs.macromol.6b00123 

C9.  P. Padmanabhan, M. Chavis, C. K. Ober, and F. A. Escobedo, "Phase behavior of PMMA-b-PHEMA with solvents methanol and THF: modelling and comparison to experiments, Soft Matter 10, 6172-6181 (2014). 

C8.  P. Padmanabhan, F. Martinez-Veracoechea, J.C. Araque, and F.A. Escobedo, "A theoretical and simulation study of the self-assembly of a binary blend of diblock copolymers",J. Chem. Phys.136, 234905 (2012).

C7.  V. Kalra, F. A. Escobedo and Y.L. Joo, "Effect of shear on nanoparticle dispersion in polymer melts: A coarse-grained molecular dynamics study", J. Chem. Phys. 132, 024901 (2010).

C6.  F. Martinez-Veracoechea and F.A. Escobedo, "The Plumber's Nightmare Phase in DBC/Homopolymer blends. A Self-Consistent Field Theory Study", Macromolecules 42, 9058  (2009).

C5.  F. Martinez-Veracoechea and F.A. Escobedo, "Bicontinuous Phases in Diblock Copolymer/ Homopolymer Blends: Simulation and Self-Consistent Field Theory", Macromolecules 42, 1775 (2009).

C4.  V. Kalra, S. Mendez, F.A. Escobedo and Y.L. Yoo "Coarse-grained molecular dynamics simulation on the placement within symmetric diblock copolymers under flow", J. Chem. Phys. 128, 164909 (2008).

C3.  F. Martinez-Veracoechea and F.A. Escobedo "Monte Carlo study of the stabilization of complex bicontinuous phases in Diblock Copolymer Systems" Macromolecules 40, 7354 (2007).

C2.  F. Martinez-Veracoechea and F.A. Escobedo, "Simulation of the Gyroid phase in off-lattice models of pure diblock copolymer melts", J. Chem. Phys. 125, 104907 (2006).

C1.  F.J. Martinez-Veracoechea and F.A. Escobedo "Lattice Monte Carlo simulations of the Gyroid phase in monodisperse and bidisperse block copolymer systems", Macromolecules, 38, 8522 (2005).


D. On microscopic and macroscopic behavior of oligomers and polymers

D14. C. Liu, K. Kubo, E. Wang, F. Yang, G. Chen, F.A. Escobedo, G.W. Coates, and P. Chen, “Single polymer growth dynamics”, Science 358, 352-355 (2017). DOI: 10.1126/science.aan6837.

D13. S. Turgman-Cohen, E. Giannelis, and F.A. Escobedo "Transport properties of amine/Carbondioxide reactive mixtures and implications to carbon capture technologies", ACS Appl. Mater. Interfaces 7, 17603 (2015).

D12.  K. Hur, R.G. Hennig, F.A. Escobedo, and U. Wiesner, "Predicting Chiral Nanostructures, Lattices and Superlattices in Complex Multicomponent Nanoparticle Self-Assembly", Nano Letters 12, 3218 (2012).

D11.  S. Goyal and F.A. Escobedo, "Structure and transport properties of polymer grafted nanoparticles", J. Chem. Phys. 135, 184902 (2011).

D10.  B. Hong, F. A. Escobedo and A.Z. Panagiotopoulos, "Diffusivities and Viscosities of Poly(ethylene oxide) Oligomers", J. Chem. Eng. Data 55, 4273 (2010).

D9.  M. Kobaslija, A.R. Bogdan, S.L. Poe, F.A. Escobedo and D.T. McQuade, "Creating microenvironments using encapsulated polymers", J. Polymer Sci. A 46, 2309 (2008).

D8.  Z. Chen, I. Gospodinov and F.A. Escobedo, "Monte Carlo simulation of the topology and conformational behavior of hyperbranched molecules: Pd-Diimine catalyzed polyethylene", Macromol. Theory & Simul. 11, 126 (2002).

D7.  F.A. Escobedo and J.J. de Pablo, "On the Scaling of the Upper Critical Solution Temperature of Binary Polymer Blends with Chain Length", Macromolecules 32, 900 (1999).

D6. S.K. Nath, F.A. Escobedo and J.J. de Pablo, "Simulation of Phase Equilibria for Alkane Mixtures", Ind. Eng. Chem. Res. 37, 3195 (1998).

D5. S.K. Nath, F.A. Escobedo and J.J. de Pablo, "On the Simulation of Vapor-Liquid Equilibrium for Alkanes", J. Chem. Phys. 108, 9905 (1998).

D4. J.K. Suen, F.A. Escobedo and J.J. de Pablo, "Monte Carlo Simulation of Polymer Chain Collapse in an Athermal Solvent", J. Chem. Phys. 106, 1288 (1997).

D3.  F.A. Escobedo and J.J. de Pablo, "Simulation and Prediction of Vapour-Liquid Equilibria for Chain Molecules", Molec. Phys. 87, 347 (1996).

D2.  F.A. Escobedo and J.J. de Pablo, "Simulation of Chain Molecules for Prediction of Thermodynamic Properties", Fluid Phase Equil. 116, 312 (1996).

D1.  F.A. Escobedo and J.J. de Pablo, "Chemical Potential and Equations of State of Hard Core Chain Molecules", J. Chem. Phys. 103, 1946 (1995).


E. On the TENSILE behavior of networks and elastomers

E17. C. Nowak and F.A. Escobedo, “Optimizing the network topology of block copolymer liquid crystal elastomers for enhanced extensibility and toughness”, Physical Rev. Materials 1, 0356601 (2017). DOI:

E16. E. Wang and F.A. Escobedo, “Swelling and Tensile Properties of Tetra-Polyethylene Glycol via Coarse-grained Molecular Models”, Macromolecular Theory and Simulation 26, 1600098, (2017). DOI: 10.1002/mats.201600098.

E15. C. Nowak and F.A. Escobedo, "Tuning the saw-tooth tensile response and toughness of multiblock copolymer diamond networks", Macromolecules 49 , 6711-6721 (2016). DOI: 10.1021/acs.macromol.6b00733 

E14. E. Wang and F.A. Escobedo, "Mechanical properties of tetra-polyethylene and tetra-polyethylene oxide diamond networks via molecular dynamics simulations", Macromolecules 49, 2375-2386 (2016). DOI: 10.1021/acs.macromol.5b02516 

E13.  B. M. Aguilera-Mercado, C. Cohen, and F. A. Escobedo, "Saw-tooth Tensile Response of Model Semi-flexible and Block-Copolymer Elastomers", Macromolecules 47, 840-850 (2014).

E12.  B. M. Aguilera-Mercado, G. D. Genesky, F. A. Escobedo, T. M. Duncan and C. Cohen, "2H-NMR and Simulation Studies of Chain Segment Orientation in PDMS Bimodal Networks", Macromolecules43, 7173 (2010).

E11.  B. Aguilera, C. Cohen and F.A. Escobedo "Segment orientation distributions in polymer networks via inversion of 2H-NMR spectra through the Maximum-Entropy method", Macromolecules 42, 8889 (2009).

E10.  G.D. Genesky, B.M. Aguilera-Mercado, D.M. Bhawe, F.A. Escobedo and C. Cohen "Experiments and Simulations: Enhanced Mechanical Properties of End-Linked Bimodal Elastomers", Macromolecules 41, 8231 (2008). 

E9.  D. Bhawe, C. Cohen and F.A. Escobedo, "Effect of chain stiffness and entanglements on the elastic behavior of model elastomers", J. Chem. Phys. 123, 014909 (2005).

E8.  D. Bhawe, C. Cohen and F.A. Escobedo, "Step-wise elastic behavior in a model elastomer", Phys. Rev. Lett. 93, 257804 (2004).

E7.  D. Bhawe, C. Cohen and F.A. Escobedo, "Formation and characterization of semi-flexible networks via Monte Carlo simulations", Macromolecules 37, 3924 (2004).

E6.  Z. Chen, C. Cohen and F.A. Escobedo, "Monte Carlo simulation of the effect of entanglements on the swelling & deformation of end-linked polymeric networks", Macromolecules 35, 3296 (2002).

E5. F.A. Escobedo and J.J. de Pablo, "Molecular Simulation of Polymeric Networks and Gels: Phase behavior and Swelling", Physics Reports 318, 85 (1999).

E4. F.A. Escobedo and J.J. de Pablo, "Simulation of Swelling in Polymeric Gels with Sub- & Super-critical Solvents", J. Chem. Phys. 110, 1290 (1999).

E3. F.A. Escobedo and J.J. de Pablo, "Simulation and Theory of the Swelling of Athermal Gels", J. Chem. Phys. 106, 793 (1997).

E2. F.A. Escobedo and J.J. de Pablo, "Phase Behavior of Model Polymeric Networks and Gels", Molec. Phys. 90, 437 (1997).

E1. F.A. Escobedo and J.J. de Pablo, "Monte Carlo Simulation of Branched and Crosslinked Polymers", J. Chem. Phys. 104, 4788 (1996).


F. On interfacial & FLUID properties and systems

F13. U. Gupta, T. Hanrath, and F.A. Escobedo, “Modeling the orientational and positional behavior of polyhedral nanoparticles at fluid-fluid interfaces”, Phys. Rev. Materials 1, 055602 (2017).

F12. L. Stutzman, J.W. Tester and F.A. Escobedo, “Heat capacities of supercritical fluids via Grand Canonical ensemble”, Molecular Simulation 44, 147-155 (2017).

F11. M.P.E. Ishmael, L.B. Stutzman, M.Z. Lukawski, F.A. Escobedo, and J.W. Tester, “Heat capacities of supercritical fluid mixtures: Comparing experimental measurements with Monte Carlo molecular simulations for carbon dioxide-methanol mixtures”, J. Supercritical Fluids 123, 40-49 (2017); available online 15 December, 2016. DOI:10.1016/j.supflu.2016.11.013.

F10. B. Savoy and F.A. Escobedo, "Molecular simulation of the effects of humidity and interfacial Si- and B-hydroxyls on the adhesion energy between glass plates", J. Colloid & Interface Sci. 465, 233-241 (2016). DOI:10.1016/j.jcis.2015.11.024.

F9.  S. Turgman-Cohen, J.C. Araque, E. Hoek, and F.A. Escobedo, "Molecular Dynamics of Equilibrium and Pressure-Driven Transport Properties of Water through LTA-type Zeolites", Langmuir 29, 12389-99 (2013).

F8.  B. Savoy and F.A. Escobedo, "Simulation study of free-energy barriers in the wetting transition of an oily fluid on a rough surface with re-entrant geometry", Langmuir28, 16080-90 (2012).

F7.  S. L. Meadley and F.A. Escobedo, "Thermodynamics and kinetics of bubble nucleation: Simulation methodology", J. Chem. Phys. 137, 074109 (2012).

F6.  B. Savoy and F.A. Escobedo, "Molecular simulations of wetting of a rough surface by an oily fluid: Effect of topology, chemistry and droplet size on wetting transition rates", Langmuir 28, 3412 (2012).

F5.  D. Choudhary, P. Clancy, R. Shetty and F.A. Escobedo "Computational study of sub-monolayer growth of pentacene", Advanced Functional Materials 16, 1768 (2006).

F4.  Z. Chen and F.A. Escobedo, "Influence of polymer architecture and polymer-wall interaction on partitioning of polymers into a slit", Phys. Rev. E, 69, 021802 (2004).

F3.  Z. Chen and F.A. Escobedo, "Simulation of chain-length partitioning in a microfabricated channel via entropic trapping", Molecular Simulation 29, 417 (2003).

F2.  Z. Chen and F.A. Escobedo, "Conformational Properties and Entropic Partitioning of Topologically Complex Polymers under Confinement", Macromolecules 34, 8802 (2001).

F1. F.A. Escobedo, D.S. Fryer and J.J. de Pablo, "Study of Thermophysical properties of Ultrathin Photoresist Films", Proc. SPIE  3332, 735 (1998).


G. On new simulation methods for material property predictions

G30. L. Stutzman, J.W. Tester and F.A. Escobedo, “Heat capacities of supercritical fluids via Grand Canonical ensemble”, Molecular Simulation, (2017).

G29. V. Thapar and  F.A. Escobedo, "Simultaneous estimation of free energies and rates using Forward Flux Sampling and Mean First Passage Times", J. Chem. Phys. 143, 244113 (2015).

G28. F.A. Escobedo, "Mapping coexistence lines via free-energy extrapolation. Application to order-disorder phase transitions of hard-core mixtures", J. Chem. Phys. 140, 094102 (2014).

G27. E.E. Borrero and F.A. Escobedo, "Simulating the kinetics and thermodynamics of transitions via forward flux/umbrella sampling", J. Phys. Chem. B 113, 6434 (2009).

G26. E. E. Borrero and F.A. Escobedo "Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes",J. Chem. Phys.129, 024115 (2008).

G25.  F.A. Escobedo and F.J. Martinez-Veracoechea "Optimization of expanded ensemble methods", J. Chem. Phys.129, 154107 (2008).

G24.  F.J. Martinez-Veracoechea and F.A. Escobedo "Variance Minimization of Free Energy Estimates from Optimized Expanded Ensembles", J. Phys. Chem. B. 112, 8120 (2008).

G23.  E. E. Borrero and F.A. Escobedo "Reaction coordinates and transition pathways of rare events via forward flux sampling", J. Chem. Phys. 127, 164101 (2007).

G22.  F.A. Escobedo and F. Martinez-Veracoechea, "Optimized expanded ensembles for simulations involving molecular insertions & deletions. I. closed systems", J. Chem. Phys. 127, 174103 (2007).

G21.  F.A. Escobedo  "Optimized expanded ensembles for simulations involving molecular insertions and deletions. II. Open systems", J. Chem. Phys. 127, 174104 (2007).

G20.  F.A. Escobedo and C.R.A. Abreu, "On the use of Transition Matrix methods with extended ensembles", J. Chem. Phys. 124, 104110 (2006).

G19.  I. Gospodinov and F.A. Escobedo "Probability density of macrostates and density of states for multicomponent mixtures from semi-empirical equations of state", Molecular Phys., 103, 3115 (2005).

G18.  C.R.A. Abreu and F.A. Escobedo "A novel Configurational-Bias Monte Carlo method for lattice polymers", Macromolecules, 38, 8532 (2005).

G17.  I. Gospodinov and F.A. Escobedo, "Multicanonical schemes for mapping out free energy landscapes of single and multi-component systems", J. Chem. Phys. 122, 164103 (2005).

G16.  I. Gospodinov and F.A. Escobedo, "Bridging continuum and statistical thermodynamics via equations of states and the density of states", J. Chem. Phys. 120, 10699 (2004).

G15.  M. Fenwick and F.A. Escobedo, "On the use of Acceptance Ratio methods in Multicanonical type simulations", J. Chem. Phys., 120, 3066 (2004).

G14.  M. Fenwick and F.A. Escobedo, "Expanded Ensemble and Replica Exchange methods for simulation of protein-like systems", J. Chem. Phys. 110, 11998 (2003).

G13.  R. Shetty, F.A. Escobedo, D. Choudhary and P. Clancy, "Characterization of order in simple materials. A pattern recognition approach", J. Chem. Phys. 117, 4000 (2002).

G12.  R. Shetty and F.A. Escobedo, "On the use of Virtual Gibbs ensembles for the direct simulation of fluid-fluid and solid-fluid phase coexistence", J. Chem. Phys. 116, 7957 (2002).

G11.  F.A. Escobedo and Z. Chen, "Simulation of Isoenthalps and Joule-Thomson Inversion Curves of Pure Fluids and Mixtures", Molecular Simulation 26, 395 (2001).

G10.  Z. Chen and F.A. Escobedo, "A Configurational-bias Approach for the Simulation of Inner sections of Linear and Cyclic Molecules", J. Chem. Phys. 113, 11382 (2000).

G9.  F.A. Escobedo, "Molecular & Macroscopic Modeling of Phase Separation", AIChE J. 46, 2086 (2000).

G8.  F.A. Escobedo, "Tracing Coexistence Lines in Multicomponent Fluid Mixtures by Molecular Simulation", J. Chem. Phys. 110, 11999 (1999).

G7. F.A. Escobedo and J.J. de Pablo, "Pseudo Ensemble Simulations and Gibbs-Duhem Integrations for Polymers" J. Chem. Phys. 106, 2911 (1997).

G6. F.A. Escobedo, "Gibbs-Duhem Integrations in Lattice Systems", Europhys. Lett. 40, 111 (1997).

G5. F.A. Escobedo and J.J. de Pablo, "Expanded Grand Canonical and Gibbs Ensemble Monte Carlo Simulation of Polymers", J. Chem. Phys. 105, 4391 (1996).

G4. F.A. Escobedo and J.J. de Pablo, "Chemical Potential and Dimensions of Chain Molecules in Athermal Environments", Molec. Phys. 89, 1733 (1996).

G3.  F.A. Escobedo and J.J. de Pablo, "Monte Carlo Simulation of the Chemical Potential of Polymers in an Expanded Ensemble", J. Chem. Phys. 103, 2703 (1995).

G2.  F.A. Escobedo and J.J. de Pablo, "Extended Configurational Bias Monte Carlo Methods for Simulation of Flexible Molecules", J. Chem. Phys. 102, 2636 (1995).

G1.  F.A. Escobedo and J.J. de Pablo, "A New Method for Generating Volume Changes in Isobaric-Isothermal Monte Carlo Simulation", Macromol. Theory Simul. 4, 691 (1995).


H. On the generalization and unification of simulation methods

H8. K. Hur, R. G. Hennig, F. A. Escobedo and U. Wiesner, "Mesoscopic Structure Prediction of Nanoparticle Assembly and Co-Assembly: Theoretical Foundation", J. Chem. Phys. 133, 194108 (2010).  

H7. F.A. Escobedo "Simulation of the density of states in isothermal and adiabatic ensembles", Phys. Rev. E 73, 056701 (2006).

H6.  C.R.A. Abreu and F.A. Escobedo "A general framework for non-Boltzmann Monte Carlo sampling", J. Chem. Phys. 124, 054116 (2006).

H5.  F.A. Escobedo, "A unified methodological framework for the simulation of nonisothermal ensembles", J. Chem. Phys. 123, 044110 (2005).

H4.  F.A. Escobedo, "Simulation of Bulk, Confined, and Polydisperse Systems. I. A Unified Methodological Framework", J. Chem. Phys. 115, 5642 (2001).

H3.  F.A. Escobedo, "Simulation of Bulk, Confined, and Polydisperse Systems. II. Application to Chain Systems", J. Chem. Phys. 115, 5653 (2001).

H2.  F.A. Escobedo, "Simulation and Extrapolation of Coexistence Properties with Single-phase and Two-phase ensembles", J. Chem. Phys. 113, 8444 (2000).

H1.  F.A. Escobedo, "Novel Pseudo-ensembles for Simulation of Multicomponent Phase Equilibria", J. Chem. Phys. 108, 8761 (1998).


I. General papers & REVIEWS on molecular simulation

I6. F.A. Escobedo "Engineering Entropy in Soft Matter: The Bad, the Ugly, and the Good", A Tutorial Review, Soft Matter, (2014). DOI: 10.1039/C4SM01646G.

I5. F.A. Escobedo, "Molecular Simulation as a Tool for Product Design in Chemical Engineering", especial issue in "Revista Ingeniería Química UNSA" (50-year anniversary) edited by the Chemical Eng. Dept. of the National University of San Agustin, Arequipa, Peru, November 2011.

I4. J. J. de Pablo and F.A. Escobedo, "Perspective: Molecular Simulations in Chemical Engineering: Present and Future", AIChE J. 48, 2716 (2002).

I3. J.J. de Pablo, Q.L. Yan and F.A. Escobedo, "Simulation of Phase Transitions in Fluids", Annual Rev. Phys. Chem. 50, 377 (1999).

I2. J.J. de Pablo and F.A. Escobedo, "Monte Carlo Simulation Methods for Polymers", chapter in the Encyclopedia of Computational Chemistry, Ed. G. Schaeffer, J. Wiley & Sons, England, 1999.

I1. J.J. de Pablo and F.A. Escobedo, "Monte Carlo Methods for Polymeric Systems", in Monte Carlo Methods in Chemical Physics; Adv. Chem. Phys. 105, 337 (1999).


B. On structure and dynamics of bio-molecules

B12. S. Pooja Mahajan, C. Velez-Vega and F.A. Escobedo, "Tilting the balance between Canonical and non-Canonical conformations for the H1 hypervariable loop of a Llama VHH through point mutations", J. Phys. Chem. B . 117, 13-24 (2013).

B11. C. Velez-Vega and F.A. Escobedo, "Characterizing the structural behavior of selected Ab-42 monomers with different solubilities", J. Phys. Chem. B 115, 4900 (2011).

B10. C. Velez-Vega, E. E. Borrero and F.A. Escobedo, "Kinetics and mechanism of the unfolding N-L transition of Trp-cage in explicit solvent via optimized Forward Flux Sampling simulations", J. Chem. Phys. 133, 105103 (2010).

B9.  E. Borrero, L. Contreras, M. DeLisa and F.A. Escobedo, "Reaction coordinates and kinetics of protein-fragment reassembly via Forward-flux sampling", Biophysical J. 98 1911 (2010).

B8.  F.A. Escobedo, E. Borrero and J.C. Araque, "Transition path sampling and forward flux sampling. Applications to biological systems", J. Physics – Cond. Matter 21, 333101 (2009).

B7.  C. Velez-Vega, E. Borrero and F.A. Escobedo, "Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol", J. Chem. Phys.  130, 225101 (2009).

B6.  M.K. Fenwick and F.A. Escobedo, "Exploration of Factors Affecting the Onset of Follicular Lymphoma through Simulations of the Germinal Center", Bulletin of Mathematical Biology 71, 1432 (2009).

B5.  C. Velez-Vega, M.K. Fenwick and F.A. Escobedo, "Simulated Mutagenesis of the Hypervariable Loops of a Llama VHH Domain for the Recovery of Canonical Conformations", J. Phys. Chem. B 113, 1785 (2009)

B4.  L. Contreras Martinez, E.E. Borrero, F.A. Escobedo and M.P. DeLisa, "In silico protein fragmentation reveals the importance of critical nuclei on domain reassembly", Biophysical J. 94, 1575 (2008).

B3.  E. Borrero and F.A. Escobedo, "Folding kinetics of a lattice protein via a forward flux sampling approach", J. Chem. Phys. 125, 164904 (2006).

B2.  L. Contreras, F. Martinez-Veracoechea, P. Pohkarel, A.D. Stroock, F.A. Escobedo and M.P. DeLisa "Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study", Biotechnology and Bioengineering  94, 105 (2006).

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