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Massachusetts Institute of Technology
Department of Chemical Engineering
 

 

 




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Trout Group Publications, Presentations and Invited Talks

Publications

  1. López-Mejías, V., Myerson, A.S., Trout, B.L. “Geometric Design of Heterogeneous Nucleation Sites on Biocompatible Surfaces,” Journal of the American Chemical Society, submitted (2013).

  2. Smejkal, B., Agrawal, N.J., Mechelke, M., Ortner, F., Heckmeier, P., Helk, B., Schulz, H., Giffard, M., Trout, B.L., Hekmat, D. “Fast and scalable purification of a therapeutic full-length antibody based on process crystallization,” Journal Biotechnology and Bioengineering, submitted (2012).

  3. Chadwick, K., Chen, J., Santiso, E. and Trout, B.L. “Molecular Modeling Applications in Crystallization,” Handbook of Industrial Crystallization. submitted (2012).

  4. Musolino, N., Santiso, E., and Trout, B.L. “Design of linear ligands for selective separation using a genetic algorithm applied to molecular architecture,” Journal of Chemical Informatics, submitted (2012).

  5. Trout, B.L. “"Understanding the Role of Arginine and Citrate as Eluents in Affinity Chromatography," Highlights in Biotechnology and Bioprocessing. ACS Symposium Series volume, submitted (2012).

  6. Musolino, N. and Trout, B.L. “Insight into the molecular mechanism of water evaporation via the finite temperature string method,” The Journal of Chemical Physics, submitted (2012).

  7. Zhou, L., Su, M., Benyahia, B., Singh, A., Barton, P.I., Trout, B.L., Myerson, A.S. and Braatz, R.D. “Mathematical modeling and design of layer crystallization in a concentric annulus with and without recirculation,” AIChE Journal, in press (2013).

  8. Quon, J., Chadwick, K., Wood, G., Sheu, I., Brettmann, B., Myerson, A.S., Trout, B.L., "Templated Nucleation of Acetaminophen on Spherical Excipient Agglomerates," Langmuir, accepted (2012).

  9. Xi, L., Shah, M., Trout, B.L. “Hopping of water in a glassy polymer studied via transition path sampling and likelihood maximization,” Journal of Physical Chemistry, in press (2012).

  10. Wong, S.Y., Tatusko, A., Trout, B.L., Myerson, A. “Development of Continuous Crystallization Processes using a Single-stage MSMPR Crystallizer with Recycle,” Crystal Growth & Design, in press (2012).

  11. Agrawal, N.J., Helk, B., and Trout, B.L. “A computational tool to predict the protein-protein interaction hot-spot residues from the structure of the unbound protein”, J. Mol. Biol., submitted (2012).

  12. Vagenende, V., Han, A.X., Mueller, M., and Trout, B.L. “Protein-associated cation-clusters in aqueous arginine solutions and their effect on protein stability and size,” J. Am. Chem. Soc., in press (2012).

  13. Kayser, V., Francon, A., Pinton, H., Saluzzo, J., Trout, B.L. “Rational Design of Rabies Vaccine Formulation for Enhanced Stability”, Journal of General Virology, submitted (2012).

  14. Vagenende, V., Trout, B.L. “Quantitative Characterization of Local Protein Solvation To Predict Solvent Effects on Protein Structure”, Biophysical Journal, 103, 6, 1354–1362 DOI: 10.1016/j.bpj.2012.08.011 (2012). link

  15. Wang, M., Rutledge, G.C., Myerson, A.S., Trout, B.L. “Production and characterization of carbamazepine nanocrystals by electrospraying for continuous pharmaceutical manufacturing”, Journal of Pharmaceutical Sciences, 101, 3, 1178-1188, DOI: 10.1002/jps.23024 (2012) link

  16. Brettmann, B.K., Cheng, K., Myerson, A.S., and Trout, B.L. “Electrospun Formulations Containing Crystalline Active Pharmaceutical Ingredients”, Pharmaceutical Research, DOI: 10.1007/s11095-012-0868-4 (2012). link

  17. Lauer, T., Agrawal, N. J., Chennamsetty, N., Egodage, K., Helk B., Trout B. L., “Developability Index: A rapid in silico tool for the screening of antibody aggregation propensity,” J. Pharm. Sci., 101, 1, 102-115 (2012). link

  18. Chadwick, K., Chen, J., Myerson, A.S., and Trout, B. L., "Towards the Rational Design of Crystalline Surfaces for Heteroepitaxy: The Role of Molecular Functionality," Crystal Growth & Design, 12, 3, 1159–1166 DOI: 10.1021/cg2010858 (2012). link

  19. Brettmann, B.K., Myerson, A.S., and Trout, B.L. “Solid-state nuclear magnetic resonance study of the physical stability of electrospun drug and polymer solid solutions”, J Pharm Sci., 101, 6, 2185–2193, DOI: 10.1002/jps.23107 (2012). link

  20. Quon, J., Zhang, H., Alvarez, A., Evans, J., Myerson, A., and Trout, B.L., “Continuous Crystallization of Aliskiren Hemifumarate,” Crystal Growth & Design, 12, 6, 3036-3044 DOI: 10.1021/cg300253a (2012) . link

  21. Zhang, H., Quon, J., Alvarez, A., Evans, J., Myerson, A.S, and Trout, B. L., “Development of Continuous Anti-solvent-cooling Crystallization Process using Cascaded Crystallizers” Org. Pro. Res. Dev., 2012, 16, 915–924 DOI: 10.1021/op2002886. link

  22. Brettmann, B. K., Bell, E., Myerson, A.S., and Trout, B. L., "Solid-state NMR characterization of high-loading solid solutions of API and excipients formed by electrospinning", J. Pharm. Sci. 101, 4, 1538-1545 (2012). link

  23. Kayser, V., Chennamsetty, N., Voynov, V., Helk, B., Forrer, K., and Trout, B. L. "A Screening Tool for Therapeutic Monoclonal Antibodies: Identifying the Most Stable Protein and Its Best Formulation Based on Thioflavin T Binding", Biotechnology Journal, 7, 1, 127-132 (2012). link

  24. Brettmann, B.K., Tsang, S., Forward, K., Rutledge, G., Myerson, A. S., and Trout, B. L., "Free Surface Electrospinning of Microparticles," Langmuir, 28, 25, 9714-9721 (2011). link

  25. Diao, Y., Helgeson, M., Siam, Z., Doyle, P., Myerson, A.S., Hatton, A., and Trout, B. L., “Gel-Induced Selective Crystallization of Polymorphs,” J. Am. Chem. Soc., 134,1, 673–684 DOI: 10.1021/ja210006t (2011). link

  26. Diao, Y., Helgeson, M., Siam, Z., Doyle, P., Myerson, A. S., Hatton, A., and Trout, B. L., "Nucleation under Soft Confinement: Role of Polymer-Solute Interactions", Crystal Growth & Design, 12, 1, 508-517 (2012). link

  27. Schneider C.*, Shukla, D.*, and Trout, B. L., “Effects of Solute-Solute Interactions on Protein Stability Studied Using Various Counterions and Dendrimers,” PLoS ONE, 6 (11) e27665 (2011). link

  28. Shukla, D., Schneider C., and Trout, B. L., “Complex Interactions between Molecular Ions in Solution and Their Effect on Protein Stability,” J. Am. Chem. Soc., 133, 46, 18713-18718, DOI: 10.1021/ja205215t (2011). link

  29. Chadwick, K., Myerson, A. S., and Trout, B. L., "Polymorphic Control by Heterogeneous Nucleation – A New Method for Selecting Crystalline Substrates", Cryst. Eng. Comm., 13, 6625-6627 (2011). link

  30. Shukla, D.*, Schneider C.*, and Trout, B. L., “Effect of PAMAM Dendrimer Salts on Protein Stability”, J. Phys. Chem. Lett., 2(14), pp 1782-1788. (2011) link

  31. Diao, Y., Harada, T., Myerson, A. S., Hatton, T. A., and Trout, B. L., “The Role of Nanopore Shape in Surface-Induced Crystallization,” Nature Materials, 10, 867-871 (2011). link Featured in Nature Materials News and Views, Nature Materials, 10, 809-810 (2011)

  32. Chunsrivirot, S., Santiso, E. E., and Trout, B. L., “Binding Affinity of a Small Molecule to an Amorphous Polymer in a Solvent. Part 2: Preferential Binding to a Surface,” Langmuir, 27, 20, 12396-12404, DOI: 10.1021/la202593u (2011). link

  33. Chunsrivirot, S., Diao, Y., and Trout, B. L., “Binding Affinity of a Small Molecule to an Amorphous Polymer in a Solvent. Part 1: Free Energy of Binding to a Binding Site,” Langmuir, 27, 20, 12396-12404, DOI: 10.1021/la201508m(2011). link

  34. Shukla, D., and Trout, B. L., “Understanding the Synergistic Effect of Arginine and Glutamic Acid Mixtures on Protein Solubility,” Submitted, J. Phys. Chem. B, 115, 11831 (2011). link

  35. Shah, M., Santiso E. E., and Trout, B. L., “Computer Simulations of Homogeneous Nucleation of Benzene from the Melt,” J. Phys. Chem. B, 115, 10400-10412 (2011). link

  36. Agrawal, N. J.*, Kumar, S.*, Wang, X., Helk, B., Singh, S. K., Trout, B.L., “Aggregation in Protein-based Biotherapeutics: Computational Studies and Tools to Identify Aggregation Prone Regions,” J. Pharm. Sci., 100, 12, 5081-5095 (2011). link

  37. Shukla, D.*, Schneider C.*, and Trout, B. L., “Molecular Level Insight Into Intra-Solvent Interaction Effects on Protein Stability and Aggregation,” Adv. Drug. Dev. Rev., 63, 1074, (2011). link

  38. Kayser, V., Chennamsetty, N., Voynov, V., Helk, B., Forrer, K., and Trout, B. L. "Conformational Stability and Aggregation of Therapeutic Monoclonal Antibodies Studied with ANS and Thioflavin T Binding", mAbs, 3, 4, 408-411 (2011). link

  39. Schaber, S. D., Gerogiorgis, D. I., Ramachandran, R., Evans, J. M. B. Barton, P.I., and Trout, B. L., “Economic Analysis of Integrated Continuous and Batch Pharmaceutical Manufacturing: A Case Study,” I&EC, 50, 17, 10083-10092, DOI: 10.1021/ie2006752 (2011). link

  40. Schneider C.*, Shukla, D.*, and Trout, B. L., “Arginine and the Hofmeister Series: The Role of Ion-Ion Interactions In Protein Aggregation Suppression”, J. Phys. Chem. B, 115, 22, 7447-7458 (2011). link

  41. Chunsrivirot, S., and Trout, B. L., “Free Energy of Binding of a Small Molecule to an Amorphous Polymer in a Solvent,” Langmuir, 27, 11, 6910-6919 (2011). link

  42. Pan, B., Ricci, M., and Trout, B. L., “A Molecular Mechanism of Hydrolysis of Peptide Bonds at Neutral pH Using a Model Compound”, J. Phys. Chem. B, 115, 19, 5958-5970, (2011). link

  43. Diao, Y., Hatton, T.A., Myerson, A., and Trout, B. L., “Surface Design for Controlled Crystallization: The Role of Surface Chemistry and Nanoscale Pores in Heterogeneous Nucleation,” Langmuir, 27, 9, 5324-5334, (2011). link

  44. Kayser, V., Chennamsetty, N., Voynov, V., Helk, B., Forrer, K., and Trout, B. L. "Evaluation of a non-Arrhenius Model for Therapeutic Monoclonal Antibody Aggregation", J. Pharm. Sci., 100, 2526 (2011) link

  45. Diao, Y.*, Helgeson, M.*, Myerson, A., Hatton, T. A., Doyle, P., and Trout, B. L. "Controlled Nucleation from Solution Using Polymer Microgels", J. Am. Chem. Soc., 133, 11, 3756-3759, (2011). link

  46. Shukla, D., Zamolo L., Cavallotti C., and Trout, B. L., “Understanding The Role of Arginine as an Eluent in Affinity Chromatography via Molecular Computations,” J. Phys. Chem. B, 115, 11, 2645-2654, (2011). link

  47. Santiso, E. E., and Trout, B. L., “A General Set of Order Parameters For Molecular Crystals,” J. Chem. Phys., 134, 064109, (2011). link

  48. Chennamsetty N., Voynov V., Kayser V., Helk B., and Trout B. L., “Prediction of protein binding regions,” Proteins Struc. Func. Bioinformatics, 79, 3, 888-897, (2011). pdf

  49. Shukla, D., and Trout, B. L., “Preferential Interaction Coefficients of Proteins in Aqueous Arginine Solutions and their Molecular Origins,” J. Phys. Chem. B, 115, 5, 1243-1253, (2011). pdf

  50. Kayser, V., Chennamsetty, N., Voynov, V., Helk, B., and Trout, B. L. "Tryptophan-Tryptophan energy transfer and classification of tryptophan residues in proteins: Therapeutic monoclonal antibody as a model", J. Fluores., 21, 1, 275-288, (2011). pdf

  51. Kayser, V., Voynov, V., Chennamsetty, N., Forrer, K., Helk, B., and Trout, B. L. "Glycosylation influence stability and aggregation of therapeutic monoclonal antibodies", Biotec. J., 6, 1, 38-44, (2011). pdf

  52. Chen, J., and Trout, B. L ., “A Computational Study of the Mechanism of the Selective Crystallization of alpha and beta Glycine from Water and Methanol-Water Mixture,” J. Phys. Chem. B, 114, 43, 13764-13772 (2010). pdf

  53. Chen, J., and Trout, B. L ., “Computer-Aided Solvent Selection for Improving the Morphology of Needle-like Crystals: A Case Study of 2,6-Dihydroxybenzoic Acid,” Cryst. Growth Des., 10, 4379-4388 (2010). pdf

  54. Shukla, D., and Trout, B. L., “Interaction of Arginine With Proteins and the Mechanism by Which it Inhibits Aggregation,” J. Phys. Chem. B, 114, 42, 13426-13438, (2010). pdf

  55. Chennamsetty N., Voynov V., Kayser V., Helk B., and Trout B. L., “Prediction of aggregation prone regions of therapeutic proteins,” J. Phys. Chem. B, 114, 19, 6614-6624 (2010). pdf

  56. Pan B., Ricci M. S., and Trout B. L., “Molecular Mechanism of Acid-Catalyzed Hydrolysis of Peptide Bonds Using a Model Compound,” J. Phys. Chem. B, 114, 13, 4389-4399 (2010). pdf

  57. Voynov V., Chennamsetty N., Kayser V., Wallny H., Helk B., and Trout B. L., “Design and Application of Antibody Cysteine Variants,” Bioconjug. Chem., 21, 2, 385-392 (2010). pdf

  58. Ovchinnikov V., Trout, B. L., and Karplus M. “Mechanical Coupling in Myosin V: A simulation study,” J. Mol. Bio., 395, 4, 815-833 (2010). pdf

  59. Voynov V., Chennamsetty N., Kayser V., Helk B., Forrer K., Zhang H., Fritsch C., Heine H., and Trout B. L., “Dynamic Fluctuations of Protein-Carbohydrate Interactions Promote Protein Aggregation” Plos one , 4, 12, e8425 (2009). pdf

  60. Voynov V., Chennamsetty N., Kayser V., Helk B., and Trout B. L., “Predictive tools for stabilization of therapeutic proteins,” mAbs, 1, 580-581 (2009). pdf

  61. Vagenende V., Yap G. S. M., and Trout, B. L., “Mechanisms of Protein Stabilization and Prevention of Protein Aggregation by Glycerol,” Biochemistry, 48, 46, 11084-11096 (2009). pdf

  62. Shukla, D., Shinde C., and Trout, B. L., “Molecular Computations of Preferential Interaction Coefficients of Proteins,” J. Phys. Chem. B, 113, 37, 12546-12554 (2009). pdf

  63. Vagenende V., Yap G. S. M., and Trout, B. L., “Molecular Anatomy of Preferential Interaction Coefficients by Elucidating Protein Solvation in Mixed Solvents: Methodology and Application for Lysozyme in Aqueous Glycerol,” J. Phys. Chem. B, 113, 34, 11743-11753 (2009). pdf

  64. Chennamsetty N., Helk B., Voyonov V., Kayser V., and Trout B. L., "Aggregation-Prone motifs in Human Immunoglobulin G", J. Mol. Bio., 391, 2, 404-413 (2009). pdf

  65. Chennamsetty N.*, Voyonov V.*, Kayser V., Helk B., and Trout B. L., “Design of Therapeutic proteins with enhanced stability”, Proc. Nat. Acad. Sci., 106, 29, 11937-11942 (2009). pdf Featured in Nature Research highlight Unstuck by Design Nature, 460, 155, (2009).

  66. Schneider, C. P. and Trout, B. L., “Investigation of Cosolute-Protein Preferential Interaction Coefficients: New Insight into the Mechanism by Which Arginine Inhibits Aggregation,” J. Phys. Chem. B, 113, 2050 (2009). pdf

  67. Peters, B., Nils E.R. Zimmermann, N.E.R, Beckham, G.T., Tester, J.W., and Trout, B.L., “Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism,” J.A.C.S., 130, 51, 17342 (2008). pdf

  68. Trout, B. L., “Why Philosophical History is Essential to Teaching the Second Law of Thermodynamics,” International Thermodynamics Symposium held in Honor and Memory of Joseph H Keenan, OCT 04-05, 2007 Cambridge, MA, Meeting the Entropy Challenge, AIP Conference Proceedings, 1033, 288 (2008). pdf

  69. Chen, J. and Trout, B. L., “Computational study of the solvent effects on the molecular self-assembly of tetrolic acid in solution and consequent polymorph formed from crystallization,” J. Phys. Chem. B, 112, 7794 (2008). pdf

  70. Beckham, G. T., Peters, B., and Trout, B. L ., “Evidence for a size dependent mechanism in solid state polymorph transformations,” J. Phys. Chem. B, 112, 7460 (2008). pdf

  71. Pong, B.-K., Trout, B. L., and Lee, J. Y., “Modified Ligand-exchange for Efficient Solubilisation of CdSe/ZnS Quantum Dots in Water: A Procedure Guided by Computational Studies,” Langmuir, 24, 5270 (2008). pdf

  72. Chong, G., Lustig, S., Jackson, C. and Trout, B. L., ” Surface adsorption behavior of soluble peptide molecules at the air/water interface,” J. Phys. Chem. B, 112, 2970 (2008). pdf

  73. Maresh, J., Giddings, L.A., Friedrich, A., Loris, E., Panjikar, S., Trout, B.L., Stockigt, J., Peters, B., O'Connor, S.,"Strictosidine synthase: mechanism of a Pictet-Spengler catalyzing enzyme," J.A.C.S., 130, 710 (2008). pdf

  74. Peters, B., Beckham, G. T., and Trout, B. L.,” Extensions to the likelihood maximization approach for finding reaction coordinates,” J. Chem. Phys., 127, 34109 (2007). pdf

  75. McNeill, V. F., Geiger, F. M., Loerting, T., Trout, B. L., and Molina, M. J., “The interaction of hydrogen chloride with ice surfaces: The effects of grain size, surface roughness, and surface disorder,” J. Phys. Chem. A, 111, 6274 (2007). pdf

  76. Pong, B.-K., Elim, H. I., Chong, J.-X., Ji, W., Trout, B. L., and Lee, J.-Y., “New insights on the nanopartical growth mechanism in the citrate reduction of gold (III) salt: formation of the Au nanowire intermediate and its non-linear optical properties,” J. Phys. Chem. C, 111, 6281 (2007). pdf

  77. Beckham, G. T., Peters, B., Starbuck, C., Variankaval, N., and Trout, B. L., “Surface-mediated nucleation in the solid-state polymorph transformation of terephthalic acid,” J.A.C.S., 129, 4714 (2007). pdf

  78. Anderson, B. J., Radhakrishnan, R., Peters, B., Borghi, G. P., Tester, J. W., and Trout, B. L., “Molecular simulations of gas hydrate nucleation,” in Physics and Chemisty of Ice, Royal Society, Cambridge (2007). pdf

  79. Pan, B., Abel, J, Ricci, M. S., Brems, D. N., Wang, D. I.C. and Trout, B. L. “Comparative oxidation studies of methionine residues reflect the structural effect on chemical kinetics,” Biochemistry, 45, 15430 (2006). pdf

  80. Peters, B. and Trout, B.L., “Obtaining reaction coordinates by likelihood maximization,” J. Chem. Phys, 125, 54108 (2006). pdf

  81. Rempel, J.Y., Trout, B.L., Bawendi, M.G., Jensen, K.F. "Density functional theory study of ligand binding on CdSe (0001), (0001), and (1120) single crystal relaxed and reconstructed surfaces: implications for nanocrystalline growth," Journal of Physical Chemistry B, 110, 18007 (2006). pdf

  82. Tang, H. and Trout, B. L., "Rational design of selective, sulfur-resistant, oxidation emissions catalysts," J. Phys. Chem. B, 110, 6856 (2006). pdf

  83. McNeill, V. F., Loerting, T., Geiger, F. M., Trout, B. L. and Molina, M. J. "Hydrogen chloride-induced surface disordering on ice, Proc. Nat. Acad. Sci., 103 (25), 9422 (2006). pdf

  84. Peters, B. and Trout, B. L. "Asparagine deamidation: pH dependent mechanism from density functional theory," Biochemistry, 45 (16), 5384 (2006). pdf

  85. Gu, C., Lustig, S., and Trout, B.L., "Solvation model based on order parameters and a fast sampling method for the calculation of solvation free energies of peptides, " J. Phys. Chem. B, 110 (3), 1476 (2006). pdf

  86. Anderson, B.J., Tester, J.W., Borghi, G.P. and Trout, B.L., "Properties of inhibitors of methane hydrate formation via molecular dynamics simulations," J.A.C.S., 127, 17852 (2005). pdf

  87. Pong, B.K., Lee, J.Y., and Trout, B.L., "First principles computational study for understanding the interactions between ssDNA and gold nanoparticles: Adsorption of methylamine on gold nanoparticulate surfaces," Langmuir, 21, 11599 (2005). pdf

  88. Tang, H.R. and Trout, B.L., "NO chemisorption on Pt(111), Rh/Pt(111), and Pd/Pt(111)," J. Phys. Chem. B, 109, 17630 (2005). pdf

  89. Rempel, J.Y., Trout, B.L., Bawendi, M.G., and Jensen, K.F., "Properties of the CdSe(0001), (0001), and (1120) single crystal surfaces: relaxation, reconstruction, and ad-atom and ad-molecule adsorption," J. Phys. Chem. B, 109, 19320 (2005). pdf

  90. Lo, C.S., Radhakrishan, R., and Trout, B.L., "Application of transition path sampling methods in catalysis: a new mechanism for C-C bond formation in the methanol coupling reaction in Chabazite," Catalysis Today, 105, 93 (2005). pdf

  91. Anderson, B. J., Bazant, M.Z., Tester, J. W., and Trout, B.L., "Application of the cell potential method to predict phase equilibria of multi-component gas hydrate systems," J. Phys. Chem. B, 109(16), 8153 (2005). pdf

  92. Tang, H. and Trout, B.L., "Electronic composition-property relationship applied to SO2 chemisorption on Pt(111) surfaces, alloys, and overlayers," J. Phys. Chem. B, 109(15), 6948 (2005). pdf

  93. Baynes, B.M., Wang, D.I.C., and Trout, B.L., "The role of arginine in the stabilization of proteins against aggregation," Biochemistry, 44, 4919 (2005). pdf

  94. Chu, J.W., Brooks, B.R. and Trout, B.L, "Oxidation of methionine residues in aqueous solutions, free methionine and methionine in G-CSF," J.A.C.S., 126, 16601 (2004). pdf

  95. Radhakrishnan, R. and Trout, B. L. "Order parameter approach to understanding and quantifying the physico-chemical behavior of complex systems," in Handbook of Materials Modeling, vol. 6, Reactivity Processes, Kluwer, New York, 2005.

  96. Anderson, B., Tester, J. W., and Trout, B. L., "Accurate potenials for argon - water and methane - water interactions via ab initio methods and their application to clathrate hydrates," J. Phys. Chem. B., 108(48), 18705 (2004). pdf

  97. Yin, J., Chu, J.W., Speed Ricci, M., Brems, D.N., Wang, D.I.C. and Trout, B.L., "Effects of antioxidants on the non-site-specific oxidation of methionine residues in granulocyte colony-stimulating factor (G-CSF) and human parathyroid hormone (hPTH) fragment 13-34," Pharm. Res., 21, 2378 (2004). pdf

  98. Yin, J., Chu, J.W., Speed Ricci, M., Brems, D.N., Wang, D.I.C. and Trout, B.L., "Effects of excipients on the hydrogen perioxide induced oxidation of methionine residues in granulocyte colony-stimulating factor (G-CSF)," Pharm. Res., 22, 140 (2005). pdf

  99. Chu, J.W., Yin, J., Brooks, B.R., Wang, D.I.C., Speed Ricci, M., Brems, D.N. and Trout, B.L., "A comprehensive picture of 'non-site-specific' oxidation of methionine residues by peroxides in protein pharmaceuticals," J. Pharm. Sci., 93, 3096 (2004). pdf

  100. Chu, J.W., Yin, J., Wang, D.I.C. and Trout, B.L., "A structural and mechanistic study of the oxidation of methionine residues in hPTH(1-34) via experiment and simulations," Biochemistry, 43,14139 (2004). pdf

  101. Lin, X., Schneider, W.F. and Trout, B.L., "Chemistry of sulfur oxide on transition metals III: oxidation of SO2 and self-diffusion of O, SO2, and SO3 on Pt," J. Phys. Chem. B., 108, 13329 (2004). pdf

  102. Lo, C. and Trout, B. L., “Density functional theory characterization of acid sites in chabazite,” J. Catal., 227, 77 (2004). pdf

  103. Baynes, B.M. and Trout, B.L. "Rational design of solution additives for the prevention of protein aggregation," Biophys. J., 87, 1631 (2004). pdf

  104. Tang, H., van der Ven, A. F. and Trout, B. L., “Phase diagram of oxygen atoms adsorbed on platinum(111) by first principles investigation,” Phys. Rev. B, 70, 045420 (2004). pdf

  105. Lo, C., Giurumescu, C. A., Radhakrishnan, R. and Trout, B. L., “Methanol coupling in the zeolite chabazite studied via Car-Parrinello molecular dynamics,” Molecular Physics, 102, 281 (2004). pdf

  106. Tang, H., van der Ven, A. F. and Trout, B. L., “Lateral interactions between oxygen atoms adsorbed on platinum(111) by first principles,” Molecular Physics, 102, 273 (2004). pdf

  107. Chu, J. W., Yin., J., Wang, D. I. C. and Trout, B. L.,“Molecular dynamic simulations and experimental oxidation rates of methionine residues of granulocyte colony-stimulating factor (G-CSF) at different pH values,” Biochemistry, 43, 1019 (2004). pdf

  108. Chu, J. W. and Trout, B. L., “On the Mechanisms of Oxidation of Organic Sulfides by H2O2 in Aqueous Solutions,” J.A.C.S., 126, 900 (2004). pdf

  109. Lin, X., Schneider, W. F. and Trout, B. L., “Chemistry of sulfur oxides on transition metals II: thermodynamics of sulfur oxides on Pt(111),” J. Phys. Chem. B, 108, 250 (2004). pdf

  110. Chu, J. W., Trout, B. L. and Brooks, B. R., “A super-linear minimization scheme for the nudged elastic band method,” J. Chem. Phys., 119, 12708 (2003). pdf

  111. Baynes, B. M., and Trout, B. L., “Proteins in mixed solvents: a molecular-level perspective,” J. Phys. Chem. B, 107, 14058 (2003). pdf

  112. Radhakrishnan, R. and Trout, B. L., “Nucleation of hexagonal (Ih) ice in liquid water,” J.A.C.S., 125, 7743 (2003). pdf

  113. Radhakrishnan, R. and Trout, B. L., “Nucleation of crystalline phases of water in homogeneous and inhomogeneous environments,” Phys. Rev. Lett., 90, 158301 (2003). pdf

  114. Radhakrishnan, R., Demurov, A., Herzog, H. and B. L. Trout, “A consistent and verifiable macroscopic model for the dissolution of liquid CO2 in water under hydrate forming conditions,” Energ. Convers. Manage., 44, 773 (2003). pdf

  115. Lin, X., Hass, K. C., Schneider, W. F., and Trout, B. L., “Chemistry of sulfur oxides on transition metals I: configurations, energetics, orbital analyses, and surface coverage effects of SO2 on Pt(111),” J. Phys. Chem. B, 106, 12575 (2002). pdf

  116. Mantz, Y. A., Geiger, F. M., Molina, L. T., Molina, M. J., and Trout, B. L., “A theoretical study of the interaction of HCl with crystalline NAT,” J. Phys. Chem. A, 106, 6972 (2002). pdf

  117. Lin, X. and Trout, B. L., “Chemistry of sulfur oxides on transition metal surfaces,” in Interfacial Applications in Environmental Engineering, ed. Keane, M., ACS Symposium Proceedings, 2002, pp. 55-68.

  118. Cao, Z., Tester, J. W., and Trout, B. L., “Sensitivity analysis of hydrate thermodynamic reference properties using experimental data and ab initio Methods,” J. Phys. Chem. B, 106, 7681 (2002). pdf

  119. Radhakrishnan, R. and Trout, B. L., “A new approach for studying nucleation phenomena using molecular simulations: application to CO2 hydrate clathrates,” J. Chem. Phys., 117, 1786 (2002). pdf

  120. Cao, Z., Anderson, B. J., Tester, J. W., and Trout, B. L., “Development and application of an ab initio methane-water potential for the study of phase equilibria of methane hydrates,” in Accurate Description of Low-lying Electronic States and Potential Energy Surfaces, ed. Hoffmann, M. R. and Dyall, K. G., ACS Symposium Series 828, 2002, pp. 418-444.

  121. Demurov, A., Radhakrishnan, R., and Trout, B. L., “Computations of Diffusivities in Ice and CO2 Clathrate Hydrates via Molecular Dynamics and Monte Carlo Simulations,” J. Chem. Phys., 116, 702 (2002). pdf

  122. Cao, Z., Sparks, K. A., Tester, J. W., and Trout, B. L., “Molecular Computations Using Robust Hydrocarbon-Water Potentials for Describing Hydrate Phase Equilibria,” J. Phys. Chem. B, 105, 10950 (2001). pdf

  123. Mantz, Y. A., Geiger, F. M., Molina, L. T., Molina, M. J., and Trout, B. L., “The Interaction of HCl with the (0001) Face of Hexagonal Ice Studied Theoretically via Car-Parrinello Molecular Dynamics,” Chem. Phys. Lett., 348, 285 (2001). pdf

  124. Bazant, M. and Trout, B. L., “A method to extract potentials from the temperature dependence of Langmuir constants for clathrate-hydrates,” Physica A, 300, 139 (2001). pdf

  125. Lin, X., Ramer, N. J., Rappe, A. M., Hass, K. C., Schneider, W. F., and Trout, B. L., “Effect of Particle Size on the Adsorption of O and S Atoms on Pt: A Density-Functional Theory Study,” J. Phys. Chem. B, 105, 7739 (2001). pdf

  126. Girumescu, C. A. and Trout, B. L., “Quantum Calculations and Car-Parrinello Simulations of Processes in the Zeolite Chabazite,” in Foundations of Molecular Modeling and Simulation, eds. Cummings, P. T., Westmoreland, P. R., and Carnahan, B., AIChE Symposium Series, 97 (2001).

  127. Mantz, Y. A., Geiger, F. M., Molina, L. T., Molina, M. J., and Trout, B. L., “First-Principles Theoretical Study of Molecular HCl Adsorption on a Hexagonal Ice (001) Surface,” J. Phys. Chem. A., 105, 7037 (2001). pdf

  128. Cao, Z., Tester, J. W., and Trout, B. L., “Computation of the Methane–Water Potential Energy Hypersurface via ab initio Methods,” J. Chem. Phys., 115, 2550 (2001). pdf

  129. Trout, B. L., “Car-Parrinello Methods in Chemical Engineering: Their Scope and Potential,” Adv. Chem. Eng., Academic Press: San Diego, 28, 353, (2001).

  130. Trout, B. L., White, D., Suits, B. H., and Gorte, R. J., “Molecular motions of hydrogen bonded CH3CN in CHA: Comparison of first-principles molecular dynamics simulations with results from 1H, 2H, and 13C NMR,” J. Phys. Chem B, 104, 11734 (2000). pdf

  131. Mantz, Y. A., Geiger, F. M., Molina, L. T., Molina, M. J., and Trout, B. L., “First-principles molecular dynamics study of surface disordering of the (0001) face of hexagonal ice,” J. Chem. Phys., 113, 10733 (2000). pdf

  132. Lau, K. K. S., Gleason, K. K., and Trout, B. L., “Thermochemistry of gas phase CF2 reactions: a density functional theory study,” J. Chem. Phys., 113, 4103 (2000). pdf

  133. Trout, B. L. and M. Parrinello, M., “Analysis of the dissociation of H2O in water using first-principles molecular dynamics,” J. Phys. Chem. B, 103, 7340 (1999). pdf

  134. Sparks, K. A., Tester, J. W., Cao, Z., and Trout, B. L., “Configurational properties of water clathrates: Monte Carlo and multidimensional integration versus the Lennard-Jones and Devonshire approximation,” J. Phys. Chem. B, 103, 6300 (1999). pdf

  135. Trout, B. L. and Parrinello, M., “The dissociation mechanism of H2O in water studied by first-principles molecular dynamics,” Chem. Phys. Lett., 288, 343 (1998). pdf

  136. Trout, B. L., Chakraborty, A. K., and Bell, A. T., “Diffusion and reaction in ZSM-5 studied by dynamic Monte Carlo,” Chem. Eng. Sci., 52, 2276 (1997). pdf

  137. Trout, B. L., Chakraborty, A. K., and Bell, A. T., “Analysis of the thermochemistry of NOx decomposition over CuZSM-5 based on quantum chemical and statistical mechanical calculations,” J. Phys. Chem., 100, 17582 (1996). pdf

  138. Trout, B. L., Chakraborty, A. K., and Bell, A. T., “Local spin density functional theory study of copper ion-exchanged ZSM-5,” J. Phys. Chem., 100, 4173 (1996). pdf

Publications (not peer reviewed)

  • N.J. Agrawal, T.M. Lauer, F. Hernandez-Guzman, B. Helk and B.L. Trout; "Novel computational tools could mitigate antibody aggregation", Pharmaceutical Formulation and Quality, Feb/Mar 2012. pdf
  • Buck, P.M., Kumar, S., Wang, X., Agrawal, N.J., Trout, B.L., and Singh, S.K., "Computational Methods to Predict Biotherapertic Protein Aggregation" , Therapeutic Proteins: Methods and Protocols, Second Edition, Springer, Humana Press. 2012

  • Radhakrishnan, R., Demurov, A., Herzog, H. J. and B. L. Trout, “Modeling the dissolution of liquid CO2 in water under hydrate forming conditions,” Proceedings of the Fourth International Conference on Gas Hydrates, Yokohama, Japan, May 2002, pp. 262- 266.

  • Cao, Z., Anderson, B., Tester, J. W. and B. L. Trout, “Computations of the thermodynamics of methane hydrates using ab initio data,” Proceedings of the Fourth International Conference on Gas Hydrates, Yokohama, Japan, May 2002, pp. 315- 320.

  • Anderson, B., Bazant, M. Z. and B. L. Trout, “Application of an analytical method to extract molecular potentials from Langmuir curve data,” Proceedings of the Fourth International Conference on Gas Hydrates, Yokohama, Japan, May 2002, pp. 418-423.

  • Radhakrishnan, R. and B. L. Trout, “Mechanism for the nucleation of CO2 hydrate clathrates studied using a Monte Carlo based approach,” Proceedings of the Fourth International Conference on Gas Hydrates, Yokohama, Japan, May 2002, pp. 494-497.

Presentations and Invited Talks

  • March 28-29, 2011, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization" ACS, Anaheim, CA (Plenary Lecture).
  • March 15-16, 2011, “Transforming Pharmaceutical Manufacturing Continuous: The Ultra Lean Way of Manufacturing" ISPE-NJ.
  • November, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” AAPS Annual Meeting, New Orleans, LA.
  • October, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” PEGS Biotechnology conference, Hannover, Germany.
  • September, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” Ipsen Corporation, Milford, MA.
  • September, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” IBC Protein Formulation Conference, Providence, RI.
  • August, 2010, “Molecular Modeling for the Rational Control of Polymorphism and Morphology,” Sepracor Corporation, Marlborough, MA.
  • July, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” MedImmune Corporation, Gaithersburg, MD.
  • July, 2010, “Continuous Manufacturing: The Ultimate in Quality by Design,” Sepracor Corporation, Marlborough, MA.
  • May, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” Accelrys Annual International Conference, Boston, MA.
  • April, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” ISPE Biotech Meeting, Cambridge, MA.
  • April, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” Merck, West Point, PA.
  • March, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” Genzyme, MA.
  • March, 2010, “Molecular Modeling for the Rational Control of Polymorphism and Morphology,” Gilead Corporation, Foster City, CA.
  • March, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” Genentech, South San Francisco, CA.
  • March, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” Amgen, Thousand Oaks, CA.
  • March, 2010, “Modeling Protein Degradation Processes and the Development of Rational Approaches to Stabilization and Protein-Cosolute Interactions: A New Strategy of Molecular QbD,” Biogen-Idec, Cambridge, MA.
  • December, 2009, “Continuous Manufacturing of Small Molecule Pharmaceuticals,” Leaders for Global Manufacturing, MIT, Cambridge, MA.
  • November, 2009, “Order parameter methods for reactions in complex systems,” Princeton Center for Theoretical Sciences, Department of Physics, Princeton, NJ.
  • October, 2009, “Rational approaches to protein and antibody stabilization,” Schering-Plough, Elizabeth, NJ.
  • September, 2009, “Rational approaches to protein and antibody stabilization,” Merck & Co., West Point, PA.
  • September, 2009, “Modeling of crystallization processes,” Merck Research Laboratories, Rahway, NJ.
  • September, 2009, “Rational approaches to pharmaceutical manufacturing,” Merck Research Laboratories, Rahway, NJ.
  • July, 2009, “Continuous manufacturing: the ultra lean way of manufacturing,” Biochemical Engineering XVI, Burlington, VT.
  • June, 2009, “Rational approaches to protein and antibody stabilization,” Bristol-Meyers Squibb, New Brunswick, NJ.
  • April, 2009, “Reactivity in complex systems,” University of Washington.
  • March, 2009, “Reactivity in complex systems,” North Carolina Theory Seminar. February, 2009, “Reactivity in complex systems,” UCLA.
  • September, 2008, “Continuous manufacturing of pharmaceuticals: the ultra lean way of manufacturing,” Global Pharmaceutical Manufacturing Summit, Chicago.
  • June, 2008, Rational design of solvent formulations via molecular computations, American Association of Pharmaceutical Science National Biotechnology Conference, Toronto, Canada.
  • April, 2008, Frontiers in chemical reactivity and pharmaceutical manufacturing, Department of Chemical Engineering, University of South Carolina.
  • March, 2008, Frontiers in chemical reactivity and pharmaceutical manufacturing, Department of Chemical Engineering, University of Puerto-Rico.
  • March, 2008, Frontiers in chemical reactivity and pharmaceutical manufacturing, Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign.
  • Oct., 2007, Formulation approaches for the future, IBC Life Sciences on Formulation Strategies for Protein Therapeutics, Hynes Convention Center, Boston, Keynote Address.
  • July, 2007, Understanding reaction processes in complex media such as liquids, Gordon Conference on the Chemistry of Liquids, Holderness School, New Hampshire.
  • June, 2007, Molecular Design of New Excipients for Large Molecule Stabilization, AAP National Biotechnology Conference, San Diego, CA.
  • March, 2007, Finding reactions coordinates for complex processes via likelihood maximization, ACS Spring Meeting, Chicago, IL.
  • November, 2006, Understanding complex reaction processes, Department of Chemical Engineering, University of Buffalo, Buffalo, New York.
  • July, 2006, Molecular simulations of ice and gas hydrate nucleation, Physics and Chemistry of Ice Conference, Bremerhaven, Germany, Keynote Address.
  • June, 2006, Reaction coordinates from likelihood maximization, U.S.-Poland Workshop on Nanoscience and Nanostructured Materials, Poznan, Poland.
  • June, 2006, Understanding complex reaction processes with applications to pharmaceuticals and heterogeneous catalysis, Department of Chemistry, University of Western Ontario, London, Ontario, Canada.
  • February, 2006, Statistical physics applied to the development of biopharmaceuticals, Department of Physics, University of RomeLa Sapienza, Rome, Italy.
  • February, 2006, Statistical physics applied to the development of biopharmaceuticals, SISSA, International School for Advanced Studies, Trieste, Italy.
  • September, 2005, Molecular engineering of chemical systems, Department of Chemical Engineering, Drexel University, Philadelphia, Pennsylvania.
  • September, 2005, Molecular engineering of chemical systems, Department of Chemical Engineering, Texas A&M, College Station, Texas.
  • September, 2005, Reactivity in complex systems, Meeting in honor of Michele Parrinello's 60th Birthday, Agno, Switzerland.
  • July, 2005, Molecular computational engineering: mechanism of methionine oxidation and rational design of additives for hindering aggregation, Protein Stability Conference, Breckenridge, Colorado.
  • March, 2005, Molecular computations for predictions of clathrate-hydrate nucleation and phase-behavior of multi-component hydrates, Hydrate Symposium at the American Chemical Society Spring Meeting, San Diego, California.
  • March, 2005, Water structuring in phase transitions and in chemical reactions at sulfur sites in proteins, Water: Structure, Dynamics and Reactions Across the Phase Diagram at the American Chemical Society Spring Meeting, San Diego, California.
  • July, 2004, A unified approach for the nucleation of ice and ice-like systems in homogeneous and inhomogeneous environments, Telluride Workshop on Studies of ice, icy particles, ice surfaces, and ice-adsorbate interactions: a molecular view, Telluride, Colorado.
  • April, 2004, Molecular analyses and design for the stabilization of therapeutic proteins, Department of Chemical Engineering, Tufts University, Medford, Massachusetts.
  • April 2004, Molecular analyses and design for the stabilization of therapeutic proteins, Department of Chemistry, Boston University, Boston, Massachusetts.
  • March, 2004, Molecular analyses and design for the stabilization of therapeutic proteins, Department of Chemical Engineering, Cornell University, Ithaca, New York.
  • March, 2004, Rochester University, Department of Chemical Engineering Seminar, Rochester, New York.
  • February, 2004 CAMP, Copenhagen, Denmark
  • November, 2003, "Ordering of Water in Phase Transitions and Biological Systems," Washington University, Department of Chemistry Seminar, St. Louis, MO.
  • November, 2003, "Ordering of Water in Phase Transitions and Biological Systems," University of Missouri, Department of Chemistry Seminar, Columbus, MO.
  • October, 2003, "Nucleation and Growth of Clathrate-Hydrates and Ice and a New Theoretical Framework to Address Those," Dartmouth University, Thayer School of Engineering, Dartmouth, NH.
  • September, 2003, "Finding reaction pathways for industrial chemical problems," Statistical Mechanics of Rare Events, Paris, France.
  • September, 2003, "Analyses of reactions in acid zeolites and of proteins via nudged elastic band calculations and Car-Parrinello simulations," CECAM Workshop on Reactivity, Lyon, France.
  • May, 2003, "Reactivity of acidic zeolites via quantum chemical and Car-Parrinello molecular dynamical methods," Advances in the Understanding and Application of Catalysis, Moscow, Russia, Plenary Lecture.
  • April, 2003, Department Seminar, Department of Chemical Engineering, Princeton University, Princeton, NJ.
  • April, 2003, Department Seminar, Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, PA.
  • March, 2003, Department Seminar, Department of Chemical Engineering, University of Texas, Austin, TX.
  • March, 2003, invited talk in “Mechanistic Surface Chemistry,” Spring Meeting of the American Chemical Society, New Orleans, LA.
  • March, 2003, invited talk in “Symposium in Honor of Professor Clayton J. Radke, recipient of the American Chemical Society Award in Colloid Chemistry,” Spring Meeting of the American Chemical Society, New Orleans, LA.
  • March, 2003, Department Seminar, Department of Chemical Engineering, Stanford University, Palo Alto, CA.
  • February, 2003, Department Seminar, Department of Chemical Engineering, North Carolina State University, Raleigh, NC.
  • November, 2002, “Solvation effects in clathrate-hydrates and biological systems,” Department of Chemical Engineering, University of California, Berkeley, CA.
  • November, 2002, “Solvation effects in clathrate-hydrates and biological systems,” Department of Chemical Engineering, California Institute of Technology, Pasadena, CA.
  • July, 2002, “Nucleation of and transport in clathrate-hydrates and ice,” Physics and Chemistry of Ice Conference, New Foundland, Canada.
  • April, 2002, “Molecular simulations for the stabilization of therapeutic proteins and thequantification of nucleation of clathrate-hydrates,” Rensselear Polytechnic Institute, Troy, NY.
  • April, 2002, “Quantification of reactive sites in zeolitic and transition metal catalysts via first-principles,” ACS Meeting, Orlando, Fl.
  • February, 2002, “The identification and study of sites of varying activity in zeolites and transition metal catalysts,” First-Principles Catalysis, Vienna, Austria.
  • February, 2002, “Order-disorder transitions on the surface of ice and in bulk ice and clathrate-hydrates,” Swiss Center for Computational Sciences, Manno, Switzerland.
  • February, 2002, “Molecular simulations for the stabilization of therapeutic proteins and the quantification of nucleation of clathrate-hydrates,” Colorado School of Mines, Golden, CO.
  • August, 2001, “Car-Parrinello simulations of the disordering of ice and dissociation of HCl, relevant to stratospheric chemistry,” ACS Meeting, Chicago, IL.
  • July, 2001, “Insight into the stabilization of therapeutic proteins via molecular simulations,” National University of Singapore, Singapore.
  • June, 2001, “Insight into the stabilization of therapeutic proteins via molecular simulations,” Hong Kong University of Science and Technology, Hong Kong.
  • April, 2001, “Multi-scale modeling of hydrate-clathrates from first-principles to macroscopic thermodynamics,” University of Connecticut, Storr, CT.
  • February, 2001, “Multi-scale modeling of hydrate-clathrates from first-principles to macroscopic thermodynamics,” Georgia Institute of Technology, Atlanta, GA.
  • January, 2001, “Multi-scale modeling of hydrate-clathrates from first-principles to macroscopic thermodynamics,” National University of Singapore, Singapore.
  • June, 1999, “Application of molecular modeling to automotive catalysis,” Workshop held at Ford Motor Company, Dearborn.
  • March, 1999, “Defect structure and its relation to methanol activation”, ACS Annual Conference, Annaheim, CA.
  • April, 1998, “Quantum mechanical methods in catalysis: a primer”, New England Catalysis Society, Worchester, MA.
  • September, 1996, “Dynamic Monte Carlo study of reaction and diffusion sites in ZSM-5 Zeolites”, Technical University of Athens, Athens, Greece.

 

Last Updated: March 1, 2013