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OpenMM 4.0: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

Stanford
P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, & V. S. Pande
Journal of Chemical Theory & Computation, 9, 1, 461-469, (2013).

Understanding the Role of Arginine and Citrate as Eluents in Affinity Chromatography.

Book ChapterMIT
D. Shukla and B. L. Trout
Developments in Biotechnology and Bioprocessing, ACS Symposium Series, Vol 1125, 67-86, 2013

Effects of Solute-Solute Interactions on Protein Stability Studied Using Various Counterions and Dendrimers.

MIT
D. Shukla*, C. P. Schneider* and B. L. Trout
PLoS One, Vol.6, No. 11, e27665, 2011

Complex Interactions between Molecular Ions in Solution and Their Effect on Protein Stability.

MIT
D. Shukla, C. P. Schneider and B. L. Trout
Journal of American Chemical Society, 133, 46, 18713-18718, 2011.

Understanding the Synergistic Effect of Arginine and Glutamic Acid Mixtures on Protein Solubility.

MIT
D. Shukla and B. L. Trout
Journal of Physical Chemistry B, 115, 41, 11831-11839, 2011.

Effect of PAMAM Dendrimer Salts on Protein Stability.

MIT
D. Shukla, C. P. Schneider and B. L. Trout
Journal of Physical Chemistry Letters, 2, 14, 1782-1788, 2011.

Molecular Level Insight Into Intra-Solvent Interaction Effects on Protein Stability and Aggregation.

MIT
D. Shukla, C. P. Schneider and B. L. Trout
Advanced Drug Delivery Reviews, 63, 1074-1085 , 2011.

Arginine and the Hofmeister Series: The Role of Ion-Ion Interactions in Protein Aggregation Suppression.

MIT
D. Shukla*, C. P. Schneider* and B. L. Trout
Journal of Physical Chemistry B, 115, 22, 7447-7458, 2011.

Understanding The Role of Arginine as an Eluent in Affinity Chromatography via Molecular Computations.

MIT
D. Shukla, L. Zamolo, C. Cavallotti, and B. L. Trout
Journal of Physical Chemistry B, 115, 11, 2645-2654, 2011.

Preferential Interaction Coefficients of Proteins in Aqueous Arginine Solutions and its Molecular Origins.

MIT
D. Shukla and B. L. Trout
Journal of Physical Chemistry B, 115, 5, 1243-1253, 2011.

Interaction of Arginine with Proteins and the Mechanism by Which it Inhibits Aggregation.

MIT
D. Shukla and B. L. Trout
Journal of Physical Chemistry B, 114, 42, 13426-13438, 2010.

Molecular Computations of Preferential Interaction Coefficients of Proteins.

MethodsMIT
D. Shukla, C. Shinde and B. L. Trout
Journal of Physical Chemistry B, 113, 37, 12456-12554, 2009.

Modeling of the Formation of Nanoparticles in Reverse Micellar Systems.

IIT Bombay
D. Shukla, and A. Mehra
Proceeding of the 17th International Congress of Chemical and Process Engineering, Prague, Czech Republic, 2006.

CaCO3 Nanoparticle Synthesis by Carbonation of Lime Solution in Microemulsion Systems

IIT Bombay
A. K. Sugih, D. Shukla, H. J. Heeres and A. Mehra
Nanotechnology, 18, 035607, 2007

A Monte Carlo Model for the Formation of Core-Shell Nanocrystals in Reverse Micellar Systems.

IIT Bombay
R. Jain, D. Shukla and A. Mehra
Industrial & Engineering Chemistry Research, 45, 1, 2249-2254, 2006.

Coagulation of Nanoparticles in Reverse Micellar Systems: A Monte Carlo Model.

IIT Bombay
R. Jain, D. Shukla and A. Mehra
Langmuir, 21, 1, 11528-11533, 2005.