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Dusan Bratko

Professor Physical Chemistry (804) 828-1865 dbratko@vcu.edu and Research Scientist UC Berkeley (510) 642-8979 dnb@berkeley.edu

Modeling Course [PDF]

Professional preparation

Ph.D., University of Ljubljana , SIovenia
Senior Fulbright Scholar: SUNY at Stony Brook, N.Y.

Research interests
Solution theories

Our research in solution theories is directed toward understanding and control of the behavior of colloidal, biopolymeric and electrolyte systems relevant to biophysics and chemical engineering. We have been developing and applying analytic methods and advanced computational techniques based on principles of statistical mechanics. These include molecular and mesoscopic simulations, integral equation theory of liquids, and field-theoretic methods for studies of soft matter and disordered materials. The goal is to explain microscopic mechanisms behind observed macroscopic behaviors in order to predict new designs or improved conditions optimizing biological function or pragmatic performance of the material.

Our work is often synergistic with experimental groups in respective fields. Systems we have studied include solutions of synthetic and biological polyelectrolytes such as DNA, surfactant self-assemblies, liquid and quenched ionic media and protein solutions. This research has helped elucidate several crucial aspects of solution electrostatics and solvation phenomena that affect the structure and phase behavior of colloidal solutions, including the important role of ion-ion correlations in intercolloidal attraction. Recently, special attention has been paid to protein-protein interactions and aggregation. The ability to control or reverse protein aggregation is vital to numerous technological processes in protein solutions and may be the key to prevention of a number of serious diseases. Complementing collaborative experimental work, we perform computational studies of molecular mechanisms involved in different stages of aggregation as a competitive process to protein folding. We apply polypeptide models with different degrees of coarse-graining and empirical inter-residue potentials derived from a statistical analysis of protein structures from the Protein Data Bank. The huge separation of time scales between monomeric motions and conformational rearrangements requires intense efforts in developing algorithms for efficient dynamic sampling in multichain systems. Specific ionic effects crucial to many properties of proteins and other biomacromolecules are analyzed by a combination of simulations and analytic integral equation approaches. These efforts are being extended to solutions of nanoparticles with ionic ingredients. In view of close relation with physics of ionic colloids, our studies of protein solutions also impact several topics in colloidal theory, including solvation and confinement effects, ion-specificity and multipolar electrostatic interactions. 

Selected publications

1. Frozen Phases of Random Heteropolymers in Disordered Media, Phys. Rev. Letters 76, 1844 (1996), with A. K. Chakraborty and E. I. Shakhnovich.
2. Interaction between Like-Charged Colloidal Spheres in Electrolyte Solutions, Proc. Natl. Acad. Sci. U.S., 95, 15169 (1998), with J. Z. Wu and J. M. Prausnitz.
3. Competition between Protein Folding and Aggregation: A Three-Dimensional Lattice-Model Simulation, J. Chem. Phys. 114, 561 (2001), with H. W. Blanch.
4. Effect of Secondary Structure on Protein Aggregation. A Replica Simulation Study, J. Chem. Phys. 118, 5185 (2003), with H. W. Blanch.
5. Interactions of Charged Dipolar Proteins in Reverse Micelles, J. Chem. Phys. 120, 11941 (2004), with J. Pinero and L. B. Bhuiyan.
6. The Role of Salt-Macroion van der Waals Interactions  inthe Colloid-Colloid Potential of Mean Force, Current Opinion in Colloid & Interface Sci. 90, 81 (2004), with F. W. Tavares and J. M. Prausnitz.
7. Gas Solubility in Hydrophobic Confinement, J. Phys. Chem. B 109, 22545 (2005), with A. Luzar.
8. Protein Folding Landscapes in Multichain systems, Proc. Natl. Acad. Sci. U.S. 102, 11692 (2005), with T. Cellmer, J. M. Prausnitz and H. W. Blanch.
9. Specific Ion Effects in Solutions of Globular Proteins: Comparison between Analytical Models and Simulation, J. Phys. Chem. B 109, 24489 (2005), with M. Bostroem, F. W. Tavares, and B. W. Ninham.
10. Effect of Single-Point Sequence Alterations on the Aggregation Propensity of a Model Protein, J. Am. Chem. Soc. 128, 1683 (2006), with T. Cellmer, J. M. Prausnitz and H. W. Blanch.

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