Professor Colina obtained her Ph.D. at the North Carolina State University (2004) and her B.S. (1993) and M.Sc. (1994) at Simón Bolívar University. She was a Postdoctoral Research Associate in the Department of Chemistry at the University of North Carolina at Chapel Hill. She was previously a faculty member at Simón Bolívar University and joined the Department of Materials Science and Engineering at The Pennsylvania State University as Associate Professor in January 2007. She won the 1999 Award for Outstanding Teaching Achievement (at the Assistant Professor level) at Simón Bolívar University, as well as several other awards from the Venezuelan’s National Committees from the Development of Higher Education and for the Academic Advancement.
Dr. Colina has several international collaborations and has presented the results of her research globally in more than 200 national and international conferences. She has published over 90 papers (including conference proceedings), recently edited a book and serve in several national and international commitees.
David is a postdoctoral associate in Dr. Coray M. Colina’s group in the Department of Chemistry at the University of Florida. He graduated with a bachelor’s degree in Chemical Engineering from the University of Pittsburgh in the spring of 2011. In the fall of 2011 he entered the Chemical Engineering Ph.D. program at North Carolina State University where he joined Dr. Carol Hall’s research group. With Dr. Hall, he investigated the structures and phases formed by systems of multipolar colloidal particles. He defended his thesis in November 2016 and joined Dr. Colina’s group in June 2017.
Dylan Anstine is from southern Kansas City, Missouri. He completed his undergraduate studies in nanoscience with an emphasis in physics at Northwest Missouri State University in May 2016 under the supervision of Dr. Himadri Chakraborty. His undergraduate research was focused on computational simulations of carbon fullerenes, photoionization, and endohedrally confined gases. The work involved using perturbation theory to investigate the field of ultra-fast optics and correlative electron behavior.
Dylan arrived in the Colina group July 2016 where he began studying the mechanical properties of amorphous polymers using all-atomistic models and non-equilibrium molecular dynamics. His current research interest is in examining hydrogel networks and developing algorithmic approaches to generate controlled in silico hydrogel topologies. Traditionally it is difficult to analyze and characterize hydrogel structure; creating a classical problem of defining structure-property relationships. Defining the effects that hydrogel network structure has on gel mechanical properties will have a significant impact on the fields of soft mechanics and modeling, cell culture, and tissue engineering.
Alex received his master’s degree at Saint-Petersburg State University (Russia) in computational and applied physics. His undergraduate research project was on the topic of the self-adapting algorithm based on the super-convergence of the solution applied for the finite elements method solver of elliptic partial derivative equations.
After graduating from the university, Alex worked in the German Federal Institute of Materials Research and Testing (BAM). Continuing in the field of his undergraduate studies, he worked with mathematical simulation of the physical processes in laser-induced micro-sparks. More specifically, the topic of the research project was the calibration-free spectral analysis of the spectra from laser-induced micro-spark plasmas.
At the beginning of 2017 he joined Dr. Coray Colina’s group with research aimed towards the molecular dynamic simulations of amorphous polymeric systems, focusing on the development of automated tools for molecular dynamic simulations.
Mike Fortunato grew up in Willow Grove in southeastern Pennsylvania. He did his undergraduate studies at the Pennsylvania State University where he earned his B. S. in Materials Science and Engineering with an option in Polymers Science and Engineering and a minor in Chemistry. In the summer of 2011, Mike participated in the REU in Soft Materials at the Pennsylvania State University studying biomaterials and water wetting.
Mike joined the Colina group in the Summer of 2012 and focused his study on the solution behavior of immunoglobulin G using fully-atomistic and coarse-grained simulation models. Immunoglobulin G is a glycoprotein that is often used as a template in designing monoclonal antibodies for use in therapeutic treatment. This work was the subject of the thesis for his M. Sc. degree which he earned in Spring 2015.
Following completion of his M. Sc. degree, the focus of his research switched to amorphous polymer simulations. Mike is one of the developers of pysimm, a python package designed to facilitate the construction and simulation of molecular systems.
Fortunato, M. E.; Colina, C. M. “pysimm: A Python Package for Simulation of Molecular Systems.” SoftwareX, 2017, 6, 7-12. [doi]
Fortunato, M. E.; Colina, C. M. “Effects of Galactosylation in Immunoglobulin G from All-Atom Molecular Dynamics Simulations.” J. Phys. Chem. B, 2014, 118 (33), 9844–9851. [doi]
Fortunato, M. E.; Colina, C. M. “Python Simulation Interface for Molecular Modeling,” http://pysimm.org, 2016.
Fortunato, M. E.; Abbott, L. J; Hart, K. E.; Colina, C. M. “nuSIMM: nanoHUB user Simulation Interface for Molecular Modeling,” https://nanohub.org/tools/nusimm, 2015.
CCP5 Methods in Molecular Simulation Summer School, Manchester University, Manchester, UK, July 21-30, 2013.
Grit received his B.S. and M.S. degree in chemical engineering from Oklahoma State University. During his undergraduate studies, he was involved in surface science research and studied peroxide reaction on tungsten hydrogen bronze surfaces for thin film sensor applications. During his M.S., his research focused on improving a gene delivery system using a genetically modified adenovirus in combination with synthetic materials. His M.S. research also involved studying pH effects and excipients screening to stabilize modified viral vectors for pharmaceutical use.
Grit joined Dr. Coray Colina’s group during the fall of 2014. He is currently working on developing novel nanoporous materials using molecular simulation with focuses on hypercrosslink polymers. The ability to accurately predict the structure-property relationship of these polymeric materials from molecular simulations will have a tremendous impact on the energy industry (gas storage and separation).
Aravinda Munasinghe is from Colombo, Sri Lanka. He graduated from University of Colombo with B.Sc. in Computational Chemistry in January 2014. As an undergraduate student, under the supervision of Prof. Nalin de Silva and Dr. Rohini de Silva, he studied electronic and dynamic properties of graphene sheets when intercalated with small particles.
At the beginning of fall 2015 he joined Dr. Coray Colina’s group with research aimed at studying dynamic properties of Osteoprotegerin (OPG) with RANKL. Understanding how OPG interact with RANKL at the atomistic scale is important due to active contribution of the RANKL/OPG/RANK pathway in many bone diseases including different forms of common osteoporosis.
Following the completion of this research project, currently his research interests are focused on studying effects of polymers on proteins upon bioconjugation.
Farhad is a Ph.D. student in the Chemistry department at the University of Florida. He received his bachelor’s degree in physics from Sharif University of Technology in Tehran, Iran in 2013. He then joined Prof. Mehmet Sayar’s group at Koc University in Istanbul, Turkey. His study examined the transferability of atomistic and coarse-grained models with the example of an amphiphilic peptide with lysine-leucine repeating residues (LK) using molecular dynamics simulations. During that time he developed a transferable coarse-grained model for peptides that displays an environment driven conformational transition. He earned his master’s degree in computational sciences from Koc University in Spring 2015.
He joined Dr. Colina’s group in Fall 2015, where he works on gel formation of mucus glycoproteins employing coarse-grained molecular dynamics. In this work, he presents a simple coarse-grained model to study the structure and dynamics of polymerized MUC5AC and entangled networks of them upon gel-formation. This model was constructed based on sequence information, domain, and composition analysis. After taking into account the information of submolecular architecture from high-resolution images of single extended molecules, he proposed a coarse-grained model consisting of four different bead types, each representing a molecular domain in MUC5AC.
Shalini is from Chennai, Tamil Nadu, India. She graduated from the National Institute of Technology, Trichy, India with a B.Tech degree in Metallurgical and Materials Engineering in August 2014. Her undergraduate research was focused on synthesis and characterization of MAX phase compound Ti3SiC2 and Al-Si alloy foams for aerospace and automotive applications. She also studied phase separation and grain growth in alloys using Monte Carlo simulations.
She joined the Colina group in fall 2014. She focused her study on Ionomers of Intrinsic Microporosity (IonomIMs) which consist of Polymers of Intrinsic Microporosity (PIMs) with ionic functional groups (such as carboxylate, sulfate) covalently attached to the polymer backbone, and extra framework counter ions (Li+, Na+, K+, Rb+ and Mg2+). The effect of different counter-ions on the porosity, carbon dioxide (CO2) adsorption and mixed gas selectivity was studied using Molecular Dynamics and Monte Carlo simulations. The goal of the project was to enhance CO2 gas separation performance under industrially relevant conditions.
Her current research focuses on enzyme responsive polyethylene glycol diacrylate (PEGDA)-peptide hydrogels for drug delivery applications. The goal of the project is to evaluate the mesh size, swelling ratio and solvent accessible surface area (SASA) as a function of molecular weight of PEGDA monomers, cross-link densities and peptide sequence. Predictive molecular dynamics simulations on an atomistic scale will aid the experimental design of these hydrogels for controlled drug release.
Akash Mathavan grew up in Davie in South Florida. He is currently an undergraduate sophomore student at the University of Florida, where he is pursuing a B. S. in Biomedical Engineering with minors in Mathematics and Computer Science.
Akash joined the Colina group in the Winter of 2016. Currently, he is working on atomistic simulations of Immunoglobulin G and the role of disulfide bonds in protein stability. IgG is a glycoprotein and the most common type of antibody found in the human body. It serves as the basis of monoclonal antibody therapy.
Akshay Mathavan, a second-year student at the University of Florida, grew up in Davie, Florida. He is pursuing a bachelor’s degree in Biomedical Engineering with minors in Computer Science and Mathematics.
In winter of 2016, Akshay starting working with Dr. Colina’s research group. Currently, he is performing atomistic simulations on Bovine Serum Albumin in order to analyze protein structures after cleaving disulfide bonds. Bovine Serum Albumin, commonly known as BSA, is often used in biomedical practices for concentration standards.