Research Projects

1. Biomaterials and Biotechnologies

1.1 Protein Adsorption
Fundamental study of interfacial phenomena between biomolecules and substrate surface is critical to the development of novel anti-biofouling materials and biotechnologies. Our lab has developed a multi-scale simulation framework, incorporating quantum, atomisitic and coarse-grained simulation as well as free energy computations in combination with experiments such as FTIR/ATR (see Fig. 1) to explain protein adsorption behavior and assess anti-fouling functionalities of various materials (crystal, polymers, self-assembled monolayers (SAMs) and lipid layers). Simulations show protein the first hydration shell acts as an energy barrier for protein adsorption, whereas the surface tension, especially that from the hydrophobic surface such as graphene (see Fig. 2), can effectively promote adsorption. Protein mobility is highly correlated with surface structures. For example, a lysozyme can have large mobility (1.8 × 10-5 cm2/s) as it is initially adsorbed on a graphene surface, however, it displays extremely low mobility (2.42 × 10-9 cm2/s) on trans-Azobenzene SAMs with 50% coverage (see Fig. 3). The condense hydration water protects protein's structures.

Fig 1. FTIR-ATR experiment to measure protein adsorption (​​J. Phys. Chem. C, 2009, 113 (6), 2053.)

Fig. 2. Lysozyme adsorption on a graphene surface simulated with MD and free energy computation. First hydration water is colored orange. (Appl. Phys. Lett., 2015, 106, 153701)

1.2 Molecular Design of (Anti-)biofouling Materials
Based on the fundamental studies of protein adsorption behavior, our lab works on molecular design of (anti)biofouling and photo-responsive surface by using simulations and experiments. For photoresponsive azobenzene-terminated self-assembled monolayer surfaces (Azo-SAMs) (see Fig. 3), our atomistic molecular dynamics (MD) results showed that the surface morphology and the terminal benzene rings’ packing are highly correlated with surface density and the isomer state. Higher surface coverage and trans-isomer state lead to more ordered polycrystalline backbone as well as more ordered local packing of benzene rings. On the Azo-SAM surface, water retains high interfacial diffusivity, whereas the adsorbed lysozyme can be immobilized with extremely low mobility but relative stable secondary structure. Our free energy computations show that lysozyme desorption free energy is~60 kT. Currently we work on the development of antibiofouling peptide mimics (peptoid) (see Fig. 4) and zwitterionic materials.

Fig. 3. Lysozyme adsorption on photo-responsive Azo-benzene SAMs grafted on silica surfaces simulated with MD. (Langmuir, 2015, 31, 13543)

Fig. 4. Lysozyme adsorption on the peptoid SAMs surface grafted on TiO2 substrate surfaces simulated with MD (the water first hydration shell is colored cyan).

1.3 Biosensor Development to Detect Protein-ligand Binding
Biomolecule's interfacial behavior can induce electron transfer or surface polarization, which can be utilized for bio-sensing​. Detection of Protein-ligand interactions without disturbances (e.g., surface immobilization, fluorescent labeling, and crystallization) presents a key question due to its scientific significance and practical applications in protein chemistry and drug discovery. In collaboration with Professor Yu-hwa Lo's research group at University of California at San Diego, we use multiscale simulations (atomistic, coarse-grained (CG) and CFD) to facilitate the development of novel effective experimental method, Transient Induced Molecular Electronic Spectroscopy (TIMES) to detect protein-ligand interactions without additional disturbances in a microfluidic channel (see the top of Fig. 5). CFD computation demonstrates that the surface’s electric polarization signal originates from the induced image charges during the transition state of surface mass transport, which is governed by the overall effects of protein concentration, hydraulic forces, and surface fouling due to protein adsorption. Hybrid atomistic molecular dynamics (MD) simulations and free energy computation show that ligand binding affects lysozyme structure and stability, producing different adsorption orientation and surface polarization (see the bottom of Fig. 5) to give the characteristic TIMES signals. (This project featured as a NSF media report, Nov, 2016.)

Fig. 5. TIMES measurement (top) and the equipment's mechanism (bottom): Lysozyme adsorption with first hydration water (magenta) and the induced electrostatic potential of the polarized Au(111) surface measured above the surface of 0.3 nm (atomistic MD and pulling in umbrella sampling windows); multiple-protein adsorption in a static fluidic environment (CG simulation); and the reduced mass flux in a flowing cell as a function of reduced time and Peclect number, i.e. bulk velocity (CFD computation). (from the left to the right) (ACS Central Science 2016, 2, 834; ​​​Applied Physics Letters 2017, 110, 073703)

1.4 Biointerfacial Electon Transfer for Bioremedation and Bioenergy
Reduction and oxidation (redox) reactions govern a variety of energy-conversion processes in biology such as respiration. Metal-reducing bacteria, such as Shewanella Oneidensis utilizes multiple-cytochrom protein assembly to harness energy from the anaerobic environment during its cycling of Fe with redox and ET processes, involving dissimilatory reduction of mineral oxides. Enzyme direct ET has promising applications in bio-energy, bio-detection and bio-remediation of contaminated soil or water.​Emergent electrical properties of multi-heme cytochromes also have promising applications in biofuel fuel cells (BFCs) and biosensors. Our group lab and our collaborators recently developed a simulation framework, which consists of homology modeling, MD simulation, protein docking, binding free energy computations, Divide-Conquer-Recombine kinetic Monte Carlo (KMC), and 3D visualization tools to study ET between the decaheme cytoheme protein complex and the ET across the adsorbed protein on the Au(111) surfaces in water (see Fig. 6). Our unique multiscale simulation approach and fundamental research of bio-nano interfacial ET and Redox are also for crucial for the application in water-energy-food nexus by using microbial electrosynthesis technique to covert organic wastes from biorefineries or food industry into new/clean energy. (This project featured as a NSF media report, Nov, 2016.)

Fig. 6. 3D visualization and nonequilibrium steady-state ET transfer between protein complex computed from KMC; predicted adsorption conformation and ET across MtrF protein on Au(111) surface in water. (from the left to the right) (​ J. Mol. Graph. Model. 2016, 65; J. Phys. Chem. Lett. 2016, 7, 929 )

1.5 Molecular Design of Nucleic Acid SAMs for Cancer Detection
​Nucleic acid fragments SAMs have been shown as a new class of novel diagnostic markers for diseases, such as cancers and HIV. However, the ability to accurate and rapidly quantify them still remain challenging due the nature of their abundance compounded by the detection probes’ low hybridization efficiency, which is highly correlated with the SAMs morphology. Our MD simulations demonstrate the hybridized paired strands show rigid rod-like double helix structure, whereas unhybridized strands display flexible coil structure (see Fig. 7). We also extend this research to design nanocarriers for targeted cancer treatment. (This project was recently given a media report: "Diagnosing Biomarkers in the Bloodstream with a Microscopic Lab-on-a-Chip", June, 2017) (Scientific Reports, 2018, 8, 3157)

Fig. 7. DNA SAMs surface without hybridization (left) and with full hybridization (right). ​Ma H, Wei T, "Study of ion behavior, morphology and hybridization on DNA self assembled membrane via molecular dynamics", AICHE Fall National Meeting, San Francisco, 2016

1.6 Lipids Membrane for Drug Delivery
Fundamental studies of the supra-molecular layer structures, dynamics and water permeation free energy of lipid membrane are crucial for drug delivery. Our group simulated the bilayer of hexa-acyl-chain lipid A and its analogue of tetra-acyl chains. Our atomistic MD simulation for the first time illustrated hexagonal compact packing of the hydrocarbon acyl chains within lipid A membrane, while the analogue was found with less ordered ripple structures (see Fig. 6). The analysis of dynamics showed that highly hydrated hydrophilic diglucosamine backbone is structurally stable, whereas the interdigitated hydrophobic acyl chain tails inside the membrane with faster dynamics screen the aqueous environment from the lipid interior and also reinforce the membrane’s structural stability. Our study also demonstrated slower dynamics and broader free energy barrier for water permeation for lipid A, compared with that of the analogue (see Fig. 8).

Fig. 8. ​Morphology of Lipid A (hexa-acyl (left)) and its analogue (tetra-acyl (right)) and water permeation free energy simulated with MD simulation and CIW free energy computation. (J. Phys. Chem, B, 2014, 118, 13202)

1.7 Nanoparticle's Interactions with the Cell's Membrane
Engineered metal (oxide) nanoparticles (NPs) have extensive applications in drug delivery, environment, bioremediation, biodetections and energy industries. Our lab uses multiscale simulations from quantum, atomistic and mesoscopic scales in combination with experiments to study chemical modified NPs' interactions with the cell's membrane, which includes lipids and transmembrane proteins. Fig. 9 shows our study of Au NP interacting with the lipid bilayer in the aqueous environment using coarse-grained molecular dynamics (CG MD) simulations at the mesoscopic level. Our goal is to understand the kinetic properties, thermodynamic driving forces and physicochemical processes to achieve structure-function design of NPs for specific applications.

Fig. 9. A gold nanoparticle interacting with the lipid bilayer in water (green: counter ions; grey: water molecules) simulated with CG MD.

2. Functional Materials

2.1 Semiconducting Rod-coil Block Copolymers for Polymer Photovoltaics
Semiconducting rod-coil block copolymers have promising applications in organic optoelectronics, e.g., polymer solar cells, and biomaterials. Due to its additional coupling of liquid-crystalline ordering with microphase separation, rod-coil block copolymer displays more complicated phase behavior than coil-coil polymer. Such coupling yields novel supramolecular structures (nanoscale architecture and tunable domain size). With our collaborator, we work on mesoscopic-scale lattice Monte Carlo (MC) simulations combined with atomistic MD simulations to study polymer phase morphology (see Fig. 10) and thin film. Another focus is to study the exciton separation and transfer inside polymeric nanostructures at quantum and atomistic scales.

Fig. 10. Rod-coil block copolymers phase morphology predicted with lattice MC simulations.

2.2 Crosslinked Polymers & Polymer-nanocomposites Membrane for Water Treatment
Polyamide reverse osmosis (RO) membrane is one of the most successfully commercialized membranes for desalination and purification. The current big challenges are to increase water permeation (to low down the energy cost) and enhance the antibifouling capability. Although microscopic structure is believed to be highly correlated with membrane's performance, there is still no practical tool available for building and investigating crosslinked membrane in atomistic scale. Our lab developed a simulation approach to construct a reliable cross-linked polyamide membrane with atomistic resolutions and with properties, matching experimental measurements, e.g. pore size distribution (see Fig. 11). Our bottom-up simulation approach enables to elucidate the relationship of membrane's microstructure and membrane performance, and thus to facilitate the experimental molecular design of the membrane and to optimize the operation conditions in both equilibrium and nonequilibrium conditions. Another aim is to develop polymer-nanoparticle composites materials by using both experiments and mesoscopic simulations (see Fig. 12). The effects of integrating nanoparticles (e.g. CNT, grahene and TiO2) on membrane's performance (water permeation, anti-biofouling capability and mechanical properties) are evaluated by both simulations and experiments. (This project featured as a NSF media report, March, 2017.)

Fig. 11. Crosslinked polyamide membrane of experimental SEM image and MD simulation: water heterogeneous diffusivity inside the membrane and membrane's pore size distribution measured with MC simulation (from the left to the right) (J. Phys. Chem. B 2016, 7, 929)

Fig 12. Polymer-Nanoparticle composites: crosslinked nanoparticles (left) and agglomerated uncrosslinked nanaoparticle (right) simulated with mesoscopic simulations and coarse-grained models.

2.3 Nanoporous Materials for Energy and Environment
Nanoporous materials, such as zeolites, metal organic frameworks (MOFs), and polyelectrolyte membranes (PEMs), play important roles in energy and environmental projects ranging from hydrogen and natural gas separation or storage, CO2 capture, fuel cells, to water treatment technologies. An understanding of non-equilibrium steady-state transport inside or through nanopores at atomistic/molecular level is critical to the design of porous materials and separation technologies. One focus of our project is to study molecular transfer through a membrane at both equilibrium and nonequilibrium conditions (see Fig. 13). Another focus is to study chemical reactions inside the nanopores coupled with molecular transfer. We use the efficient method of reactive MD to simulate complicated chemical reactions from atomistic scales validated by quantum computations (see the example of Fig. 14). Such simulation methodology is also applicable for the simulation and optimization of lithium ion batteries through the use of nanomaterials, or for the environmental applications, such as water purification and air pollution control with nanotechnologies.

Fig. 13. Separation of CH4 and CO2 with zeolite membrane at nonequilibrium steady-state simulated with house-developed software of hybrid MD/grand canonical Monte Carlo (GCMC).

2.4 Materials at Severe Conditions
Fundamental studies of material behaviors at severe conditions, such as high temperature and high pressure gradient, have various critical applications such as the space program, geology, and petrochemistry industry. Fig. 14 shows our research to explore the possible application of silicon carbide (SiC) ceramic material in hydrocarbon pyrolysis in petrochemistry industry. The severe high-temperature operation conditions of ethylene thermal cracking pose a necessity for the development of new corrosion-resistant, coking-resistant and highly thermal conductive materials of radiant coil tubes. Our results with reactive atomistic simulations show SiC surfaces undergo hydrothermal corrosion accompanied with coking formation at temperature above 1500 K at the presence of added water.

Fig. 14. Chemical reactions simulated from atomistic scale by using reactive MD: C6H14 pyrolysis with addition of water on SiC surfaces at 2500 K (yellow: silicon; pink: carbon; cyan: hydrogen; red: oxygen; blue: carbon in coking structure ).(Langmuir, 2017, 33, 11102)

2.5 Particle Simulations
The properties and behaviors of flowing particles are essential to the characteristics of associated micro- and macro-fluid mechanics applicable to biological and MEMs systems and environmental research in particle pollution (such as PM2.5). Our lab employed hybrid discrete element method and computational fluid dynamics (DEM-CFD) to study the soft particles’ fluidization (see Fig. 15) and adsorption. Particle dynamic motions (aggregation in the bulk and adsorption/desorption/exchange adjacent to the wall) are analyzed as a function of the wall boundary confinement and the particles’ size, density and rigidity.

Fig. 15. Fluidized Particles simulated with DEM-CFD


Thomas Brings Home a Win from 2018 Annual AIChE Meeting

Mon, December 10, 2018

Chemical Engineering Junior Jamaka Thomas won second place in the Food, Pharmaceutical and Biotechnology category at the 2018 Annual AIChE Meeting for her research submission titled: “Enrichment of Oat Protein by Means of Gravity and Electrostatic Forces.” Thomas co-authored her submission with Chemical Engineering Graduate Student Dinara Konakbayeva.Read More >>

Assistant Professor Patrick Ymele-Leki Mentors Postdoctoral Researcher and 2018 Research Week Winner

Fri, April 20, 2018

Chemical Engineering postdoctoral researcher Jyothirmai Simhadri was announced as the Post Doc/Resident/Fellow/Research Associate winner in the Physical Sciences and Engineering category for her research submission titled: "Development of Shewanella Oneidensis MR-1 Biofilms for Iodate Reduction in Groundwater". Read More >>


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