Research Categories

Chemistry and Chemical Engineering

This category covers:

  • Advanced Chemical Processes
  • Biological Chemistry
  • Catalysis
  • Chiral & Pharmaceutical Engineering
  • Green Chemistry
  • Inorganic chemistry
  • Medicinal Chemistry
  • Molecular Modeling
  • Natural Product Synthesis
  • Organic Synthesis
  • Physical Chemistry
  • Process Systems Engineering/Process Control
  • Statistical Thermodynamics
  • Stereochemistry
  • Theoretical / Computational / Physical Chemistry
  • Theoretical Chemistry
  • Spectroscopy

Process System and Multi-Scale Modeling
The group focuses on the research subjects of four principles spanning from quantum/statistical mechanics to macroscopic systems; first-principle and ab-initio calculations, molecular modeling and simulation, hydrodynamics, and control and optimization of chemical processes. In our group, while individual subjects are of great importance to pose potential impacts on scientific recognitions, any parallel and series of combination of the specified principles can be autonomously engineered to yield theoretical generality by undertaking inductive and deductive approaches. While our paradigm is based on bridging characteristics of researches, our group takes on the following individual projects as initiatives:

First-Principle and Ab-Initio Calculations
By quantum mechanics and density functional calculations, we study heterogeneous catalytic reactions, surface sciences phenomena, as well as surface thermodynamics and kinetics studies to bridge between surface science’s experiments and real industrial scale reactions.

Molecular Modeling and Simulation
Molecular Dynamics and Monte Carlo simulation methodology are applied for studying defects in crystals, confined fluids, phase equilibria, and fluids in catalytic membrane. Current modules are built upon basis of simple potentials such as hard sphere and square well, and more realistically, Lennard-Jones and Morse potentials. While abstract understandings of the real systems are possible through those models, our intention is to extend the projects by adopting semi-empirical/empirical potentials or by developing one, hence to incarnate real systems.

We develop simplified minimal molecular dynamics model for applications such as microflows, turbulence, and multiphase flows. The ultimate goal is to create the so called minimal molecular Dynamics, which constitutes small but realistic model of fluid flows. In such modeling approaches, one tries to create molecular dynamics stripped to its bare essentials. The basic idea is to create a simple molecular dynamics with smallest possible number of degree of freedoms. The advantage of such an approach is becoming increasingly recognized as for an example: lattice Boltzmann models are now routinely used for computer simulations of fluid flows and for hydrodynamics of complex fluids.

Control and Optimization of Chemical Processes
We develop dynamic models of chemical systems including catalytic reactors, crystallizers, solid oxide fuel cells and bioreactors to better understand their behaviors, optimize their performance in the face of uncertainty and design control structures. In addition, data based methods to detect and diagnose faults in industrial processes and analyze underlying phenomenon in biomedical processes using multivariate statistics are being explored. Chemometric techniques are also being developed to improve the calibration of spectroscopic sensors that forms the basis of on-line process optimization and control.

Related Links:
Centre for Chiral & Pharmaceutical Engineering
Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences

NameResearch Interests
Dr Alessandra BonanniBiosensor technologies Biosensors are analytical tools which combine a biorecognition agent which provides selectivity and a transducer that confers sensitivity and can convert the biorecognition event into a measurable electronic signal. The advantage of using biosensor over traditional techniques is represented by their low costs, small dimensions, portability, and fast response. The different areas for potential biosensor applications are mainly medical diagnosis, environmental monitoring and food analysis. DNA analysis DNA analysis is of extreme importance to solve problems of different nature such as investigation on genetic diseases, detection of food and water contamination by microorganism, studies on breeding origins or tissue matching, and solution of forensic issues. The techniques for genome identification are nowadays mainly based on DNA sequencing by using fluorescent labels and optical detectors. They require a few days for the analysis to be completed and the costs are prohibitive to the general public. Demand has never been greater for innovative technologies which can provide fast, inexpensive and reliable genome information. The focus of my research is on the development of analytical tools (biosensors) for the rapid, reliable and low cost identification of DNA sequences. In order to achieve that, different electrochemical techniques are used for the detection of the analytical signal. The developed biosensors are based on various platforms (such as gold, carbon and silicon) and different nanomaterials (i.e. gold nanoparticles, graphene nanoplatelets and several quantum dots) are employed for the amplification of the obtained signal and the improvement of detection limit. The final step of this work is the application of the developed genosensor to real sample analysis. Once this second part is successfully accomplished, the analytical tool could be eventually integrated into a DNA amplification process, resulting in a portable device for point-of-care diagnostic tests and for very sensitive detection of SNPs correlated to different diseases. Food Analysis This field includes research in the two following areas: - Application of DNA genosensors to identify of DNA sequences correlated to bacteria involved in food contamination (i.e. Salmonella spp, Listeria monocytogenes, Escherichia coli) - Development of electrochemical biosensors for the detection of antioxidant capacity of food and beverages
Assoc Prof Atsushi GotoPolymer Chemistry and Polymer Materials 1) Controlled syntheses of polymers 2) Development of new living radical polymerization via organic catalysis 3) Creation of new advance polymer materials using structurally controlled polymers
Prof Atul N. ParikhMembrane biophysics biologically inspired materials biosensors synthetic chemical biology
Prof Bo Gunnar LiedbergThe research interests of Prof. Bo Liedberg can be divided into three main areas Surface Chemistry and Self Assembled Monolayers This part of the research concerns fundamental studies of adsorbates and ultrathin molecular architectures, like Self-Assembled Monolayers (SAMs), on solid supports. The group was very early in studying self-assembly of substituted alkylthiols on gold substrates. A key activity has been to study temperature driven phenomena occurring in such assemblies as well as in adsorbed layers on top such SAMs. Oligo(ethylene glycol) and oligosaccharide SAMs have attracted considerable attention, both experimentally and theoretically, because of their structural characteristics and advantageous properties in contact with biofluids. Another area concerns interfacial water and ice. Temperature programmed studies have been undertaken to improve the understanding of the nucleation and microscopic wetting behavior of water/ice. The complexity of the SAMs has increased over the years and we are today focusing on architectures based on SAMs bearing multivalent chelator heads, helix-loop-helix polypeptides and receptor functions. Bioinspired and Biomimetic Nanoscience This research concerns the development of nanoscale architectures fabricated using either top-down or bottom-up protocols (or a combination of both). We are, for example, developing plasmonic arrays based on 100 nm gold nano dots on silicon and glass surface for amplification of optical fluorescence signals, so-called metal enhanced fluorescence (MEF). We are also developing composite materials based on a combination of de novo designed peptide scaffolds, planar surfaces and nanoparticles of controlled size and shape. A novel concept based on peptide folding has been used for controlled assembly of gold nanoparticles. The group is also involved in the development of Dip Pen Nanolithography (DPN) for patterning of surfaces on the 30-100 nm length scale. This work is performed jointly with a previous student of the group who nowadays is setting up a nanolaboratory at the Institute of Physics, Vilnius. We are also involved in several EC projects where different types of micro- and nanoscale patterning tools are employed for production of coatings for biofouling, sensing and biomedical applications. Optical Biosensors, micro- and nanoarrays The group has a long experience in developing optical transducers for biosensing application. We were the first to demonstrate the use of surface plasmon resonance for studies of bioaffinity interactions at surfaces, a technology that today form the backbone in SPR/Biacore instruments developed for biospecific interaction analysis (BIA). We are today using it in combination with ellipsometric interrogation and imaging optics for microarraying, and in combination with nanoparticle for studies optical enhancement phenomena. This includes, for example, microarray chips for protein multiplexing. The group is also working on the development of generic biochips for studies of ligand-receptor binding. Besides working on microarray fabrication for protein detection and analysis we are also developing biochips for the safety and security area. Selected publications 1. Tinazli, A., Tang, J., Valiokas, R., Picuric, S., Lata, S., Piehler, J., Liedberg, B., Tampe, R., Chem. Eur. J. 11, 5249-5259 (2005). 2. Aili, D., Enander, K., Tai, F-I., Baltzer, L., Liedberg, B., Angew. Chem., 120, 5636-5638 (2008). 3. Aili, D., Enander, K., Baltzer, L., Liedberg, B., Nano Letters, 8, 2473-2478 (2008). 4. Andersson, O., Ulrich, C., Björefors, F., Liedberg, B., Sensors&Actuators B: Chemical, 134, 545-550 (2008). 5. Klenkar, G., Liedberg, B., Anal. Bioanal. Chem. 391, 1679-1688 (2008). 6. Aili, D., Selegård. R., Baltzer, L., Enander, K., Liedberg, Small, 5, 2445-2452 (2009). 7. Lee, H.-H., Ruzele, Z., Malysheva, L., Onipko, A., Gutes, A., Björefors, F., Valiokas, R., Liedberg, B., Langmuir, 25(24), 13959–71 (2009).
Assoc Prof Cai WenjianProf Cai's areas of expertise are system modelling, control and optimization, multivariable system identification and control, sensor and instrumentation, mechanical system simulation and design, and intelligent systems. His current research works focus on industry applications in building HVAC processes, renewable energy processes and environmental processes.
Prof Chan Bee Eng, MaryDr Chan-Park has interest and expertise in nanoimprint, micro- and nano-patterning, biomaterials, tissue engineering and carbon nanotubes. She has published more than 80 journal papers and holds more than 15 patents/patent applications in these areas. She has supervised more than 12 PhD students and 15 postdoctoral fellows.
Asst Prof Chen GangDr Gang CHEN has been interested in probing the molecular recognition interactions responsible for RNA structures, stabilities, dynamics, and functions since 2001. He has worked on a variety of RNA structures including non-Watson-Crick base pairs (such as isoG-isoC, G-A, A-A, U-U, U-C, G-U, and A-C pairs), base triples, and pseudoknots. The triplex structures present in RNA pseudoknots inspired the current work on targeting RNA by dsRNA-binding chemically modified peptide nucleic acids (PNAs, see below), which show selective recognition of dsRNAs over ssRNAs and dsDNAs. 1. Yang, L., Zhong, Z., Tong, C., Jia, H., Liu, Y., and Chen, G.* (2018) Single-molecule mechanical folding and unfolding of RNA hairpins: Effects of single A-U to A∙C pair substitutions and single proton binding and implications for mRNA structure-induced −1 ribosomal frameshifting. J. Am. Chem. Soc. 140, 8172-8184. (IF: 14.357) 2. Patil, K.M., Toh, D.F.K., Yuan, Z., Meng, Z., Shu, Z., Zhang, H., Ong, A.A.L., Krishna, M.S., Lu, L., Lu, Y.,* and Chen, G.* (2018) Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A-U pairs in dsRNAs. Nucleic Acids Res. 46, 7506-7521. (IF: 11.561) 3. Krishna, M.S., Toh, D.F.K., Meng, Z., Ong, A.A.L., Wang, Z., Lu, Y., Xia, K., Prabakaran, M., and Chen, G.* (2019) Sequence- and structure-specific probing of RNAs by short nucleobase-modified dsRNA-binding PNAs incorporating a fluorescent light-up uracil analog. Anal. Chem., 91, 5331-5338. (IF: 6.042) 4. Kesy, J., Patil, K.M., Kumar, S.M. Shu, Z., Yee, Y.H., Zimmermann, L., Ong, A.A.L., Toh, D.F.K., Krishna, M.S., Yang, L., Decout, J.L., Luo, D., Prabakaran, M.,* Chen, G.,* and Kierzek, E.* (2019) A short chemically modified dsRNA-binding PNA (dbPNA) inhibits influenza viral replication by targeting viral RNA panhandle structure. Bioconjugate Chem., 30, 931-943. (IF: 4.485) 5. Puah, R.Y. Jia, H., Maraswami, M., Toh, D.F.K., Ero, R., Yang, L., Patil, K.M., Ong, A.A.L., Krishna, M.S., Sun, R., Tong, C., Huang, M., Chen, X., Loh, T.P., Gao, Y.G., Liu, D.X.,* and Chen, G.* (2018) Selective binding to mRNA duplex regions by chemically modified peptide nucleic acids stimulates ribosomal frameshift. Biochemistry 57, 149-159. (IF: 2.997) 6. Toh, D.F.K., Devi, G., Patil, K.M., Qu, Q., Maraswami, M., Xiao, Y., Loh, T.P., Zhao, Y.,* and Chen, G.* (2016) Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine-purine inversion site of an RNA duplex. Nucleic Acids Res. 44, 9071-9082. (IF: 11.561) 7. Devi, G., Yuan, Z., Lu, Y., Zhao, Y.,* and Chen, G.* (2014) Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes. Nucleic Acids Res. 42, 4008-4018. (IF: 11.561)
Prof Chen XiaodongCurrently, Prof. Chen's research focuses on two directions: (1) Integrated nano-bio interface: to develop programmable nanostructure-biomaterial hybrid systems for monitoring, manipulating, and mimicking biological processes. (2) Programmable materials for energy conversion: to explore programmable modules for electrochemical energy conversion and storage.
Assoc Prof Chew Jia WeiFluidized bed technology represents an important industrial application, spanning energy production, chemical synthesis, and pharmaceutical processes, among others. However, due in part to the limitations of measurement techniques, processes employing particulate flows often operate below design capacity, and operations are generally based on experience rather than theory. Thus, my research focuses on the important need for the development of measurement and/or analytical solutions for understanding and diagnostic purposes. Another area of research is scaling analysis of fluidized bed systems to develop design heuristics. In fluidized bed systems an added complexity involves instabilities that have to be included in a comprehensive model. To date, the prediction of the characteristic instability length (e.g., the bubble or cluster size) remains elusive, despite its importance in enhancing our comprehension of various phenomena (e.g., species segregation and clustering) in polydisperse fluidized beds. To this end, systematic scaling analysis is expected to be useful in the design and optimization of fluidized bed systems. Membrane technology also spans wide-ranging applications, such as water purification, gas separation, and dialysis. However, optimal performance remains elusive due inevitably to concentration polarization and fouling. Specifically for membrane distillation, although rigorous equations have been developed, the inability to account for the wide spectrum of pore sizes of the membrane and/or biofouling layer inhibits the use of such models for predicting the performance. In particular, membrane distillation enables the production of potable water using waste heat from industrial processes, thus makes for a promising Green Technology. Hence, one area of my research will be towards developing new techniques for characterizing pore sizes (such as evapoporometry), which is expected to lead to a better understanding and optimization of membrane processes. Another thrust involves study of an integrated hybrid process comprising a fluidized bed and a membrane for water purification. More specifically, the addition of particles to a tubular membrane module has been shown to significantly enhance the water permeation flux due to promoting turbulence. For the system to become a feasible and reliable method for separations, further enhancement of performance is warranted.
Prof Chi Yonggui RobinOrganoCatalysis, Chemical Synthesis, Functional Molecules