Overall
My group specializes in molecular simulation in application to chemical engineering problems, material science and bimolecular systems. Over the last 50 years, since the first Monte Carlo simulations by Metropolis and co-workers, molecular simulations have been playing an increasingly important role in a range of research areas, from thermodynamic properties of matter to material design and drug discovery. There are several reasons for this. Simulations often provide an efficient alternative to experiments when conditions of interest are difficult or expensive to achieve (such as extreme pressures and temperatures); moreover, we can consider a much larger number of systems and conditions, thus significantly reducing the optimization cycle. Using computer one can imagine unphysical, chimerical systems, properties of which nevertheless may provide an important thermodynamic insight. This ‘what if?’ approach has been particularly useful in proposing new materials and structures for specific applications.  Most importantly, molecular simulations provide a unique look at the system on a detailed molecular scale, thus underpinning physical effects responsible for its behaviour.

Specific research directions in the group

1. CO2 capture and storage
Global warming and climate change is one of the greatest challenges faced by the mankind today. Reduction of CO2 emissions is the primary objective of greener energy strategies. As a part of the larger UK consortia (EP/G062129/1 £1,958,116), starting September 2009 my group will use computer simulations and theoretical approaches to evaluate promising carbon adsorbents for CO2 capture and separations.  This research will be continued at and extended to probe a range of other promising materials such as hypercrosslinked polymers. Initially, we will focus on flue gases, but optimization of materials for other processes (such as air capture) will be also considered.

Edinburgh school of engineering carbon capture team: http://www.see.ed.ac.uk/carbon capture/

2. Efficient technologies for automotive industry
The current research project sponsored by the Royal Shell Global solutions (£65,000) is aimed to understand the effect of carbon porous deposits inside the combustion engine in a car on the engine’s performance. In general presence of these deposits leads to diminished performance of the engine. One proposed mechanism of this effect suggests that these carbon deposits selectively adsorb components of the pre-ignited fuel and therefore lower its octane number. We are testing this hypothesis using adsorption experiments and simulations and have been able to confirm that it is indeed a viable mechanism of performance deterioration. Jose Costa is a PhD student on this project. Recently, Jose presented these results at the Society of Automotive Engineers meeting in Detroit; and an article has been also recently published in the journal of Carbon. These research directions will be further extended with a focus on more detailed characterization of the deposit structure, the role of water adsorption, the design of possible additives to the fuel that would prevent the deposition process.

Pinto da Costa, J. M. C., Cracknell, R. F., Sarkisov, L., and Seaton, N. A., “Structural Characterization of Carbonaceous Combustion-Chamber Deposits”  Carbon, 2009, 47, 3322.

3. Biomimetic materials for drug delivery, sensing and security applications
Polymeric materials capable of biomimetic molecular recognition functions can be used in a number of applications such as sensing, separations, drug delivery and catalysis. However, design of these materials with tailored functionalities remains an intricate and vastly empirical art. In our group we focus on the development of computational strategies aimed to streamline the design process. As a first step we focused on the better understanding of the mechanism of molecular recognition in these materials. We proposed the first theoretical model featuring and explaining molecular recognition effects in these materials. Currently we are extending these studies to propose new molecularly imprinted polymers for drug purification and delivery applications. This research is funded by the EPSRC (£230,000 EP/D074762/1) and current group members working on this project include one PhD candidate.

We intend to further extend this project to security applications. Quick and reliable detection of explosives in real life settings, such as the airport baggage terminal, has been of a major importance due to the rise of global terrorism threat in the recent years. Any technique developed for explosive detection must satisfy certain requirements. Specifically, it must be able to sense very low levels of warfare agents and it should be able to discriminate the warfare agents from other similar but benign compounds to avoid unnecessary (and very costly) false alarms. Imprinted polymers can be used for sensing explosives, as a part of microcantilever detector. The problem is that a large variety of building blocks is available for these materials and search for the best options in experiments is expensive, time consuming and in the case of many warfare agents simply dangerous. Instead, we will use computer simulations where we imitate experimental systems on molecular scale. Initially, we will focus on optimization of molecular recognition functionality for TNT as a model theoretical system, but other warfare agents can be considered at later stages.

Dourado, E. M. A and Sarkisov, L, Emergence of molecular recognition phenomena in a simple model of imprinted porous materials, J. Chem. Phys. 2009, 130(21), 214701.

Herdes, C. and Sarkisov, L, Computer simulation of VOCs adsorption in atomistic models of molecularly imprinted polymers. Langmuir 2009, 25 (9), pp 5352–5359

4. Molecular engineering of efficient drug delivery systems
In order to be effective drug molecules have to get inside a diseased cell. This is not a simple task, as cells are protected by membranes that allow only specific groups of molecules to cross. This is a major obstacle in the development of new efficient drugs, particularly when the drug molecules are large as in genetic therapy. Viruses are able to cross the cell membrane and one way to deliver drugs into a cell is to use special viruses to ‘infect’ the cells with drug molecules. Unfortunately, this technology is expensive, and there are health risks associated with using the viruses.  There is a great need for new ways of getting drugs safely into cells. In this project we construct virtual molecular carriers and explore their ability to cross lipid membranes. Initially, we focused on peptide systems, and in the process managed to provide some general fundamental insights peptide-membrane interactions. Evi Gkeka is a PhD student on this project who recently, using these course grained computer simulations, explained the mechanism of barrel-stave pore formation in lipid membranes. Currently we investigate nanoparticle-bilayer interactions, phase behaviour of lipids and viral translocation.

Gkeka, P. and Sarkisov, L, Spontaneous formation of a barrel-stave pore in a coarse-grained model of the synthetic LS3 peptide and a DPPC lipid bilayer. Journal of Physical Chemistry B, 2008, 113(1), pp: 6-8

5. Sensing & capture of estrogens from water resources using novel polymeric materials
Contamination of fresh water resources with endocrine disruptive chemicals (EDCs) presents a serious environmental threat. It is a particularly important issue for very potent EDC, such as estrogens, that can cause adverse impact on the environment and human health even in trace concentrations (ng/L). Current water treatment systems are not designed or efficient in detection or removal of these chemicals. We aim to develop a project that provides a comprehensive, rational strategy for design of new porous polymer materials for microcantilever sensors and nanofiltration membranes technologies. At the heart of the approach are novel molecularly imprinted and hyper-crosslinked polymers. Starting with the already available materials, we will use molecular modelling to design new structures and guide the synthetic protocol (in collaboration with synthetic chemists). The developed materials will be tested for their ability to sense and remove potent EDC chemicals from diverse water resources.

6. Protein crystallization solutions for proteomic research
Protein crystallization is a crucial step in the determination of protein 3D structure from X-ray crystallography and it depends on many physical and chemical factors, including solution properties. As a consequence, favourable crystallization conditions are sought through extensive trial-and-error procedures which are both time and money consuming. For example, recent experiments in the field of structural genomics show that the successful rate of proceeding to structural determination from protein clones is about 10%. To address this issue we need to generate a clear, unambiguous picture of how proteins interact in water solutions under crystallization conditions. Preliminary studies have been conducted through the two HPC-Europa projects in 2007-2008 with Dr. Pellicane as the visitor in my group. In these preliminary studies, published in Physical Review Letters, we characterized for the first time effective interactions involved in the formation of two hydrophobic crystal contacts and showed that the depth of the potential does not exceed 2kT, however the shape of the potential does depend on the specific features of the interface. This will have important implications in our understanding of the protein phase behaviour. These studies will be extended to a broader range of protein systems and conditions, with a view of construction a proper multiscale model of protein behaviour in solution.

Pellicane, G., Smith, G. and Sarkisov, L, Molecular dynamics characterization of protein crystal contacts in aqueous solutions. Physical Review Letters, 2008, 101(24) 248102.

7. Other themes
In general, we are also interested in a number of topics related to structural characterization of porous materials. In this endeavour we utilize a diverse arsenal of tools from integral equatios to Monte Carlo methods. Specifically, we developed a range of tools to calculate surface area and pore size distributions in various materials such as Metal Organic Frameworks. These programmes are available in the archived form below along with the manuals and well documented test cases.

7.1 Poreblazer 1.1: comprehensive structure analysis package for ordered and disordered materials

- Accessible surface area
- Geometric pore size distribution
- Pore percolation analysis
- Structure connectivity analysis
- Orthorhombic and non-orthorhombic unit cells
- Available upon request

- Poreblazer 1.2 has the following additional functions (available upon request):
- Pore volume (geometric, He)
- Free energy profiles, local and global Henry's coefficients and selectivities

Other codes in our group are not yet "client" ready, but we would be happy to discuss opportunities to use them in other groups:

7.3 Replica Ornstein-Zerinke/ RISM codes: the code allows one to consider multicomponent mixtures of rigid molecules (of any geometry) interacting via a square-well, Lennard-Jones, hard sphere potential. The code utilizes Percus-Yevick, MSA, HNC, Martynov-Sarkisov closures. ROZ functionality of the code allows to consider any molecular mixture confined within a quenched molecular matrix (of arbitrary complexity and number of components).

7.4 Lipid bilayer structure analysis package: a set of codes that takes Gromacs/MARTINI configurations as an input to generate information about bilayer surface area, bond angle distribution, cluster phases, cluster connectivity, 2D radial distribution functions: lba_1.1

7.5 Potential of mean force from Umbrella/WHAM: the in-house code uses Gromacs trajectories along a reaction coordinate to calculate PMF based on Umbrella/WHAM equations

7.6 We also have in-house GCMC, MD and lattice density functional codes

7.7 Link to Multipurpose Simulation Code (MuSiC) developed in Prof. Randy Snurr group at Northwestern University: http://zeolites.cqe.northwestern.edu/Music/music.html

Link: IRMOF1_CO2