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Papers by Zak Hughes

Nanoscale, Jan 2, 2015

Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy... more Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.

Journal of colloid and interface science, Jan 15, 2014

We report the structure of the electrical double layer, determined from molecular dynamics simula... more We report the structure of the electrical double layer, determined from molecular dynamics simulations, for a range of saline solutions (NaCl, KCl, MgCl2 and CaCl2) at both 0.16 and 0.60 mol kg(-1) on different facets of the gold and silver aqueous interfaces. We consider the Au/Ag(111), native Au/Ag(100) and reconstructed Au(100)(5×1) facets. For a given combination of metallic surface and facet, some variations in density profile are apparent across the different cations in solution, with the corresponding chloride counterion profiles remaining broadly invariant. All density profiles at the higher concentration are predicted to be very similar to their low-concentration counterparts. We find that each electrolyte responds differently to the different metallic surface and facets, particularly those of the divalent metal ions. Our findings reveal marked differences in density profiles between facets for a given metallic interface for both Mg(2+) and Ca(2+), with Na(+) and K(+) showi...

Langmuir, 2014

Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and... more Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.

NATO Science Series II: Mathematics, Physics and Chemistry, 2005

This article describes some of the progress made towards the simulation of liquid crystalline pol... more This article describes some of the progress made towards the simulation of liquid crystalline polymers and dendrimers within our laboratory. We describe the use of hybrid models, where a mixture of spherical and nonspherical potentials can be linked together to form model macromolecules. Results are presented for hybrid models of a side-chain and a main chain liquid crystal polymer, which have been studied by molecular dynamics simulation. Preliminary results are also presented from a modelling study of a third generation carbosilane liquid crystalline dendrimer. These involve molecular dynamics studies of single molecules in a solvent using a hybrid Gay-Berne/Lennard-Jones model; and studies of the bulk phases of the dendrimer using a coarse-grained hybrid spherocylinder/Lennard-Jones model. We also review briefly some of the progress made with other models for liquid crystals and polymers, point to the problems still faced and some of the current developments designed to overcome them.

Biophysical Journal, 2014

The vitrification solutions used in the cryopreservation of biological samples aim to minimize th... more The vitrification solutions used in the cryopreservation of biological samples aim to minimize the deleterious formation of ice by dehydrating cells and promoting the formation of the glassy state of water. They contain a mixture of different cryoprotective agents (CPAs) in water, typically polyhydroxylated alcohols and/or dimethyl sulfoxide (DMSO), which can damage cell membranes. Molecular dynamics simulations have been used to investigate the behavior of pure DPPC, pure DOPC, and mixed DOPC-β-sitosterol bilayers solvated in a vitrification solution containing glycerol, ethylene glycol, and DMSO at concentrations that approximate the widely used plant vitrification solution 2. As in the case of solutions containing a single CPA, the vitrification solution causes the bilayer to thin and become disordered, and pores form in the case of some bilayers. Importantly, the degree of thinning is, however, substantially reduced compared to solutions of DMSO containing the same total CPA concentration. The reduction in the damage done to the bilayers is a result of the ability of the polyhydroxylated species (especially glycerol) to form hydrogen bonds to the lipid and sterol molecules of the bilayer. A decrease in the amount of DMSO in the vitrification solution with a corresponding increase in the amount of glycerol or ethylene glycol diminishes further its damaging effect due to increased hydrogen bonding of the polyol species to the bilayer headgroups. These findings rationalize, to our knowledge for the first time, the synergistic effects of combining different CPAs, and form the basis for the optimization of vitrification solutions.

The journal of physical chemistry. B, Jan 4, 2012

Molecular dynamics simulations have been used to investigate the effect of DMSO on 1,2-dipalmitoy... more Molecular dynamics simulations have been used to investigate the effect of DMSO on 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) phospholipid bilayers. The concentration of DMSO was varied between 0 and 25.0 mol %. For both lipids, DMSO causes the membrane to expand in the plane of the membrane while thinning normal to that plane. Above a critical concentration, pores in the membrane form spontaneously, and if the concentration is increased further, then the bilayer structure is destroyed. Even at concentrations below those required to induce pores, DMSO readily diffuses across the bilayers. The free-energy profile associated with the diffusion of a DMSO molecules across the membrane has been calculated. The simulations suggest that the DOPC bilayer is more resistant to the deleterious effects of DMSO, both increasing the stability of the membranes and decreasing the rate at which DMSO diffuses across the membrane. In thi...

Chemistry of Materials, 2014

ABSTRACT Controllable 3D assembly of multicomponent inorganic nanomaterials by precisely position... more ABSTRACT Controllable 3D assembly of multicomponent inorganic nanomaterials by precisely positioning two or more types of nanoparticles to modulate their interactions and achieve multifunctionality remains a major challenge. The diverse chemical and structural features of biomolecules can generate the compositionally specific organic/inorganic interactions needed to create such assemblies. Toward this aim, we studied the materials-specific binding of peptides selected based upon affinity for Ag (AgBP1 and AgBP2) and Au (AuBP1 and AuBP2) surfaces, combining experimental binding measurements, advanced molecular simulation, and nanomaterial synthesis. This reveals, for the first time, different modes of binding on the chemically similar Au and Ag surfaces. Molecular simulations showed flatter configurations on Au and a greater variety of 3D adsorbed conformations on Ag, reflecting primarily enthalpically driven binding on Au and entropically driven binding on Ag. This may arise from differences in the interfacial solvent structure. On Au, direct interaction of peptide residues with the metal surface is dominant, while on Ag, solvent-mediated interactions are more important. Experimentally, AgBP1 is found to be selective for Ag over Au, while the other sequences have strong and comparable affinities for both surfaces, despite differences in binding modes. Finally, we show for the first time the impact of these differences on peptide mediated synthesis of nanoparticles, leading to significant variation in particle morphology, size, and aggregation state. Because the degree of contact with the metal surface affects the peptides ability to cap the nanoparticles and thereby control growth and aggregation, the peptides with the least direct contact (AgBP1 and AgBP2 on Ag) produced relatively polydispersed and aggregated nanoparticles. Overall, we show that thermodynamically different binding modes at metallic interfaces can enable selective binding on very similar inorganic surfaces and can provide control over nanoparticle nucleation and growth. This supports the promise of bionanocombinatoric approaches that rely upon materials recognition.

ABSTRACT This chapter contains sections titled: Introduction Molecular Simulations of Polymeric M... more ABSTRACT This chapter contains sections titled: Introduction Molecular Simulations of Polymeric Membrane Materials for Water Treatment Applications Molecular Simulation of Inorganic Desalination Membranes Molecular Simulation of Membrane Fouling References

Proceedings of The National Academy of Sciences, 2009

Phase-change materials are functionally important materials that can be thermally interconverted ... more Phase-change materials are functionally important materials that can be thermally interconverted between metallic (crystalline) and semiconducting (amorphous) phases on a very short time scale. Although the interconversion appears to involve a change in local atomic coordination numbers, the electronic basis for this process is still unclear. Here, we demonstrate that in a nearly vacancy-free binary GeSb system where we can

The Journal of Physical Chemistry C, 2011

ABSTRACT Desalination by reverse osmosis is an increasingly important source of potable water in ... more ABSTRACT Desalination by reverse osmosis is an increasingly important source of potable water in many countries. The interest in developing new, more effective membranes is, therefore, great. One set of materials that have been suggested as a possible new type of desalination Membrane are nanoporous materials. In this work computational methods are used to investigate the behavior of water within five different zeolitic systems. Quantum mechanical calculations are used to construct a set of force-field parameters for two atomistic.:models, Molecular dynamics simulations Of. the zeolites show that Water will diffuse through zeolites at a rate faster than that obtained with the composite membranes currently used in commercial desalination. In addition, the thermodynamics of salt rejection have been investigated using the free energy perturbation method. The results of these calculations show that the chloride ion finds the zeolitic environment strongly unfavorable compared to the bulk solution. In the case of the sodium ion, the energetic difference between the zeolite environment and solution is less significant, but charge separation prevents sodium from permeating the membrane.

The Journal of Physical Chemistry B, 2013

Polyhydroxylated alcohols and DMSO are common cryosolvents that can damage cell membranes at suff... more Polyhydroxylated alcohols and DMSO are common cryosolvents that can damage cell membranes at sufficiently high concentrations. The interaction of representative plant cell membranes composed of mixed 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)-β-sitosterol bilayers, at a range of compositions, with a variety of cryosolvent molecules (DMSO, propylene glycol, ethylene glycol, glycerol, and methanol) has been investigated using molecular dynamics simulations. All the cryosolvents cause the bilayers to thin and become disordered; however, DMSO and propylene glycol have a greater disordering effect on the bilayer. Propylene glycol is shown to have the ability to cause the formation of pores in pure DOPC bilayers in a manner similar to that previously shown for DMSO. As the concentration of β-sitosterol within the bilayer increases, the membranes become more resistant to the deleterious effects of the cryosolvents. All three polyhydroxylated species are observed to form hydrogen bonds to multiple phospholipid molecules, effectively acting as cross-linkers, with glycerol being the most effective cross-linker. Increases in the concentration of β-sitosterol reduce overall hydrogen bonding of the bilayer with the cryosolvents as well as cross-linking, with glycerol and ethylene glycol being the most affected. The ability of all of these cryosolvents to affect the integrity of cell membranes appears to be the result of the balance of their ability to disorder lipid bilayers, to diffuse across them, and to interact with the lipid head groups.

Soft Matter, 2013

ABSTRACT Cell membrane phospholipid bilayers can be damaged by the large amounts of dimethyl sulp... more ABSTRACT Cell membrane phospholipid bilayers can be damaged by the large amounts of dimethyl sulphoxide (DMSO) commonly used in cryopreservation. The interaction of DMSO with model bilayers consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and β-sitosterol has been studied using molecular dynamics simulations. Initially the effect of sterol concentration and temperature upon bilayers solvated in pure water was determined, and membranes containing β-sitosterol were compared with membranes containing cholesterol. These simulations showed that the presence of sterols has a condensing effect on the phospholipids, causing a reduction in the area per lipid as the sterol concentration increases, up to a phospholipid–sterol ratio of 2:1. The incorporation of sterols into the bilayer also increased the thickness and order of the phospholipid acyl tails. DOPC–β-sitosterol bilayers at different relative concentrations were simulated in solutions of 2.5 and 25.0 mol% DMSO. The interaction of DMSO with the bilayers caused the bilayers to expand laterally, while thinning normal to the plane of the bilayer expansion. The same qualitative behaviour has been shown to occur in pure phosphocholine bilayers. However, the presence of sterols made the membranes more resistant to the effects of DMSO, to the extent that the membranes where able to maintain their integrity in 25.0 mol% DMSO, a concentration that would otherwise cause the destruction of a pure DOPC bilayer. Increasing the concentration of β-sitosterol within the bilayers reduced the rate of DMSO diffusion across the bilayer and, if the concentration was large enough, caused the diffusion mechanism to change. DMSO was observed to disorder the membranes enough to cause an increase in the number of sterol “flip–flops”. The findings of this work provide a more realistic description of how DMSO interacts with cell membranes and the role of the composition of the membrane.

Soft Matter, 2005

Coarse-grained simulations are described in which the behaviour of a system of model liquid cryst... more Coarse-grained simulations are described in which the behaviour of a system of model liquid crystalline dendrimer molecules is studied in both liquid and smectic-A liquid crystalline phases. The model system is based on a third generation carbosilane dendrimer, which is functionalised at the surface by short polymeric chains terminated in mesogenic units. The design of the coarsegrained model is based on initial Monte Carlo studies of a single carbosilane molecule at an atomistic level, which yield structural data. The coarse-grained dendrimer is represented in terms of a combination of spherical sites representing the dendrimer core and polymer chains, and spherocylinders representing the mesogenic groups. A strong coupling is seen between internal molecular structure and molecular environment, with individual dendrimer molecules undergoing a remarkable transition from spherical to rod-shaped at the isotropic-smectic phase transition. The driving force for mesophase formation is provided by nanoscale microphase separation of mesogens and the dendrimer core.

Nanoscale, 2014

To fully harness the enormous potential offered by interfaces between graphitic nanostructures an... more To fully harness the enormous potential offered by interfaces between graphitic nanostructures and biomolecules, detailed connections between adsorbed conformations and adsorption behaviour are needed. To elucidate these links, a key approach, in partnership with experimental techniques, is molecular simulation. For this, a force-field (FF) that can appropriately capture the relevant physics and chemistry of these complex bio-interfaces, while allowing extensive conformational sampling, and also supporting inter-operability with known biological FFs, is a pivotal requirement. Here, we present and apply such a force-field, GRAPPA, designed to work with the CHARMM FF. GRAPPA is an efficiently implemented polarisable force-field, informed by extensive plane-wave DFT calculations using the revPBE-vdW-DF functional. GRAPPA adequately recovers the spatial and orientational structuring of the aqueous interface of graphene and carbon nanotubes, compared with more sophisticated approaches. We apply GRAPPA to determine the free energy of adsorption for a range of amino acids, identifying Trp, Tyr and Arg to have the strongest binding affinity and Asp to be a weak binder. The GRAPPA FF can be readily incorporated into mainstream simulation packages, and will enable large-scale polarisable biointerfacial simulations at graphitic interfaces, that will aid the development of biomolecule-mediated, solution-based graphene processing and self-assembly strategies.

Langmuir, 2013

The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the dev... more The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the development of bionanotechnology applications. In line with advances in polarizable force fields for adsorption at aqueous gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calculated using first-principles approaches for a wide range of different but biologically relevant small molecules, including water. Here, we present such first-principles data for a comprehensive range of bio-organic molecules obtained from plane-wave density functional theory calculations using the vdW-DF functional. As reported previously for the gold force field, GolP-CHARMM (Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force-fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616-1630), we have used these data to construct a a new force field, AgP-CHARMM, suitable for the simulation of biomolecules at the aqueous Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. Our force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. We also calculate and compare the structuring (spatial and orientational) of liquid water adsorbed at both silver and gold. Finally, we report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aqueous interfaces, calculated using metadynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. Our findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. Our analysis suggests that the relatively stronger structuring of the first water layer on silver, relative to gold, could give rise to these differences.

Journal of Materials Chemistry, 2010

... Zak E. Hughes * and Julian D. Gale. Nanochemistry Research Institute, Department of Chemistry... more ... Zak E. Hughes * and Julian D. Gale. Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, PO Box U1987 ... by a cosine term, while the intermolecular interactions are represented by a Coulomb interaction and Lennard-Jones potentials. ...

Computer Physics Communications, 2008

The phase behaviour of three soft core spherocylinder models is investigated with a view to produ... more The phase behaviour of three soft core spherocylinder models is investigated with a view to producing an effective potential for use in coarsegrained simulations of liquid crystal phases and polymers composed of rigid and flexible segments. Provided potentials are not made too soft, two of the soft core models are found to work well in terms of successfully reproducing mesophases and in providing considerable improvements in computational speed over other commonly used coarse-grained models. In Monte Carlo simulations a soft-core spherocylinder model in which a cut and shifted Lennard-Jones potential is truncated with a linear tangential potential is found to be particularly effective; while for molecular dynamics a better model is provided by a DPD-like quadratic potential. Here, computational speed-ups of 20-30× are seen in equilibration times in comparison to the well-known soft repulsive spherocylinder (SRS) model. The quadratic potential is used in an additional set of coarse-grained simulations of a liquid crystal with a flexible chain, which exhibits spontaneous formation of a nematic phase. The use of different types of interaction sites is also illustrated by the simulation of a spherocylinder with two "tails" formed from spheres. Here, varying the hardness of the sphere-spherocylinder interaction potential allows the formation of a smectic-A phase which exhibits microphase separation.

Agricultural Sciences in China, 2010

We have performed coarse grained molecular dynamics simulations (CGMD) to investigate the interac... more We have performed coarse grained molecular dynamics simulations (CGMD) to investigate the interactions of generation 7, 5 and 3 (G7, G5 and G3) charge-neutral polyamidoamine (PAMAM) dendrimers with a DPPC (dipalmitoylphosphatidylcholine) monolayer at the air-water interface (model pulmonary surfactant) during the end-expiration process. Our results show that different generations of PAMAM dendrimers have different influences on the DPPC monolayer. Generally, G3 PAMAM dendrimers show little influence on the DPPC monolayer's structure and relative properties. While G7 and G5 PAMAM dendrimers tend to induce the formation of largely deformed structures of the DPPC monolayer and inhibit or even reverse the normal phase transition of the interfacial DPPC molecules during the process of compression. Besides, we find that the formation processes of these disrupted structures are energy-favorable based on analyzing van der Waals interaction energy between PAMAM dendrimers and the whole system.

Nanoscale, Jan 2, 2015

Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy... more Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.

Journal of colloid and interface science, Jan 15, 2014

We report the structure of the electrical double layer, determined from molecular dynamics simula... more We report the structure of the electrical double layer, determined from molecular dynamics simulations, for a range of saline solutions (NaCl, KCl, MgCl2 and CaCl2) at both 0.16 and 0.60 mol kg(-1) on different facets of the gold and silver aqueous interfaces. We consider the Au/Ag(111), native Au/Ag(100) and reconstructed Au(100)(5×1) facets. For a given combination of metallic surface and facet, some variations in density profile are apparent across the different cations in solution, with the corresponding chloride counterion profiles remaining broadly invariant. All density profiles at the higher concentration are predicted to be very similar to their low-concentration counterparts. We find that each electrolyte responds differently to the different metallic surface and facets, particularly those of the divalent metal ions. Our findings reveal marked differences in density profiles between facets for a given metallic interface for both Mg(2+) and Ca(2+), with Na(+) and K(+) showi...

Langmuir, 2014

Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and... more Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.

NATO Science Series II: Mathematics, Physics and Chemistry, 2005

This article describes some of the progress made towards the simulation of liquid crystalline pol... more This article describes some of the progress made towards the simulation of liquid crystalline polymers and dendrimers within our laboratory. We describe the use of hybrid models, where a mixture of spherical and nonspherical potentials can be linked together to form model macromolecules. Results are presented for hybrid models of a side-chain and a main chain liquid crystal polymer, which have been studied by molecular dynamics simulation. Preliminary results are also presented from a modelling study of a third generation carbosilane liquid crystalline dendrimer. These involve molecular dynamics studies of single molecules in a solvent using a hybrid Gay-Berne/Lennard-Jones model; and studies of the bulk phases of the dendrimer using a coarse-grained hybrid spherocylinder/Lennard-Jones model. We also review briefly some of the progress made with other models for liquid crystals and polymers, point to the problems still faced and some of the current developments designed to overcome them.

Biophysical Journal, 2014

The vitrification solutions used in the cryopreservation of biological samples aim to minimize th... more The vitrification solutions used in the cryopreservation of biological samples aim to minimize the deleterious formation of ice by dehydrating cells and promoting the formation of the glassy state of water. They contain a mixture of different cryoprotective agents (CPAs) in water, typically polyhydroxylated alcohols and/or dimethyl sulfoxide (DMSO), which can damage cell membranes. Molecular dynamics simulations have been used to investigate the behavior of pure DPPC, pure DOPC, and mixed DOPC-β-sitosterol bilayers solvated in a vitrification solution containing glycerol, ethylene glycol, and DMSO at concentrations that approximate the widely used plant vitrification solution 2. As in the case of solutions containing a single CPA, the vitrification solution causes the bilayer to thin and become disordered, and pores form in the case of some bilayers. Importantly, the degree of thinning is, however, substantially reduced compared to solutions of DMSO containing the same total CPA concentration. The reduction in the damage done to the bilayers is a result of the ability of the polyhydroxylated species (especially glycerol) to form hydrogen bonds to the lipid and sterol molecules of the bilayer. A decrease in the amount of DMSO in the vitrification solution with a corresponding increase in the amount of glycerol or ethylene glycol diminishes further its damaging effect due to increased hydrogen bonding of the polyol species to the bilayer headgroups. These findings rationalize, to our knowledge for the first time, the synergistic effects of combining different CPAs, and form the basis for the optimization of vitrification solutions.

The journal of physical chemistry. B, Jan 4, 2012

Molecular dynamics simulations have been used to investigate the effect of DMSO on 1,2-dipalmitoy... more Molecular dynamics simulations have been used to investigate the effect of DMSO on 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) phospholipid bilayers. The concentration of DMSO was varied between 0 and 25.0 mol %. For both lipids, DMSO causes the membrane to expand in the plane of the membrane while thinning normal to that plane. Above a critical concentration, pores in the membrane form spontaneously, and if the concentration is increased further, then the bilayer structure is destroyed. Even at concentrations below those required to induce pores, DMSO readily diffuses across the bilayers. The free-energy profile associated with the diffusion of a DMSO molecules across the membrane has been calculated. The simulations suggest that the DOPC bilayer is more resistant to the deleterious effects of DMSO, both increasing the stability of the membranes and decreasing the rate at which DMSO diffuses across the membrane. In thi...

Chemistry of Materials, 2014

ABSTRACT Controllable 3D assembly of multicomponent inorganic nanomaterials by precisely position... more ABSTRACT Controllable 3D assembly of multicomponent inorganic nanomaterials by precisely positioning two or more types of nanoparticles to modulate their interactions and achieve multifunctionality remains a major challenge. The diverse chemical and structural features of biomolecules can generate the compositionally specific organic/inorganic interactions needed to create such assemblies. Toward this aim, we studied the materials-specific binding of peptides selected based upon affinity for Ag (AgBP1 and AgBP2) and Au (AuBP1 and AuBP2) surfaces, combining experimental binding measurements, advanced molecular simulation, and nanomaterial synthesis. This reveals, for the first time, different modes of binding on the chemically similar Au and Ag surfaces. Molecular simulations showed flatter configurations on Au and a greater variety of 3D adsorbed conformations on Ag, reflecting primarily enthalpically driven binding on Au and entropically driven binding on Ag. This may arise from differences in the interfacial solvent structure. On Au, direct interaction of peptide residues with the metal surface is dominant, while on Ag, solvent-mediated interactions are more important. Experimentally, AgBP1 is found to be selective for Ag over Au, while the other sequences have strong and comparable affinities for both surfaces, despite differences in binding modes. Finally, we show for the first time the impact of these differences on peptide mediated synthesis of nanoparticles, leading to significant variation in particle morphology, size, and aggregation state. Because the degree of contact with the metal surface affects the peptides ability to cap the nanoparticles and thereby control growth and aggregation, the peptides with the least direct contact (AgBP1 and AgBP2 on Ag) produced relatively polydispersed and aggregated nanoparticles. Overall, we show that thermodynamically different binding modes at metallic interfaces can enable selective binding on very similar inorganic surfaces and can provide control over nanoparticle nucleation and growth. This supports the promise of bionanocombinatoric approaches that rely upon materials recognition.

ABSTRACT This chapter contains sections titled: Introduction Molecular Simulations of Polymeric M... more ABSTRACT This chapter contains sections titled: Introduction Molecular Simulations of Polymeric Membrane Materials for Water Treatment Applications Molecular Simulation of Inorganic Desalination Membranes Molecular Simulation of Membrane Fouling References

Proceedings of The National Academy of Sciences, 2009

Phase-change materials are functionally important materials that can be thermally interconverted ... more Phase-change materials are functionally important materials that can be thermally interconverted between metallic (crystalline) and semiconducting (amorphous) phases on a very short time scale. Although the interconversion appears to involve a change in local atomic coordination numbers, the electronic basis for this process is still unclear. Here, we demonstrate that in a nearly vacancy-free binary GeSb system where we can

The Journal of Physical Chemistry C, 2011

ABSTRACT Desalination by reverse osmosis is an increasingly important source of potable water in ... more ABSTRACT Desalination by reverse osmosis is an increasingly important source of potable water in many countries. The interest in developing new, more effective membranes is, therefore, great. One set of materials that have been suggested as a possible new type of desalination Membrane are nanoporous materials. In this work computational methods are used to investigate the behavior of water within five different zeolitic systems. Quantum mechanical calculations are used to construct a set of force-field parameters for two atomistic.:models, Molecular dynamics simulations Of. the zeolites show that Water will diffuse through zeolites at a rate faster than that obtained with the composite membranes currently used in commercial desalination. In addition, the thermodynamics of salt rejection have been investigated using the free energy perturbation method. The results of these calculations show that the chloride ion finds the zeolitic environment strongly unfavorable compared to the bulk solution. In the case of the sodium ion, the energetic difference between the zeolite environment and solution is less significant, but charge separation prevents sodium from permeating the membrane.

The Journal of Physical Chemistry B, 2013

Polyhydroxylated alcohols and DMSO are common cryosolvents that can damage cell membranes at suff... more Polyhydroxylated alcohols and DMSO are common cryosolvents that can damage cell membranes at sufficiently high concentrations. The interaction of representative plant cell membranes composed of mixed 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)-β-sitosterol bilayers, at a range of compositions, with a variety of cryosolvent molecules (DMSO, propylene glycol, ethylene glycol, glycerol, and methanol) has been investigated using molecular dynamics simulations. All the cryosolvents cause the bilayers to thin and become disordered; however, DMSO and propylene glycol have a greater disordering effect on the bilayer. Propylene glycol is shown to have the ability to cause the formation of pores in pure DOPC bilayers in a manner similar to that previously shown for DMSO. As the concentration of β-sitosterol within the bilayer increases, the membranes become more resistant to the deleterious effects of the cryosolvents. All three polyhydroxylated species are observed to form hydrogen bonds to multiple phospholipid molecules, effectively acting as cross-linkers, with glycerol being the most effective cross-linker. Increases in the concentration of β-sitosterol reduce overall hydrogen bonding of the bilayer with the cryosolvents as well as cross-linking, with glycerol and ethylene glycol being the most affected. The ability of all of these cryosolvents to affect the integrity of cell membranes appears to be the result of the balance of their ability to disorder lipid bilayers, to diffuse across them, and to interact with the lipid head groups.

Soft Matter, 2013

ABSTRACT Cell membrane phospholipid bilayers can be damaged by the large amounts of dimethyl sulp... more ABSTRACT Cell membrane phospholipid bilayers can be damaged by the large amounts of dimethyl sulphoxide (DMSO) commonly used in cryopreservation. The interaction of DMSO with model bilayers consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and β-sitosterol has been studied using molecular dynamics simulations. Initially the effect of sterol concentration and temperature upon bilayers solvated in pure water was determined, and membranes containing β-sitosterol were compared with membranes containing cholesterol. These simulations showed that the presence of sterols has a condensing effect on the phospholipids, causing a reduction in the area per lipid as the sterol concentration increases, up to a phospholipid–sterol ratio of 2:1. The incorporation of sterols into the bilayer also increased the thickness and order of the phospholipid acyl tails. DOPC–β-sitosterol bilayers at different relative concentrations were simulated in solutions of 2.5 and 25.0 mol% DMSO. The interaction of DMSO with the bilayers caused the bilayers to expand laterally, while thinning normal to the plane of the bilayer expansion. The same qualitative behaviour has been shown to occur in pure phosphocholine bilayers. However, the presence of sterols made the membranes more resistant to the effects of DMSO, to the extent that the membranes where able to maintain their integrity in 25.0 mol% DMSO, a concentration that would otherwise cause the destruction of a pure DOPC bilayer. Increasing the concentration of β-sitosterol within the bilayers reduced the rate of DMSO diffusion across the bilayer and, if the concentration was large enough, caused the diffusion mechanism to change. DMSO was observed to disorder the membranes enough to cause an increase in the number of sterol “flip–flops”. The findings of this work provide a more realistic description of how DMSO interacts with cell membranes and the role of the composition of the membrane.

Soft Matter, 2005

Coarse-grained simulations are described in which the behaviour of a system of model liquid cryst... more Coarse-grained simulations are described in which the behaviour of a system of model liquid crystalline dendrimer molecules is studied in both liquid and smectic-A liquid crystalline phases. The model system is based on a third generation carbosilane dendrimer, which is functionalised at the surface by short polymeric chains terminated in mesogenic units. The design of the coarsegrained model is based on initial Monte Carlo studies of a single carbosilane molecule at an atomistic level, which yield structural data. The coarse-grained dendrimer is represented in terms of a combination of spherical sites representing the dendrimer core and polymer chains, and spherocylinders representing the mesogenic groups. A strong coupling is seen between internal molecular structure and molecular environment, with individual dendrimer molecules undergoing a remarkable transition from spherical to rod-shaped at the isotropic-smectic phase transition. The driving force for mesophase formation is provided by nanoscale microphase separation of mesogens and the dendrimer core.

Nanoscale, 2014

To fully harness the enormous potential offered by interfaces between graphitic nanostructures an... more To fully harness the enormous potential offered by interfaces between graphitic nanostructures and biomolecules, detailed connections between adsorbed conformations and adsorption behaviour are needed. To elucidate these links, a key approach, in partnership with experimental techniques, is molecular simulation. For this, a force-field (FF) that can appropriately capture the relevant physics and chemistry of these complex bio-interfaces, while allowing extensive conformational sampling, and also supporting inter-operability with known biological FFs, is a pivotal requirement. Here, we present and apply such a force-field, GRAPPA, designed to work with the CHARMM FF. GRAPPA is an efficiently implemented polarisable force-field, informed by extensive plane-wave DFT calculations using the revPBE-vdW-DF functional. GRAPPA adequately recovers the spatial and orientational structuring of the aqueous interface of graphene and carbon nanotubes, compared with more sophisticated approaches. We apply GRAPPA to determine the free energy of adsorption for a range of amino acids, identifying Trp, Tyr and Arg to have the strongest binding affinity and Asp to be a weak binder. The GRAPPA FF can be readily incorporated into mainstream simulation packages, and will enable large-scale polarisable biointerfacial simulations at graphitic interfaces, that will aid the development of biomolecule-mediated, solution-based graphene processing and self-assembly strategies.

Langmuir, 2013

The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the dev... more The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the development of bionanotechnology applications. In line with advances in polarizable force fields for adsorption at aqueous gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calculated using first-principles approaches for a wide range of different but biologically relevant small molecules, including water. Here, we present such first-principles data for a comprehensive range of bio-organic molecules obtained from plane-wave density functional theory calculations using the vdW-DF functional. As reported previously for the gold force field, GolP-CHARMM (Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force-fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616-1630), we have used these data to construct a a new force field, AgP-CHARMM, suitable for the simulation of biomolecules at the aqueous Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. Our force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. We also calculate and compare the structuring (spatial and orientational) of liquid water adsorbed at both silver and gold. Finally, we report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aqueous interfaces, calculated using metadynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. Our findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. Our analysis suggests that the relatively stronger structuring of the first water layer on silver, relative to gold, could give rise to these differences.

Journal of Materials Chemistry, 2010

... Zak E. Hughes * and Julian D. Gale. Nanochemistry Research Institute, Department of Chemistry... more ... Zak E. Hughes * and Julian D. Gale. Nanochemistry Research Institute, Department of Chemistry, Curtin University of Technology, PO Box U1987 ... by a cosine term, while the intermolecular interactions are represented by a Coulomb interaction and Lennard-Jones potentials. ...

Computer Physics Communications, 2008

The phase behaviour of three soft core spherocylinder models is investigated with a view to produ... more The phase behaviour of three soft core spherocylinder models is investigated with a view to producing an effective potential for use in coarsegrained simulations of liquid crystal phases and polymers composed of rigid and flexible segments. Provided potentials are not made too soft, two of the soft core models are found to work well in terms of successfully reproducing mesophases and in providing considerable improvements in computational speed over other commonly used coarse-grained models. In Monte Carlo simulations a soft-core spherocylinder model in which a cut and shifted Lennard-Jones potential is truncated with a linear tangential potential is found to be particularly effective; while for molecular dynamics a better model is provided by a DPD-like quadratic potential. Here, computational speed-ups of 20-30× are seen in equilibration times in comparison to the well-known soft repulsive spherocylinder (SRS) model. The quadratic potential is used in an additional set of coarse-grained simulations of a liquid crystal with a flexible chain, which exhibits spontaneous formation of a nematic phase. The use of different types of interaction sites is also illustrated by the simulation of a spherocylinder with two "tails" formed from spheres. Here, varying the hardness of the sphere-spherocylinder interaction potential allows the formation of a smectic-A phase which exhibits microphase separation.

Agricultural Sciences in China, 2010

We have performed coarse grained molecular dynamics simulations (CGMD) to investigate the interac... more We have performed coarse grained molecular dynamics simulations (CGMD) to investigate the interactions of generation 7, 5 and 3 (G7, G5 and G3) charge-neutral polyamidoamine (PAMAM) dendrimers with a DPPC (dipalmitoylphosphatidylcholine) monolayer at the air-water interface (model pulmonary surfactant) during the end-expiration process. Our results show that different generations of PAMAM dendrimers have different influences on the DPPC monolayer. Generally, G3 PAMAM dendrimers show little influence on the DPPC monolayer's structure and relative properties. While G7 and G5 PAMAM dendrimers tend to induce the formation of largely deformed structures of the DPPC monolayer and inhibit or even reverse the normal phase transition of the interfacial DPPC molecules during the process of compression. Besides, we find that the formation processes of these disrupted structures are energy-favorable based on analyzing van der Waals interaction energy between PAMAM dendrimers and the whole system.