Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Free energy functional expansion as the generalized approach to the equation of state of dense fluids

A version of the thermodynamic perturbation theory based on a scaling transformation of the partition function has been applied to the statistical derivation of the equation of state in a highpressure region. Two modifications of the equations of state have been obtained on the basis of the free energy functional perturbation series. The comparative analysis of the experimental PV T- data on the isothermal compression for the supercritical fluids of inert gases has been carried out. © 2012.

Can surface energy measurements predict the impact of catalyst hydrophobicity upon fatty acid esterification over sulfonic acid functionalised periodic mesoporous organosilicas?

Sulfonic acid functionalised periodic mesoporous organosilicas (PrSO3 H-PMOs) with tunable hydrophobicity were synthesised via a surfactant-templating route, and characterised by porosimetry, TEM, XRD, XPS, inverse gas chromatography (IGC) and ammonia pulse chemisorption. IGC reveals that incorporation of ethyl or benzyl moieties into a mesoporous SBA-15 silica framework significantly increases the non-specific dispersive surface energy of adsorption for alkane adsorption, while decreasing the free energy of adsorption of methanol, reflecting increased surface hydrophobicity. The non-specific dispersive surface energy of adsorption of PMO-SO3H materials is strongly correlated with their activity towards palmitic acid esterification with methanol, demonstrating the power of IGC as an analytical tool for identifying promising solid acid catalysts for the esterification of free fatty acids. A new parameter [-ΔGCNP-P], defined as the per carbon difference in Gibbs free energy of adsorption between alkane and polar probe molecules, provides a simple predictor of surface hydrophobicity and corresponding catalyst activity in fatty acid esterification. © 2014 Elsevier B.V.

Threshold-induced phase transitions in perceptrons

Error rates of a Boolean perceptron with threshold and either spherical or Ising constraint on the weight vector are calculated for storing patterns from biased input and output distributions derived within a one-step replica symmetry breaking (RSB) treatment. For unbiased output distribution and non-zero stability of the patterns, we find a critical load, α p, above which two solutions to the saddlepoint equations appear; one with higher free energy and zero threshold and a dominant solution with non-zero threshold. We examine this second-order phase transition and the dependence of α p on the required pattern stability, κ, for both one-step RSB and replica symmetry (RS) in the spherical case and for one-step RSB in the Ising case.

Error-correcting codes on a Bethe-like lattice

We analyse Gallager codes by employing a simple mean-field approximation that distorts the model geometry and preserves important interactions between sites. The method naturally recovers the probability propagation decoding algorithm as a minimization of a proper free-energy. We find a thermodynamical phase transition that coincides with information theoretical upper-bounds and explain the practical code performance in terms of the free-energy landscape.

Structure, dynamics, and energetics of siRNA-cationic vector complexation:a molecular dynamics study

The design and synthesis of safe and efficient nonviral vectors for gene delivery has attracted significant attention in recent years. Previous experiments have revealed that the charge density of a polycation (the carrier) plays a crucial role in complexation and the release of the gene from the complex in the cytosol. In this work, we adopt an atomistic molecular dynamics simulation approach to study the complexation of short strand duplex RNA with six cationic carrier systems of varying charge and surface topology. The simulations reveal detailed molecular-level pictures of the structures and dynamics of the RNA-polycation complexes. Estimates for the binding free energy indicate that electrostatic contributions are dominant followed by van der Waals interactions. The binding free energy between the 8(+)polymers and the RNA is found to be larger than that of the 4(+)polymers, in general agreement with previously published data. Because reliable binding free energies provide an effective index of the ability of the polycationic carrier to bind the nucleic acid and also carry implications for the process of gene release within the cytosol, these novel simulations have the potential to provide us with a much better understanding of key mechanistic aspects of gene-polycation complexation and thereby advance the rational design of nonviral gene delivery systems.

A mean field theory of coded CDMA systems

We present a mean field theory of code-division multiple access (CDMA) systems with error-control coding. On the basis of the relation between the free energy and mutual information, we obtain an analytical expression of the maximum spectral efficiency of the coded CDMA system, from which a mean field description of the coded CDMA system is provided in terms of a bank of scalar Gaussian channels whose variances in general vary at different code symbol positions. Regular low-density parity-check (LDPC)-coded CDMA systems are also discussed as an example of the coded CDMA systems.

Novel hydrogel copolymers and semi-interpenetraing polymer networks

Interpenetrating polymer networks (lPN's), have been defined as a combination of two polymers each in network form, at least one of which has been synthesised and / or crosslinked in the presence of the other. A semi-lPN, is formed when only one of the polymers in the system is crosslinked, the other being linear. lPN's have potential advantages over homogeneous materials presently used in biomedical applications, in that their composite nature gives them a useful combination of properties. Such materials have potential uses in the biomedical field, specifically for use in hard tissue replacements, rigid gas permeable contact lenses and dental materials. Work on simply two or three component systems in both low water containing lPN's supplemented by the study of hydrogels (water swollen hydrophilic polymers) can provide information useful in the future development of more complex systems. A range of copolymers have been synthesised using a variety of methacrylates and acrylates. Hydrogels were obtained by the addition of N-vinyl pyrrolidone to these copolymers. A selection of interpenetrants were incorporated into the samples and their effect on the copolymer properties was investigated. By studying glass transition temperatures, mechanical, surface, water binding and oxygen permeability properties samples were assessed for their suitability for use as biomaterials. In addition copolymers containing tris-(trimethylsiloxy)-y-methacryloxypropyl silane, commonly abbreviated to 'TRlS', have been investigated. This material has been shown to enhance oxygen permeability, a desirable property when considering the design of contact lenses. However, 'TRIS' has a low polar component of surface free energy and hence low wettability. Copolymerisation with a range of methacrylates has shown that significant increases in surface wettability can be obtained without a detrimental effect on oxygen permeability. To further enhance to surface wettability 4-methacryloxyethyl trimellitic anhydride was incorporated into a range of promising samples. This study has shown that by careful choice of monomers it is possible to synthesise polymers that possess a range of properties desirable in biomedical applications.

Cellular interactions with hydrogels

An efficient means of evaluating potential biomaterials is to use the in vitro fibroblast cell culture model. However, the chemistry which influences cell adhesion on polymer substrates is poorly understood. The work in this thesis aims to rationalise several theories of current opinion and introduce new chemical techniques that may predict cellular behaviour. The keratoprosthesis is a typical example of the need to be able to manipulate cell adhesion of materials since both adhesive and non adhesive sections are needed for proper integration and optical function. Calcein AM/ethidium homodimer-1 and DAPI assays were carried out using 3T3 and EKl.BR cells. Poly(HEMA) was found to be the most cell adhesive hydrogel tested. The reactivity of monomers and the resulting sequence distribution were found to affect surface properties and this may explain the poor levels of cell adhesion seen on NVP/MMA copolymers. Surface free energy is shown to be dependent on the polar and non polar groups present along the backbone chain of the polymers. Dehydrated and hydrated contact angle measurements show the effect of rotation of surface groups around the backbone chain. This effect is most apparent on hydrogels containing methacrylic acid. Dynamic contact angle measurements confirm sequence distribution irregularities and demonstrate the mobility of surface groups. Incorporation of NVI or DEAEMA into the hydrogels does not affect the mobility of the surface groups despite their bulkiness. Foetal calf serum was used for the first time as a test solution in an attempt to mimic a biological environment during surface experiments. A Vroman effect may be present, and may involve different surface proteins for each material tested. This interdisciplinary study combines surface characterisation and biological testing to further the knowledge of the biomaterial/host interface. Surface chemistry techniques appear to be insufficiently sensitive to predict cellular behaviour. The degree of ionisation of hydrogels containing ionic groups depends on the nature of the functional groups as well as the concentration and this is an important parameter to consider when comparing charged materials.

Variational inference for diffusion processes

Diffusion processes are a family of continuous-time continuous-state stochastic processes that are in general only partially observed. The joint estimation of the forcing parameters and the system noise (volatility) in these dynamical systems is a crucial, but non-trivial task, especially when the system is nonlinear and multimodal. We propose a variational treatment of diffusion processes, which allows us to compute type II maximum likelihood estimates of the parameters by simple gradient techniques and which is computationally less demanding than most MCMC approaches. We also show how a cheap estimate of the posterior over the parameters can be constructed based on the variational free energy.

Statistical physics of error-correcting codes

In this thesis we use statistical physics techniques to study the typical performance of four families of error-correcting codes based on very sparse linear transformations: Sourlas codes, Gallager codes, MacKay-Neal codes and Kanter-Saad codes. We map the decoding problem onto an Ising spin system with many-spins interactions. We then employ the replica method to calculate averages over the quenched disorder represented by the code constructions, the arbitrary messages and the random noise vectors. We find, as the noise level increases, a phase transition between successful decoding and failure phases. This phase transition coincides with upper bounds derived in the information theory literature in most of the cases. We connect the practical decoding algorithm known as probability propagation with the task of finding local minima of the related Bethe free-energy. We show that the practical decoding thresholds correspond to noise levels where suboptimal minima of the free-energy emerge. Simulations of practical decoding scenarios using probability propagation agree with theoretical predictions of the replica symmetric theory. The typical performance predicted by the thermodynamic phase transitions is shown to be attainable in computation times that grow exponentially with the system size. We use the insights obtained to design a method to calculate the performance and optimise parameters of the high performance codes proposed by Kanter and Saad.

Protein deposition at polymer surfaces:the bulk and surface structure-property effects of hydrogels

The primary objective of this research has been to investigate the interfacial phenomenon of protein adsorption in relation to the bulk and surface structure-property effect s of hydrogel polymers. In order to achieve this it was first necessary to characterise the bulk and surface properties of the hydrogels, with regard to the structural chemistry of their component monomers. The bulk properties of the hydrogels were established using equilibrium water content measurements, together with water-binding studies by differential scanning calorimetry (D.S.C.). Hamilton and captive air bubble-contact angle techniques were employed to characterise the hydrogel-water interface and from which by a mathematical derivation, the interfacial free energy (ðsw) and the surface free energy components (ð psv, ðdsv, ðsv) were obtained. From the adsorption studies using the radio labelled iodinated (125I) proteins of human serum albumin (H.S.A.) and human fibrinogen (H.Fb.), it was Found that multi-layered adsorption was occurring and that the rate and type of this adsorption was dependent on the physico-chemical behaviour of the adsorbing protein (and its bulk concentration in solution), together with the surface energetics of the adsorbent polymer. A potential method for the invitro evaluation of a material's 'biocompatibility' was also investigated, based on an empirically observed relationship between the adsorption of albumin and fibrinogen and the 'biocompatibility' of polymeric materials. Furthermore, some consideration was also given to the biocompatibility problem of proteinaceous deposit formation on hydrophilic soft' contact lenses and in addition a number of potential continual wear contact lens formulations now undergoing clinical trials,were characterised by the above techniques.

Computer simulation of moist agglomerate collisions

This thesis considers the computer simulation of moist agglomerate collisions using the discrete element method (DEM). The study is confined to pendular state moist agglomerates, at which liquid is presented as either absorbed immobile films or pendular liquid bridges and the interparticle force is modelled as the adhesive contact force and interstitial liquid bridge force. Algorithms used to model the contact force due to surface adhesion, tangential friction and particle deformation have been derived by other researchers and are briefly described in the thesis. A theoretical study of the pendular liquid bridge force between spherical particles has been made and the algorithms for the modelling of the pendular liquid bridge force between spherical particles have been developed and incorporated into the Aston version of the DEM program TRUBAL. It has been found that, for static liquid bridges, the more explicit criterion for specifying the stable solution and critical separation is provided by the total free energy. The critical separation is given by the cube root of liquid bridge volume to a good approximation and the 'gorge method' of evaluation based on the toroidal approximation leads to errors in the calculated force of less than 10%. Three dimensional computer simulations of an agglomerate impacting orthogonally with a wall are reported. The results demonstrate the effectiveness of adding viscous binder to prevent attrition, a common practice in process engineering. Results of simulated agglomerate-agglomerate collisions show that, for colinear agglomerate impacts, there is an optimum velocity which results in a near spherical shape of the coalesced agglomerate and, hence, minimises attrition due to subsequent collisions. The relationship between the optimum impact velocity and the liquid viscosity and surface tension is illustrated. The effect of varying the angle of impact on the coalescence/attrition behaviour is also reported. (DX 187, 340).

Charge-balanced copolymer hydrogels:potential as biomedical materials

Polyzwitterionic-containing hydrogel materials been proposed for use in biomaterial applications. Polyzwitterions contain anions and cations in the same monomeric unit, unlike polyampholytes which contain them in different monomeric units. The use of cationic and anionic monomers in stoichiometrically equivalent proportions produces charge-balanced polyampholytes (PA) copolymers. Membranes prepared using either betaine-containing (BT) polyzwitterionic copolymers or PA copolymers can share similar properties, but the range of EWCs offered by membranes incorporating BT and PA monomers is greater than that for conventional neutral hydrogels and methacrylic acid-based systems. Here we compare properties of BT-containing and PA-containing copolymer membranes, relevant to their potential as biomedical materials. Membranes of the copolymers were prepared as previously described. Surface energy was determined using a GBX Digidrop (GBX Scientific Instruments), with diidomethane and water as probes. The absorption of proteins was determined by soaking the membranes in 1mg/ml protein solutions for a predetermined time, and measuring UV absorption of the membranes at certain wavelengths. The BT and PA copolymer membranes displayed similar values for the polar components and dispersive components of total surface free energy. This was perhaps not surprising when the structures of the monomers were considered. The BT and PA copolymer membranes displayed differences in their protein absorption over time, with the PA demonstrating higher uptake of protein than the BT. In addition to the aforementioned greater EWC range, the use of BT and PA copolymer membranes also avoids some of the problems associated with net anionicity. Comparison of the BT copolymer with the “pseudo” zwitterionic PA copolymers shows that controlled molecular architecture is required to gain the benefits of balancing the charges present in the copolymers in a way that will make them beneficial to hydrogel design.

Charge effects on the hindered transport of macromolecules across the endothelial surface glycocalyx layer

A fluid mechanical and electrostatic model for the transport of solute molecules across the vascular endothelial surface glycocalyx layer (EGL) was developed to study the charge effect on the diffusive and convective transport of the solutes. The solute was assumed to be a spherical particle with a constant surface charge density, and the EGL was represented as an array of periodically arranged circular cylinders of like charge, with a constant surface charge density. By combining the fluid mechanical analyses for the flow around a solute suspended in an electrolyte solution and the electrostatic analyses for the free energy of the interaction between the solute and cylinders based on a mean field theory, we estimated the transport coefficients of the solute across the EGL. Both of diffusive and convective transports are reduced compared to those for an uncharged system, due to the stronger exclusion of the solute that results from the repulsive electrostatic interaction. The model prediction for the reflection coefficient for serum albumin agreed well with experimental observations if the charge density in the EGL is ranged from approximately -10 to -30 mEq/l.