Biomedical subjects

Mark J Biggs

Publications and source records attributed to Mark J Biggs.

3 recordsLinked to original sources

PubMed2006

Ab initio protein fold prediction using evolutionary algorithms: influence of design and control parameters on performance.

True ab initio prediction of protein 3D structure requires only the protein primary structure, a physicochemical free energy model, and a search method for identifying the free energy global minimum. Various characteristics of evolutionary algorithms (EAs) mean they are in principle well suited to the latter. Studies to date have been less than encouraging, however. This is because of the limited consideration given to EA design and control parameter issues. A comprehensive study of these issues was, therefore, undertaken for ab initio protein fold prediction using a full atomistic protein model. The performance and optimal control parameter settings of twelve EA designs where first established using a 15-residue polyalanine molecule-design aspects varied include the encoding alphabet, crossover operator, and replacement strategy. It can be concluded that real encoding and multipoint crossover are superior, while both generational and steady-state replacement strategies have merits. The scaling between the optimal control parameter settings and polyalanine size was also identified for both generational and steady-state designs based on real encoding and multipoint crossover. Application of the steady-state design to met-enkephalin indicated that these scalings are potentially transferable to real proteins. Comparison of the performance of the steady state design for met-enkephalin with other ab initio methods indicates that EAs can be competitive provided the correct design and control parameter values are used.

Algorithms↗

PubMed2004

Absolute assessment of adsorption-based porous solid characterization methods: comparison methods.

The design and use of microporous solids depends on having access to characteristics such as the pore volume and surface area. Comparison methods such as the alpha(s) method are one of the most widely used means of determining these parameters. An assessment of this group of methods was undertaken by comparing estimates obtained from them using adsorption isotherms generated by grand canonical Monte Carlo simulation on a selection of model nanoporous solids with exactly known surface areas and pore volumes. Conclusions are drawn from this absolute assessment in regard to the validity of the alpha(s) method for determining the micropore volume, the mesopore surface area, and the separation of pore groups based on the concept of primary and cooperative filling, the subtracting pore effect (SPE) method, and the required character of the reference surface.

Journal Article↗

PubMed2004

Molecular simulation evidence for solidlike adsorbate in complex carbonaceous micropore structures.

Adsorption of a model nitrogen vapor on a range of complex nanoporous carbon structures is simulated by grand canonical Monte Carlo simulation for a single subcritical temperature above the bulk freezing point. Adsorption and desorption isotherms, heats of adsorption, and three-dimensional singlet distribution functions (SDFs) were generated. Inspection of the SDFs reveals significant levels of solidlike adsorbate at saturation even in the most complex of the microporous solids considered. This strongly suggests that solidlike adsorbate will also occur for simple subcritical vapors adsorbed on real noncrystalline solids such as microporous carbons at temperatures above the bulk freezing point, supporting indirect experimental observations. The presence of significant levels of solidlike adsorbate has implications for characterization of microporous solids where adsorbate density is used (e.g., determination of pore volume from loading). Detailed consideration of the SDF at different loadings for a model microporous solid indicates solidlike adsorbate forms at distributed points throughout the pore space at pressures dependent on the nature of the local porosity. The nature of the local porosity also dictates the freezing mechanism. A local freezing/ melting/refreezing process is also observed. Introduction of mesoporosity into the model causes hysteresis between the adsorption and desorption isotherms. Adsorption in the hysteresis loop occurs by a series of local condensation events. It appears as if the presence of adjacent microporosity and/or adsorbate within it affects the pressure at which these events occur. Reversal of the condensation during desorption occurs throughout the mesoporosity at a single pressure; this pressure is unaffected by the presence of adjacent microporosity or the adsorbate within it. It is also shown that the empirical concept of "pore size" is not consistent for describing adsorption in the complex solids considered here. A new concept is, therefore, proposed that seeks to account for the factors that affect local adsorption energy: local geometry, microtexture, surface atom density, and surface chemistry.

Journal Article↗