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Biomedical subjects

Roy L Johnston

Publications and source records attributed to Roy L Johnston.

13 recordsLinked to original sources
PubMed2006

Topographical complexity of multidimensional energy landscapes.

A scheme for visualizing and quantifying the complexity of multidimensional energy landscapes and multiple pathways is presented employing principal component-based disconnectivity graphs and the Shannon entropy of relative "sizes" of superbasins. The principal component-based disconnectivity graphs incorporate a metric relationship between the stationary points of the system, which enable us to capture not only the actual assignment of the superbasins but also the size of each superbasin in the multidimensional configuration space. The landscape complexity measure quantifies the degree of topographical complexity of a multidimensional energy landscape and tells us at which energy regime branching of the main path becomes significant, making the system more likely to be kinetically trapped in local minima. The path complexity measure quantifies the difficulty encountered by the system to reach a connected local minimum by the path in question, implying that the more significant the branching points along the path the more difficult it is to end up in the desired local minimum. As an illustrative example, we apply this analysis to two kinds of small model protein systems exhibiting a highly frustrated and an ideal funnel-like energy landscape.

Computer Graphics↗
PubMed2006

Characterizing potential surface topographies through the distribution of saddles and minima.

Three related clusters of thirteen particles bound by pairwise Morse potentials with different ranges are the vehicles for relating the dynamics and kinetics of these clusters to the topographies of their energy landscapes. The analyses are based on the distributions of minima and saddles, on the asymmetries of the barriers and the kinetics of passage among the energy bands that the distributions of minima display. While all three of the examples are essentially structure-seekers, the extent of this character is clearly related to the range of the potential.

Journal Article↗
PubMed2006

Spectroscopy of growing and evaporating water droplets: exploring the variation in equilibrium droplet size with relative humidity.

We demonstrate that the thermodynamic properties of a single liquid aerosol droplet can be explored through the combination of a single-beam gradient force optical trap with Raman spectroscopy. A single aqueous droplet, 2-6 microm in radius, can be trapped in air indefinitely and the response of the particle to variations in relative humidity investigated. The Raman spectrum provides a unique fingerprint of droplet composition, temperature, and size. Spontaneous Raman scattering is shown to be consistent with that from a bulk phase sample, with the shape of the OH stretching band dependent on the concentration of sodium chloride in the aqueous phase and on the polarization of the scattered light. Stimulated Raman scattering at wavelengths commensurate with whispering gallery modes is demonstrated to provide a method for determining the size of the trapped droplet with nanometer precision and with a time resolution of 1 s. The polarization dependence of the stimulated scatter is consistent with the dependence observed for the spontaneous scatter from the droplet. By characterizing the spontaneous and stimulated Raman scattering from the droplet, we demonstrate that it is possible to measure the equilibrium size and composition of an aqueous droplet with variation in relative humidity. For this benchmark study we investigate the variation in equilibrium size with relative humidity for a simple binary sodium chloride/aqueous aerosol, a typical representative inorganic/aqueous aerosol that has been studied extensively in the literature. The measured equilibrium sizes are shown to be in excellent agreement with the predictions of Köhler theory. We suggest that this approach could provide an important new strategy for characterizing the thermodynamic properties and kinetics of transformation of aerosol particles.

Journal Article↗
PubMed2006

Analyzing energy landscapes for folding model proteins.

A new benchmark 20-bead HP model protein sequence (on a square lattice), which has 17 distinct but degenerate global minimum (GM) energy structures, has been studied using a genetic algorithm (GA). The relative probabilities of finding particular GM conformations are determined and related to the theoretical probability of generating these structures using a recoil growth constructor operator. It is found that for longer successful GA runs, the GM probability distribution is generally very different from the constructor probability, as other GA operators have had time to overcome any initial bias in the originally generated population of structures. Structural and metric relationships (e.g., Hamming distances) between the 17 distinct GM are investigated and used, in conjunction with data on the connectivities of the GM and the pathways that link them, to explain the GM probability distributions obtained by the GA. A comparison is made of searches where the sequence is defined in the normal (forward) and reverse directions. The ease of finding mirror image solutions are also compared. Finally, this approach is applied to rationalize the ease or difficulty of finding the GM for a number of standard benchmark HP sequences on the square lattice. It is shown that the relative probabilities of finding particular members of a set of degenerate global minima depend critically on the topography of the energy landscape in the vicinity of the GM, the connections and distances between the GM, and the nature of the operators used in the chosen search method.

Algorithms↗
PubMed2005

Strategies for increasing the efficiency of a genetic algorithm for the structural optimization of nanoalloy clusters.

An improved genetic algorithm (GA) is described that has been developed to increase the efficiency of finding the global minimum energy isomers for nanoalloy clusters. The GA is optimized for the example Pt12Pd12, with specific investigation of: the effect of biasing the initial population by seeding; the effect of removing specified clusters from the population ("predation"); and the effect of varying the type of mutation operator applied. These changes are found to significantly enhance the efficiency of the GA, which is subsequently demonstrated by the application of the best strategy to a new cluster, namely Pt19Pd19.

Journal Article↗
PubMed2005

Global optimization of bimetallic cluster structures. I. Size-mismatched Ag-Cu, Ag-Ni, and Au-Cu systems.

A genetic algorithm approach is applied to the optimization of the potential energy of a wide range of binary metallic nanoclusters, Ag-Cu, Ag-Ni, Au-Cu, Ag-Pd, Ag-Au, and Pd-Pt, modeled by a semiempirical potential. The aim of this work is to single out the driving forces that make different structural motifs the most favorable at different sizes and chemical compositions. Paper I is devoted to the analysis of size-mismatched systems, namely, Ag-Cu, Ag-Ni, and Au-Cu clusters. In Ag-Cu and Ag-Ni clusters, the large size mismatch and the tendency of Ag to segregate at the surface of Cu and Ni lead to the location of core-shell polyicosahedral minimum structures. Particularly stable polyicosahedral clusters are located at size N = 34 (at the composition with 27 Ag atoms) and N = 38 (at the composition with 32 and 30 Ag atoms). In Ag-Ni clusters, Ag32Ni13 is also shown to be a good energetic configuration. For Au-Cu clusters, these core-shell polyicosahedra are less common, because size mismatch is not reinforced by a strong tendency to segregation of Au at the surface of Cu, and Au atoms are not well accommodated upon the strained polyicosahedral surface.

Journal Article↗
PubMed2005

Global optimization of bimetallic cluster structures. II. Size-matched Ag-Pd, Ag-Au, and Pd-Pt systems.

Genetic algorithm global optimization of Ag-Pd, Ag-Au, and Pd-Pt clusters is performed. The 34- and 38-atom clusters are optimized for all compositions. The atom-atom interactions are modeled by a semiempirical potential. All three systems are characterized by a small size mismatch and a weak tendency of the larger atoms to segregate at the surface of the smaller ones. As a result, the global minimum structures exhibit a larger mixing than in Ag-Cu and Ag-Ni clusters. Polyicosahedral structures present generally favorable energetic configurations, even though they are less favorable than in the case of the size-mismatched systems. A comparison between all the systems studied here and in the previous paper (on size-mismatched systems) is presented.

Journal Article↗
PubMed2005

How many dimensions are required to approximate the potential energy landscape of a model protein?

A scheme to approximate the multidimensional potential energy landscape in terms of a minimal number of degrees of freedom is proposed using a linear transformation of the original atomic Cartesian coordinates. For one particular off-lattice model protein the inherent frustration can only be reproduced satisfactorily when a relatively large number of coordinates are employed. However, when this frustration is removed in a Go-type model, the number of coordinates required is significantly lower, especially around the global potential energy minimum. To aid our interpretation of the results we consider modified disconnectivity graphs where a measure of the structural diversity and a metric relation between the stationary points are incorporated.

Computer Simulation↗
PubMed2004

Rationalizing the structural properties of bupivacaine base--a local anesthetic--directly from powder X-ray diffraction data.

Bupivacaine belongs to a family of 1-alkyl-2',6'-pipecoloxylidides, which has shown promise as reversible action potential blockers that can introduce prolonged local anesthetic effects. The crystal structure of the free-base form of bupivacaine has been determined directly from powder X-ray diffraction data using the Genetic Algorithm technique for structure solution, followed by Rietveld refinement. This work further emphasizes the scope and utility of ab initio structure solution directly from powder X-ray diffraction data for tackling structural problems within the biomedical field, leading to opportunities for the investigation of structure-property relationships.

Anesthetics, Local↗
PubMed2003

Development of a multipopulation parallel genetic algorithm for structure solution from powder diffraction data.

Previously, the genetic algorithm (GA) approach for direct-space crystal structure solution from powder diffraction data has been applied successfully in the structure determination of a range of organic molecular materials. In this article, we present a further development of our approach, namely a multipopulation parallel GA (PGA), which is shown to give rise to increased speed, efficiency, and reliability of structure solution calculations, as well as providing new opportunities for further optimizing our GA methodology. The multipopulation PGA is based on the independent evolution of different subpopulations, with occasional interaction (e.g., transfer of structures) allowed to occur between the different subpopulations. Different strategies for carrying out this interpopulation communication are considered in this article, and comparisons are made to the conventional single-population GA. The increased power offered by the PGA approach creates the opportunity for structure determination of molecular crystals of increasing complexity.

Journal Article↗
PubMed2003

Polymorphism of a novel sodium ion channel blocker.

2-[[4-(4-Fluorophenoxy)phenyl]-methylene]-hydrazinecarboxamide, a member of the semicarbazone family which has shown potential therapeutic use as anticonvulsants, has been found to exist in two polymorphic forms denoted A and B. In addition to reporting aspects of the physical characterization of both forms, the crystal structure of polymorph A has been determined directly from powder X-ray diffraction data using the Genetic Algorithm technique for structure solution, followed by Rietveld refinement. This structure is compared with that of polymorph B, which was determined previously from single crystal X-ray diffraction data. Knowledge of the crystal structures of the two polymorphs provides the opportunity for establishing structure-property relationships. This work further emphasizes the scope and utility of ab initio structure solution from powder X-ray diffraction data in the pharmaceuticals field.

Calorimetry, Differential Scanning↗
PubMed2002

Geometry optimisation of aluminium clusters using a genetic algorithm.

The application of a Genetic Algorithm, for optimising the geometry of aluminium clusters with 21-55 atoms bound by the many-body Murrell-Mottram potential, is described. In this size regime, a number of different structural motifs are identified--face-centred cubic, hexagonal close packed, decahedral and icosahedral structures. The larger clusters consist of hollow icosahedral geometric shells, with Al55 having a centred icosahedral structure. Evolutionary Progress Plots for Al19 and Al38 reveal how the best structure evolves from generation to generation upon operation of the Genetic Algorithm.

Journal Article↗