Comparative analysis of the cutting angle and simulated annealing methods in global optimization
- Authors: Bagirov, Adil , Zhang, Jiapu
- Date: 2003
- Type: Text , Journal article
- Relation: Optimization Vol. 52, no. 4-5 (2003), p. 363-378
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- Description: This article presents a comparative analysis of two methods of global optimization: the simulated annealing method and a method based on a combination of the cutting angle method and a local search. This analysis is carried out using results of numerical experiments. These results demonstrate that the combined method is more effective than the simulated annealing method.
- Description: C1
- Description: 2003000436
The discrete gradient evolutionary strategy method for global optimization
- Authors: Abbas, Hussein , Bagirov, Adil , Zhang, Jiapu
- Date: 2003
- Type: Text , Conference paper
- Relation: Paper presented at the Congress on Evolutionary Computation CEC 2003, Canberra : 8th December, 2003
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- Description: Global optimization problems continue to be a challenge in computational mathematics. The field is progressing in two streams: deterministic and heuristic approaches. In this paper, we present a hybrid method that uses the discrete gradient method, which is a derivative free local search method, and evolutionary strategies. We show that the hybridization of the two methods is better than each of them in isolation.
- Description: E1
- Description: 2003000440
Derivative-free hybrid methods in global optimization and their applications
- Authors: Zhang, Jiapu
- Date: 2005
- Type: Text , Thesis , PhD
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- Description: In recent years large-scale global optimization (GO) problems have drawn considerable attention. These problems have many applications, in particular in data mining and biochemistry. Numerical methods for GO are often very time consuming and could not be applied for high-dimensional non-convex and / or non-smooth optimization problems. The thesis explores reasons why we need to develop and study new algorithms for solving large-scale GO problems .... The thesis presents several derivative-free hybrid methods for large scale GO problems. These methods do not guarantee the calculation of a global solution; however, results of numerical experiments presented in this thesis demonstrate that they, as a rule, calculate a solution which is a global one or close to it. Their applications to data mining problems and the protein folding problem are demonstrated.
- Description: Doctor of Philosophy
Local optimization method with global multidimensional search
- Authors: Bagirov, Adil , Rubinov, Alex , Zhang, Jiapu
- Date: 2005
- Type: Text , Journal article
- Relation: Journal of Global Optimization Vol. 32, no. 2 (2005), p. 161-179
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- Description: This paper presents a new method for solving global optimization problems. We use a local technique based on the notion of discrete gradients for finding a cone of descent directions and then we use a global cutting angle algorithm for finding global minimum within the intersection of the cone and the feasible region. We present results of numerical experiments with well-known test problems and with the so-called cluster function. These results confirm that the proposed algorithms allows one to find a global minimizer or at least a deep local minimizer of a function with a huge amount of shallow local minima. © Springer 2005.
- Description: C1
- Description: 2003001351
Optimization approach for clustering datasets with weights
- Authors: Ghosh, Ranadhir , Rubinov, Alex , Zhang, Jiapu
- Date: 2005
- Type: Text , Journal article
- Relation: Optimization Methods & Software Vol. 20, no. 2-3 (Apr-Jun 2005), p. 329-345
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- Description: We introduce datasets with weights and suggest using the minimization of some highly nonsmooth functions for clustering of such datasets. Datasets with weights often appear as the result of an approximation of large-scale datasets. We examine such approximations and also consider the application of datasets with weights to examine self-organizing maps. Results of some numerical experiments are presented and discussed.
- Description: C1
- Description: 2003001366
A multidimensional descent method for global optimization
- Authors: Bagirov, Adil , Rubinov, Alex , Zhang, Jiapu
- Date: 2009
- Type: Text , Journal article
- Relation: Optimization Vol. 58, no. 5 (2009), p. 611-625
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- Description: This article presents a new multidimensional descent method for solving global optimization problems with box-constraints. This is a hybrid method where local search method is used for a local descent and global search is used for further multidimensional search on the subsets of intersection of cones generated by the local search method and the feasible region. The discrete gradient method is used for local search and the cutting angle method is used for global search. Two-and three-dimensional cones are used for the global search. Such an approach allows one, as a rule, to escape local minimizers which are not global ones. The proposed method is local optimization method with strong global search properties. We present results of numerical experiments using both smooth and non-smooth global optimization test problems. These results demonstrate that the proposed algorithm allows one to find a global or a near global minimizer.
Studies on the structural stability of rabbit prion probed by molecular dynamics simulations
- Authors: Zhang, Jiapu
- Date: 2009
- Type: Text , Journal article
- Relation: Journal of Biomolecular Structure and Dynamics Vol. 27, no. 2 (2009), p. 159-162
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- Description: Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect humans and animals. Rabbits are the only mammalian species reported to be resistant to infection from prion diseases isolated from other species (I. Vorberg et al., Journal of Virology 77 (3), 2003-2009 (2003)). At the end of 2007 the NMR structure of rabbit prion (124-228) was deposited into protein data bank (PDB entry 2FJ3). This paper studies the inhibition mechanism of rabbit prion at molecular structural level by molecular dynamics simulations. ©Adenine Press (2009).
Compare the replica exchange sampling strategy with the Metropolis-Hastings sampling strategy of Markov Chain Monte Carlo simulations for the H1N1 influenza pandemic infectious disease model
- Authors: Zhang, Jiapu
- Date: 2010
- Type: Text , Journal article
- Relation: International Journal of Mathematical Modeling, Simulation and Applications Vol. 3, no. 1 (2010), p. 99-109
- Full Text: false
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Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils probed by hybrid local and global optimization searches
- Authors: Zhang, Jiapu , Sun, Jie
- Date: 2010
- Type: Text , Conference paper
- Relation: International Conference on Optimization and Control 2010 p. 91-112
- Full Text: false
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- Description: In recent years large-scale global optimization (GO) problems have drawn considerable attention. These problems have many applications, in particular in data mining and biochemistry. Numerical methods for GO are often very time consuming and could not be applied for high-dimensional non-convex and/or non-smooth optimization problems. The study of new algorithms which allow one to solve large-scale GO problem is very important. One technique is to use hybrid of global and local/global search algorithms. This paper presents two hybrid methods for solving the large-scale Lennard-Jones potential GO problem. The methods do not guarantee the calculation of a global solution; however results of numerical experiments show that they, as a rule, calculate a solution which is global one or close to it. One hybrid method is successfully applied to the construction of optimal atomic-resolution structures of prion (113-120) AGAAAAGA amyloid fibrils. Two successful structures constructed in this paper might be useful in furthering the goals of medicinal chemistry in this field.
Studies on the structural stability of rabbit prion probed by molecular dyanamics simulations of its wild-type and mutants
- Authors: Zhang, Jiapu
- Date: 2010
- Type: Text , Journal article
- Relation: Journal of Theoretical Biology Vol. 264, no. (2010), p. 119-122
- Full Text: false
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- Description: Prion diseases are invariabiably fatal and highly infectious neurodegenerative diseases that affect humans and animals. Rabbits are the only mammalian species reported to be resistant to infection from prion diseases isolated from other species (Vorber et.al., 2003). Fortunately, the NMR structure of rabbit prion (124-228) (PDB entry 2FJ3), the NMR structure of rabbit prion protein mutation s173N (PDB entry 2JOH) and the NMR structure of rabbit prion protein I214V [PDB entry 2JOM} were released recently. This paper studies these NMR structures by molecular dyanmaics simulations. Simulation results confirm the structural ability of wild-type rabbit prion, and show that the salt bridge between D177 and R163 greatly contributes to the structural stability of rabbity prion. Crown Copyright Published by Elsevier.
A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling
- Authors: Zhang, Jiapu , Gao, David , Yearwood, John
- Date: 2011
- Type: Text , Journal article
- Relation: Journal of Theoretical Biology Vol. 284, no. 1 (2011), p. 149-157
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- Description: Many experimental studies have shown that the prion AGAAAAGA palindrome hydrophobic region (113-120) has amyloid fibril forming properties and plays an important role in prion diseases. However, due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, to date structural information on AGAAAAGA region (113-120) has been very limited. This region falls just within the N-terminal unstructured region PrP (1-123) of prion proteins. Traditional X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy experimental methods cannot be used to get its structural information. Under this background, this paper introduces a novel approach of the canonical dual theory to address the 3D atomic-resolution structure of prion AGAAAAGA amyloid fibrils. The novel and powerful canonical dual computational approach introduced in this paper is for the molecular modeling of prion AGAAAAGA amyloid fibrils, and that the optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils presented in this paper are useful for the drive to find treatments for prion diseases in the field of medicinal chemistry. Overall, this paper presents an important method and provides useful information for treatments of prion diseases. © 2011.
An effective simulated annealing refined replica exchange Markov chain Monte Carlo algorithm for the infectious disease model of H1N1 influenza pandemic
- Authors: Zhang, Jiapu
- Date: 2011
- Type: Text , Journal article
- Relation: World Journal of Modelling and Simulation Vol. 7, no. 1 (2011), p. 29-39
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- Description: This paper is concerned with a computational algorithm for fitting a deterministic MSEIRS (immune-susceptible-exposed-infectious-recovered-susceptible) epidemic model for the transmission of influenza (H1N1) to mortality data. The model-fitting is carried out using a simulated annealing refined replica exchange Markov chain Monte Carlo algorithm. The effectiveness of the algorithm is illustrated using the triple wave data from five English towns collected during the 1918 ~ 1919 influenza pandemic. Numerical results show that the replica exchange (refined by simulated annealing) sampling technique is superior to other existing sampling techniques such as the Gibbs sampling technique, the Metropolis-Hastings sampling technique, the Multiple-try Metropolis technique for the Markov chain Monte Carlo computation. The algorithm presented in this paper has great promise to be used for carrying out some numerical computations of the current complex 2009 ∼ 2010 influenza pandemic.
Comparison studies of the structural stability of rabbit prion protein with hyman and mouse prion proteins
- Authors: Zhang, Jiapu
- Date: 2011
- Type: Text , Journal article
- Relation: Journal of Theoretical biology Vol. 269, no. 1 (2011), p. 88-95
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- Description: Background: Prion diseases are fatal and infectious neurodegenerative diseases affecting humans and animals. Rabbits are one of the few mammalian species reported to be resistant to infection from prion diseases isolated from other species (I. Vorberg et al., Journal of Virology 77 (3) (2003) 2003-2009). Thus the study of rabbit prion protein structure to obtain insight into the immunity of rabbits to prion diseases is very important. Findings: The paper is a straight forward molecular dynamics simulation study of wild-type rabbit prion protein (monomer cellular form) which apparently resists the formation of the scrapie form. The comparison analyses with human and mouse prion proteins done so far show that the rabbit prion protein has a stable structure. The main point is that the enhanced stability of the C-terminal ordered region especially helix 2 through the D177-R163 salt-bridge formation renders the rabbit prion protein stable. The salt bridge D201-R155 linking helixes 3 and 1 also contributes to the structural stability of rabbit prion protein. The hydrogen bond H186-R155 partially contributes to the structural stability of rabbit prion protein. Conclusions: Rabbit prion protein was found to own the structural stability, the salt bridges D177-R163, D201-R155 greatly contribute and the hydrogen bond H186-R155 partially contributes to this structural stability. The comparison of the structural stability of prion proteins from the three species rabbit, human and mouse showed that the human and mouse prion protein structures were not affected by the removing these two salt bridges. Dima et al. (Biophysical Journal 83 (2002) 1268-1280 and Proceedings of the National Academy of Sciences of the United States of America 101 (2004) 15335-15340) also confirmed this point and pointed out that "correlated mutations that reduce the frustration in the second half of helix 2 in mammalian prion proteins could inhibit the formation of PrPSc".
Molecular dynamics studies on the structural stability of wild-type dog prion protein
- Authors: Zhang, Jiapu , Liu, David
- Date: 2011
- Type: Text , Journal article
- Relation: Journal of Biomolecular Structure and Dynamics Vol. 28, no. 6 (2011), p. 861-869
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- Description: Prion diseases such as Creutzfeldt-Jakob disease, variant Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, Fatal Familial Insomnia, Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (or ‘mad-cow’ disease) and chronic wasting disease in cattle are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. However, by now there have not been some effective therapeutic approaches to treat all these prion diseases. In 2008, canine mammals including dogs (canis familials) were the first time academically reported to be resistant to prion diseases (Vaccine 26: 2601-2614 (2008)). Thus, it is very worth studying the molecular structures of dog prion protein to obtain insights into the immunity of dogs to prion diseases. This paper studies the molecular structural dynamics of wild-type dog prion protein. The comparison analyses with rabbit prion protein show that the dog prion protein has stable molecular structures whether under neutral or low pH environments. We also find that the salt bridges such as D177-R163 contribute to the structural stability of wild-type rabbit prion protein under neutral pH environment.
The structural stability of wild-type horse prion protein
- Authors: Zhang, Jiapu
- Date: 2011
- Type: Text , Journal article
- Relation: Journal of Biomolecular Structure and Dynamics Vol. 29, no. 2 (2011), p. 369-377
- Full Text: false
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- Description: Prion diseases (e.g. Creutzfeldt-Jakob disease (CJD), variant CJD (vCJD), Gerstmann-Sträussler-Scheinker syndrome (GSS), Fatal Familial Insomnia (FFI) and Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (BSE or 'mad-cow' disease) and chronic wasting disease (CWD) in cattles) are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. However, by now there have not been some effective therapeutic approaches or medications to treat all these prion diseases. Rabbits, dogs, and horses are the only mammalian species reported to be resistant to infection from prion diseases isolated from other species. Recently, the β2-α2 loop has been reported to contribute to their protein structural stabilities. The author has found that rabbit prion protein has a strong salt bridge ASP177-ARG163 (like a taut bow string) keeping this loop linked. This paper confirms that this salt bridge also contributes to the structural stability of horse prion protein. Thus, the region of β2-α2 loop might be a potential drug target region. Besides this very important salt bridge, other four important salt bridges GLU196-ARG156-HIS187, ARG156-ASP202 and GLU211-HIS177 are also found to greatly contribute to the structural stability of horse prion protein. Rich databases of salt bridges, hydrogen bonds and hydrophobic contacts for horse prion protein can be found in this paper. ©Adenine Press (2011).
Molecular dynamics studies on the structural stability of wild-type rabbit prion protein: Surface electrostatic charge distributions
- Authors: Zhang, Jiapu
- Date: 2012
- Type: Text , Book chapter
- Relation: Bioinformatics Research: New Developments p. 131-138
- Full Text: false
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- Description: Prion diseases cover a large range of neurodegenerative diseases in humans and animals, which are invariably fatal and highly infectious. By now there have not been some effective therapeutic approaches or medications to treat all prion diseases. Fortunately, numerous experimental experiences have showed that rabbits are resistant to infection from prion diseases isolated from other species, and recently the molecular structures of rabbit prion protein and its mutants were released into protein data bank. Prion diseases are "protein structural conformational" diseases. Thus, in order to reveal some secrets of prion diseases, it is amenable to study rabbits by techniques of the molecular structure and its dynamics. Wen et al. (PLoS One 5(10) e13273 (2010), Journal of Biological Chemistry 285(41) 31682-31693 (2010)) reported the surface of NMR RaPrPC(124-228) molecular snapshot has a large land of continuous positive charge distribution, which contributes to the structural stability of rabbit prion protein. This is just the property at one snapshot. This paper confirms a large land of positive charge distribution has still been reserved during the long molecular dynamics of 30 nanoseconds in many environments, but the continuous of the land has not been always reserved yet. These results may be useful for the medicinal treatment of prion diseases. © 2012 Nova Science Publishers, Inc. All rights reserved.
The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils
- Authors: Zhang, Jiapu , Hou, Yating , Wang, Yiju , Wang, Changyu , Zhang, Xiangsun
- Date: 2012
- Type: Text , Journal article
- Relation: Natural Science Vol. 4, no. 12A (2012), p. 1097-1108
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- Description: Experimental X-ray crystallography, NMR (Nu- clear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein); theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduc- es some optimization algorithms used in these research fields and presents a new theoretical computational method—An improved LBFGS Quasi-Newtonian mathematical optimization me- thod—to produce 3D structures of prion AGAA- AAGA amyloid fibrils (which are unstable, non-crystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic re-gion AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experi-mental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.
Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136)
- Authors: Zhang, Jiapu , Zhang, Yuanli
- Date: 2013
- Type: Text , Journal article
- Relation: Acta Biochimica et Biophysica Sinica Vol. 45, no. 6 (2013), p. 509-519
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- Description: Prion diseases, traditionally referred to as transmissible spongiform encephalopathies, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species, manifesting as scrapie in sheep, bovine spongiform encephalopathy (or 'madcow' disease) in cattle, and Creutzfeldt-Jakob disease, Gerstmann-Strussler-Scheinker syndrome, fatal familial insomnia (FFI), and Kulu in humans, etc. These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrPC) into insoluble abnormally folded infectious prions (PrPSc). The hydrophobic region PrP(109-136) controls the formation of diseased prions: the normal PrP(113-120) AGAAAAGA palindrome is an inhibitor/blocker of prion diseases and the highly conserved glycine-xxx-glycine motif PrP(119- 131) can inhibit the formation of infectious prion proteins in cells. This article gives detailed reviews on the PrP(109- 136) region and presents the studies of its three-dimensional structures and structural dynamics. © The Author 2013.
- Description: 2003011134
Recent advances in the immunity research of rabbits to Prion Diseases
- Authors: Zhang, Jiapu
- Date: 2013
- Type: Text , Journal article
- Relation: Biochemistry & Pharmacology Vol. 2, no. e143 (2013), p. 1-2
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A survey and a molecular dynamics study on the (central) hydrophobic region of prion proteins
- Authors: Zhang, Jiapu , Wang, Feng
- Date: 2014
- Type: Text , Journal article
- Relation: Current Pharmaceutical Biotechnology Vol. 15, no. 11 (2014), p. 1026-1048
- Full Text: false
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- Description: Prion diseases which are serious neurodegenerative diseases that affect humans and animals occur in various of species. Unlike many other neurodegenerative diseases affected by amyloid, prion diseases can be highly infectious. Prion diseases occur in many species. In humans, prion diseases include the fatal human neurodegenerative diseases such as Creutzfeldt-Jakob Disease (CJD), Fatal Familial Insomnia (FFI), Gerstmann-Strussler-Scheinker syndrome (GSS) and Kuru etc. In animals, prion diseases are related to the bovine spongiform encephalopathy (BSE or ‘mad-cow’ disease) in cattle, the chronic wasting disease (CWD) found in deer and elk, and scrapie seen in sheep and goats, etc. More seriously, the fact that transmission of the prion diseases across the species barrier to other species such as humans has caused a major public health concern worldwide. For example, the BSE in Europe, the CWD in North America, and variant CJDs (vCJDs) in young people of UK. Fortunately, it is discovered that the hydrophobic region of prion proteins (PrP) controls the formation of diseased prions (PrPSc), which provide some clues in control of such diseases. This article provides a detailed survey of recent studies with respect to the PrP hydrophobic region of human PrP(110–136) using molecular dynamics studies. © 2014 Bentham Science Publishers.