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Evolutionary Methods (evolutionary + methods)

Distribution by Scientific Domains

Life Sciences	50%
Engineering	50%

Selected Abstracts

Optimized evolution in the cytostat: A Monte Carlo simulation

BIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009
Alan Gilbert
Abstract Rational genetic alterations of a microorganism for a specific purpose are not possible in many situations where our knowledge of the relationship between phenotype and genotype is limited. In such cases evolutionary techniques must be applied. Evolutionary methods are usually time consuming; therefore, more efficient techniques are highly desirable. In this work we present the optimization of strain development in a cytostat. The time required for mutant strain isolation is dependent on the total cells present, the wild-type specific growth rate, the beneficial mutation probability, the mutant specific growth rate, and several bioreactor operating conditions. These parameters are highly related, and a theoretical model, as developed here, is needed to define the conditions that optimize the isolation. The model is based on a discrete, stochastic description of mutant formation and selection in the background of abundant wild-type cells. Using the model, we determined the optimal cytostat operating strategy for mutant isolation that varies according to the probability of beneficial mutations. It is also shown that mutants with as little as a 5% growth advantage can be isolated in less than 15 days which is significantly faster than in a chemostat. The described optimal mutant isolation procedure is expected to be particularly useful for the generation of industrial strains that are robust in challenging growth conditions. Biotechnol. Bioeng. 2009;102: 221,231. © 2008 Wiley Periodicals, Inc. [source]

Virus-evolutionary linear genetic programming

ELECTRONICS & COMMUNICATIONS IN JAPAN, Issue 1 2008
Kenji Tamura
Abstract Many kinds of evolutionary methods have been proposed. GA and GP in particular have demonstrated their effectiveness in various problems recently, and many systems have been proposed. One is Virus-Evolutionary Genetic Algorithm (VE-GA), and the other is Linear Genetic Programming in C (LGPC). The performance of each system has been reported. VE-GA is the coevolution system of host individuals and virus individuals. That can spread schema effectively among the host individuals by using virus infection and virus incorporation. LGPC implements the GP by representing the individuals to one dimension as if GA. LGPC can reduce a search cost of pointer and save machine memory, and can reduce the time to implement GP programs. We have proposed that a system introduce virus individuals in LGPC, and analyzed the performance of the system on two problems. Our system can spread schema among the population, and search solution effectively. The results of computer simulation show that this system can search for solution depending on LGPC applying problem's character compared with LGPC. © 2008 Wiley Periodicals, Inc. Electron Comm Jpn, 91(1): 32, 39, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.10030 [source]

An efficient hybrid evolutionary algorithm based on PSO and ACO for distribution feeder reconfiguration

EUROPEAN TRANSACTIONS ON ELECTRICAL POWER, Issue 5 2010
Taher Niknam
Abstract A new formulation based on norm2 method for the multi objective distribution feeder reconfiguration (DFR) is introduced in order to minimize the real power loss, deviation of the nodes' voltage, the number of switching operations, and to balance the loads on the feeders. In the proposed method, since the objective functions are not the same and commensurable, the objective functions are considered as a vector and the aim is to maximize the distance (norm2) between the objective function vector and the worst objective function vector while the constraints are met. The status of the tie and sectionalizing switches are considered as the control variables. The proposed DFR problem is a multi objective and non-differentiable optimization problem so a hybrid evolutionary algorithm based on Particle Swarm Optimization (PSO) and Ant Colony Optimization (ACO), called HPSO, is proposed to solve it. The feasibility of the HPSO algorithm and the proposed DFR is demonstrated and compared with the solutions obtained by other approaches and evolutionary methods such as genetic algorithm (GA), ACO and the original PSO, over different distribution test systems. Copyright © 2009 John Wiley & Sons, Ltd. [source]

Heterotachy and Functional Shift in Protein Evolution

IUBMB LIFE, Issue 4-5 2003
Hervé Philippe
Abstract Study of structure/function relationships constitutes an important field of research, especially for modification of protein function and drug design. However, the fact that rational design (i.e. the modification of amino acid sequences by means of directed mutagenesis, based on knowledge of the three-dimensional structure) appears to be much less efficient than irrational design (i.e. random mutagenesis followed by in vitro selection) clearly indicates that we understand little about the relationships between primary sequence, three-dimensional structure and function. The use of evolutionary approaches and concepts will bring insights to this difficult question. The increasing availability of multigene family sequences that has resulted from genome projects has inspired the creation of novel in silico evolutionary methods to predict details of protein function in duplicated (paralogous) proteins. The underlying principle of all such approaches is to compare the evolutionary properties of homologous sequence positions in paralogs. It has been proposed that the positions that show switches in substitution rate over time--i.e., 'heterotachous sites'--are good indicators of functional divergence. However, it appears that heterotachy is a much more general process, since most variable sites of homologous proteins with no evidence of functional shift are heterotachous. Similarly, it appears that switches in substitution rate are as frequent when paralogous sequences are compared as when orthologous sequences are compared. Heterotachy, instead of being indicative of functional shift, may more generally reflect a less specific process related to the many intra- and inter-molecular interactions compatible with a range of more or less equally viable protein conformations. These interactions will lead to different constraints on the nature of the primary sequences, consistently with theories suggesting the non-independence of substitutions in proteins. However, a specific type of amino acid variation might constitute a good indicator of functional divergence: substitutions occurring at positions that are generally slowly evolving. Such substitutions at constrained sites are indeed much more frequent soon after gene duplication. The identification and analysis of these sites by complementing structural information with evolutionary data may represent a promising direction to future studies dealing with the functional characterization of an ever increasing number of multi-gene families identified by complete genome analysis. IUBMB Life, 55: 257-265, 2003 [source]