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In building practical applications of evolutionary computation (EC), two optimizations are essential. First, the parameters of the search method need to be tuned to the domain in order to balance exploration and exploitation effectively.…
Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene…
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
The evolution of an open system is usually associated with the interaction of the system with an environment. A new method to study the open-type system evolution of a qubit (two-level atom) state is established. This evolution is…
Most physical and other natural systems are complex entities composed of a large number of interacting individual elements. It is a surprising fact that they often obey the so-called scaling laws relating an observable quantity with a…
Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…
We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. We…
We study the role of recombination, as practiced by genetically-competent bacteria, in speeding up Darwinian evolution. This is done by adding a new process to a previously-studied Markov model of evolution on a smooth fitness landscape;…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
Evolution of a multiplicity distribution can be described with the help of master equation. We first look at 3rd and 4th factorial moments of multiplicity distributions and derive their equilibrium values. From them central moments and…
We propose an extension of the standard model with an extra U(1)' abelian symmetry, three Higgs doublets and one Higgs singlet, where the new U(1)' charges are flavour non-universal. As a result, the model introduces an enlarger particle…
The living organism is considered as an open system, whereas Prigogine's approach to the thermodynamics of such systems is used. The approach allows one to formulate the law of individual growth and development (ontogenesis) of the living…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
A flagellated bacterium navigates fluid environments by rotating its helical flagellar bundle. The wobbling of the bacterial body significantly influences its swimming behavior. To quantify the three underlying motions--precession,…
We conducted a three-dimensional numerical simulation of bioconvection generated by oxygen-reactive chemotactic bacteria. This study investigated the bioconvection patterns, interference between plumes, and the wavelength of bioconvection…
Recent observations suggest that Hubble's constant is large, and hence that the Universe appears to be younger than some of its constituents. The traditional escape route, which assumes that the expansion is accelerating, appears to be…
We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system…
Ecology and evolution under changing environments are important in many subfields of biology with implications for medicine. Here, we explore an example: the consequences of fluctuating environments on the emergence of antibiotic…