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We present the novel approach to mathematical modeling of information processes in biosystems. It explores the mathematical formalism and methodology of quantum theory, especially quantum measurement theory. This approach is known as {it quantum-like} and it should be distinguished from study of genuine quantum physical processes in biosystems (quantum biophysics, quantum cognition). It is based on quantum information representation of biosystems state and modeling its dynamics in the framework of theory of open quantum systems. This paper starts with the non-physicist friendly presentation of quantum measurement theory, from the original von Neumann formulation to modern theory of quantum instruments. Then, latter is applied to model combinations of cognitive effects and gene regulation of glucose/lactose metabolism in Escherichia coli bacterium. The most general construction of quantum instruments is based on the scheme of indirect measurement, in that measurement apparatus plays the role of the environment for a biosystem. The biological essence of this scheme is illustrated by quantum formalization of Helmholtz sensation-perception theory. Then we move to open systems dynamics and consider quantum master equation, with concentrating on quantum Markov processes. In this framework, we model functioning of biological functions such as psychological functions and epigenetic mutation.
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In this paper we briefly discuss the necessity of using quantum mechanics as a fundamental theory applicable to some key functional aspects of biological systems. This is especially relevant to three important parts of a neuron in the human brain, namely the cell membrane, microtubules (MT) and ion channels. We argue that the recently published papers criticizing the use of quantum theory in these systems are not convincing.
Photosynthesis is the basic process used by plants to convert light energy in reaction centers into chemical energy. The high efficiency of this process is not yet understood today. Using the formalism for the description of open quantum systems by means of a non-Hermitian Hamilton operator, we consider initially the interplay of gain (acceptor) and loss (donor). Near singular points it causes fluctuations of the cross section which appear without any excitation of internal degrees of freedom of the system. This process occurs therefore very quickly and with high efficiency. We then consider the excitation of resonance states of the system by means of these fluctuations. This second step of the whole process takes place much slower than the first one, because it involves the excitation of internal degrees of freedom of the system. The two-step process as a whole is highly efficient and the decay is bi-exponential. We provide, if possible, the results of analytical studies, otherwise characteristic numerical results. The similarities of the obtained results to light harvesting in photosynthetic organisms are discussed.
Is there a functional role for quantum mechanics or coherent quantum effects in biological processes? While this question is as old as quantum theory, only recently have measurements on biological systems on ultra-fast time-scales shed light on a possible answer. In this review we give an overview of the two main candidates for biological systems which may harness such functional quantum effects: photosynthesis and magnetoreception. We discuss some of the latest evidence both for and against room temperature quantum coherence, and consider whether there is truly a functional role for coherence in these biological mechanisms. Finally, we give a brief overview of some more speculative examples of functional quantum biology including the sense of smell, long-range quantum tunneling in proteins, biological photoreceptors, and the flow of ions across a cell membrane.
Invited contribution to Quantum Aspects of Life, D. Abbott Ed. (World Scientific, Singapore, 2007).
An approximate exponential quantum projection filtering scheme is developed for a class of open quantum systems described by Hudson- Parthasarathy quantum stochastic differential equations, aiming to reduce the computational burden associated with online calculation of the quantum filter. By using a differential geometric approach, the quantum trajectory is constrained in a finite-dimensional differentiable manifold consisting of an unnormalized exponential family of quantum density operators, and an exponential quantum projection filter is then formulated as a number of stochastic differential equations satisfied by the finite-dimensional coordinate system of this manifold. A convenient design of the differentiable manifold is also presented through reduction of the local approximation errors, which yields a simplification of the quantum projection filter equations. It is shown that the computational cost can be significantly reduced by using the quantum projection filter instead of the quantum filter. It is also shown that when the quantum projection filtering approach is applied to a class of open quantum systems that asymptotically converge to a pure state, the input-to-state stability of the corresponding exponential quantum projection filter can be established. Simulation results from an atomic ensemble system example are provided to illustrate the performance of the projection filtering scheme. It is expected that the proposed approach can be used in developing more efficient quantum control methods.
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