scholarly journals Quantum Biology: An Update and Perspective

2021 ◽  
Vol 3 (1) ◽  
pp. 80-126
Author(s):  
Youngchan Kim ◽  
Federico Bertagna ◽  
Edeline M. D’Souza ◽  
Derren J. Heyes ◽  
Linus O. Johannissen ◽  
...  
Keyword(s):  
Equilibrium State ◽  
Fluorescent Proteins ◽  
Building Blocks ◽  
Living Systems ◽  
Quantum Mechanical ◽  
Biological Processes ◽  
Biological Functions ◽  
Biomolecular Systems ◽  
Quantum Biology ◽  
Quantum Mechanical Effects

Understanding the rules of life is one of the most important scientific endeavours and has revolutionised both biology and biotechnology. Remarkable advances in observation techniques allow us to investigate a broad range of complex and dynamic biological processes in which living systems could exploit quantum behaviour to enhance and regulate biological functions. Recent evidence suggests that these non-trivial quantum mechanical effects may play a crucial role in maintaining the non-equilibrium state of biomolecular systems. Quantum biology is the study of such quantum aspects of living systems. In this review, we summarise the latest progress in quantum biology, including the areas of enzyme-catalysed reactions, photosynthesis, spin-dependent reactions, DNA, fluorescent proteins, and ion channels. Many of these results are expected to be fundamental building blocks towards understanding the rules of life.

scholarly journals The future of quantum biology

2018 ◽  
Vol 15 (148) ◽  
pp. 20180640 ◽  
Author(s):  
Adriana Marais ◽  
Betony Adams ◽  
Andrew K. Ringsmuth ◽  
Marco Ferretti ◽  
J. Michael Gruber ◽  
...  
Keyword(s):  
Equilibrium State ◽  
Quantum Mechanical ◽  
Biological Processes ◽  
Future Directions ◽  
Quantum Biology ◽  
Classical Physics ◽  
Current State ◽  
Small Scales ◽  
Quantum Mechanical Effects ◽  
Observational Techniques

Biological systems are dynamical, constantly exchanging energy and matter with the environment in order to maintain the non-equilibrium state synonymous with living. Developments in observational techniques have allowed us to study biological dynamics on increasingly small scales. Such studies have revealed evidence of quantum mechanical effects, which cannot be accounted for by classical physics, in a range of biological processes. Quantum biology is the study of such processes, and here we provide an outline of the current state of the field, as well as insights into future directions.

The Possibility of Quantum Medicine in Cancer Research: A Review

2021 ◽  
pp. 1-20
Author(s):  
Mahsa Faramarzpour ◽  
Mohammadreza Ghaderinia ◽  
Hamed Abadijoo ◽  
Hossein Aghababa
Keyword(s):  
Quantum Mechanics ◽  
Cancer Biology ◽  
Quantum Physics ◽  
Review Paper ◽  
Building Blocks ◽  
Physical World ◽  
Quantum Mechanical ◽  
Quantum Biology ◽  
Biological Phenomena ◽  
Game Changer

There is no doubt that quantum mechanics has become one of the building blocks of our physical world today. It is one of the most rapidly growing fields of science that can potentially change every aspect of our life. Quantum biology is one of the most essential parts of this era which can be considered as a game-changer in medicine especially in the field of cancer. Despite quantum biology having gained more attention during the last decades, there are still so many unanswered questions concerning cancer biology and so many unpaved roads in this regard. This review paper is an effort to answer the question of how biological phenomena such as cancer can be described through the quantum mechanical framework. In other words, is there a correlation between cancer biology and quantum mechanics, and how? This literature review paper reports on the recently published researches based on the principles of quantum physics with focus on cancer biology and metabolism.

scholarly journals An evolutionary perspective on immunometabolism

Science ◽  
2019 ◽  
Vol 363 (6423) ◽  
pp. eaar3932 ◽  
Author(s):  
Andrew Wang ◽  
Harding H. Luan ◽  
Ruslan Medzhitov
Keyword(s):  
Cell Fate ◽  
Life History Theory ◽  
De Novo ◽  
Building Blocks ◽  
Biological Processes ◽  
Biological Functions ◽  
Cell Fate Decisions ◽  
Ecological Principles ◽  
Proliferation And Differentiation ◽  
Cell Quiescence

Metabolism is at the core of all biological functions. Anabolic metabolism uses building blocks that are either derived from nutrients or synthesized de novo to produce the biological infrastructure, whereas catabolic metabolism generates energy to fuel all biological processes. Distinct metabolic programs are required to support different biological functions. Thus, recent studies have revealed how signals regulating cell quiescence, proliferation, and differentiation also induce the appropriate metabolic programs. In particular, a wealth of new studies in the field of immunometabolism has unveiled many examples of the connection among metabolism, cell fate decisions, and organismal physiology. We discuss these findings under a unifying framework derived from the evolutionary and ecological principles of life history theory.

Applications of Density Functional Theory to Biological Systems

1998 ◽  
Author(s):  
Tomasz Adam Wesolowski ◽  
Jacques Weber
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Biological Systems ◽  
Quantum Mechanical ◽  
Biological Processes ◽  
Biological Functions ◽  
Functional Theory ◽  
Hartree Fock ◽  
Functional Units

The term biological systems may be used in reference to a wide class of polyatomic systems. They can be defined as minimal functional units which perform specific biological functions: enzymatic reactions, transport across membranes, or photosynthesis. At present, such systems as a whole are not amenable to quantum-chemistry studies because of their large size. The smallest enzymes are built of few thousands of atoms (e.g., lysozyme consists of 129 amino-acid subunits), the smallest nucleic acids are of similar size (e.g., t-RNA molecules consist of about 80 nucleotide subunits), whereas biological membranes are even larger and include different biological macromolecules embedded in a phospholipide medium. On the other hand, a common-sense definition of the term biological systems refers to any chemical molecule or molecular complex which is involved in biological or biochemical processes. The latter definition, which will be used throughout this review, covers not only complete functional units performing biological functions but also fragments of such units. Theoretical studies have provided data on properties of such fragments and have helped understanding of the biological processes at the molecular level. Depending upon the size of such fragments, they can be studied by means of various quantum-chemical methods. Molecular systems of up to a few thousands of atoms can be studied using semi-empirical methods. For the Hartree-Fock or Kohn-Sham density functional theory (DFT) calculations, the current size limit is a few hundreds of atoms. (Throughout the text, Hartree-Fock refers to ab initio Self-Consistent Field calculations using the approximation of linear combination of atomic orbitals.) When the desired accuracy requires the calculation of electron correlation at the ab initio level, only systems containing no more than few tens of atoms can be treated. Therefore, a theoretician aiming at the elucidation of biological processes by quantum-mechanical calculations faces two crucial issues. The first one is the selection of a fragment for modeling at the quantum-mechanical level. The second one is the assessment of the effects associated with parts of the system which cannot be modeled at the quantum-mechanical level. In this review, the DFT studies of biological systems are divided into two groups corresponding to different ways of addressing the second aforementioned issue.

Comparison and Analysis of Computational Methods for Identifying N6 - methyladenosine Sites in Saccharomyces Cerevisiae

2020 ◽  
Vol 26 ◽  
Author(s):  
Pengmian Feng ◽  
Lijing Feng ◽  
Chaohui Tang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Computational Methods ◽  
Computational Analysis ◽  
Computational Prediction ◽  
Experimental Methods ◽  
Biological Processes ◽  
Biological Functions ◽  
Precise Location ◽  
Future Directions ◽  
The Past

Background and Purpose: N 6 -methyladenosine (m6A) plays critical roles in a broad set of biological processes. Knowledge about the precise location of m6A site in the transcriptome is vital for deciphering its biological functions. Although experimental techniques have made substantial contributions to identify m6A, they are still labor intensive and time consuming. As good complements to experimental methods, in the past few years, a series of computational approaches have been proposed to identify m6A sites. Methods: In order to facilitate researchers to select appropriate methods for identifying m6A sites, it is necessary to give a comprehensive review and comparison on existing methods. Results: Since researches on m6A in Saccharomyces cerevisiae are relatively clear, in this review, we summarized recent progresses on computational prediction of m6A sites in S. cerevisiae and assessed the performance of existing computational methods. Finally, future directions of computationally identifying m6A sites were presented. Conclusion: Taken together, we anticipate that this review will provide important guides for computational analysis of m 6A modifications.

Capabilities

2018 ◽  
Author(s):  
Paul F. M. J. Verschure
Keyword(s):  
Building Blocks ◽  
Living Systems ◽  
System Level ◽  
Cognitive Architectures ◽  
Multiple Components ◽  
Perception Action

This chapter introduces the “Capabilities” section of the Handbook of Living Machines. Where the previous section considered building blocks, we recognize that components or modules do not automatically make systems. Hence, in the remainder of this handbook, the emphasis is toward the capabilities of living systems and their emulation in artifacts. Capabilities often arise from the integration of multiple components and thus sensitize us to the need to develop a system-level perspective on living machines. Here we summarize and consider the 14 contributions in this section which cover perception, action, cognition, communication, and emotion, and the integration of these through cognitive architectures into systems that can emulate the full gamut of integrated behaviors seen in animals including, potentially, our own capacity for consciousness.

scholarly journals Engineering motile aqueous phase-separated droplets via liposome stabilisation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shaobin Zhang ◽  
Claudia Contini ◽  
James W. Hindley ◽  
Guido Bolognesi ◽  
Yuval Elani ◽  
...  
Keyword(s):  
Aqueous Phase ◽  
Marangoni Effect ◽  
Living Systems ◽  
Biological Processes ◽  
Biological Applications ◽  
Emulsion System ◽  
Biotechnological Potential ◽  
New Directions ◽  
Directional Motion ◽  
The Stability

AbstractThere are increasing efforts to engineer functional compartments that mimic cellular behaviours from the bottom-up. One behaviour that is receiving particular attention is motility, due to its biotechnological potential and ubiquity in living systems. Many existing platforms make use of the Marangoni effect to achieve motion in water/oil (w/o) droplet systems. However, most of these systems are unsuitable for biological applications due to biocompatibility issues caused by the presence of oil phases. Here we report a biocompatible all aqueous (w/w) PEG/dextran Pickering-like emulsion system consisting of liposome-stabilised cell-sized droplets, where the stability can be easily tuned by adjusting liposome composition and concentration. We demonstrate that the compartments are capable of negative chemotaxis: these droplets can respond to a PEG/dextran polymer gradient through directional motion down to the gradient. The biocompatibility, motility and partitioning abilities of this droplet system offers new directions to pursue research in motion-related biological processes.

scholarly journals Comparison of Quantitative Morphology of Layered and Arbitrary Patterns: Contrary to Visual Perception, Binary Arbitrary Patterns Are Layered from a Structural Point of View

2021 ◽  
Vol 11 (14) ◽  
pp. 6300
Author(s):  
Igor Smolyar ◽  
Daniel Smolyar
Keyword(s):  
Boolean Function ◽  
Layer Structure ◽  
Central Element ◽  
Morphological Characteristics ◽  
Building Blocks ◽  
Point Of View ◽  
Living Systems ◽  
Seismic Profiles ◽  
Contour Maps ◽  
Anisotropic Layers

Patterns found among both living systems, such as fish scales, bones, and tree rings, and non-living systems, such as terrestrial and extraterrestrial dunes, microstructures of alloys, and geological seismic profiles, are comprised of anisotropic layers of different thicknesses and lengths. These layered patterns form a record of internal and external factors that regulate pattern formation in their various systems, making it potentially possible to recognize events in the formation history of these systems. In our previous work, we developed an empirical model (EM) of anisotropic layered patterns using an N-partite graph, denoted as G(N), and a Boolean function to formalize the layer structure. The concept of isotropic and anisotropic layers was presented and described in terms of the G(N) and Boolean function. The central element of the present work is the justification that arbitrary binary patterns are made up of such layers. It has been shown that within the frame of the proposed model, it is the isotropic and anisotropic layers themselves that are the building blocks of binary layered and arbitrary patterns; pixels play no role. This is why the EM can be used to describe the morphological characteristics of such patterns. We present the parameters disorder of layer structure, disorder of layer size, and pattern complexity to describe the degree of deviation of the structure and size of an arbitrary anisotropic pattern being studied from the structure and size of a layered isotropic analog. Experiments with arbitrary patterns, such as regular geometric figures, convex and concave polygons, contour maps, the shape of island coastlines, river meanders, historic texts, and artistic drawings are presented to illustrate the spectrum of problems that it may be possible to solve by applying the EM. The differences and similarities between the proposed and existing morphological characteristics of patterns has been discussed, as well as the pros and cons of the suggested method.

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