Quantum Biology: an Update and Perspective
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Glossary - Cellbiology
1 Glossary - Cellbiology Blotting: (Blot Analysis) Widely used biochemical technique for detecting the presence of specific macromolecules (proteins, mRNAs, or DNA sequences) in a mixture. A sample first is separated on an agarose or polyacrylamide gel usually under denaturing conditions; the separated components are transferred (blotting) to a nitrocellulose sheet, which is exposed to a radiolabeled molecule that specifically binds to the macromolecule of interest, and then subjected to autoradiography. Northern B.: mRNAs are detected with a complementary DNA; Southern B.: DNA restriction fragments are detected with complementary nucleotide sequences; Western B.: Proteins are detected by specific antibodies. Cell: The fundamental unit of living organisms. Cells are bounded by a lipid-containing plasma membrane, containing the central nucleus, and the cytoplasm. Cells are generally capable of independent reproduction. More complex cells like Eukaryotes have various compartments (organelles) where special tasks essential for the survival of the cell take place. Cytoplasm: Viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus. The part of the cytoplasm not contained in any organelle is called the Cytosol. Cytoskeleton: (Gk. ) Three dimensional network of fibrous elements, allowing precisely regulated movements of cell parts, transport organelles, and help to maintain a cell’s shape. • Actin filament: (Microfilaments) Ubiquitous eukaryotic cytoskeletal proteins (one end is attached to the cell-cortex) of two “twisted“ actin monomers; are important in the structural support and movement of cells. Each actin filament (F-actin) consists of two strands of globular subunits (G-Actin) wrapped around each other to form a polarized unit (high ionic cytoplasm lead to the formation of AF, whereas low ion-concentration disassembles AF). -
Quantum Mechanics and Biology
QUANTUM MECHANICS AND BIOLOGY H. C. LONGUET-HIGGINS From the University of Cambridge, England I should like to begin by saying that I feel very diffident about speaking on the subject which the organizers of this Conference invited me to discuss with you. What I have to say will inevitably be limited by the extreme superficiality of my acquaintance with modem biochemistry and biophysics. The only apology which I can offer for being here at all is that I feel, in common with most scientists, that it is a good thing for workers in quite different fields to meet occasionally and compare notes so as to discover whether the methods of one discipline can usefully be applied to the problems of another. It will soon become apparent to you that my opinions on the usefulness of quantum mechanics to biologists are decidedly con- servative; but if these opinions are not generally shared, perhaps at least they will provoke discussion. The thesis which I want to develop in the next few minutes will seem to many of you to be rather pedestrian. Briefly I want to suggest that for many years to come the student of living matter will have much more need for an understanding of physical chemistry than for a knowledge of quantum mechanics. However much one may marvel at the variety and versatility of living things, it cannot be denied that all organisms are in one sense physico-chemical machines. Ingenious and baffling as their structure and function may seem to be, it is therefore proper, in attempting to understand them, to compare their component parts with those in- animate systems which the physical chemist now understands more or less thor- oughly. -
Biophysics 1
Biophysics 1 on interactions between proteins involved in Notch signaling using BIOPHYSICS modern biophysical methods. Thermodynamics of association and allosteric effects are determined by spectroscopic, ultracentrifugation, http://biophysics.jhu.edu/ and calorimetric methods. Atomic structure information is being obtained by NMR spectroscopy. The ultimate goal is to determine the The Department of Biophysics offers programs leading to the B.A., M.A., thermodynamic partition function for a signal transduction system and and Ph.D. degrees. Biophysics is appropriate for students who wish interpret it in terms of atomic structure. to develop and integrate their interests in the physical and biological sciences. NMR Spectroscopy (Dr. Lecomte) Research interests in the Department cover experimental and Many proteins require stable association with an organic compound computational, molecular and cellular structure, function, and biology, for proper functioning. One example of such “cofactor” is the heme membrane biology, and biomolecular energetics. The teaching and group, a versatile iron-containing molecule capable of catalyzing a research activities of the faculty bring its students in contact with broad range of chemical reactions. The reactivity of the heme group biophysical scientists throughout the university. Regardless of their choice is precisely controlled by interactions with contacting amino acids. of research area, students are exposed to a wide range of problems of Structural fluctuations within the protein are also essential to the fine- biological interest. For more information, and for the most up-to-date list tuning of the chemistry. We are studying how the primary structure of of course offerings and requirements, consult the department web page at cytochromes and hemoglobins codes for heme binding and the motions biophysics.jhu.edu (http://biophysics.jhu.edu/). -
Origin of Probability in Quantum Mechanics and the Physical Interpretation of the Wave Function
Origin of Probability in Quantum Mechanics and the Physical Interpretation of the Wave Function Shuming Wen ( [email protected] ) Faculty of Land and Resources Engineering, Kunming University of Science and Technology. Research Article Keywords: probability origin, wave-function collapse, uncertainty principle, quantum tunnelling, double-slit and single-slit experiments Posted Date: November 16th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-95171/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Origin of Probability in Quantum Mechanics and the Physical Interpretation of the Wave Function Shuming Wen Faculty of Land and Resources Engineering, Kunming University of Science and Technology, Kunming 650093 Abstract The theoretical calculation of quantum mechanics has been accurately verified by experiments, but Copenhagen interpretation with probability is still controversial. To find the source of the probability, we revised the definition of the energy quantum and reconstructed the wave function of the physical particle. Here, we found that the energy quantum ê is 6.62606896 ×10-34J instead of hν as proposed by Planck. Additionally, the value of the quality quantum ô is 7.372496 × 10-51 kg. This discontinuity of energy leads to a periodic non-uniform spatial distribution of the particles that transmit energy. A quantum objective system (QOS) consists of many physical particles whose wave function is the superposition of the wave functions of all physical particles. The probability of quantum mechanics originates from the distribution rate of the particles in the QOS per unit volume at time t and near position r. Based on the revision of the energy quantum assumption and the origin of the probability, we proposed new certainty and uncertainty relationships, explained the physical mechanism of wave-function collapse and the quantum tunnelling effect, derived the quantum theoretical expression of double-slit and single-slit experiments. -
Graduate Group in Biochemistry and Molecular Biophysics General Information for Incoming Students
Graduate Group in Biochemistry and Molecular Biophysics General Information for Incoming Students Student mailboxes are located on the left as you enter the Mail Room (257 Anatomy-Chemistry Building) of the Dept. of Biochemistry and Biophysics. Use the following address to have mail sent to you at this location: Department of Biochemistry and Biophysics, 257 Anatomy-Chemistry Bldg., Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104- 6059. The Student Room is located in 250 Anatomy-Chemistry Building. Keys to this room have been placed in your mailbox. The room has two computers (1 MAC, 1 PC) and a printer. Please make sure the door is locked and securely closed when you leave the room. Lockers: Please contact Kelli McKenna if you would like a locker. They are located in the hallway outside of Rm 234 Anatomy- Chemistry. Advising: You will be meeting individually with the Advising Committee to select your fall courses and for guidance on your rotations. Course registration forms should be returned to Kelli McKenna as soon as possible after your meeting. Any changes in your fall schedule should be made within two weeks of the start of the semester and need to be approved by one of the members of the Advising Committee. Lab Rotation Approval forms are to be completed by Friday, September 13, 2021. You can find the forms for course registration and lab rotation on the BMB webpage: www.med.upenn.edu/bmbgrad under the resources page. Seminars which you are expected to attend: · Raiziss Rounds: Thursdays at noon (Austrian Auditorium, Clinical Research Building). -
Physics, Biology and the Origin of Life: the Physicians' View Geoffrey Goodman Phd1 and M
IMAJ • VOL 13 • DeceMber 2011 PERSPECTIVE Physics, Biology and the Origin of Life: The Physicians' View Geoffrey Goodman PhD1 and M. Eric Gershwin MD2 1Kfar Vradim, Israel 2Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Davis, CA, USA environment and were very much concerned with the insepa- ABSTRACT: Physicians have a great interest in discussions of life and its rable issue of 'what' is life and 'how' it relates to inanimate origin, including life's persistence through successive cycles matter. Physicians of those eras were more concerned about of self-replication under extreme climatic and man-made religion and the role of man and God than about physical sci- trials and tribulations. We review here the fundamental ence. One wonders what they would think today, with physical processes that, contrary to human intuition, life may be science dominated and puzzled by the apparent incompatibility seen heuristically as an ab initio, fundamental process between two fundamental concepts: general relativity (gravi- at the interface between the complementary forces of tational) theory that views matter-energy as an expression of gravitation and quantum mechanics. Analogies can predict a time-space continuum and quantum theory that considers applications of quantum mechanics to human physiology matter-energy in terms of discrete quantities (quanta) and in addition to that already being applied, in particular to waves and their counterintuitively weird behavior. The long- aspects of brain activity and pathology. This potential will also extend eventually to, for example, autoimmunity, held desire to unify these two fundamental laws of physics in genetic selection and aging. -
Catalysishub NEWSLETTER
CatalysisHub NEWSLETTER The UK Catalysis Hub has created a thriving and successful network of catalytic scientists who are developing and promoting catalytic science in the UK. The Hub has succeeded in coordinating the community and is contributing to the development of new approaches and techniques in the field. It has provided substantial added value and is now recognised widely both in the UK and internationally. It will provide an excellent base for the future development of this crucial area of science in the UK. “The Hub has demonstrated resilience in the current pandemic with the community coming together to support each other through webinars and training courses and we will continue these in more normal times. Our proposal round was very successful with a large number of high quality proposals submitted and we have funded an excellent portfolio of research. The next few months will hopefully see an easing of the lockdown and an increase in our ability to do research. We hope that all are keeping well and safe and we look forward to meeting in person when we can and discussing catalytic research face to face.” ~ Professor Christopher Hardacre, Director Events Highlights of 2020 online via our website, so they will be a future resource for the whole catalysis community. COVID-19 has had a major impact on scientific network and dissemination due to travel UKCC 2020, 7 - 9 January 2020 restrictions and social distancing making face to face meetings and conferences unfeasible. The UK Catalysis Hub winter conference was held virtually and we worked on a vibrant programme of webinars, scientific discussions and other online events. -
Restricted Agents in Thermodynamics and Quantum Information Theory
Research Collection Doctoral Thesis Restricted agents in thermodynamics and quantum information theory Author(s): Krämer Gabriel, Lea Philomena Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010858172 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Diss. ETH No. 23972 Restricted agents in thermodynamics and quantum information theory A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by Lea Philomena Kr¨amer Gabriel MPhysPhil, University of Oxford born on 18th July 1990 citizen of Germany accepted on the recommendation of Renato Renner, examiner Giulio Chiribella, co-examiner Jakob Yngvason, co-examiner 2016 To my family Acknowledgements First and foremost, I would like to thank my thesis supervisor, Prof. Renato Renner, for placing his trust in me from the beginning, and giving me the opportunity to work in his group. I am grateful for his continuous support and guidance, and I have always benefited greatly from the discussions we had | Renato without doubt has a clear vision, a powerful intuition, and a deep understanding of physics and information theory. Perhaps even more importantly, he has an exceptional gift for explaining complex subjects in a simple and understandable way. I would also like to thank my co-examiners Giulio Chiribella and Jakob Yngvason for agreeing to be part of my thesis committee, and for their input and critical questions in the discussions and conversations we had. -
Neuroreceptor Activation by Vibration-Assisted Tunneling
OPEN Neuroreceptor Activation by SUBJECT AREAS: Vibration-Assisted Tunneling BIOPHYSICAL CHEMISTRY Ross D. Hoehn1, David Nichols2, Hartmut Neven3 & Sabre Kais4,5,6 MECHANISM OF ACTION 1Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA, 2Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA,3 Google, Venice, CA 90291, USA,4 Department of Received 5 20 October 2014 Chemistry, Purdue University, West Lafayette, IN 47907, USA, Departments of Physics, Purdue University, West Lafayette, IN 47907, USA,6 Qatar Environment and Energy Research Institute, Qatar Foundation, Doha, Qatar. Accepted 20 March 2015 G protein-coupled receptors (GPCRs) constitute a large family of receptor proteins that sense molecular Published signals on the exterior of a cell and activate signal transduction pathways within the cell. Modeling how an 24 April 2015 agonist activates such a receptor is fundamental for an understanding of a wide variety of physiological processes and it is of tremendous value for pharmacology and drug design. Inelastic electron tunneling spectroscopy (IETS) has been proposed as a model for the mechanism by which olfactory GPCRs are activated by a bound agonist. We apply this hyothesis to GPCRs within the mammalian nervous system Correspondence and using quantum chemical modeling. We found that non-endogenous agonists of the serotonin receptor share requests for materials a particular IET spectral aspect both amongst each other and with the serotonin molecule: a peak whose should be addressed to intensity scales with the known agonist potencies. We propose an experiential validation of this model by S.K. (kais@purdue. utilizing lysergic acid dimethylamide (DAM-57), an ergot derivative, and its deuterated isotopologues; we also provide theoretical predictions for comparison to experiment. -
On Quantum Tunnelling with and Without Decoherence and the Direction of Time
On the effect of decoherence on quantum tunnelling. By A.Y. Klimenko † The University of Queensland, SoMME, QLD 4072, Australia (SN Applied Sciences, 2021, 3:710) Abstract This work proposes a series of quantum experiments that can, at least in principle, allow for examining microscopic mechanisms associated with decoherence. These experiments can be interpreted as a quantum-mechanical version of non-equilibrium mixing between two volumes separated by a thin interface. One of the principal goals of such experiments is in identifying non-equilibrium conditions when time-symmetric laws give way to time-directional, irreversible processes, which are represented by decoher- ence at the quantum level. The rate of decoherence is suggested to be examined indirectly, with minimal intrusions | this can be achieved by measuring tunnelling rates that, in turn, are affected by decoherence. Decoherence is understood here as a general process that does not involve any significant exchanges of energy and governed by a particular class of the Kraus operators. The present work analyses different regimes of tunnelling in the presence of decoherence and obtains formulae that link the corresponding rates of tunnelling and decoherence under different conditions. It is shown that the effects on tunnelling of intrinsic decoherence and of decoherence due to unitary interactions with the environment are similar but not the same and can be distinguished in experiments. Keywords: decoherence, quantum tunnelling, non-equilibrium dynamics 1. Introduction The goal of this work is to consider experiments that can, at least in principle, examine time-directional quantum effects in an effectively isolated system. Such experiments need to be conducted somewhere at the notional boundary between the microscopic quantum and macroscopic thermodynamic worlds, that is we need to deal with quantum systems that can exhibit some degree of thermodynamic behaviour. -
Synthetic Biology
From Molecular Biology to Synthetic Biology, what’s new? Sandra Taylor, Senior Research Technician, BSc (Hons), Mphil, Rsci, MIScT [email protected] (0161) 306 5131 Small beginnings in Norwich, after my first degree • 1987 - First lab job veterinary tests: Bacteriology, post mortems, blood, urine, faeces tests etc. Plant Molecular Genetics 1988 to 1998 – the lab grew from 6 to 16 people and several papers were published on the way that flowering is controlled. 1998 to 2001: Biochemistry Division, School of Biological Sciences, Manchester University – I supported 6 research groups, sharing expertise. Topics from cell division (in toads) to asthma (in horses and people), and cultured human cells. Career Break from 2001 to 2007 • Starting again after 6 years was a challenge but I soon got back up to speed. Technical roles are very varied, never boring, a bit like being a Mum! 2007 to present • I spent 7 years in the Michael Smith Building (Life Sciences) – various roles (cell culture, cloning, yeast two-hybrid) • In 2014 I moved to the MIB – more Chemistry/Biochemistry focussed Nano-scale 3D printing?! Micro-titre plates with 96, 384 or even 1536 sample wells – technology is being developed to “write” strings of DNA into these tiny wells using 3D nano-printing technology. Present Challenges Supporting SYNBIOCHEM • New subject(s) and equipment to learn about • The new SYMBIOCHEM team is 10 people and 4 robots! • IT technology means writing electronic lab notebooks instead of paper ones! • The new team is multidisciplinary so lots to learn but good fun! • This is now the age of writing DNA, as opposed to just reading it Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle) Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARA/Endofin with HD-PTP. -
LETTER Doi:10.1038/Nature11653
LETTER doi:10.1038/nature11653 Revealing the quantum regime in tunnelling plasmonics Kevin J. Savage1, Matthew M. Hawkeye1, Rube´n Esteban2, Andrei G. Borisov2,3, Javier Aizpurua2 & Jeremy J. Baumberg1 When two metal nanostructures are placed nanometres apart, their probe dynamically controlled plasmonic cavities and reveal the onset of optically driven free electrons couple electrically across the gap. The quantum-tunnelling-induced plasmonics in the subnanometre regime. resulting plasmons have enhanced optical fields of a specific colour Two gold-nanoparticle-terminated atomic force microscope (AFM) tightly confined inside the gap. Many emerging nanophotonic tech- tips are oriented tip-to-tip (Fig. 1a). The tip apices define a cavity nologies depend on the careful control of this plasmonic coupling, supporting plasmonic resonances created via strong coupling between including optical nanoantennas for high-sensitivity chemical and localized plasmons on each tip7,27. This dual AFM tip configuration biological sensors1, nanoscale control of active devices2–4, and provides multiple advantages. First, independent nanometre-precision improved photovoltaic devices5. But for subnanometre gaps, co- movement of both tips is possible with three-axis piezoelectric stages. herent quantum tunnelling becomes possible and the system enters Second, conductive AFM probes provide direct electrical connection a regime of extreme non-locality in which previous classical treat- to the tips, enabling simultaneous optical and electrical measurements. ments6–14 fail. Electron correlations across the gap that are driven Third, the tips are in free space and illuminated from the side in a by quantum tunnelling require a new description of non-local dark-field configuration (Fig. 1b, c and Supplementary Information).