Article

Prediction of Tubulin Resonant Frequencies Using the Resonant Recognition Model (RRM)

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  • AMALNA Consulting
  • AMALNA Consulting
  • AMALNA Consulting
Article

Prediction of Tubulin Resonant Frequencies Using the Resonant Recognition Model (RRM)

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Abstract

We analyzed tubulin proteins using Resonant Recognition Model to predict possible electromagnetic resonances in tubulin and microtubules. These electromagnetic resonances are proposed to be caused by charge transfer through protein molecule. The frequencies of these electromagnetic resonances depend on charge velocity. Using different velocities of charge transfer, we predicted resonant frequencies in different frequency ranges from KHz to THz. We also proposed that these resonant frequencies could be relevant for taxol binding as well as to possible role of microtubules as macromolecular computer.

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... RRM is based upon the finding that protein function may be controlled by periodic distribution in the energy of their delocalized electrons, thereby modulating protein-protein interplay, as well as protein-DNA interactions, a fundamental step in DNA remodeling and the epigenetic control of biological properties in living organisms. Viewing vibration of molecules as an insepara-ble convergence of mechanical and electromagnetic forces, the RRM also postulated that protein conductivity could be associated with defined spectral signatures, resulting from electromagnetic radiation/absorption patterns generated by the flow of electric charges through the protein backbone [34,35]. In particular, the RRM proposes that not only the characteristics of single molecules, but also the molecular interactions that control the biological processes rely upon electromagnetic resonances between interacting biomolecules at specific electromagnetic frequencies within the infra-red, visible, and ultraviolet frequency ranges. ...
... Interestingly, the spectral signatures predicted by RRM for resonance frequencies of tubulin have been verified and supported by experimental evidence [5,35]. In fact, STM, coupled with an artificial cell replica developed to deliver electromagnetic fields of specific frequencies to tubulin molecules assembling onto platinum nanoelectrodes, has shown that tubulins, tubulin dimers, and microtubules exhibited electric conductivity profiles resonating only with specific electromagnetic frequencies applied through the cell replica system [5]. ...
... Within the context discussed herein, microtubuli may be considered as an elastic matrix of nanowires capable of mechanical and electromagnetic oscillatory patterns with radiation characteristics, while, taking into account the previously discussed RRM [32][33][34][35], signaling molecules may be equated to oscillators, behaving as resonators for frequencies in the range of 10 13 -10 15 Hz, consonant with the length of amino acid chains. With an inter-amino acid distance of about 3.8 Ä, the estimated velocity of electric charge along the protein chain has been estimated around 7.87 × 10 5 m/s [32,33], which led to considerations of the establishment of protein-mediated resonance frequency ranges with radiation characteristics. ...
Article
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We discuss emerging views on the complexity of signals controlling the onset of biological shapes and functions, from the nanoarchitectonics arising from supramolecular interactions, to the cellular/multicellular tissue level, and up to the unfolding of complex anatomy. We highlight the fundamental role of physical forces in cellular decisions, stressing the intriguing similarities in early morphogenesis, tissue regeneration, and oncogenic drift. Compelling evidence is presented, showing that biological patterns are strongly embedded in the vibrational nature of the physical energies that permeate the entire universe. We describe biological dynamics as informational processes at which physics and chemistry converge, with nanomechanical motions, and electromagnetic waves, including light, forming an ensemble of vibrations, acting as a sort of control software for molecular patterning. Biomolecular recognition is approached within the establishment of coherent synchronizations among signaling players, whose physical nature can be equated to oscillators tending to the coherent synchronization of their vibrational modes. Cytoskeletal elements are now emerging as senders and receivers of physical signals, “shaping” biological identity from the cellular to the tissue/organ levels. We finally discuss the perspective of exploiting the diffusive features of physical energies to afford in situ stem/somatic cell reprogramming, and tissue regeneration, without stem cell transplantation.
... The RRM model has been previously presented in detail [4][5][6][7][8][9][10][11][12][13][14][15][16][17] and is here presented within the Supplementary File. In summary, the RRM model analyses the distribution of free electron energies along protein and DNA macromolecules. ...
... In summary, the RRM model analyses the distribution of free electron energies along protein and DNA macromolecules. It has been previously established [4][5][6][9][10][11][12][13][14][15][16][17] that specific periodicities within this energy distribution [7,8] are related to a specific biological function of proteins and consequently to their specificity to interact with their targets, including other proteins, protein receptors and DNA. In the case of the interaction between the protein and the protein receptor, it has been established that phases at the specific interaction frequency (wavelength) should be opposite. ...
... This means that a phase difference at this characteristic frequency between interacting macromolecules should be close to π (3.14 rad). The physical meaning of these interaction frequencies (wavelengths) has been established once when the charge transfer through the protein backbone was investigated [4][5][6][9][10][11][12][13][14][15][16][17]. It was found that these wavelengths correspond directly to electromagnetic radiation wavelengths in the range between ultra-violet, visible, infra-red and far infra-red light. ...
Article
Full-text available
Featured Application: The results of this research can be used in development of improved, cheaper and targeted techniques for differentiation of stem cells into specific tissues using the identified frequencies of electromagnetic radiation. Abstract: Differentiation of stem cells into different tissues is a promising approach to treat a large number of diseases, as well as for tissue transplantation and repair. It has been shown that parathyroid hormone, similarly to stromal self-derived factor, and the radiation of specific electromagnetic frequencies of blue and green light, can encourage stem cell differentiation into osteoblasts. Here, we analysed parathyroid hormone, its receptor and stromal self-derived factor using the Resonant Recognition Model, which proposes that protein function is based on specific frequencies of electromagnetic radiation within ultraviolet , visible, infra-red and far infra-red light. The purpose of this research is to predict the characteristic frequencies related to parathyroid hormone activities, particularly differentiation of stem cells into osteoblasts. We have found that the most effective wavelength for stem cell differentiation would be 502 nm, which is between 420 nm and 540 nm, already experimentally proven to be effective in stimulating osteoblast differentiation. Thus, we propose that wavelength radiation of 502 nm will be even more efficient for differentiation of stem cells into osteoblasts.
... According to the RRM principles, by analysing a protein primary structure, the critical information about its functionality can be obtained. The RRM postulates that protein (DNA) interactions present a resonant energy transfer between the interacting molecules at the frequency specific for each observed function/interaction [10,[26][27][28][29]. ...
... The RRM postulates that there is a significant correlation between spectra of the numerical presentation of amino acids and their biological activity [9,25]. Through extensive computational studies utilizing the RRM theory, it was found that the RRM frequencies present the characteristic features of different protein biological functions or interactions [9,10,[25][26][27][28][29]. These characteristic RRM frequencies were shown to be relevant parameters for mutual recognition between biomolecules and are important in describing the selectivity of interaction between proteins and their substrates or targets but are not chemical binding [9,10,[25][26][27][28][29]. ...
... Through extensive computational studies utilizing the RRM theory, it was found that the RRM frequencies present the characteristic features of different protein biological functions or interactions [9,10,[25][26][27][28][29]. These characteristic RRM frequencies were shown to be relevant parameters for mutual recognition between biomolecules and are important in describing the selectivity of interaction between proteins and their substrates or targets but are not chemical binding [9,10,[25][26][27][28][29]. To be regarded as the characteristic feature of a particular protein biological function, the RRM frequency should satisfy the following criteria: ...
Article
Heat-shock protein (HSP)-based immunotherapy is believed to be a promising area of development for cancer treatment as such therapy is characterized by a unique approach to every tumour. It was shown that by inhibition of HSPs it is possible to induce apoptotic cell death in cancer cells. Interestingly, there are a great number of disordered regions in proteins associated with cancer, cardiovascular and neurodegenerative diseases, signalling, and diabetes. HSPs and some specific enzymes were shown to have these disordered regions in their primary structures. The experimental studies of HSPs confirmed that their intrinsically disordered (ID) regions are of functional importance. These ID regions play crucial roles in regulating the specificity of interactions between dimer complexes and their interacting partners. Because HSPs are overexpressed in cancer, predicting the locations of ID regions and binding sites in these proteins will be important for developing novel cancer therapeutics. In our previous studies, signal processing methods have been successfully used for protein structure-function analysis (i.e. for determining functionally important amino acids and the locations of protein active sites). In this paper, we present and discuss a novel approach for predicting the locations of ID regions in the selected cancer-related HSPs.
... The Resonant Recognition Model (RRM) model proposes that macromolecular selective interactions are based on electromagnetic resonant energy transfer between macromolecules in the range of infra-red, visible and ultra-violet light, and, thus, could mimic the specificity enabled by different frequencies (wavelengths) of sunlight [3,4]. By applying RRM, it is possible to identify and calculate relevant frequencies, critical for resonant activation of specific biological activities of proteins and DNA [5][6][7][8][9][10][11]. ...
... RRM is based on the findings that certain periodicities within the distribution of energy of delocalized electrons along a protein (DNA/RNA) molecule are critical for protein (DNA/RNA) biological function and/or interaction with their targets [3,4,12]. If charge transfer through these macromolecules is introduced, then the charge moving through the macromolecular backbone can produce electromagnetic radiation, absorption and resonance with spectral characteristics corresponding to the energy distribution [3][4][5][6][7][8]. ...
... where λ is the wavelength of light irradiation in nm, which can influence a particular biological process, frrm is a RRM numerical frequency, and K is coefficient of this linear correlation. We applied this concept to a number of proteins and DNA examples [3][4][5][6][7][8]. The concept has been also experimentally tested by predicting the electromagnetic frequencies for L-Lactate Dehydrogenase [8], whereby radiating L-Lactate Dehydrogenase with predicted calculated electromagnetic frequencies achieved a significant change in enzyme activity. ...
Article
Full-text available
The meaning and influence of light to biomolecular interactions, and consequently to health, has been analyzed using the Resonant Recognition Model (RRM). The RRM proposes that biological processes/interactions are based on electromagnetic resonances between interacting biomolecules at specific electromagnetic frequencies within the infra-red, visible and ultraviolet frequency ranges, where each interaction can be identified by the certain frequency critical for resonant activation of specific biological activities of proteins and DNA. We found that: (1) the various biological interactions could be grouped according to their resonant frequency into super families of these functions, enabling simpler analyses of these interactions and consequently analyses of influence of electromagnetic frequencies to health; (2) the RRM spectrum of all analyzed biological functions/interactions is the same as the spectrum of the sun light on the Earth, which is in accordance with fact that life is sustained by the sun light; (3) the water is transparent to RRM frequencies, enabling proteins and DNA to interact without loss of energy; (4) the spectrum of some artificial sources of light, as opposed to the sun light, do not cover the whole RRM spectrum, causing concerns for disturbance to some biological functions and consequently we speculate that it can influence health.
... The Resonant Recognition Model (RRM) model proposes that macromolecular selective interactions are based on electromagnetic resonant energy transfer between macromolecules in the range of infra-red, visible and ultra-violet light and thus could mimic specificity enabled by different frequencies (wavelengths) of the Sun light [5,6]. By applying the RRM, it is possible to identify and calculate relevant frequencies critical for resonant activation of specific biological activities of proteins and DNA [7][8][9][10][11][12][13]. ...
... The RRM is based on the findings that certain periodicities within the distribution of energy of delocalized electrons along a protein/DNA/RNA molecule are critical for protein/DNA/RNA biological function and/or interaction with their targets [5,6,14]. If charge transfer through these macromolecules is introduced, then charge moving through macromolecular backbone can produce electromagnetic radiation, absorption and resonance with spectral characteristics corresponding to the energy distribution [5][6][7][8][9][10]. ...
... We applied this concept on a number of proteins and DNA examples [5][6][7][8][9][10]. The concept has been also experimentally tested by predicting the electromagnetic frequencies for L-Lactate Dehydrogenase [10], where by radiating L-Lactate Dehydrogenase with predicted calculated electromagnetic frequencies the significant change in enzyme activity was achieved. ...
Conference Paper
Full-text available
Nikola Tesla's work was related to analysis and usage of electromagnetic resonances. Among many of his technical interests he was also interested in bioresonances. His particular interest was in the electromagnetic resonance of the Earth (Schumann Resonance) and the Sun light influence to living organisms. Here, we present some of our earlier work on how Schumann Resonance affects human brain activity, as well as how they are related to acupuncture meridian resonances. We also present here influence and importance of the Sun light and other environmental light to biological processes in living cells, in particular to activity of macromolecules like proteins, DNA and RNA. We have shown that these macromolecular activities/interactions are based on electromagnetic resonances between interacting macromolecules using our own Resonant Recognition Model (RRM).
... Whereas earlier this disease used to affect more on chemotherapy, uncontrolled sugar, people undergoing any kind of transplant and the elderly. This fungus reaches the rest of the body through the nose [30,31]. Usually this fungus is in the air and goes into the nose through the breath. ...
... From the nose and mouth to the attack, the black fungus reaches the eyes very quickly. If infected with this, re-transplant B of the eye is not possible [30]. ii. ...
... Numbness in hands and feet is common but face is rare. So if you feel like this too, then you need to get tested [30]. iii. ...
Article
As everyone knows that in today’s time Artificial Intelligence, Machine Learning and Deep Learning are being used extensively and generally researchers are thinking of using them everywhere. At the same time, we are also seeing that the second wave of corona has wreaked havoc in India. More than 4 lakh cases are coming in 24 h. In the meantime, news came that a new deadly fungus has come, which doctors have named Mucormycosis (Black fungus). This fungus also spread rapidly in many states, due to which states have declared this disease as an epidemic. It has become very important to find a cure for this life-threatening fungus by taking the help of our today’s devices and technology such as artificial intelligence, data learning. It was found that the CT-Scan has much more adequate information and delivers greater evaluation validity than the chest X-Ray. After that the steps of Image processing such as pre-processing, segmentation, all these were surveyed in which it was found that accuracy score for the deep features retrieved from the ResNet50 model and SVM classifier using the Linear kernel function was 94.7%, which was the highest of all the findings. Also studied about Deep Belief Network (DBN) that how easy it can be to diagnose a life-threatening infection like fungus. Then a survey explained how computer vision helped in the corona era, in the same way it would help in epidemics like Mucormycosis.
... Here, we have utilised our own Resonant Recognition Model (RRM), to distinguish between immune system activation and inflammation functions by analysing both IL-12 and IL-23 pathways. The RRM is based on the findings that certain periodicities within the distribution of energy of delocalized electrons along protein molecules are critical for their biological functions and/or interactions with their targets (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) . If charge transfer through protein macromolecules is introduced, then charge moving through macromolecular backbone can produce electromagnetic radiation, absorption and resonance with spectral characteristics corresponding to the energy distribution and charge velocity (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) . ...
... The RRM is based on the findings that certain periodicities within the distribution of energy of delocalized electrons along protein molecules are critical for their biological functions and/or interactions with their targets (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) . If charge transfer through protein macromolecules is introduced, then charge moving through macromolecular backbone can produce electromagnetic radiation, absorption and resonance with spectral characteristics corresponding to the energy distribution and charge velocity (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) . ...
... Here, we present and use our own nonconventional, biophysical, theoretical Resonant Recognition Model (RRM), which is based on the findings that certain periodicities within the distribution of energy of delocalized electrons along protein molecules are critical for protein biological functions and/or interactions with their targets (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) . The RRM model has been extensively published and experimentally successfully tested . ...
Article
Full-text available
The main organism defence against pathogens is immune system, but unfortunately its activity is always associated with unwanted inflammation. It would be beneficial, if it is possible to understand immune activation and inflammation, as well as to identify parameters that can distinguish between immune activation and inflammation. For that purpose, we have used our own nonconventional, biophysical, theoretical Resonant Recognition Model, which we applied to Interleukin-12 (IL-12) and Interleukin-23 (IL-23) pathways. We have identified the separate parameters for those two pathways, and we assigned them separately to immune activation and inflammation biological functions. These results could be used in diminishing effects of unwanted inflammation in number of health conditions.
... Here, we have analyzed ion channel proteins and neurotoxins proteins from UniProt database [5]. We have applied the Resonant Recognition Model (RRM) [6][7][8][9][10][11], which proposes that activation of proteins is based on electromagnetic radiation of the certain frequency characterizing the specific biological function of proteins. Thus, by using the RRM, we can calculate characteristic electromagnetic frequency of the pain related ion channel activation and consequently propose that the TERP patches conductive imprint can interfere with this frequency. ...
... The Resonant Recognition Model (RRM) is based on the findings that certain periodicities within the distribution of energy of delocalized electrons along protein/DNA molecules are critical for protein/DNA biological functions and/or interactions with their targets [6][7][8]. If charge transfer through these macromolecules is introduced, then charge moving through macromolecular backbone can produce electromagnetic radiation, absorption and resonance with spectral characteristics corresponding to the energy distribution and charge velocity [6][7][8][9][10][11]. The RRM enables the calculation of these spectral characteristics, by assigning each amino acid a physical parameter representing the energy of delocalized electrons of each amino acid. ...
... This correlation can be represented as following: λ = K / frrm where λ is the wavelength of light irradiation in nm, which can influence specific biological process, frrm is a RRM numerical frequency and K is coefficient of this linear correlation. We applied this concept on number of proteins and DNA examples [6][7][8][9][10][11][12]. The concept has been also experimentally tested by predicting the electromagnetic frequencies for L-Lactate Dehydrogenase [13], where by radiating L-Lactate Dehydrogenase with predicted calculated electromagnetic frequencies the significant change in enzyme activity was achieved. ...
Article
Tuning Element Relief Patches (TERP) are silicon based Titanium Salt infused adhesive patches that have been developed by Tuning Element. A number of anecdotal reports have shown that TERP patches diffuse pain, including chronic, inflammatory and neuropathic. Pain is a very complex biochemical and electrical process involving sensory part, nerve transmission and brain perception of pain. We concentrated our research on nerve transmission, which is electrical signal along the nerve (axon). This electrical signal is created by complex activity of opening and closing of pain related ion channels and redistribution of electrically charged ions on the nerve cell membrane. Ion channels are made of different proteins, which are involved with the complex processes of opening and closing ion channels. Here, we apply Resonant Recognition Model (RRM) to analyze ion channel proteins related to the pain transmission in order to find out, how imprints and particles within TERP patches can interfere with pain related activity of ion channels.
... Based on this finding, we have developed Resonant Recognition Model (RRM) [3,4], which is able to calculate these frequencies from periodicities within the distribution of energy of delocalised electrons along protein, DNA and/or RNA molecules using charge velocity through these macromolecules. We have applied this concept on number of proteins, DNA and/or RNA examples [1,[3][4][5], as well as on some medical conditions like: Crigler-Najjar syndrome [6], pain [7] and influence of environmental light to health [8]. This concept has been also experimentally tested by predicting the electromagnetic frequencies for activation of l-lactate dehydrogenase [9] and has been tested independently on experimental measurements of photon emission from dying melanoma cells [10], on photon emission from lethal and non-lethal Ebola strains [11], as well as on differentiation of osteoblasts stem cells [12]. ...
... The comprehensive analysis done so far confirms that all protein sequences with the common biological function have common frequency component, which is specific feature for the observed function/interaction [1,[3][4][5][6][7][8][23][24][25] . In order to understand the meaning of the characteristic frequency, it is important to clarify what is meant by the biological function of proteins. ...
... Thus, these frequencies must represent oscillations of some physical field which can transmit through water dipoles. One of the possibilities is that this field is electromagnetic in nature [1,[3][4][5]. Phase circles at RRM frequency of 0.2764 for human leptin protein (+0.96 rad) in blue and human leptin receptor protein (−2.10 rad) in red. It can be easily observed that these phases are opposite to each other, supporting the RRM approach that protein and protein receptors should have opposite phases at RRM frequency characterising their recognition and interaction. ...
Chapter
This chapter represents review of our work on Resonant Recognition Model (RRM), which proposes that certain resonant rhythms are critical for protein and DNA/RNA macromolecular biological functions. These macromolecules express their biological function through selective interactions with their target molecules. We have discovered, within the RRM model, that these selective interactions are based on resonant electromagnetic energy transfer between interacting molecules. The RRM enables frequencies (wavelengths) of this energy transfer to be identified, which then can be applied for design of de novo bioactive peptides with desired biological function or to influence biological functions with either electromagnetic radiation of specific frequency (wavelength) or with conductive elements like titanium salt or nanophotonic particles. All these RRM applications can be used in pharmacology, drug design, treatment of diseases, agriculture or even in electronics. The RRM approach is completely changing the paradigm of understanding the specificity of macromolecular activity and interactions, and as such is opening completely new future horizons for science.
... Whereas earlier this disease used to affect more on chemotherapy, uncontrolled sugar, people undergoing any kind of transplant and the elderly. This fungus reaches the rest of the body through the nose [30,31]. Usually this fungus is in the air and goes into the nose through the breath. ...
... From the nose and mouth to the attack, the black fungus reaches the eyes very quickly. If infected with this, re-transplant B of the eye is not possible [30]. ii. ...
... Numbness in hands and feet is common but face is rare. So if you feel like this too, then you need to get tested [30]. iii. ...
Article
Full-text available
As everyone knows that in today’s time Artificial Intelligence, Machine Learning and Deep Learning are being used extensively and generally researchers are thinking of using them everywhere. At the same time, we are also seeing that the second wave of corona has wreaked havoc in India. More than 4 lakh cases are coming in 24 h. In the meantime, news came that a new deadly fungus has come, which doctors have named Mucormycosis (Black fungus). This fungus also spread rapidly in many states, due to which states have declared this disease as an epidemic. It has become very important to find a cure for this life-threatening fungus by taking the help of our today’s devices and technology such as artificial intelligence, data learning. It was found that the CT-Scan has much more adequate information and delivers greater evaluation validity than the chest X-Ray. After that the steps of Image processing such as pre-processing, segmentation, all these were surveyed in which it was found that accuracy score for the deep features retrieved from the ResNet50 model and SVM classifier using the Linear kernel function was 94.7%, which was the highest of all the findings. Also studied about Deep Belief Network (DBN) that how easy it can be to diagnose a life-threatening infection like fungus. Then a survey explained how computer vision helped in the corona era, in the same way it would help in epidemics like Mucormycosis.
... In the case of protein-protein receptor interactions, it has been found that phases at the characteristic interaction frequency should be opposite, i.e., should be close to π (3.14 rad) [1][2][3][4][5][6][7]. If charge transfer through these macromolecules is introduced, then charge moving through the macromolecular backbone can produce electromagnetic radiation, absorption, and resonance, with spectral characteristics corresponding to the energy distribution and charge velocity [1][2][3][13][14][15][16]. These wavelengths are found to correspond to electromagnetic radiation wavelengths in the range of far infra-red, infra-red, visible, and ultra-violet spectrum. ...
... The RRM concept has been already extensively published [1][2][3][4][5][6][7][13][14][15][16]21] and is presented in detail within the Supplementary Material. ...
Article
Full-text available
Featured Application: The results of this research can be used in combating obesity and overweight, which are becoming increasing health problems in modern society. Abstract: Obesity is a medical condition in which excess body fat may have a negative effect on health and lifestyle, and it is becoming an increasing problem within modern society. Leptin is the key protein that regulates body energy balance by inhibiting hunger, and it could potentially be used in treatment of obesity and overweight. Here, we applied our own Resonant Recognition Model, which is capable of analyzing the selectivity of any protein-receptor interaction on an example of leptin-leptin receptor. We have identified a specific characteristic parameter for leptin activity through the leptin receptor, and this parameter could be used in development of new treatments for obesity.
... We have empirical evidence for this possibility [9]. Irena Cosic [10], the originator of the Resonant Recognition Model for molecular interactions , transformed each of the different amino acids within the tubulin molecule into pseudopotentials. Fast Fourier Transforms of the spectral power densities for the spatial periodicities were then converted to equivalent wavelengths. ...
... The movement of electrons produces an electromagnetic field with very specific characteristics that are primarily within the infrared and ultraviolet range. Cosic, Lazar and Cosic [10] showed that tubulin exhibits very specific resonant frequencies with peaks within the 2.05 to 2.14 μm (infrared), 440 to 470 nm (ultraviolet interface with the visible wavelength boundary) and 600 -615 nm. The PMT that we employed is maximally sensitive around the 450 nm range. ...
... RRM is a revolutionary new approach proposing that macromolecular activity is based on electromagnetic resonances [12][13][14][15][16]. In our previous work we have used the RRM to predict resonances in tubulin and microtubules and shown that these resonances are in the frequency ranges from THz to KHz [17], which has been experimentally confirmed by a recently published paper [11]. Here, we are applying the RRM to predict possible electromagnetic resonances in other proteins (telomerase), DNA (telomere) and RNA (TERT mRNA). ...
... Therefore, the estimated range for both amino acid and nucleotide macromolecules includes infra-red, visible and ultra-violet light. These computational predictions were found to be related to biological function of the macromolecules by comparison with a number of experimental measurements [12][13][14][15][16][17][18][19]. ...
Article
Full-text available
Background: It has been shown that there are electromagnetic resonances in biological molecules (proteins, DNA and RNA) in the wide range of frequencies including THz, GHz, MHz and KHz. These resonances could be important for biological function of macromolecules, as well as could be used in development of devices like molecular computers. As experimental measurements of macromolecular resonances are timely and costly there is a need for computational methods that can reliably predict these resonances. We have previously used the Resonant Recognition Model (RRM) to predict electromagnetic resonances in tubulin and microtubules. Consequently, these predictions were confirmed experimentally. Methods: The RRM is developed by authors and is based on findings that protein, DNA and RNA electromagnetic resonances are related to the free electron energy distribution along the macromolecule. Results: Here, we applied the Resonant Recognition Model (RRM) to predict possible electromagnetic resonances in telomerase as an example of protein, telomere as an example of DNA and TERT mRNA as an example of RNA macromolecules. Conclusion: We propose that RRM is a powerful model that can computationally predict protein, DNA and RNA electromagnetic resonances.
... RRM is a revolutionary new approach proposing that macromolecular activity is based on electromagnetic resonances [12][13][14][15][16]. In our previous work we have used the RRM to predict resonances in tubulin and microtubules and shown that these resonances are in the frequency ranges from THz to KHz [17], which has been experimentally confirmed by a recently published paper [11]. Here, we are applying the RRM to predict possible electromagnetic resonances in other proteins (telomerase), DNA (telomere) and RNA (TERT mRNA). ...
... Therefore, the estimated range for both amino acid and nucleotide macromolecules includes infra-red, visible and ultra-violet light. These computational predictions were found to be related to biological function of the macromolecules by comparison with a number of experimental measurements [12][13][14][15][16][17][18][19]. ...
... To discern the spatial spectral power density of the amino acid sequence of each of these components of the pathway, each amino acid for each molecule was assigned the psuedopotential value as described by Cosic [1,5]. The pseudo potential is the estimated electron-ion interaction potential (EIIP) that describes the average energy states of all valence electrons for each amino acid. ...
... According to Cosic [1,5], each specific biological function within a protein (or DNA) is characterized by one frequency that in turn predicts a peak wavelength for photon emissions. From an aggregate or field perspective specific biological functions of a "serial" pathway might be described by a specific spectral profile or pattern of peak frequencies. ...
Article
Full-text available
The duality of matter-energy as particle-waves was applied to the classic ERK-MAP signaling pathways between the plasma cell membrane and the nucleus and was tested with Cosic’s Resonance Recognition Method. Spectral analyses of sequences of pseudopotentials that reflect de-localized electrons of amino acids for the 11 proteins in the pathway were computed. The spectral power density of the terminal protein (cFOS) was shown to be the average of the profiles of the precursor proteins. The results demonstrated that in addition to minute successive alterations in molecular structure wave-functions and resonant patterns can also describe complex molecular signaling pathways in cells. Different pathways may be defined by a single resonance profile. The separations between the peaks of wavelengths from Cosic’s predictions for photon emissions in the visible spectrum that define the ERK-MAP pathway were within the range of 10-20 J. This quantity has been shown to be a fundamental unit of energy within the universe. The involvement of photon patterns indicates that non-local effects could accompany the serial causality (locality) assumed to connect molecular pathways.
... We have empirical evidence for this possibility [9]. Irena Cosic [10], the originator of the Resonant Recognition Model for molecular interactions, transformed each of the different amino acids within the tubulin molecule into pseudopotentials. Fast Fourier Transforms of the spectral power densities for the spatial periodicities were then converted to equivalent wavelengths. ...
... The movement of electrons produces an electromagnetic field with very specific characteristics that are primarily within the infrared and ultraviolet range. Cosic, Lazar and Cosic [10] showed that tubulin exhibits very specific resonant frequencies with peaks within the 2.05 to 2.14 μm (infrared), 440 to 470 nm (ultraviolet interface with the visible wavelength boundary) and 600 -615 nm. The PMT that we employed is maximally sensitive around the 450 nm range. ...
Article
Full-text available
The specific diameter of microtubules was shown to be a primary solution when magnetic energy was set equal to Casimir energy. To discern if this spatial containment could be foci for information photon emissions were measured from preparations of microtubules (MTs) while they were exposed in sequential 4 min intervals to various patterns of weak magnetic fields whose intensities ranged from 3 to 10 μT. Calculations from the median mass of a tubulin dimer, its summed charges and the applied magnetic field as well as the change in magnetic moment derived from the energy of the hydrogen line when applied to our experimental fields predicted a dynamic shift (Δf) between 0.03 and 0.21 Hz. Spectral power densities (SPD) indicated marked enhancements in photon numbers during periods of magnetic field exposures within the 7.6 to 7.8 Hz increment. The total SPD units for the shift were 10-18 to 10-17 J per s. Five of the eight patterns elicited a split spectrum of power within this range. Separate factor analyses of the SPDs of the serial values that composed the points of the actual field patterns indicated those that evoked the split-spectrum (Δf = 0.05 to 0.13 Hz) displayed significantly higher loadings on the same factor compared to those that did not. If this shift in photon energy reflects a phase modulation of the coherence frequency (8 MHz) of MTs, the increment of energy per MHz frequency would be within the energy of the neutral hydrogen line. These results suggest that the intrinsic structure or information from specific intensity magnetic fields when applied to MTs is reflected in photon energy densities vacillating around the fundamental Schumann Resonance that could be an interface between Casimir and magnetic sources.
... We have empirical evidence for this possibility [9]. Irena Cosic [10], the originator of the Resonant Recognition Model for molecular interactions, transformed each of the different amino acids within the tubulin molecule into pseudopotentials. Fast Fourier Transforms of the spectral power densities for the spatial periodicities were then converted to equivalent wavelengths. ...
... The movement of electrons produces an electromagnetic field with very specific characteristics that are primarily within the infrared and ultraviolet range. Cosic, Lazar and Cosic [10] showed that tubulin exhibits very specific resonant frequencies with peaks within the 2.05 to 2.14 μm (infrared), 440 to 470 nm (ultraviolet interface with the visible wavelength boundary) and 600 -615 nm. The PMT that we employed is maximally sensitive around the 450 nm range. ...
... Thus, with the same periodicities within proteins sequences, as determined by the RRM, different modalities of charge transfer can produce different resonant frequencies, which are not necessarily related to their protein biological function, but could be related to the protein and DNA/RNA resonances, in general. Such approach has been tested with tubulin and microtubule [27] and results have been experimentally proved [18]. In addition we have applied this approach to telomerase as example of proteins, telomere as example of DNA sequences, as well as TERT mRNA as an example of RNA macromolecules [28]. ...
... The roles played by these proteins are very diverse, however our results are showing that there is common characteristic frequency for all these proteins analyzed and thus we propose that the frequency of f = 0.002 is a key role player for Plasmodium vitality. In addition, we also narrow down to charge velocity, as proposed by Cosic's scenario, which has been shown in the past to be relevant for biological function of the proteins [27,28]. Thus, we propose here that the most probable frequency to be used to interfere parasite activity is frequency of 2-5THz. ...
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The absence of clear breakthrough in malaria combat could support the need for different ways of tackling the disease that are substantiated by conceptually new bases. The main idea of this research is to analyze possibility to interfere with malaria parasite activity using specific resonant electromagnetic frequencies. Although the idea to combat malaria infection with electromagnetic frequencies is not new, we will here present unique approach, so called Resonant Recognition Model (RRM) to specifically identify electromagnetic frequencies mostly important for interference with malaria infection. The RRM is calculating periodicities (frequencies) in distribution of free electron energies along protein sequence which are relevant for protein function/interaction. When charge transfer through protein backbone is considered then it can produce electromagnetic radiation of specific frequency depending on charge velocity. Ten groups of proteins relevant for Plasmodium interactions were analyzed. Each of ten groups of proteins have at least one significant characteristic frequency peak at one of the following RRM frequencies: f = 0.002, f = 0.11 or f = 0.34. This suggests that the diversity of proteins participating in Plasmodium invasion could be represented with only three RRM frequencies. Depending on the charge transfer mechanism (velocity) along the protein, different electromagnetic resonant frequencies are expected. Based on presented results, we suggest that the RRM frequency of f = 0.002 (related to 2-5THz), to be regarded as crucial for Plasmodium infectivity and possibly for interfering with invasion process. Although this far infrared electromagnetic frequency cannot penetrate human body more than down to 4 cm, such radiation can be of great help in combating Plasmodium, since a sizeable part of parasite remain in the skin for hours after the mosquito bite. In addition the specific RRM frequency is capable to resonantly initiate a whole cascade of protein-protein (DNA, RNA) interactions directed to the specific biological activity which could contra-act Plasmodium infection.
... Williams et al., 2005). Augmenting endogenous signal transduction by various wavelengths of IR/red/blue light (Cosic et al., 2014; Hanczyc et al., 2013; Karbowski et al., 2015; Rativa et al., 2010; Samoc et al., 2006). 2. Application of LLLT to heal tendon and muscle tears in injuries (including sports injuries) by optimizing dose and wavelength. ...
... The theory confirms the dipole characteristics of the tubulin states that mediate computation and entanglement as electric or magnetic, the latter being more prominent as demonstrated by Bandyopadhyay Coherence at alternating currents of gigahertz, megahertz and kilohertz frequencies at room temperature (Sahu et al 2013). Entanglement and interference patterns within the microtubules support the formation of holographic images, which forms the basis of consciousness (Hameroff 2014;Pitkanen 2014;Cosic et al 2015;Mitchel and Staretz 2011). ...
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Everything around seems phenomenal and appears driven by a conscious experience. Everything is an experience and for the experiencer appears eternally phenomenal and subjective. The conscious 'How' can be easily explained by the many reductive based advances in science and other disciplines, but the conscious 'Why' persists as phenomenal. The 'How' however can be reduced only to a precise limit i.e. the limits of scientific exploration, beyond which it persists to be phenomenal. This paper is an inter-disciplinary understanding of how science and phenomenology can complement each other to help decipher and conform to the hypothetical approach, that everything around is phenomenal.
... The dipole characteristics within these structures mediate the computation and entanglement as electric or magnetic at alternating currents of gigahertz, megahertz and kilohertz frequencies at room temperature (Sahu et al., 2013a;Sahu et al., 2013b) which could answer the decoherence problem of the ORCH-OR theory (Hagan et al 2001;Hameroff and Penrose, 2014b). The Resonant Recognition Model (RRM) has also demonstrated higher frequencies in gigahertz to terahertz ranges within the microtubules suggesting that these higher frequencies are related to transmission velocities for solitons and excitons and are therefore purely electromagnetic in nature similar to a quantum information communication system (Cosic et al., 2015). ...
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Origin of life on earth transpired once and from then on, it emerges as an endless eternal process. Matter and energy are constants of the cosmos and the hypothesis is that the origin of life is a moment when these constants intertwined or interacted. Energy from the cosmos interacted with inorganic matter to support matter with retention of this riveted energy, as energy to be circulated within the primitive channelized structures to conserve energy by the materialization of the proton homeostasis mechanisms developed from the obtainable inorganic matter. The driver for these processes as we now confirm, exists in the quantum world and through quantum phenomenal processes could have combined these constants to create the magic of life. Primitive earth was a chemical reactive system that triggered a macromolecular evolution by means of open thermodynamic systems, driven by cyclic gradients of temperature, electromagnetic radiation and chemical potentials which sustained life and proto-consciousness in the first life forms driven by the quantum processes. The origin of life is always an intriguing topic but the purpose for finding the cause should never be inclined towards obliterating it; for if that is the case, the further we seek, the farther it will go.
... Cosic et al. [103,104] H-bond strength in MTs has been recently computationally estimated [105] as ranging from 11.9 k/mol for the weakest bond to 42.2 kJ/mol for the strongest one and a total of 462 kJ/mol for the α-tubulin/α-tubulin interactions and 472 kJ/mol for the α-tubulin/β-tubulin interactions, which based on the Planck relationship between frequency and energy translates into a range of frequency values between 0.3 × 10 14 Hz and 1.3 × 10 15 Hz. Again, these frequencies are much too high to be affected by TTFields. ...
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Long-standing research on electric and electromagnetic field interactions with biological cells and their subcellular structures has mainly focused on the low-and high-frequency regimes. Biological effects at intermediate frequencies between 100 and 300 kHz have been recently discovered and applied to cancer cells as a therapeutic modality called Tumor Treating Fields (TTFields). TTFields are clinically applied to disrupt cell division, primarily for the treatment of glioblastoma multiforme (GBM). In this review, we provide an assessment of possible physical interactions between 100 kHz range alternating electric fields and biological cells in general and their nano-scale subcellular structures in particular. This is intended to mechanistically elucidate the observed strong disruptive effects in cancer cells. Computational models of isolated cells subject to TTFields predict that for intermediate frequencies the intracellular electric field strength significantly increases and that peak dielectrophoretic forces develop in dividing cells. These findings are in agreement with in vitro observations of TTFields’ disruptive effects on cellular function. We conclude that the most likely candidates to provide a quantitative explanation of these effects are ionic condensation waves around microtubules as well as dielectrophoretic effects on the dipole moments of microtubules. A less likely possibility is the involvement of actin filaments or ion channels.
... Each heterodimer is an electric dipole with 18 Ca ions located in the dimer center and a negative charge in the α tubulin before hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and in the β tubulin after hydrolysis-Satarić et al., Tuszyński et al. [22,23]. After irradiation by external electromagnetic field and consequent measurement, Sahu et al. disclosed electromagnetic activity and resonance spectra in a wide frequency range from radio frequencies up to the UV band [24][25][26]; further frequencies have been predicted by Cosic et al. [27]. The excitation of the microtubule inner circular cavity is possible in the UV region. ...
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The general mechanism of controlling, information and organization in biological systems is based on the internal coherent electromagnetic field. The electromagnetic field is supposed to be generated by microtubules composed of identical tubulin heterodimers with periodic organization and containing electric dipoles. We used a classical dipole theory of generation of the electromagnetic field to analyze the space–time coherence. The structure of microtubules with the helical and axial periodicity enables the interaction of the field in time shifted by one or more periods of oscillation and generation of coherent signals. Inner cavity excitation should provide equal energy distribution in a microtubule. The supplied energy coherently excites oscillators with a high electrical quality, microtubule inner cavity, and electrons at molecular orbitals and in ‘semiconduction’ and ‘conduction’ bands. The suggested mechanism is supposed to be a general phenomenon for a large group of helical systems.
... The introduction of the issue of protein conductivity in RRM development, led to the consideration that a charge moving through the protein backbone would generate an electromagnetic irradiation or absorption with spectral signatures corresponding to energy distribution along the protein [19,20]. These theoretically calculated spectra were confirmed experimentally [11,21]. Moreover, RRM allows designing of new peptides with desired spectral characteristics, and biological activities [22]. ...
... The protein 67 interactions can be considered a transfer of resonant energy 68 between interacting molecules through an oscillating physical field 69 that could be expressed within the domain of classic photons. 70 While investigating a persistent anomaly that some complex 71 molecular structures with quite different geometries displayed 72 similar functional characteristics Cosic [3,4] This traditional approach attempts to simulate structural similari-281 ties at the interface of molecular interactions rather than the simi-282 larities of the system's resonance. 283 Perhaps the most significant result of these analyses is the sug-284 gestion of three peaks (two major) of SPDs that could define or at the differences between the first two was 1 Â 10 À20 J and between 292 the second and third wavelength was 1.6 Â 10 À20 J. ...
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Cosic discovered that spectral analyses of a protein sequence after each constituent amino acid had been transformed into an appropriate pseudopotential predicted a resonant energy between interacting molecules. Several experimental studies have verified the predicted peak wavelength of photons within the visible or near-visible light band for specific molecules. Here, this concept has been applied to a classic signaling pathway, JAK-STAT, traditionally composed of nine sequential protein interactions. The weighted linear average of the spectral power density (SPD) profiles of each of the eight “precursor” proteins displayed remarkable congruence with the SPD profile of the terminal molecule (CASP-9) in the pathway. These results suggest that classic and complex signaling pathways in cells can also be expressed as combinations of resonance energies.
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PKMζ is a brain-specific protein kinase that has been suggested as playing a key role in memory consolidation mechanisms. It is identical to catalytic portion of another protein kinase, PKCζ. Lacking the regulatory end, PKMζ is several times more active than PKCζ. However, knowledge about PKMζ mechanisms in memory consolidation is patchy, and sometimes contradictory. The resonant recognition model (RRM) might shed some light in understanding PKMζ role on memory consolidation. This is the first attempt in literature to apply the RRM to the study of PKMζ and PKCζ. We obtained that PKMζ presents a spectral peak at the resonant recognition frequency of fRRM= 0.063 (likely, corresponding to the infrared frequency of 3190 nm) and another peak at fRRM =0.211(950 nm in the near infrared). Peak at fRRM= 0.063 is also shared by PKCζ, and the peak at fRRM =0.211 is similar to the one recently reported in literature for regulatory proteins. We hypothesize that irradiating with a weak light infrared source at these frequencies would modify long term potentiation results. Finally, a scheme for resonant interactions in PKMζ and PKCζ is proposed. Palabras claves: long term potentiation, protein kinases, resonant recognition model, bioinformatics. RESUMEN PKMζ es una proteína quinasa específica del cerebro que se ha sugerido que desempeña un papel clave en los mecanismos de consolidación de la memoria. Es idéntica a la porción catalítica de otra proteína quinasa, PKCζ. Al carecer de la porción regulatoria, PKMζ es varias veces más activa que PKCζ. Sin embargo, el conocimiento sobre los mecanismos de PKMζ in en la consolidación de la memoria es parcial, y a veces contradictorio. El modelo de reconocimiento resonante (RRM) podría esclarecer la comprensión del papel de PKMζ en la consolidación de la memoria. Este es el primer intento en la literatura para aplicar el MRR al estudio de Revista Cubana de Informática Médica 2017:9(2)121-134 http://scielo.sld.cu 122 PKMζ y PKCζ. Se obtuvo que PKMζ presenta un pico espectral a la frecuencia de reconocimiento resonante fRRM = 0,063 (probablemente, correspondiente a la frecuencia infrarroja de 3190 nm) y otro pico a fRRM = 0,211 (950 nm en el infrarrojo cercano). Pico en fRRM = 0,063 es también compartida por PKCζ, y el pico a fRRM = 0,211 es similar a la recientemente informado en la literatura para las proteínas reguladoras. Se plantea la hipótesis de que la irradiación con una fuente de luz infrarroja débil a estas frecuencias podría modificar los resultados de potenciación a largo plazo. Finalmente, se propone un esquema para interacciones resonantes en PKMζ y PKC.
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imprinted in Tuning Element 5Minute Relief PatchesTM(5MRP) as an adjunct support in postsurgical pain management. 10 postsurgical patient were treated with 5MRP as an adjunct to standard postoperative opioid medication and 10 were treated only with standard postoperative opioid medication. Our study concluded that ELEMF in 5MRP increase pain tolerance threshold in postsurgical pain management thus requiring significant reduction in usage of opioid medication.
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Tubulin is a promising target for designing anti-cancer drugs. Identification of hotspots in multifunctional Tubulin protein provides insights for new drug discovery. Although machine learning techniques have shown significant results in prediction, they fail to identify the hotspots corresponding to a particular biological function. This paper presents a signal processing technique combining resonant recognition model (RRM) and Stockwell Transform (ST) for the identification of hotspots corresponding to a particular functionality. The characteristic frequency (CF) representing a specific biological function is determined using the RRM. Then the spectrum of the protein sequence is computed using ST. The CF is filtered from the ST spectrum using a time-frequency mask. The energy peaks in the filtered sequence represent the hotspots. The hotspots predicted by the proposed method are compared with the experimentally detected binding residues of Tubulin stabilizing drug Taxol and destabilizing drug Colchicine present in the Tubulin protein. Out of the 53 experimentally identified hotspots, 60% are predicted by the proposed method whereas around 20% are predicted by existing machine learning based methods. Additionally, the proposed method predicts some new hot spots, which may be investigated.
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Rhythmic oscillatory patterns sustain cellular dynamics, driving the concerted action of regulatory molecules, microtubules, and molecular motors. We describe cellular microtubules as oscillators capable of synchronization and swarming, generating mechanical and electric patterns that impact biomolecular recognition. We consider the biological relevance of seeing the inside of cells populated by a network of molecules that behave as bioelectronic circuits and chromophores. We discuss the novel perspectives disclosed by mechanobiology, bioelectromagnetism, and photobiomodulation, both in term of fundamental basic science and in light of the biomedical implication of using physical energies to govern (stem) cell fate. We focus on the feasibility of exploiting atomic force microscopy and hyperspectral imaging to detect signatures of nanomotions and electromagnetic radiation (light), respectively, generated by the stem cells across the specification of their multilineage repertoire. The chance is reported of using these signatures and the diffusive features of physical waves to direct specifically the differentiation program of stem cells in situ, where they already are resident in all the tissues of the human body. We discuss how this strategy may pave the way to a regenerative and precision medicine without the needs for (stem) cell or tissue transplantation. We describe a novel paradigm based upon boosting our inherent ability for self-healing.
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Abstract: The cystic fibrosis is genetic disease characterised by build-up of thick mucus in the lungs, which causes difficulties in breathing. It is caused by mutations in CFTR protein. Here, we utilised the Resonant Recognition Model (RRM), which proposes that proteins specific activity is characterised by specific frequencies (wavelengths) of electromagnetic radiation. Using the RRM approach, we have identified the electromagnetic frequency (wavelength) characterising the healthy CFTR proteins, while the amplitude at this frequency is diminishing in mutated CFTR proteins. Thus, the identified characteristic frequency (wavelength) for heathy CFTR proteins could be proposed to be critical for healthy functioning of CFTR proteins and for differentiating between healthy and malfunctioning CFTR proteins related to cystic fibrosis. In addition, using the RRM approach we achieved the possible explanation on how specific temperature of 27-28°C can restore the healthy function in mutated CFTR proteins.
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There is evidence that biological processes can be induced or modulated by induction of light of particular characteristic frequencies. The frequency selective effects of light on biological processes involving protein activation involves energies of the same order and nature as electromagnetic irradiation of light. These phenomena are analysed here in terms of the Resonant Recognition Model (RRM) which proposes that protein activities (interactions) are based on resonant electromagnetic energy transfer within a range of infra-red and visible light. All proteins can be considered as linear sequences of their constitutive elements (amino acids). The RRM model interprets this linear information using signal analysis methods including spectral and space-frequency analysis. It has been found that the spectrum of the distribution of the energies of free electrons along the proteins is critical for protein's function (interaction). As there is evidence that certain charge could travel along the proteins then charge moving through the protein backbone and passing different energy stages caused by different amino acid side groups can produce sufficient conditions for the specific electromagnetic radiation or absorption. These results lead to the conclusion that specificity of protein interactions are based on the resonant electromagnetic energy transfer between interacting molecules with a specific frequency for each observed function/interaction.
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We demonstrate that a single brain-neuron-extracted microtubule is a memory-switching element, whose hysteresis loss is nearly zero. Our study shows how a memory-state forms in the nanowire and how its protein arrangement symmetry is related to the conducting-state written in the device, thus, enabling it to store and process ∼500 distinct bits, with 2 pA resolution between 1 nA and 1 pA. Its random access memory is an analogue of flash memory switch used in a computer chip. Using scanning tunneling microscope imaging, we demonstrate how single proteins behave inside the nanowire when this 3.5 billion years old nanowire processes memory-bits.
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The nature of consciousness, the mechanism by which it occurs in the brain, and its ultimate place in the universe are unknown. We proposed in the mid 1990's that consciousness depends on biologically 'orchestrated' coherent quantum processes in collections of microtubules within brain neurons, that these quantum processes correlate with, and regulate, neuronal synaptic and membrane activity, and that the continuous Schrödinger evolution of each such process terminates in accordance with the specific Diósi-Penrose (DP) scheme of 'objective reduction' ('OR') of the quantum state. This orchestrated OR activity ('Orch OR') is taken to result in moments of conscious awareness and/or choice. The DP form of OR is related to the fundamentals of quantum mechanics and space-time geometry, so Orch OR suggests that there is a connection between the brain's biomolecular processes and the basic structure of the universe. Here we review Orch OR in light of criticisms and developments in quantum biology, neuroscience, physics and cosmology. We also introduce a novel suggestion of 'beat frequencies' of faster microtubule vibrations as a possible source of the observed electro-encephalographic ('EEG') correlates of consciousness. We conclude that consciousness plays an intrinsic role in the universe.
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With a large number of DNA and protein sequences already known, the crucial question is to find out how the biological function of these macromolecules is "written" in the sequence of nucleotides or amino acids. Biological processes in any living organism are based on selective interactions between particular bio-molecules, mostly proteins. The rules governing the coding of a protein's biological function, i.e. its ability to selectively interact with other molecules, are still not elucidated. In addition, with the rapid accumulation of databases of protein primary structures, there is an urgent need for theoretical approaches that are capable of analysing protein structure-function relationships. The Resonant Recognition Model (RRM) 12 is one attempt to identify the selectivity of protein interactions within the amino acid sequence. The RRM 12 is a physico-mathematical approach that interprets protein sequence linear information using digital signal processing methods. In the RRM the protein primary structure is represented as a numerical series by assigning to each amino acid in the sequence a physical parameter value relevant to the protein's biological activity. The RRM concept is based on the finding that there is a significant correlation between spectra of the numerical presentation of amino acids and their biological activity. Once the characteristic frequency for a particular protein function/interaction is identified, it is possible then to utilize the RRM approach to predict the amino acids in the protein sequence, which predominantly contribute to this frequency and thus, to the observed function, as well as to design de novo peptides having the desired periodicities. As was shown in our previous studies of fibroblast growth factor (FGF) peptidic antagonists 23 and human immunodeficiency virus (HIV) envelope agonists 24, such de novo designed peptides express desired biological function. This study utilises the RRM computational approach to the analysis of oncogene and proto-oncogene proteins. The results obtained have shown that the RRM is capable of identifying the differences between the oncogenic and proto-oncogenic proteins with the possibility of identifying the "cancer-causing" features within their protein primary structure. In addition, the rational design of bioactive peptide analogues displaying oncogenic or proto-oncogenic-like activity is presented here.
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The book advances the premise that the cytoskeleton is the cell's nervous system, the biological controller/computer. If indeed cytoskeletal dynamics in the nanoscale (billionth meter, billionth second) are the texture of intracellular information processing, emerging ''NanoTechnologies'' (scanning tunneling microscopy, Feynman machines, von Neumann replicators, etc.) should enable direct monitoring, decoding and interfacing between biological and technological information devices. This in turn could result in important biomedical applications and perhaps a merger of mind and machine: Ultimate Computing.
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This paper considers the possibility of stochastic resonance (SR) in tubulin dimers. A formula for the signal-to-noise ratio (SNR) of tubulin as a function of temperature is derived. The effective potential experienced by a delocalized electron in such a dimer is postulated to be a symmetric bimodal well. Inter-well and intra-well motions are described by Kramers rate theory and the Langevin formalism respectively. The frequency-dependent expression for the SNR shows that the response of the electron-tubulin dimer system is enhanced by ambient dipolar oscillations in specific frequency regimes. This is a characteristic of SR. Biophysical implications of this property such as the relevance to 8.085 MHz microtubule resonance and the clocking mechanism are detailed.
Article
In their article, Is the Brain a Quantum Computer,? Litt, Eliasmith, Kroon, Weinstein, and Thagard (2006) criticize the Penrose-Hameroff "Orch OR" quantum computational model of consciousness, arguing instead for neurocomputation as an explanation for mental phenomena. Here I clarify and defend Orch OR, show how Orch OR and neurocomputation are compatible, and question whether neurocomputation alone can physiologically account for coherent gamma synchrony EEG, a candidate for the neural correlate of consciousness. Orch OR is based on quantum computation in microtubules within dendrites in cortex and other regions linked by dendritic-dendritic gap junctions ("dendritic webs") acting as laterally connected input layers of the brain's neurocomputational architecture. Within dendritic webs, consciousness is proposed to occur as gamma EEG-synchronized sequences of discrete quantum computational events acting in integration phases of neurocomputational "integrate-and-fire" cycles. Orch OR is a viable approach toward understanding how the brain produces consciousness.
Article
This chapter discusses some problems of modern bioenergetics at the molecular level, and focuses on the important role of nonlinear processes. The process of the vibrational energy and electron transfer along protein molecules is studied on the basis of nonlinear equations. A new model of the molecular mechanism of muscular contraction in animals is presented, in the chapter, using the concept of solitons. The possible role of solitons in other biological processes is also investigated in the chapter. The most active part in cell bioenergetics is played by protein molecules. They are closely connected with the basic manifestations of life. All chemical processes in the cell take place with the participation of proteins–enzymes. Proteins transform chemical energy into mechanical energy and are responsible for cellular and intracellular movement. The chapter reveals that the presence of the energy gap in the spectrum of excited states of the chain between exciton and soliton states proves to be one of the reasons for the high stability of a soliton. To destroy a soliton, that is, to split it into a free exciton and a deformation that then relaxes into a thermal motion, it is necessary to expend a considerable amount of energy.
Article
Based on a calculation of neural decoherence rates, we argue that the degrees of freedom of the human brain that relate to cognitive processes should be thought of as a classical rather than quantum system, i.e., that there is nothing fundamentally wrong with the current classical approach to neural network simulations. We find that the decoherence time scales ( approximately 10(-13)-10(-20) s) are typically much shorter than the relevant dynamical time scales ( approximately 10(-3)-10(-1) s), both for regular neuron firing and for kinklike polarization excitations in microtubules. This conclusion disagrees with suggestions by Penrose and others that the brain acts as a quantum computer, and that quantum coherence is related to consciousness in a fundamental way.
Article
The study of electron/proton transport in alpha-helix sections of proteins have illustrated the existence of soliton-like mechanisms. Recently, Ciblis and Cosic extended investigation to the existence of possible like soliton-type mechanisms in other parts of the protein. They used Quantum Hamiltonian analysis to investigate. In this paper, we investigate the same problem but we use Classical Hamiltonian analysis in our investigation.
Article
Proteins are the biomolecular workhorses driving the most biological processes in any living organism. These processes are based on selective interactions between particular proteins. So far the rules governing the coding of the protein's biological function, i.e. its ability to selectively interact with other biomolecules, have not been elucidated The resonant recognition model (RRM) is a novel physicomathematical approach established to analyze the interaction between a protein and its target. The RRM assumes that the specificities of protein interactions are based on the resonant electromagnetic energy transfer at the specific frequency for each interaction. One of the main applications of this model is to predict the location of a protein's biological active site(s) using digital signal processing. This paper incorporates the continuous wavelet transform (CWT) into the RRM to predict the active sites for a chosen protein example. We have investigated the oncogene functional group using digital signal analysis methods, in particular Fourier transform and CWT determined oncogenes' characteristic frequency and functional active sites; and performed the design of the peptide analogous. The results obtained provide new insights into the structure-function relationships of the analyzed oncogene protein family.
Review Study: Influence of Electromagnetic Radiation on Enzyme Activity and Effects of Synthetic Peptides on Cell Trans-formation
  • E Pirogova
  • V Vojisavljevic
  • T Istivan
  • P Coloe
  • I Cosic
E. Pirogova, V. Vojisavljevic, T. Istivan, P. Coloe, I. Cosic, "Review Study: Influence of Electromagnetic Radiation on Enzyme Activity and Effects of Synthetic Peptides on Cell Trans-formation", MD-Medical Data, vol. 2, no.4, pp. 317-324, 2010.
On Davydov's Alpha-Helix Solitons, Long-Time Prediction in Dynamics
  • J M Hyman
  • D W Mclaughlin
  • A C Scott
J.M. Hyman, D.W. McLaughlin, A.C. Scott, "On Davydov's Alpha-Helix Solitons, Long-Time Prediction in Dynamics", John Wiley & sons, pp. 367-394, 1983.
  • I Cosic
I. Cosic, "Macromolecular Bioactivity: Is it Resonant Interaction between Macromolecules?-Theory and Applications", IEEE Trans. on Biomedical Engineering, vol. 41, pp. 1101-1114, 1994.