Abstract

The existence of any elementary particle in universe requires the existence of some region of universe occupied by it. By taking the volume of this occupied region, the author will reformulate the relativistic quantum field theory using new 3-dimensional region-like idealization of elementary particles and hereinafter will call the total volume of all regions occupied by the elementary constituent particles of the quantum system the occupied volume. Also the author will call the set of all regions of universe filled by elementary constituent particles of the quantum system the occupied path. Always any quantum system is existed at a head of its occupied path. This path is growing by mutual filling and leaving regions of universe by its elementary constituent particles. The conservation of this elementary constituent particle requires the conservation of its occupied volume during this process. This requirement could be summarized by the following conditions: 1) the total volume of all regions of universe filled by the elementary constituent particles of the quantum system minus the total volume of all regions of universe left by these elementary constituent particles must be equal to the occupied volume of the quantum system; 2) the total increase in the occupied volume of the quantum system due to the absorption of another elementary particles from outside its occupied regions minus the total decreasing in its occupied volume due to the emission of another elementary particles outside its occupied regions must be equal to the occupied volume of it. The wave-particle duality of the elementary constituent particles implied accumulation of them as the finite set of interfered waves. This accumulation of elementary constituent particles causes the absolute probabilistic nature of event of finding the elementary consistent particle in specified interfered wave, and hence the mathematical representation of this interfered wave should take into account the value of probability amplitude of finding an elementary particle inside the region occupied specified interfered wave. In quantum theory this probability amplitude corresponds to complex amplitude of the wave function of interfered wave. Also in Hilbert’s representation of the quantum theory these wave functions are representing the components of the quantum state vector. In this paper the author will develop the transformation theory of the region-like quantum state of the quantum system. In this study, we managed to reformulate of the Relativistic Quantum Field Theory using Region-Like Idealization of the Elementary Particle Identification of an one-bead by one-compound computer-aided discovery novel peptide mimetic pharmacophore against human ovarian cancer highly expressed on conserved mRNAs-cDGX4GX6X7c associated combinatorial libraries.

Keywords

Reformulation; Relativistic Quantum Field Theory; Region-Like Idealization; Elementary Particle Identification; one-bead by one-compound; computer-aided discovery; novel peptide mimetic; pharmacophore; human ovarian cancer; highly expressed; fconserved; mRNAs-cDGX4GX6X7c; combinatorial libraries; Creation, Annihilation, Animation, Occupied Volume, Occupied Path,

Abstract

BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer’s disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD) framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.In silico designed of an Anticancer Peptide SVS-1 multipharmacophore as a potential drug-like efficator in Preceding Membrane Neutralization using a web server multi-mimotopic algorithmic approach for biclustering analysis of expression data.Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. Anticancer peptides (ACPs) are polycationic amphiphiles capable of preferentially killing a widespectrum of cancer cells relative to non-cancerous cells. Their primary mode of action is aninteraction with the cell membrane and subsequent activation of lytic effects, however it remainscontroversial the exact mechanism responsible for this mode of action. It has in previous studies been shown that utilizing zeta potential analyses it was possible to demonstrate the interaction of a small anticancer peptide with membrane modelsystems and cancer cells. Electrostatic interactions have a pivotal role in the cell killing processand in contrast to the AMPs action cell death occurs without achieving full neutralization of themembrane charge. Formation of insoluble amyloid plaques in the vascular and hippocampal areas of the brain characterizes Alzheimer’s disease, a devastating neurodegenerative disorder causing dementia. Site-specific hydrolytic catalysis of β-secretase, or BACE-1, is responsible for production of oligomerative amyloid β-peptide. As the catalytic activity of BACE-1 is pH-dependent and its structural dynamics are intrinsic to the catalysis, we examine the dependence of dynamics of BACE-1 on solution pH and its implications on the catalytic mechanism of BACE-1. Also, we highlight the importance of accurate description of protonation states of the titratable groups in computer-aided drug discovery targeting BACE-1. We hope the understanding of pH dependence of the dynamics and inhibitor binding properties of BACE-1 will aid the structure-based inhibitor design efforts against Alzheimer’s disease.In silico designed of an Anticancer Peptide SVS-1 multipharmacophore as a potential drug-like efficator in Preceding Membrane Neutralization using a web server multi-mimotopic algorithmic approach for biclustering analysis of expression data.Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. The advent of microarray technology has revolutionized the search for genes that are differentially expressed across a range of cell types or experimental conditions. Traditional clustering methods, such as hierarchical clustering, are often difficult to deploy effectively since genes rarely exhibit similar expression pattern across a wide range of conditions. Web-enabled service called GEMS (Gene Expression Mining Server) for biclustering microarray data where Users may upload expression data and specify a set of criteria. In this study GEMS performs bicluster mining based on a Gibbs sampling paradigm of Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria to the in silico design of an Anticancer Peptide SVS-1 multipharmacophore as a potential drug-like efficator in Preceding Membrane Neutralization using a multi-mimotopic algorithmic approach for biclustering analysis of expression data.. Here, in Biogenea we have for the first time discovered an Anticancer Peptide SVS-1 multipharmacophore with an ini silico evaluated Efficacy in Preceding Membrane Neutralization using a web server for biclustering analysis of expression data.

Keywords

In silico designed; Anticancer Peptide; SVS-1; multipharmacophore; potential; drug-like; efficator; Preceding Membrane; Neutralization; multi-mimotopic; algorithmic approach; biclustering analysis; expression data; Conformational Dynamics; Binding Free Energies; Inhibitors; BACE-1; Protonation Equilibria;

Abstract

Human T lymphotropic virus type 1 (HTLV-1) was the first isolated retrovirus and is the causative agent of Adult T cell leukemia or Tropical Spastic Paraparesis which develops in 6-10 % of HTLV-1 positive individuals. Viral transmission takes place vertically or horizontally via cell to cell contact and syncitia formation between infected and non-infected cells. The viral envelope is responsible for the attachment and entry of the virus into the host cell. Env is composed of two subunits: referred to as the surface subunit, and the gp21 transmembranous subunit. It has been proposed that gp46 is mainly involved in host cell receptor binding and gp21 is involved in post binding events resulting in the fusion of host cell membrane with the infected cell membrane. There has been no effective cure against HTLV-1 and it is resistant to conventional means. We explore the viability of using intrinsically quantum phenomena for molecular sensing. We formulate a theory for coherent sensing by combining the full analytical description of electronic relaxation processes with mass diffusion and charge transport models. This theory produces molecular-scale design criteria for sensors with responses rooted in quantum mechanical coherence phenomena. For example, the sensitivity of the detector can increase with decreased coupling between the molecular binding sites and the sensor substrate. Exploiting quantum properties of the analyte and the sensing element (e.g., electronic affinity, polarizability, etc.) enables enhanced discrimination among multiple analytes. Discovery and a computerized quantitative bio-informatic in silico Development of a Synthetic Gp 46-gp21 derived P400-P197 Peptide mimetic pharmacophore as a potential HTLV-1 Fusion Inhibitor in a mass-action law based new cluster of algorithmsSensing of molecules using quantum dynamics.Therefore investigations in possible therapeutic approaches are very important. One possible therapeutic strategy against HTLV-1 is the use of peptide fusion inhibitors to prevent transmission of the virus. Here, in Biogenea we have for the first time focused on HTVS programs with graphical user interfaces (GUIs) that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of median-effect equation of the massaction law deduced from over 300 mechanism specific-equations which has been shown to be the unified theory that serves as the common-link for complicated biomedical systems in a computer platform for the in silico discovered Synthetic Peptide mimetic multi-targeted pharmacophore as a novel Potential HTLV-1 Fusion Inhibitor Therapeutics using a mass-action law based algorithm for cost-effective approach for cancer drug discovery and development.

Keywords

Sensing of molecules; quantum dynamics, Discovery, computerized, quantitative bio-informatic, in silico, Development, Synthetic, Gp 46-gp21, derived P400-P197, Peptide mimetic, pharmacophore, HTLV-1, Fusion Inhibitor, mass-action law, new cluster of algorithms.

Abstract

Quantum key distribution is a technique to securely distribute a bit string between two parties by using the laws of quantum mechanics. The security of this technique depends on the basis of quantum mechanics rather than the difficulty of the mathematical calculation as in the classical encoding. Researches in this field have shown that the quantum key distribution will be fully func-tioning outside the laboratory in a few years. Due to the complexity and the high efficiency of the device, the verification is needed. In this article, we use PRISM to verify the security of the quan-tum key distribution protocol, which uses the entangled photon based on BB84 in silico Model Checking Development of a Synthetic Gp 46-gp21 derived P400-P197 Peptide mimetic pharmacophore as a potential HTLV-1 Fusion Inhibitor in a mass-action law based new cluster of algorithms protocol

Keywords

Analysis of Security; Quantum Key; Distribution Based; Entangled Photon Pairs; Model Checking; in silico Development; Synthetic Gp 46-gp21; P400-P197 Peptide mimetic; pharmacophore; HTLV-1 Fusion Inhibitor; mass-action law; new cluster of algorithms;Cryptography, Quantum Cryptography, Quantum Key Distribution, Model Checking

Abstract

BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer’s disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. Formation of insoluble amyloid plaques in the vascular and hippocampal areas of the brain characterizes Alzheimer’s disease, a devastating neurodegenerative disorder causing dementia. Site-specific hydrolytic catalysis of β-secretase, or BACE-1, is responsible for production of oligomerative amyloid β-peptide. As the catalytic activity of BACE-1 is pH-dependent and its structural dynamics are intrinsic to the catalysis, we examine the dependence of dynamics of BACE-1 on solution pH and its implications on the catalytic mechanism of BACE-1. Also, we highlight the importance of accurate description of protonation states of the titratable groups in computer-aided drug discovery targeting BACE-1. We hope the understanding of pH dependence of the dynamics and inhibitor binding properties of BACE-1 will aid the structure-based inhibitor design efforts against Alzheimer’s disease.Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria Discovery and a computerized quantitative bio-informatic in silico Development of a Synthetic Gp 46-gp21 derived P400-P197 Peptide mimetic pharmacophore as a potential HTLV-1 Fusion Inhibitor in a mass-action law based new cluster of algorithmsSensing of molecules using quantum dynamics. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD) framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria Discovery and a computerized quantitative bio-informatic in silico Development of a Synthetic Gp 46-gp21 derived P400-P197 Peptide mimetic pharmacophore as a potential HTLV-1 Fusion Inhibitor in a mass-action law based new cluster of algorithmsSensing of molecules using quantum dynamics.

Keywords

Conformational Dynamics; Binding Free Energies; Inhibitors of BACE-1; Perspective of Protonation; Equilibria Discovery; computerized quantitative bio-informatic; in silico Development; Synthetic Gp 46-gp21; P400-P197 Peptide mimetic; pharmacophore; HTLV-1 Fusion Inhibitor; mass-action law; new cluster of algorithms;Sensing of molecules; quantum dynamics;

Abstract

Fluorescence molecular imaging/tomography may play an important future role in preclinical research and clinical diagnostics. Time- and frequency-domain fluorescence imaging can acquire more measurement information than the continuous wave (CW) counterpart, improving the image quality of fluorescence molecular tomography. Although diffusion approximation (DA) theory has been extensively applied in optical molecular imaging, high-order photon migration models need to be further investigated to match quantitation provided by nuclear imaging. In this paper, a frequency-domain parallel adaptive finite element solver is developed with simplified spherical harmonics (SPN) approximations. To fully evaluate the performance of the SPN approximations, a fast time-resolved tetrahedron-based Monte Carlo fluorescence simulator suitable for complex heterogeneous geometries is developed using a convolution strategy to realize the simulation of the fluorescence excitation and emission. The validation results show that high-order SPN can effectively correct the modeling errors of the diffusion equation, especially when the tissues have high absorption characteristics or when high modulation frequency measurements are used. Furthermore, the parallel adaptive mesh evolution strategy improves the modeling precision and the simulation speed significantly on a realistic digital mouse phantom. This solver is a promising platform for fluorescence molecular tomography using high-order approximations to the radiative transfer equation to Represent Entangled Quantum parallel adaptive finite element simplified spherical harmonics States approximation solver for frequency domain fluorescence molecular imaging to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes for the efficient discovery of homomultimerized HIV short linear motif-like peptide mimicking lead compound on its functional binding sites.

Keywords

A parallel adaptive finite element simplified spherical harmonics approximation solver for frequency domain fluorescence molecular imagingA cursory analysis to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes for the efficient discovery of homomultimerized HIV short linear motif-like peptide mimicking lead compound on its functional binding sites. Virtual Numbers to Represent Entangled Quantum States.

Abstract

To enhance the optimization ability of particle swarm algorithm, a novel quantum-inspired particle swarm optimization algorithm is proposed. In this method, the particles are encoded by the probability amplitudes of the basic states of the multi-qubits system. The rotation angles of multi-qubits are determined based on the local optimum particle and the global optimal particle, and the multi-qubits rotation gates are employed to update the particles. At each of iteration, updating any qubit can lead to updating all probability amplitudes of the corresponding particle. The experimental results of some benchmark functions optimization show that, although its single step iteration consumes long time, the optimization ability of the proposed method is significantly higher than other similar algorithms representing for the first time a Quantum-Inspired Particle Swarm Optimization Algorithm Encoded by Probability Amplitudes of Multi-Qubit cursory analysis to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes for the efficient discovery of homomultimerized HIV short linear motif-like peptide mimicking lead compound on its functional binding sites.

Keywords

cursory analysis; global patterns; anti-HIV-1; cell cycle viral replication enzymes; discovery of homomultimerized; HIV short linear motif-like; peptide mimicking; lead compound; functional binding sites; Quantum-Inspired; Particle Swarm; Optimization Algorithm; Probability Amplitudes of Multi-Qubits;

Abstract

In the existing formalism of quantum states, probability amplitudes of quantum states are complex numbers. A composition of entangled quantum states, such as a Bell state, cannot be decomposed into its constituent quantum states, implying that quantum states lose their identities when they get entangled. This is contrary to the observation that a composition of entangled quantum states decays back to its constituent quantum states. To eliminate this discrepancy, this paper introduces a new type of numbers, called virtual numbers, which produce zero upon multiplication with complex numbers. In the proposed formalism of quantum states, probability amplitudes of quantum states are general numbers made of complex and virtual numbers. A composition of entangled quantum states, such as a Bell state, can then be decomposed into its constituent quantum states, implying that quantum states retain their identities when they get entangled. Considerable success has been achieved in the treatment of HIV-1 infection, and more than two dozen antiretroviral drugs are available targeting several distinct steps in the viral replication cycle. However, resistance to these compounds emerges readily, even in the context of combination therapy. Drug toxicity, adverse drug-drug interactions, and accompanying poor patient adherence can also lead to treatment failure. These considerations make continued development of novel poly-targeted antiretroviral therapeutics necessary. A number of rationall computer aided drug discovery steps in the HIV-1 replication cycle that represent promising targets for drug discovery have been previously highlighted. In this research article we for the first time presented a Virtual Numbers to Represent Entangled Quantum States cursory analysis to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes for the efficient discovery of homomultimerized HIV short linear motif-like peptide mimicking lead compound on its functional binding sites.

Keywords

Quantum Mechanics; Probability Amplitude; Complex Number; Entanglement; Bell State1; Pocket-Based filtering, Drug Design Methodology, hyper drug-target interactions
restricted; Boltzmann machines, Discovery; in silico computer aided, free energy potency optimization, poly-target antagonists, HIV-II viral replication protease cycle associated enzymes

Abstract

Newcomb’s problem is a game between two players, one of who has an ability to predict the future: let Bob have an ability to predict Alice’s will. Now, Bob prepares two boxes, Box1 and Box2, and Alice can select either Box2 or both boxes. Box1 contains $1. Box2 contains $1,000 only if Alice selects only Box2; otherwise Box2 is empty($0). Which is better for Alice? Since Alice cannot decide which one is better in general, this problem is called Newcomb’s paradox. In this paper, we propose quantum strategies for this paradox by Bob having quantum ability. Many other results including quantum strategies put emphasis on finding out equilibrium points. On the other hand, our results put emphasis on whether a player can predict another player’s will. Then, we show some positive solutions for Quantum Strategies for Newcomb’s Paradox cursory analysis to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes for the efficient discovery of homomultimerized HIV short linear motif-like peptide mimicking lead compound on its functional binding sites.

Keywords

Game Theory, Newcomb’s Paradox, Quantum Strategy, Meyer’s Strategy; cursory analysis; global patterns; anti-HIV-1 cell cycle viral replication enzymes; efficient discovery; homomultimerized HIV; short linear motif-like peptide mimicking; lead compound; functional binding sites; Quantum Strategies; Newcomb’s Paradox;

Abstract

We design sensors where information is transferred between the sensing event and the actuator via quantum relaxation processes, through distances of a few nanometers. We thus explore the possibility of sensing using intrinsically quantum mechanical phenomena that are also at play in photobiology, bioenergetics, and information processing. Specifically, we analyze schemes for sensing based on charge transfer and polarization (electronic relaxation) processes. These devices can have surprising properties. Their sensitivity can increase with increasing separation between the sites of sensing (the receptor) and the actuator (often a solid-state substrate). This counterintuitive response and other quantum features give these devices favorable characteristics, such as enhanced sensitivity and selectivity. Using coherent phenomena at the core of molecular sensing presents technical challenges but also suggests appealing schemes for molecular sensing and information transfer in supramolecular structures.A cursory analysis to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes for the efficient discovery of homomultimerized HIV short linear motif-like peptide mimicking lead compound on its functional binding sites. Quantum Discord of a Two-Qubit Anisotropy XXZ Heisenberg Chain with Dzyaloshinskii-Moriya Interaction. We investigate the quantum discord of a two-qubit anisotropy XXZ Heisenberg chain with Dzyaloshinskii-Moriya (DM) interaction under magnetic field. It is shown that the quantum discord highly depends on the system’s temperature T, DM interaction D, homogenous magnetic field B and the anisotropy Δ. For lower temperature T, by modulating D and B, the quantum discord can be controlled and the quantum discord switch can be realized. Considerable success has been achieved in the treatment of HIV-1 infection, and more than two dozen antiretroviral drugs are available targeting several distinct steps in the viral replication cycle. However, resistance to these compounds emerges readily, even in the context of combination therapy. Drug toxicity, adverse drug-drug interactions, and accompanying poor patient adherence can also lead to treatment failure. These considerations make continued development of novel poly-targeted antiretroviral therapeutics necessary. A number of rationall computer aided drug discovery steps in the HIV-1 replication cycle that represent promising targets for drug discovery have been previously highlighted. In this research article we for the first time presented a cursory analysis to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes associated for the efficient discovery of homomultimerized HIV proteins targeted lead compounds and its functional binding sites.A cursory analysis to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes for the efficient discovery of homomultimerized HIV short linear motif-like peptide mimicking lead compound on its functional binding sites. Quantum Discord of a Two-Qubit Anisotropy XXZ Heisenberg Chain with Dzyaloshinskii-Moriya Interaction. We explore the viability of using intrinsically quantum phenomena for molecular sensing. We formulate a theory for coherent sensing by combining the full analytical description of electronic relaxation processes with mass diffusion and charge transport models. This theory produces molecular-scale design criteria for sensors with responses rooted in quantum mechanical coherence Sensing phenomena of Quantum Discord of a Two-Qubit Anisotropy XXZ Heisenberg Chain with Dzyaloshinskii-Moriya Interaction molecules quantum dynamics cursory analysis to identify several global patterns for anti-HIV-1 cell cycle viral replication enzymes for the efficient discovery of homomultimerized HIV short linear motif-like peptide mimicking lead compound on its functional binding sites.

Keywords

Quantum Discord, Heisenberg Chain, Dzyaloshinskii-Moriya Interaction, Anisotropy, Magnetic Field, Pocket-Based filtering, Drug Design Methodology, hyper drug-target interactions
restricted Boltzmann machines, Discovery in silico, computer aided, free energy potency optimization, poly-target antagonists, HIV-II viral replication, protease cycle associated enzymes, molecular sensing, quantum relaxation processes, charge transfer, field-effect transistors, coherence,