Physics of Biology

1608 Submissions

[7] viXra:1608.0441 [pdf] submitted on 2016-08-30 14:10:56

Studies on the Viability of the Boundary Element Method for the Real-Time Simulation of Biological Organs

Authors: Kirana Kumara P
Comments: 216 Pages. This is a draft (preprint) version. (PhD registration Jan 2, 07; coursework Jan to Apr, 07; comprehensive exam Apr 20, 09; colloquium Aug 14, 15; submission Aug 20, 15; defense (oral exam) Aug 22, 16. The final version of the thesis is deposited at IISc.)

Realistic and real-time computational simulation of biological organs (e.g., human kidneys, human liver) is a necessity when one tries to build a quality surgical simulator that can simulate surgical procedures involving these organs. Currently deformable models, spring-mass models, or finite element models are widely used to achieve the realistic simulations and/or the real-time performance. It is widely agreed that continuum mechanics based numerical techniques are preferred over deformable models or spring-mass models, but those techniques are computationally expensive and hence the higher accuracy offered by those numerical techniques come at the expense of speed. Hence there is a need to study the speed of different numerical techniques, while keeping an eye on the accuracy offered by those numerical techniques. Such studies are available for the Finite Element Method (FEM) but rarely available for the Boundary Element Method (BEM). Hence the present work aims to conduct a study on the viability of BEM for the real-time simulation of biological organs, and the present study is justified by the fact that BEM is considered to be inherently efficient when compared to mesh based techniques like FEM. A significant portion of literature on the real-time simulation of biological organs suggests the use of BEM to achieve better simulations. When one talks about the simulation of biological organs, one needs to have the geometry of a biological organ in hand. Geometry of biological organs of interest is not readily available many a times, and hence there is a need to extract the three dimensional (3D) geometry of biological organs from a stack of two dimensional (2D) scanned images. Software packages that can readily reconstruct 3D geometry of biological organs from 2D images are expensive. Hence, a novel procedure that requires only a few free software packages to obtain the geometry of biological organs from 2D image sequences is presented. The geometry of a pig liver is extracted from CT scan images for illustration purpose. Next, the three dimensional geometry of human kidney (left and right kidneys of male, and left and right kidneys of female) is obtained from the Visible Human Dataset (VHD). The novel procedure presented in this work can be used to obtain patient specific organ geometry from patient specific images, without requiring any of the many commercial software packages that can readily do the job. To carry out studies on the speed and accuracy of BEM, a source code for BEM is needed. Since the BEM code for 3D elasticity is not readily available, a BEM code that can solve 3D linear elastostatic problems without accounting for body forces is developed from scratch. The code comes in three varieties: a MATLAB version, a Fortran version (sequential version), and a Fortran version (parallelized version). This is the first free and open source BEM code for 3D elasticity. The developed code is used to carry out studies on the viability of BEM for the real-time simulation of biological organs, and a few representative problems involving kidneys and liver are found to give accurate solutions. The present work demonstrates that it is possible to simulate linear elastostatic behaviour in real-time using BEM without resorting to any type of precomputations, on a computer cluster by fully parallelizing the simulations and by performing simulations on different number of processors and for different block sizes. Since it is possible to get a complete solution in real-time, there is no need to separately prove that every type of cutting, suturing etc. can be simulated in real-time. Future work could involve incorporating nonlinearities into the simulations. Finally, a BEM based simulator may be built, after taking into account details like rendering.
Category: Physics of Biology

[6] viXra:1608.0359 [pdf] submitted on 2016-08-26 07:40:35

Cortical Conscious Network

Authors: George Rajna
Comments: 32 Pages.

New research published in the New Journal of Physics tries to decompose the structural layers of the cortical network to different hierarchies enabling to identify the network's nucleus, from which our consciousness could emerge. [21] Where in your brain do you exist? Is your awareness of the world around you and of yourself as an individual the result of specific, focused changes in your brain, or does that awareness come from a broad network of neural activity? How does your brain produce awareness? [20] In the future, level-tuned neurons may help enable neuromorphic computing systems to perform tasks that traditional computers cannot, such as learning from their environment, pattern recognition, and knowledge extraction from big data sources. [19] IBM scientists have created randomly spiking neurons using phase-change materials to store and process data. This demonstration marks a significant step forward in the development of energy-efficient, ultra-dense integrated neuromorphic technologies for applications in cognitive computing. [18] An ion trap with four segmented blade electrodes used to trap a linear chain of atomic ions for quantum information processing. Each ion is addressed optically for individual control and readout using the high optical access of the trap. [17] To date, researchers have realised qubits in the form of individual electrons (aktuell.ruhr-uni-bochum.de/pm2012/pm00090.html.en). However, this led to interferences and rendered the information carriers difficult to programme and read. The group has solved this problem by utilising electron holes as qubits, rather than electrons. [16] Physicists from MIPT and the Russian Quantum Center have developed an easier method to create a universal quantum computer using multilevel quantum systems (qudits), each one of which is able to work with multiple "conventional" quantum elements – qubits. [15] Precise atom implants in silicon provide a first step toward practical quantum computers. [14] A method to produce significant amounts of semiconducting nanoparticles for light-emitting displays, sensors, solar panels and biomedical applications has gained momentum with a demonstration by researchers at the Department of Energy's Oak Ridge National Laboratory. [13] A source of single photons that meets three important criteria for use in quantum-information systems has been unveiled in China by an international team of physicists. Based on a quantum dot, the device is an efficient source of photons that emerge as solo particles that are indistinguishable from each other. The researchers are now trying to use the source to create a quantum computer based on "boson sampling". [11] With the help of a semiconductor quantum dot, physicists at the University of Basel have developed a new type of light source that emits single photons. For the first time, the researchers have managed to create a stream of identical photons. [10] Optical photons would be ideal carriers to transfer quantum information over large distances. Researchers envisage a network where information is processed in certain nodes and transferred between them via photons. [9] While physicists are continually looking for ways to unify the theory of relativity, which describes large-scale phenomena, with quantum theory, which describes small-scale phenomena, computer scientists are searching for technologies to build the quantum computer using Quantum Information. In August 2013, the achievement of "fully deterministic" quantum teleportation, using a hybrid technique, was reported. On 29 May 2014, scientists announced a reliable way of transferring data by quantum teleportation. Quantum teleportation of data had been done before but with highly unreliable methods. The accelerating electrons explain not only the Maxwell Equations and the Special Relativity, but the Heisenberg Uncertainty Relation, the Wave-Particle Duality and the electron’s spin also, building the Bridge between the Classical and Quantum Theories. The Planck Distribution Law of the electromagnetic oscillators explains the electron/proton mass rate and the Weak and Strong Interactions by the diffraction patterns. The Weak Interaction changes the diffraction patterns by moving the electric charge from one side to the other side of the diffraction pattern, which violates the CP and Time reversal symmetry. The diffraction patterns and the locality of the self-maintaining electromagnetic potential explains also the Quantum Entanglement, giving it as a natural part of the Relativistic Quantum Theory and making possible to build the Quantum Computer with the help of Quantum Information.
Category: Physics of Biology

[5] viXra:1608.0357 [pdf] submitted on 2016-08-26 07:11:36

Network Theory of Consciousness

Authors: George Rajna
Comments: 30 Pages.

Where in your brain do you exist? Is your awareness of the world around you and of yourself as an individual the result of specific, focused changes in your brain, or does that awareness come from a broad network of neural activity? How does your brain produce awareness? [20] In the future, level-tuned neurons may help enable neuromorphic computing systems to perform tasks that traditional computers cannot, such as learning from their environment, pattern recognition, and knowledge extraction from big data sources. [19] IBM scientists have created randomly spiking neurons using phase-change materials to store and process data. This demonstration marks a significant step forward in the development of energy-efficient, ultra-dense integrated neuromorphic technologies for applications in cognitive computing. [18] An ion trap with four segmented blade electrodes used to trap a linear chain of atomic ions for quantum information processing. Each ion is addressed optically for individual control and readout using the high optical access of the trap. [17] To date, researchers have realised qubits in the form of individual electrons (aktuell.ruhr-uni-bochum.de/pm2012/pm00090.html.en). However, this led to interferences and rendered the information carriers difficult to programme and read. The group has solved this problem by utilising electron holes as qubits, rather than electrons. [16] Physicists from MIPT and the Russian Quantum Center have developed an easier method to create a universal quantum computer using multilevel quantum systems (qudits), each one of which is able to work with multiple "conventional" quantum elements – qubits. [15] Precise atom implants in silicon provide a first step toward practical quantum computers. [14] A method to produce significant amounts of semiconducting nanoparticles for light-emitting displays, sensors, solar panels and biomedical applications has gained momentum with a demonstration by researchers at the Department of Energy's Oak Ridge National Laboratory. [13] A source of single photons that meets three important criteria for use in quantum-information systems has been unveiled in China by an international team of physicists. Based on a quantum dot, the device is an efficient source of photons that emerge as solo particles that are indistinguishable from each other. The researchers are now trying to use the source to create a quantum computer based on "boson sampling". [11] With the help of a semiconductor quantum dot, physicists at the University of Basel have developed a new type of light source that emits single photons. For the first time, the researchers have managed to create a stream of identical photons. [10] Optical photons would be ideal carriers to transfer quantum information over large distances. Researchers envisage a network where information is processed in certain nodes and transferred between them via photons. [9] While physicists are continually looking for ways to unify the theory of relativity, which describes large-scale phenomena, with quantum theory, which describes small-scale phenomena, computer scientists are searching for technologies to build the quantum computer using Quantum Information. In August 2013, the achievement of "fully deterministic" quantum teleportation, using a hybrid technique, was reported. On 29 May 2014, scientists announced a reliable way of transferring data by quantum teleportation. Quantum teleportation of data had been done before but with highly unreliable methods. The accelerating electrons explain not only the Maxwell Equations and the Special Relativity, but the Heisenberg Uncertainty Relation, the Wave-Particle Duality and the electron’s spin also, building the Bridge between the Classical and Quantum Theories. The Planck Distribution Law of the electromagnetic oscillators explains the electron/proton mass rate and the Weak and Strong Interactions by the diffraction patterns. The Weak Interaction changes the diffraction patterns by moving the electric charge from one side to the other side of the diffraction pattern, which violates the CP and Time reversal symmetry. The diffraction patterns and the locality of the self-maintaining electromagnetic potential explains also the Quantum Entanglement, giving it as a natural part of the Relativistic Quantum Theory and making possible to build the Quantum Computer with the help of Quantum Information.
Category: Physics of Biology

[4] viXra:1608.0071 [pdf] replaced on 2016-08-10 05:17:53

"Patch" for DNA

Authors: Mark M. Grinshtein
Comments: 5 Pages.

The article reviewed a technique of diagnosing and treating gene viral diseases by way of identification and subsequent recovery (repair) of abnormal chromosomes.
Category: Physics of Biology

[3] viXra:1608.0070 [pdf] submitted on 2016-08-07 08:30:00

Why Humans Become Old

Authors: Mark M. Grinshtein
Comments: 5 Pages.

The article considers the telomere theory which authors were awarded the Nobel Prize in 2009. The aging process is explained from the point of view of Information-Wave Medicine (IWM). The aging program is shown to be a multi-level genetic structure controlled by the body’s internal biological clock.
Category: Physics of Biology

[2] viXra:1608.0061 [pdf] submitted on 2016-08-06 04:35:50

IBM Detect Cancer

Authors: George Rajna
Comments: 27 Pages.

IBM scientists have developed a new lab-on-a-chip technology that can, for the first time, separate biological particles at the nanoscale and could enable physicians to detect diseases such as cancer before symptoms appear. [14] Scientists work toward storing digital information in DNA. [13] Leiden theoretical physicists have proven that DNA mechanics, in addition to genetic information in DNA, determines who we are. Helmut Schiessel and his group simulated many DNA sequences and found a correlation between mechanical cues and the way DNA is folded. They have published their results in PLoS One. [12] We model the electron clouds of nucleic acids in DNA as a chain of coupled quantum harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. [11] Scientists have discovered a secret second code hiding within DNA which instructs cells on how genes are controlled. The amazing discovery is expected to open new doors to the diagnosis and treatment of diseases, according to a new study. [10] There is also connection between statistical physics and evolutionary biology, since the arrow of time is working in the biological evolution also. From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. [8] This paper contains the review of quantum entanglement investigations in living systems, and in the quantum mechanically modeled photoactive prebiotic kernel systems. [7] The human body is a constant flux of thousands of chemical/biological interactions and processes connecting molecules, cells, organs, and fluids, throughout the brain, body, and nervous system. Up until recently it was thought that all these interactions operated in a linear sequence, passing on information much like a runner passing the baton to the next runner. However, the latest findings in quantum biology and biophysics have discovered that there is in fact a tremendous degree of coherence within all living systems. The accelerating electrons explain not only the Maxwell Equations and the Special Relativity, but the Heisenberg Uncertainty Relation, the Wave-Particle Duality and the electron's spin also, building the Bridge between the Classical and Quantum Theories. The Planck Distribution Law of the electromagnetic oscillators explains the electron/proton mass rate and the Weak and Strong Interactions by the diffraction patterns. The Weak Interaction changes the diffraction patterns by moving the electric charge from one side to the other side of the diffraction pattern, which violates the CP and Time reversal symmetry. The diffraction patterns and the locality of the self-maintaining electromagnetic potential explains also the Quantum Entanglement, giving it as a natural part of the Relativistic Quantum Theory and making possible to understand the Quantum Biology.
Category: Physics of Biology

[1] viXra:1608.0022 [pdf] submitted on 2016-08-02 11:37:25

Nano Drug Delivery Systems

Authors: A.S.Bhattacharyya, P.Prabhakar
Comments: 03 Pages. Working Paper

A study of polymer erosion rate during drug delivery.
Category: Physics of Biology