Reports in Advances of Physical Sciences

In the last years of the 20th century, the attention of physicists working in statistical physics moved from equilibrium processes characterized by stationary correlation functions and Poisson dynamics to biological processes exhibiting ergodicity breaking. The discovery of these processes raised a debate on whether basic properties such as the Onsager principle had to be abandoned or properly revisited. The discovery of Levy processes led many researchers to replace the conventional central limit theorem with the generalized central limit theorem, responsible for a striking departure from the ordinary Gaussian statistics. The discovery of the processes of self-organization made the study of avalanches become very popular. The observation of turbulent processes led to the discovery of new waiting time distribution densities, characterized by inverse power laws and a new stochastic central limit theorem was invented to explain the emergence of Mittag-Leffler function, which is now widely used for the foundation of fractional derivatives. The traditional Linear Response Theory of Kubo was replaced by a new form of linear response, compatible with the ergodic breakdown of complex systems, and this new form of linear response was used for the foundation of Complexity Matching (CM). I plan to prove that crucial events are responsible for ergodicity breaking and that the CM phenomenon is a manifestation of crucial events. One problem still open in this field of research is the origin of $1∕f$ noise that is traditionally interpreted as a manifestation of the Mandelbrot Fractional Brownian Motion (FBM). I plan to show that the $1∕f$ noise proposed in for the foundation of the CM phenomenon has a completely different nature, involving crucial events rather than the FBM infinite memory. A recent result of my research group proved that the progress of autonomic neuropathy makes the heartbeats of healthy individuals, dominated by crucial events, turn into FBM. Quite surprisingly, the same phenomenon of transition from the crucial event to the FBM regime was observed in the germination process of lentils in the absence of light. The transition from Levy to Gauss statistics is supposed to be generated by environmental fluctuations and I will illustrate the experimental and theoretical research works that will shed light into their nature.

Biomolecules exhibit very complex dynamical properties and are constantly exchanging energy. These systems also behave very much like non-equilibrium systems. For example, there exist systems like proteins and their dynamics, cancer tumor progression, biophotonics and many more. These principles can also be used to understand the information processing in the DNA. There have been various studies which clearly indicate that classical physics is not enough to explain these systems. The two fundamental aspects of physics which can be applied to all systems are Quantum Mechanics and Electrodynamics. Every process or interaction has inbuilt in it these two fundamental properties.

In general, the field of biomolecules is studied as a macroscopic phenomenon and the focus is mostly on the results which we detect or measure in laboratory experiments.

Quantum physics concepts have been an extremely interesting tool to see the deeper aspects of such complex systems. There has always been an interest in complex systems from the Quantum Mechanics point of view. Early researchers such as Erwin Schrödinger was also said to have an interest in the quantum aspects of life. Quantum Mechanics deals with microscopic systems at the fundamental level and gives an insight into the phenomena from the lens of the dynamics of the process. Since the early days of the formulation of Quantum Mechanics, it has expressed itself as a robust theory which can describe systems such as molecular physics and chemistry, atomic physics and even systems such as proteins. This conjunction of biomolecules and quantum physics has gained immense interest recently.

In this research, we make an attempt to describe the dynamics of biomolecules from two aspects, namely:

• (1)Fermi’s Golden Rule;
• (2)Quantum Entanglement in Biomolecules.

In this study, we will present a new idea based on an extension in Fermi’s Golden Rule and how Quantum Entanglement plays a part in explaining Fermi’s Golden Rule further. Further, we will explain how these concepts can be applied to specific complex systems in biology.

Protein aggregation is a sophisticated biological mechanism that can have detrimental consequences. It is recognized as the hallmark of neurodegenerative diseases, suffered by millions of people each year reported by World Health Organization, $\mathrm{\text{title}}=\mathrm{\text{Dementia}}$. Abnormal deposits of amyloid fibrils and/or oligomers accumulate in and around neurons causing irreparable damage that leads to severe deterioration of the surrounding brain tissue and cognitive function. As of now, early detection, therapeutic intervention and treatment options are extremely limited. Protein aggregation is known to be highly dynamic, irreversible process which is source of its difficulty to fully understand and remedy the problem. The design of our study is to interpret the mechanics of intrinsically disordered proteins that self-assemble into highly structured fibrils. The aim is to gain a deeper understanding of protein–protein interactions, environmental conditions and chaperone failure that attribute to the aggregation process. The complexity of the aggregation process cannot be modeled using statistical physics and statistical thermodynamics of equilibrium processes. There are numerous studies that suggest protein aggregation which is a non-equilibrium process. Based on non-equilibrium physics, one of the best ways to understand it is through the Langevin and Fokker–Planck equations. Langevin equations describe stochastic dynamics of non-equilibrium processes. The Fokker–Planck equation is used to calculate the probability distribution and explain the trend in entropy of a model independent protein aggregation process.

Liquid crystals are molecular systems that exhibit partial ordering of molecules similar to solids while maintaining the ability to flow like liquids. Depending upon the amount of ordering in the material, there are many types of liquid crystalline phases. The nematic phase is the most common and technologically most important one due to its use in display applications. In the nematic phase, the molecules tend to have the same alignment, but their positions are not correlated. In part due to fundamental scientific interest and driven by new technological motivations apart from displays, the existence of new stable nematics has been continuously searched. The continuing search led to a recent discovery of a new type of nematic phase,^, known as the twist-bend nematic (Ntb), in certain bent-shaped liquid crystal dimers that have been supported by various independent experimental studies. Since the Ntb phase has been discovered recently, its properties have not been fully explored and a detailed description and understanding at the molecular level are still far from complete.

The Ntb phase’s formation is highly sensitive to any slight changes in the molecular shape arising from the chemical makeup of the linking spacer, terminal moieties and mesogenic units.^, Such structural features are not accessible directly through experiments. Thus, in this work, we present a set of DFT calculations on a series of liquid crystal dimers. This work aims to probe the role of certain structural features in driving the formation of the Ntb phase. This study also reveals why this phase occurs in certain bent molecules, but not in all. Since the constituent molecules are flexible and exist in a range of conformers, comparing the conformational landscapes of the dimers-exhibiting-the-Ntb-phase against those-do-not would identify the molecular conformations promoting the formation of the Ntb phase. Overall, this study evaluates ideal molecular structural features and conformational ensembles potentially responsible for the appearance of the Ntb phase.

Fungi can be found everywhere, and their impacts on human beings are numerous and varied. Fungi have been widely used in the food, biofuel, beverage and pharmaceutical industries. However, uncontrolled fungal growth can be costly to agriculture, forestry and livestock. If they feed on humans, diseases can be induced such as ringworm, athlete’s foot and lung infections. Some effects on human health may last over years and even lifetimes. It requires timely and accurate identification of mold species to evaluate and/or prevent damage from mold growth, and minimize the consequences of mold exposure. Raman spectroscopy studies on mold spores have been proposed and implemented as a method to identify fungal species. However, the presence of fluorescence emission always hinders Raman signal detection and is virtually impossible to avoid, especially in biological specimens. Shifted excitation Raman difference spectroscopy (SERDS) is a very powerful technique to separate Raman contribution from fluorescence contribution. Herein, we adopt the SERDS modality to extract pure Raman signals from fungal conidia of different species and find that Raman signatures of spores generated from pigment molecules bounded within the cell walls. A further study of conidia of different mold species indicates that the major features of the Raman spectrum correlate with the melanin biosynthesis pathway: species that produce the same melanin exhibit similar Raman spectra.^,

Several studies have used the logistic equation to model the growth of cancer cell populations as seen in Eq. (). This has included correlated multiplicative, $ϵ(x)$ and additive, $\mathrm{\Gamma }(t)$, noise terms. These noise terms can affect the growth rate, $a$, and death rate, $b$, of tumor cells and can be induced from factors such as radiotherapy or other cancer treatments. Depending on the intensity of the noise the terms, the fluctuations can induce a phase transition. Noise-induced transitions of nonlinear stochastic systems have applications in the fields of physics, chemistry and biology.

In this paper, we study the spreading of epidemic in a network of individuals who may either contract a disease through contact with infected nearest neighbors or be vaccinated under the influence of neighbors who are already vaccinated. We show that both interaction between susceptible S and infected individuals I and the imitation of vaccination, a form of sociological interaction between susceptible S and vaccinated V individuals, may lead to a phase transition. If the spreading of epidemic is in the supercritical condition, corresponding to an unlimited growth of infection, the interaction between S and V must reach the supercritical condition to generate control of the spreading of infection, and bring the system to criticality. By adopting a theoretical perspective like that of multilayer complex networks, we study the case where the epidemiological network is under the influence of a sociological debate on whether to be vaccinated. We show that at criticality this debate generates clusters of individuals in favor of vaccination and clusters of individuals opposing it.^, We study the influence of this debate on the spread of infection. We show that because of this debate in the epidemic network, a pattern emerges mirroring the structures of the sociological network. Finally, we introduce feedback of the epidemic network on the sociological network, and we prove that because of this feedback the sociological system undergoes a process of self-organization maintaining it at criticality. This system exhibits temporal complexity and critical slowing down. We hope that these results may have an important effect of giving interesting suggestions to behavioral psychologists and information scientists actively involved in the analysis of the social debate on the moral issues connected to sexual activities.

The ab-initio determination of the thermodynamic properties of the hydrolysis of the GTP gamma-phosphate in normal and abnormal cell functions of the RAS protein mutant Thr (Q61) leads to a description of energy cycle deviations in the abnormal mitogen-activated protein kinase cascade. A predictive non-equilibrium probability statement describing the nonlinear changes for these open and finite-lifetime systems follows from reasonable enthalpy and entropy values between the normal and mutated forms based on structures of the GTPase states at the allosteric site. Recent advances in understanding entropy in terms of asymmetric and highly entropic catalysis lead to an investigation of the GTPase entropy, specifically with regard to a failure in catalysis of the phosphate fragment by a water hydrogen positioned by the enzyme. Utilizing a simple atomic metal catalyst surface displacement model, a paradigm that reduces noise from the quantum entanglement plus atomic displacement terms results in the process entropy.

The evaluation of entropies within the mixed ionic, covalent and entangled system requires a nonlinear Markovian approach utilizing von Neumann entropies achieved by a systematic accumulation of entangled potentials in a step-wise method.^, Determination of the Hamiltonian for the entangled atomic state includes pure and mixed quantum states solved within the Araki–Leib triangle boundary resulting in only hard-entangled states, and the entanglement of Coulombic and Laughlin-like states can be evaluated by slicing the Hilbert spaces and solving the pure states, or mixed states separately, and then summing them. Incorporating the resulting entanglement potentials as well as the Coulombic atomic displacement states into a derivative of the Fokker–Planck equation results in generated and produced entropy.

The resting activity of the heart, without external sensory input, has provided novel information on the interactions that occur between biological and entropic systems in the body. The intersection between multifractality and disease diagnosis has been extensively worked on in the biophysical field, and yet, it is one that still has a lot of potential for new discoveries. In this paper, I will attempt to briefly describe the current literature on the use of multifractality on disease diagnosis, in addition to briefly comment on the future of this diagnostic methodology in the fight against cancer.

A fractal is described as a never-ending pattern, one that is infinitely complex and seems to repeat a process over and over in a loop. Fractals exhibit self-similarity, meaning they are patterns that are identical or near-identical on many scales, including time scales. In the context of this paper, fractals are visible patterns in the heartbeat 1s into a time series that will also be visible 1 day into a time series. This self-similarity is described by exponents. For example, monofractal processes only scale fractally in one manner, meaning that one exponent will help define them mathematically. On a graph of a power law over time, a monofractal state would present as a linear curve, as one exponent is defining it. Multifractality, on the other hand, is a term defining a spectrum of exponents used to help mathematically define a natural state. It would present as a nonlinear curve on the graph of a power law, as multiple exponents of multiple orders are describing its self-similarity over time. A heartbeat time series, in this paper, will be defined as 1800 evenly-spaced measurements of heart rate from one patient.⁵ In addition, the term crucial renewal events, also called crucial events, will be defined as events in a heartbeat time series that store the long-term memory of the heartbeat, therefore impacting the future patterns of the heartbeat. Crucial events build upon each other, meaning that the occurrence of earlier crucial events will correlate to the occurrence of subsequent crucial events. Over time, a decrease in the correlation between crucial events would indicate the presence of Poisson-like events, which in this paper will be defined as a disturbance in the healthy physiological process of a heartbeat.

The concept that multifractality and crucial events may play a role in disease diagnosis has been presented in different ways in the past. The first method was through broad multifractal spectrum analysis, in which Ivanov et al. determined that a loss of multifractality occurs in a non-healthy state, specifically when they analyzed congestive heart failure. This finding suggested that the presence of pathology moved the heartbeat closer to a monofractal state, making the difference between healthy and pathological individuals easy to identify. The second method, presented later on, presented evidence that healthy patients were less likely to have unrelated Poisson-like events than diseased or unhealthy patients. Crucially, West and Grigolini in 2017 were able to find an intersection between these two methods by proving that increasing the percentage of unrelated Poisson-like events occurring in a system would directly correlate to a narrower multifractal spectrum, connecting the two diagnostic methods and providing a view of multifractality such that it could have a drastic impact on potential diagnosis methodologies in the future.^,

Despite its advantages, photodynamic therapy (PDT) has one major drawback: penetration depth. This limits the use of conventional PDT methods to skin (surface) tumors only, making it ineffective for deep tumors. There are four possible solutions for the light delivery for deep tumor treatment: particles activated by near-infrared (NIR) light, up-conversion of nanoparticles that absorb NIR light and emit visible light for other photosensitizers (PSs), fiber optics and ionizing X-rays. Of these options, the best is X-rays. Near-infrared light can penetrate only 5mm in tissue while retaining enough energy to activate the PSs. The use of fiber optics is neither convenient nor efficient as it cannot effectively and evenly activate the photosensitizers. It is also almost impossible for the treatment of metastatic sites or lymph nodes involved with this disease, unless they are located in the region where light delivery is feasible. In contrast with the other methods, X-rays can easily penetrate as deeply as necessary into the patients, and are convenient as they are commonly used in cancer therapy.

The use of novel copper–cysteamine (Cu–Cy) nanoparticles is a good solution for overcoming these issues because Cu–Cy nanoparticles can be effectively activated by X-rays to produce singlet oxygen, which makes it very efficient for deep cancer treatment. Here, I will discuss the use of copper–cysteamine nanoparticles to enhance radiation therapy in combination with PDT and targeting therapies.

Biophotonics is a vibrant interdisciplinary field exploring the interaction between electromagnetic radiation and biological materials such as sub-cellular structures and molecules in living organisms. Biophotonics research leads to applications in agriculture and life sciences and produces tools for medical diagnostics and therapies. Working in this general field, we have recently made advances toward ultrasensitive Raman-spectroscopic probing of viruses. Our approach is based on laser spectroscopy aided by plasmonic nanoantennas, as in tip-enhanced Raman spectroscopy (TERS). An additional enhancement in sensitivity and speed is obtained by employing the femtosecond adaptive spectroscopic technique (FAST) for coherent anti-Stokes Raman scattering (CARS). The combined approach shows promise for non-destructive label-free bioimaging with molecular-level sensitivity and with spatial resolution down to a fraction of a nanometer.

Nature has generated sophisticated and very efficient molecular motors, employed for nanoscale transport at the intracellular level. As a complementary tool to nanofluidics, these motors have been envisioned for nanotechnological devices. In order to pave the way for such applications, a thorough understanding of the mechanisms governing these motors is needed. Because of the complexity of their in vivo functions, this understanding is best acquired in vitro, where functional parameters can independently be controlled. I will report on work in my group that studies and harnesses the transport properties of molecular motors on functionalized structures of reduced dimensionality such as carbon nanotubes, lithographically designed electrodes, microwires, loops and swarms. In addition, I will show results that demonstrate the potential of this work for biomedical advances.

This paper examines the question of whether the generally accepted interpretation of a supermassive object in M87 is the only one possible. There are grounds for this, in particular, due to the detection of a magnetic field in its vicinity. For this purpose, the stability of self-gravitating objects is investigated based on the correct definition of the energy of gravitation in the framework of the bi-metric approach to the theory. It is shown that supermassive objects can be stable configurations of a partially degenerate Fermi gas, the radius of which is less than their Schwarzschild radius.

In this study, a radical hypothesis concerning the wave-particle duality exhibited by extremely small objects in nature is explored by developing a Planck lattice model of space–time that grapples with the uncertain dynamic quantum structure of space–time at the Planck scale. Upon applying the Planck lattice model to two notable experiments that most clearly demonstrate the essence of wave-particle duality, one immediately finds that it successfully shows in a relatively straightforward and physically consistent manner how parcels of matter and energy, i.e., electrons and photons, respectively, can behave like waves. The heuristic concepts regarding the underlying structure of space–time contained herein are intended to show the classical particle description of matter and energy as fundamental, while at the same time doing away with the widely held notion of a continuous space–time.

Fascinated people from the dawn of history, gravity is not understood, still. Here, we suggest that gravity is a result of a process in the material: (1) Gravitational photons are produced by all atoms that exist in nonzero temperature and or interact with radiation, similar to black body radiation. (2) Then, these photons move in the material. The electromagnetic properties of the gravitational photons and the structure of the object cause the photons’ trajectories to bend. (3) Such trajectories generate a force pointing to the center of mass of the object, due to the circular motion and the electromagnetic properties of the gravitational photons. These trajectories are radiated outwards, as in antennae, although at a much slower rate, due to that force. So basically gravity is a simple process (as black body radiation), just a sort of generalized radiation pressure due to the process of gravity in the material, resulting in antenna like radiation emission, of these unique electromagnetic waves that are pressed towards the radiating object center of mass during their circular motion in the object. Going beyond the dynamical model, we identify various possible forms of the gravitational photons, and their general invariant properties. With this theory, we (1) explain various unexplained phenomena that are related to gravity, yet also suggest (2) method and apparatus for gravity shielding, and (3) gravitational radiation energy cultivation. This theory can form the missing part for the “theory of everything”.

The standard cosmology can answer almost nothing about how the structure of a galaxy is formed. It expects a supermassive black hole at the center and dark matter in the halo to explain the circulation of stars and its velocity. However, why the visible matters are distributed in such a thin plane by the interaction with the black hole while dark matter results in a spherical distribution is a critical open question for a disc galaxy. How the elliptical, ring, and long-barred galaxies are formed is unknown either. Here, we repot simulations of structures of galaxies according to our galactic evolution model based on the energy circulation theory. The theory claims the fundamental force to work between momentums, by which various energy circulations are formed. After terminating cyclic decompositions to lower-level circulations and separations to two ones by the space expansion, a resulted circulation (galactic seed) starts to release lower-level circulations (stellar seeds). Linear releases of stellar seeds from an isolated single galactic seed show an elliptical galaxy. Simultaneous releases on the whole circumference result in stellar seeds in a ring, where the seeds continue to circulate even if the ring radius increases. Intermittent ring releases from a single galactic seed provide a disc galaxy. Ring releases from separate binary galactic seeds form a barred ring galaxy, while linear releases from binary ends give a barred arm galaxy. Ring releases from attached two galactic seeds form a double-disc galaxy. If the two seeds rotate, spiral arms come out.

It is known that very distant galaxies, much like our own, show remarkably high receding velocities, the magnitude of which increases with distance. Therefore, in this study, a gravitational analog of the photoelectric effect was investigated by replacing the classical (wave) theory of gravity with a gravity quanta hypothesis. The significance of this concept regarding the motion of distant galaxies is evaluated by comparing the results obtained for a photon traveling through a Planck lattice model of spacetime to the observational data for both the cosmological redshift and time dilation effects of light from distant Type Ia supernovae. The photogravity effect does not necessarily invalidate the standard big bang cosmology and may in fact add a layer of fidelity to its conclusions concerning the evolution and age of the universe.

Based on Bohr’s model of hydrogen atom, the main purpose of this paper is to propose a new hypothesis for the model of hydrogen atom and perform mathematical calculations and verifications using experimental values and physical constants. The new model can not only provide the explanations that the existing theories failed to provide, but also can be used to construct neutrons, atomic nuclei, and individual atoms and molecules by involving only electrons and protons and their interactions. This means we only need to know how single electron and proton interact with each other, then we can establish a full model of hydrogen atom, and then we can establish other atomic nuclei. After all, all matter in the universe is made from hydrogen atoms through nuclear fusion.

This paper proposes the hypothesis that cosmic vacuum is full of energy basic state field (EBSF), and expounds its physical connotation based on cosmological constant of general relativity and Dirac’s negative energy sea. Cosmic vacuum is a special kind of physical object with complexity that can be characterized by quantum super-fluidity; it forms Dark energy in Universe. The rationality and correctness of this hypothesis are demonstrated through the analysis in terms of energy basic distribution on the background of cosmic scale and energy scale, quantum vacuum field, the evolution of EBSF state into static quantum’s state (particles or quasiparticle) and so on. Also it estimates the vacuum energy value in the energy basic state field to the same order of energy as the energy value for driving the accelerated expansion of the universe.