Reports in Advances of Physical Sciences最新文献

{"title":"Entropy in Biochemical Failure","authors":"R. Hallford","doi":"10.1142/s2424942422400084","DOIUrl":"https://doi.org/10.1142/s2424942422400084","url":null,"abstract":"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. 1 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. 2 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. 3 , 4 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. 5 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. 6","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83943466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding Structural and Molecular Properties of Liquid Crystal Dimers: A Density Functional Approach","authors":"Anant Kumar","doi":"10.1142/s2424942422400047","DOIUrl":"https://doi.org/10.1142/s2424942422400047","url":null,"abstract":"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, 1 , 2 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. 3 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. 4 , 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.","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81535572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Entropic Analysis of Protein Aggregation using Langevin Equations and Fokker–Planck Equations","authors":"L. Cook, Preet Sharma","doi":"10.1142/s2424942422400035","DOIUrl":"https://doi.org/10.1142/s2424942422400035","url":null,"abstract":"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, [Formula: see text]. 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.","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81004943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Workshop on Latex","authors":"Jackie Dunn","doi":"10.1142/s2424942422400138","DOIUrl":"https://doi.org/10.1142/s2424942422400138","url":null,"abstract":"","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85441783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crucial Events and Biology","authors":"P. Grigolini","doi":"10.1142/s2424942422400011","DOIUrl":"https://doi.org/10.1142/s2424942422400011","url":null,"abstract":"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. 1 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. 2 The observation of turbulent processes led to the discovery of new waiting time distribution densities, characterized by inverse power laws 3 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. 4 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). 5 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 [Formula: see text] noise that is traditionally interpreted as a manifestation of the Mandelbrot Fractional Brownian Motion (FBM). 6 I plan to show that the [Formula: see text] noise proposed in 5 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 7 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 8 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.","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85659721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization and Identification of Fungal Conidia via Shifted Excitation Raman Difference Spectroscopy","authors":"Zehua Han, B. Strycker, Blake Commer, Kai Wang, Brain D. Shaw, M. Scully, A. Sokolov","doi":"10.1142/s2424942422400059","DOIUrl":"https://doi.org/10.1142/s2424942422400059","url":null,"abstract":"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. 1 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. 2 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. 3 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. 4 , 5","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"356 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73969335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnosing Disease with Multifractality","authors":"Sage Copling","doi":"10.1142/s2424942422400096","DOIUrl":"https://doi.org/10.1142/s2424942422400096","url":null,"abstract":"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 1[Formula: see text]s 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. 1 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. 3 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. 2 The second method, presented later on, presented evidence that healthy","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83052104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Novel and Common Origin of Gamma-ray Bursts: A Galactic Seed Separation with Emitting Radiations","authors":"S. Nagao","doi":"10.1142/s2424942421500055","DOIUrl":"https://doi.org/10.1142/s2424942421500055","url":null,"abstract":"The mechanism of the gamma-ray burst is uncertain while the current candidates, respectively, for short and long GRBs are rather accepted. They conflict with some observed facts. Here we examine in detail the process for an energy circulation to separate to two ones by the energy circulation theory. We derive the equations of the force and the potential energy for the separation of a galactic seed. A galactic seed divides to two seeds orthogonally. If the receding speed is high enough, two seeds separate away orthogonally. If not enough, they are trapped at the energy trough, from where a subsequent flat separation occurs. The difference in the potential energy is partly emitted as gamma-ray radiations. The proposed process nicely meets the observed features of the GRBs, which the standard cosmology cannot explain. The GRBs are an important evidence to support our proposed model of galactic evolution, which includes galactic seed separations, as well as its basis; the energy circulation theory. Another key evidence, which we reported previously, is that the model predicts a constant speed of a galaxy rotation at any radial distances without dark matter.","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"164 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88397327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Energy Basic State Field of the Universe (I)","authors":"Xiaodong Yang, Jing Hu, Yuchen Yang","doi":"10.1142/s2424942422500074","DOIUrl":"https://doi.org/10.1142/s2424942422500074","url":null,"abstract":"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.","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"52 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90067707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Langevin Equations, Fokker–Planck Equations and Entropic Analysis of a Model-Independent Classical Plasma","authors":"Kendra Jean Jacques, Preet Sharma","doi":"10.1142/s2424942421500043","DOIUrl":"https://doi.org/10.1142/s2424942421500043","url":null,"abstract":"Plasma dynamics have been studied extensively and there is a fair amount of understanding where the scientific community has reached at. However, there is still a very big gap in completely explaining plasma physics at the classical as well as the quantum level. The dynamics of plasma from an entropic approach are not very well understood or explained. There is too much chaos to account for and even a small deviation in terms of perturbations of any kind makes a sizeable difference. This study is based on the entropic approach where we take a model independent classical plasma. Then we apply Langevin equations and Fokker–Planck equations to explain the entropy generated and entropy produced. Then we study various conditions in which we apply an electric field and a magnetic field and understand the various trends in entropy changes. When we apply the electric field and the magnetic fields independently of each other and together in the plasma model, we see that there is a very important change in the increase in entropy. There are also changes in the plasma flow, but the overall flow does not drastically change since we have considered a model independent plasma. Finally, we show that there are indeed changes to the entropy in a model-independent classical plasma in the various cases as mentioned in this study.","PeriodicalId":52944,"journal":{"name":"Reports in Advances of Physical Sciences","volume":"123 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80151036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}