Physical Basis Research Articles

Chemical Exchange Saturation Transfer MRI: What Neuro-Oncology Clinicians Need To Know.

Chemical exchange saturation transfer (CEST) is a relatively novel magnetic resonance imaging (MRI) technique with an image contrast designed for in vivo measurement of certain endogenous molecules with protons that are exchangeable with water protons, such as amide proton transfer commonly used for neuro-oncology applications. Recent technological advances have made it feasible to implement CEST on clinical grade scanners within practical acquisition times, creating new opportunities to integrate CEST in clinical workflow. In addition, the majority of CEST applications used in neuro-oncology are performed without the use gadolinium-based contrast agents which are another appealing feature of this technique. This review is written for clinicians involved in neuro-oncologic care (nonphysicists) as the target audience explaining what they need to know as CEST makes its way into practice. The purpose of this article is to (1) review the basic physics and technical principles of CEST MRI, and (2) review the practical applications of CEST in neuro-oncology.

Spin-phonon coupling and magnetic relaxation in single-molecule magnets.

Electron-phonon coupling is important in many physical phenomena, e.g. photosynthesis, catalysis and quantum information processing, but its impacts are difficult to grasp on the microscopic level. One area attracting wide interest is that of single-molecule magnets, which is motivated by searching for the ultimate limit in the miniaturisation of binary data storage media. The utility of a molecule to store magnetic information is quantified by the timescale of its magnetic reversal processes, also known as magnetic relaxation, which is limited by spin-phonon coupling. Several recent accomplishments of synthetic organometallic chemistry have led to the observation of molecular magnetic memory effects at temperatures above that of liquid nitrogen. These discoveries have highlighted how far chemical design strategies for maximising magnetic anisotropy have come, but have also highlighted the need to characterise the complex interplay between phonons and molecular spin states. The crucial step is to make a link between magnetic relaxation and chemical motifs, and so be able to produce design criteria to extend molecular magnetic memory. The basic physics associated with spin-phonon coupling and magnetic relaxation was outlined in the early 20th century using perturbation theory, and has more recently been recast in the form of a general open quantum systems formalism and tackled with different levels of approximations. It is the purpose of this Tutorial Review to introduce the topics of phonons, molecular spin-phonon coupling, and magnetic relaxation, and to outline the relevant theories in connection with both the traditional perturbative texts and the more modern open quantum systems methods.

Epicurean Stability (eustatheia): A Philosophical Approach of Stress Management

Epicurus used an empirical and sensualistic approach to knowledge, creating a consistent, naturalistic, pragmatic and consequentialistic philosophy. The scientific observations of the last centuries have confirmed the basic principles of Epicurean physics, as well the psychotherapeutic approach of Epicurean ethics, which fits human nature. We know from the work “On Frank Criticism” of Epicurean philosopher Philodemus of Gadara, that the teaching methodology of Epicureans included psychoeducational counseling through therapeutic criticism based on friendly freedom of speech and aiming at τῆς ψυχῆς θεραπείαν (psychotherapy) and at knowledge of maintaining mental health and well-being. The Epicureans called εὐστάθεια (eustatheia, “stability”) the psychosomatic balance (τὸ τῆς σαρκὸς καὶ ψυχῆς εὐσταθὲς κατάστημα), which today we call homeostasis (ὁμοιόστασις), and considered it the basis of true happiness. They recognized empirically the stress that disturbed psychosomatic homeostasis as an agitation of the psyche or a painful feeling of the body and used a number of mental and affective techniques (including the tetrapharmakos) to manage stress at its onset, so that it does not evolve into the particularly troublesome conditions of anxiety and/or depression, which may become chronic psychosomatic disorders with significant social consequences. The article discusses the relation of the main ethical teachings of Epicurus with the biological basis of human brain functions and with the management of stress by cognitive and behavioral psychotherapy.

The Correspondence of G. H. Lewes and Charles Darwin

The Correspondence of G. H. Lewes and Charles Darwin

Assessment on Digitalization of Basic Physics Courses: Need Analysis on the Use of Digital-based Assessment

Assessment is essential to measure students' achievement of learning objectives. Assessments in Basic physics courses are still categorized as manual, unstructured, and outdated. Using descriptive statistics, this study aims to investigate the need for digital assessments in Basic physics courses. The samples were taken from two public universities, two private universities, and a university with Physics Education Study Programs. They were half of each university students’ number per class. The number of respondents from Public university A, Public university B, Private University C, Private University D, and University E were 91, 49, 25, 20, and 29 students, respectively. Data collection was carried out using a questionnaire via a google form. Data obtained was analyzed by calculating the percentage for each indicator. Research indicators consist of the availability of teaching materials, the application of blended models, students' interest in basic physics, and the availability of assessments of the physics learning process. The results show that the five institutions that provide Basic Physics courses have not implemented digital assessments optimally. Of the five tertiary institutions that became the research sample, only one institution achieved the minimum target, with a score of 55.31% in the class of 2021 at university A. Meanwhile, the other four tertiary institutions did not achieve 50% in the last five batches. Therefore, lecturers must develop digital assessments in basic physics courses using the Kahoot application.

Analysis of Students' Mastery of Basic Physics Concepts in Lectures Using E-Books

The use of teaching materials has many benefits for students, one of which is to make it easier for students to find information and assist in mastering concepts. This pre-experimental study aims to describe students' mastery of Basic Physics concepts in lectures using e-books. The subjects of this study consisted of all students taking Basic Physics courses at the Biology Education Study Program, University of Mataram, with a total of 27 students. The research was conducted in 7 meetings, starting from October 24 2022 to December 5 2022. The concepts studied consisted of: Static Fluid, Dynamic Fluid, Vibration and Waves, Temperature and Heat. Student concept mastery data was obtained from giving essay tests at the 8th meeting. The level of mastery of the concept is divided into 8 grades namely A, B+, B, C+, C, D+, D, E. Students are declared to have passed if they get grade C, with levels of mastery of concepts ranging from 65 to less than 70. The results showed that the grades the lowest is 66.2 (grade C), while the highest is 91.5 (grade A). The average value of concept mastery is 77.8 (grade B). Thus, it can be concluded that the percentage of students' concept mastery who obtain a pass grade of 100%. The use of e-books can be an alternative teaching material that can be used by lecturers and students in an all-digital era. E-book users can access anytime and anywhere

Adaptive dynamic analysis-based optical coherence tomography angiography for blood vessel projection artifact suppression.

Optical coherence tomography angiography (OCTA) for blood vessel 3-D structure imaging suffers from blood vessel projection artifacts/tail artifacts when using a long decorrelation time (e.g., repeat B-scan acquisition in regular OCTA) or loss of micro vessel signal when using a short decorrelation time. In this work, we developed an adaptive first-order field autocorrelation function (g1) analysis-based technique to suppress the projection artifacts under macro vessels while enhancing the dynamic signal of micro vessels. The proposed method is based on the differences of the decorrelation rate and the phase variations of g1 between the vessel voxels and the artifacts regions. A short or long decorrelation time was applied to obtain the dynamic index of the projection artifacts region or the blood vessel region, respectively. Compared to the slab subtraction-based post-image processing-based techniques, the proposed approach addresses this problem on a physical basis and shows the ability to suppress the projection artifacts while enhancing the detection of the micro vessels.

Frequency Changes in Terminal Alkynes Provide Strong, Sensitive, and Solvatochromic Raman Probes of Biochemical Environments.

The C≡C stretching frequencies of terminal alkynes appear in the "clear" window of vibrational spectra, so they are attractive and increasingly popular as site-specific probes in complicated biological systems like proteins, cells, and tissues. In this work, we collected infrared (IR) absorption and Raman scattering spectra of model compounds, artificial amino acids, and model proteins that contain terminal alkyne groups, and we used our results to draw conclusions about the signal strength and sensitivity to the local environment of both aliphatic and aromatic terminal alkyne C≡C stretching bands. While the IR bands of alkynyl model compounds displayed surprisingly broad solvatochromism, their absorptions were weak enough that alkynes can be ruled out as effective IR probes. The same solvatochromism was observed in model compounds' Raman spectra, and comparisons to published empirical solvent scales (including a linear regression against four meta-aggregated solvent parameters) suggested that the alkyne C≡C stretching frequency mainly reports on local electronic interactions (i.e., short-range electron donor-acceptor interactions) with solvent molecules and neighboring functional groups. The strong solvatochromism observed here for alkyne stretching bands introduces an important consideration for Raman imaging studies based on these signals. Raman signals for alkynes (especially those that are π-conjugated) can be exceptionally strong and should permit alkynyl Raman signals to function as probes at very low concentrations, as compared to other widely used vibrational probe groups like azides and nitriles. We incorporated homopropargyl glycine into a transmembrane helical peptide via peptide synthesis, and we installed p-ethynylphenylalanine into the interior of the Escherichia coli fatty acid acyl carrier protein using a genetic code expansion technique. The Raman spectra from each of these test systems indicate that alkynyl C≡C bands can act as effective and unique probes of their local biomolecular environments. We provide guidance for the best possible future uses of alkynes as solvatochromic Raman probes, and while empirical explanations of the alkyne solvatochromism are offered, open questions about its physical basis are enunciated.

Development of Habits of Mind Instruments in the Context of Basic Physics Practicum: EFA and Rasch Model

Assessing the habits of mind among prospective teachers is an essential part of learning. Therefore, this research aims to develop the habits of mind instrument in the context of basic physics practicum. It was conducted using the research and development method which has three stages namely (1) planning the test, (2) implementing the test, and (3) determining the validity and reliability. The sample consisted of 105 biology teacher candidates taking basic physics courses. The habits of mind instrument developed was in the form of a questionnaire consisting of 52 items and is related to basic physics practicum. Furthermore, exploratory factor analysis and the Rasch model approach were used in developing the instrument. Based on expert judgment using Fleiss Kappa, the content validity was 0.700 and was classified in the good category. The developed instrument was considered reliable based on Cronbach’s alpha value of 0.970. The exploratory factor analysis reduced the dimensions of the instrument to 11 factors. The analysis of the Rasch model met the element of unidimensionality. There is no bias on the instrument based on gender and place of residence. However, efforts are needed to overcome the lack of creative thinking habits among prospective biology teachers.

Environmental Intelligence using Machine Learning Applications

The big data deluge has presented us with a unique opportunity to observe the environment. These sensors employ the basic physics principles in sensing the environment. These include but are not limited to, remote sensing of air quality, temperature, or other biophysical variables. Although a great effort has been placed into collecting the data, a greater effort must be placed into their societal applications. Machine Learning tools can provide easy access to build such applications. Continuous monitoring and alerting the interested parties can prevent some undesirable outcomes. For example, a weather forecast is widely used to predict the temperature/precipitation a few days in advance. Similarly, new applications can be developed to practice intelligent decision-making that affects public health. Recent progress in air quality studies is promising to develop such environmental intelligence. In this review article, we illustrate the use of Machine Learning in making predictions and discuss some of the applications of the relevant data sets for Environmental Intelligence.

Good and Evil from the Point of View of Physics

The article analyzes the concepts of "good" and "evil" from the point of view of physics. Although the physical concept of “entropy” as a measure of disorder was the first candidate who could serve as the physical basis of these ethical concepts, in fact it is not suitable for this purpose. However, the “entropic potential of the event” Z (T, A) that describes the impact of the event A that occurred in the moment T0 in the system R to the entropy of this system at the future moment T (T > T0) is well suited for our analysis. The article describes methods for calculating the “entropic potential of the event” for certain real-life events and discuss several other related ideas, such as “time factor”, “averaging” and “universality”.

Measurements of Na+-occluded intermediates during the catalytic cycle of the Na+/K+-ATPase provide novel insights into the mechanism of Na+ transport

The Na+/K+-ATPase is an integral plasma membrane glycoprotein of all animal cells that couples the exchange of intracellular Na+ for extracellular K+ to the hydrolysis of ATP. The asymmetric distribution of Na+ and K+ is essential for cellular life and constitutes the physical basis of a series of fundamental biological phenomena. The pumping mechanism is explained by the Albers-Post model. It involves the presence of gates alternatively exposing Na+/K+-ATPase transport sites to the intracellular and extracellular sides and includes occluded states in which both gates are simultaneously closed. Unlike for K+, information is lacking about Na+-occluded intermediates, as occluded Na+ was only detected in states incapable of performing a catalytic cycle, including two Na+-containing crystallographic structures. The current knowledge is that intracellular Na+ must bind to the transport sites and become occluded upon phosphorylation by ATP to be transported to the extracellular medium. Here, taking advantage of epigallocatechin-3-gallate to instantaneously stabilize native Na+-occluded intermediates, we isolated species with tightly bound Na+ in an enzyme able to perform a catalytic cycle, consistent with a genuine occluded state. We found that Na+ becomes spontaneously occluded in the E1 dephosphorylated form of the Na+/K+-ATPase, exhibiting positive interactions between binding sites. In fact, the addition of ATP does not produce an increase in Na+ occlusion as it would have been expected; on the contrary, occluded Na+ transiently decreases, whereas ATP lasts. These results reveal new properties of E1 intermediates of the Albers-Post model for explaining the Na+ transport pathway.

Constructing generic effective field theory for all masses and spins

We solve the long-standing problem of operator basis construction for fields with all masses and spins. Based on the on-shell method, we propose a novel method to systematically construct a complete set of lowest dimensional amplitude bases at any given dimension through semistandard Young tableaus of Lorentz subgroup $SU(2{)}_{r}$ and global symmetry $U(N)$ ($N$ is the number of external legs), which can be directly mapped into physical operator bases. We first construct a complete set of independent monomial bases whose dimension is not the lowest and a redundant set of bases that always contains a complete set of amplitude bases with the lowest dimension. Then we decompose the bases of the redundant set into the complete monomial bases from low to high dimension and eliminate the linear correlation bases. Finally, the bases with the lowest dimension can be picked up. We also propose a matrix projection method to construct the massive amplitude bases involving identical particles. The operator bases of a generic massive effective field theory can be efficiently constructed by the computer programs. A complete set of four-vector operators at dimensions up to six is presented.

The Rise of 212 MAX Phase Borides: DFT Insights into the Physical Properties of Ti2PB2, Zr2PbB2, and Nb2AB2 [A = P, S] for Thermomechanical Applications.

In this article, ab initio calculations of unexplored Ti2PB2, Zr2PbB2, and Nb2AB2 [A = P, S] were performed wherein Ti2PB2 along with its 211 boride phase Ti2PB was predicted for the first time. The stability was confirmed by calculating the formation energy, phonon dispersion curve, and elastic stiffness constants. The obtained elastic constants, elastic moduli, and Vickers hardness values of Ti2PB2, Zr2PbB2, and Nb2AB2 [A = P, S] were found to be significantly larger than those of their counterparts 211 borides and carbides. The studied compounds are brittle, like most MAX and MAB phases. The electronic band structure and density of states revealed the metallic nature of the titled borides. Several thermal parameters were explored, certifying the suitability of Ti2PB2, Zr2PbB2, and Nb2AB2 [A = P, S] to be used as efficient thermal barrier coating materials. The response of Ti2PB2, Zr2PbB2, and Nb2AB2 [A = P, S] to the incident photon was studied by computing the dielectric constant (real and imaginary parts), refractive index, absorption coefficient, photoconductivity, reflectivity, and energy loss function. In this work, we have explored the physical basis of the improved thermomechanical properties of 212 MAX phase borides compared to their existing carbide and boride counterparts.

Identification and mechanistic basis of non-ACE2 blocking neutralizing antibodies from COVID-19 patients with deep RNA sequencing and molecular dynamics simulations.

Variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continue to cause disease and impair the effectiveness of treatments. The therapeutic potential of convergent neutralizing antibodies (NAbs) from fully recovered patients has been explored in several early stages of novel drugs. Here, we identified initially elicited NAbs (Ig Heavy, Ig lambda, Ig kappa) in response to COVID-19 infection in patients admitted to the intensive care unit at a single center with deep RNA sequencing (>100 million reads) of peripheral blood as a diagnostic tool for predicting the severity of the disease and as a means to pinpoint specific compensatory NAb treatments. Clinical data were prospectively collected at multiple time points during ICU admission, and amino acid sequences for the NAb CDR3 segments were identified. Patients who survived severe COVID-19 had significantly more of a Class 3 antibody (C135) to SARS-CoV-2 compared to non-survivors (15059.4 vs. 1412.7, p = 0.016). In addition to highlighting the utility of RNA sequencing in revealing unique NAb profiles in COVID-19 patients with different outcomes, we provided a physical basis for our findings via atomistic modeling combined with molecular dynamics simulations. We established the interactions of the Class 3 NAb C135 with the SARS-CoV-2 spike protein, proposing a mechanistic basis for inhibition via multiple conformations that can effectively prevent ACE2 from binding to the spike protein, despite C135 not directly blocking the ACE2 binding motif. Overall, we demonstrate that deep RNA sequencing combined with structural modeling offers the new potential to identify and understand novel therapeutic(s) NAbs in individuals lacking certain immune responses due to their poor endogenous production. Our results suggest a possible window of opportunity for administration of such NAbs when their full sequence becomes available. A method involving rapid deep RNA sequencing of patients infected with SARS-CoV-2 or its variants at the earliest infection time could help to develop personalized treatments using the identified specific NAbs.

Calculation of the thermal conductivity coefficient of nanocrystals

Mathematical modeling methods are powerful tools in the design of various types of nanosystems and the analysis of processes taking place in them. Note that the main tasks of mathematical modeling in nanoscale systems are: the formation of nanoelements, the interaction of individual elements of the nanosystem, the determination of the structure of the isolated nanosystem in dynamic states, the calculation of the parameters of the nanosystem during its interaction with the environment, the calculation of the macro parameters of the nanosystem. With this work, we continue the consistent presentation of theoretical foundations, methods of modeling, and results of calculations of macro characteristics of nanosystems, based on the work on modeling of processes of formation and structure of different nanosystems. This paper provides the physical basis as well as numerical methods for calculating the thermal conductivity of homogeneous nanosystems. Computer simulation of the calculation of the thermal conductivity coefficient of silicon-based nanocrystals by molecular dynamics was carried out in the LAMMPS software complex. Equations describing multi-particle MEAM potentials are considered. The problem of determining the thermal conductivity coefficient has been solved in several steps. In molecular dynamic calculations, the value of the thermal conductivity coefficient can be calculated in various ways. This work uses the Green - Kubo formalism, which associates the autocorrelation function of heat flow with the coefficient of thermal conductivity. Temperature dependencies of thermal conductivity coefficient for silicon-based materials are determined. Calculations of thermophysical characteristics of homogeneous silicon-based nanosystems were made. The curves of the temperature dependence of thermal conductivity coefficient for systems of different dimensions are presented. Data obtained using MEAM potentials were compared with experimental data. It was found that the nature of the curves and the values obtained during the simulation are well consistent with the experimental data.

The Role of Quantum Mechanics in Understanding the Phenomenon of Consciousness

The article analyzes the effectiveness of quantum theories of mental experience in relation to two ontological problems - the problem of the existence of consciousness in the material world and the problem of the interaction of consciousness and body. A critical analysis of the quantum theories of consciousness by Penrose-Hameroff, M. Tegmark, G. Stapp, M. Fischer and M.B. Mensky shows that they fail to fully explain how complex physical systems generate mental experience without violating the principle of causal closure of the physical world and the principle of epistemological completeness of physics. Quantum mechanics provides specific processes that are the physical basis of the psyche, but do not explain the phenomenal aspect of subjective reality. Nevertheless, the Heisenberg uncertainty principle gives an understanding of how the interaction of consciousness and body within the scientific picture of the world can be carried out without violating the law of energy conservation. It is shown that the quantum theories of consciousness currently being developed have a predominantly panprotopsychic character, which faces a problem due to the fact that the protomental property of physical systems must be expressed quantitatively and correspond to the value included in the physical equations. As a result, it is concluded that in order to develop quantum theories of consciousness more effectively, it is necessary to give an emergent character, not jumping from the quantum level to the psychic, but explaining the mechanism of the emergence of systemic properties during the sequential transition between different ontological regions of existence, including physical, chemical, biological, neurophysiological and psychic.

Adapting a Physical Earthquake-Aftershock Model to Simulate the Spread of COVID-19

There exists a need for a simple, deterministic, scalable, and accurate model that captures the dominant physics of pandemic propagation. We propose such a model by adapting a physical earthquake/aftershock model to COVID-19. The aftershock model revealed the physical basis for the statistical Epidemic Type Aftershock Sequence (ETAS) model as a highly non-linear diffusion process, thus permitting a grafting of the underlying physical equations into a formulation for calculating infection pressure propagation in a pandemic-type model. Our model shows that the COVID-19 pandemic propagates through an analogous porous media with hydraulic properties approximating beach sand and water. Model results show good correlations with reported cumulative infections for all cases studied. In alphabetical order, these include Austria, Belgium, Brazil, France, Germany, Italy, New Zealand, Melbourne (AU), Spain, Sweden, Switzerland, the UK, and the USA. Importantly, the model is predominantly controlled by one parameter (α), which modulates the societal recovery from the spread of the virus. The obtained recovery times for the different pandemic waves vary considerably from country to country and are reflected in the temporal evolution of registered infections. These results provide an intuition-based approach to designing and implementing mitigation measures, with predictive capabilities for various mitigation scenarios.

Basic Physics of Ultrasound Elastography

Basic Physics of Ultrasound Elastography

Acidity and metal complexation of edge surface of birnessite-type MnO2: Insight from first principles simulations.

Birnessite-type MnO2 plays key roles in scavenging trace elements in numerous natural environments and has also been regarded as a promising energy storage material. The interfacial properties of birnessite are highly pH-dependent due to the presence of various amphoteric groups on its edges, and, therefore, the acidity constants (pKa) of these groups are vital to the understanding of its electrochemical and environmental performances. However, an accurate acidity dataset for birnessite is absent yet. In this study, we employed first-principles molecular dynamics simulations and the vertical energy gap method to calculate the pKas of groups on the birnessite (010) edge. The interfacial hydration structure was characterized with a focus on the hydrogen bonding network. The obtained pKas suggest that MnOH2 is active while Mn2OH remains inert in a common pH range. Based on these results, the incorporation of transition metals on the edge surface was investigated by taking Ni2+ and Zn2+ as the model cations. The energy changes associated with the incorporation process of Ni2+ from the outer-sphere state indicate that incorporation on the edge surface is more feasible than that on the basal surface presumed in previous studies. Overall, the results obtained provide an atomic-scale insight into the acid-base chemistry of birnessite and form a physical basis for understanding the interfacial processes of birnessite.