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This article features an interview with Jingjing Sun and Angelike Stathopoulos, who conducted a study on the collective migration of caudal visceral mesoderm (CVM) cells in Drosophila embryos. They discovered that cell division coordinates two gene expression programs in migrating CVM cells. The researchers discuss their scientific backgrounds and the questions they are trying to answer in their lab. They also highlight the importance of the Drosophila system for their research. The study's key findings include the identification of two groups of genes that regulate the behaviors of CVM cells during migration, and the role of cell division in controlling gene expression programs. The researchers also discuss their motivations and future directions for their research. [Extracted from the article]

The five papers published by Hodgkin and Huxley in 1952 are seminal works in the field of physiology, earning their authors the Nobel Prize in 1963 and ushering in the era of membrane biophysics. The papers present a considerable challenge to the novice student, but this has been partly allayed by recent publications that have updated the reporting of current and voltage to reflect the modern convention and two books that describe the contents of the papers in detail. A disadvantage is that these guides contain hundreds of pages, requiring considerable time and energy on behalf of the reader. We present a concise guide to the Hodgkin and Huxley papers that includes only essential content, with the data presented in a linear and logical manner. We have color-coded figures for ease of understanding and included boxes that summarize key information for easy reference. It is our expectation that this article will act as an accessible introduction for students to the work of Hodgkin and Huxley and hopefully foster an appreciation for a fascinating story that repays in-depth study. NEW & NOTEWORTHY The Hodgkin and Huxley papers continue to inspire and intimidate, 70 years after their publication. The diverse subjects they cover include advanced experimental procedures, complex data analysis, calculus, and modeling, all of which ensure the papers can present a challenging read. We present a concise guide to the papers that includes only essential content depicted in color-coded graphs, allowing tracking of data from recordings to analysis and incorporation into the model to ease understanding. [ABSTRACT FROM AUTHOR]

Abstract In order to make 2nd-generation biofuels more competitive, high solid-matter content has to be reached. To progress towards this target, the mechanism for destructuring lignocellulose fibres in semidilute conditions has to be well understood, as this configuration shows the basic mechanism which limits transfers and efficiency. This study aims to delve deeply into the biophysical and transfer limitations occurring during enzymatic hydrolysis. A specific experimental set-up associating in-situ and ex-situ physical (rheometry, chord length analysis) and biochemical analysis was used to expand the knowledge of hydrolysis of extruded softwood paper pulp over 24 h under different substrate concentrations (1%–3%) and enzyme doses (Accellerase 1500, 5 and 25 FPU/g cellulose). Non-Newtonian behaviour associated with pronounced yield stress stand as the major factors limiting process efficiency. A critical time was deduced from viscosity evolution, and the existence of a unique, dimensionless viscosity-time curve was established, suggesting similar mechanisms for fibre degradation. In addition, chord length distribution allowed for the description of population evolution and was discussed in the light of in-situ viscosity and hydrolysis yield. Physical (viscosity, particle size) and biochemical (substrate) kinetics were modelled (second-order) and coefficients identified. A chronology of the encountered phenomenological limitations demonstrates the necessity of optimising bioprocesses by considering physical parameters. A reference feed rate is proposed in order to reach high solid loading under fed-batch strategy. Highlights • An in- & ex-situ multiscale approach was used to study the paper pulp hydrolysis. • The bio-physical and transfer limitations during hydrolysis were investigated. • A non-Newtonian behaviour was the major factor limiting process efficiency. • A unique dimensionless viscosity-time curve was identified. • A reference feed rate is proposed to reach high solid loading with fed-batch mode. [ABSTRACT FROM AUTHOR]

While mounting evidence indicates that a phylogenetically diverse group of animals detect Earth-strength magnetic fields, a magnetoreceptor has not been identified in any animal. One possible reason that identifying a magnetoreceptor has proven challenging is that, like many research fields, magnetoreception research lacks extensive independent replication. Independent replication is important because a subset of studies undoubtedly contain false positive results and without replication it is difficult to determine whether the outcome of an experiment is a false positive. However, we report here a reanalysis of a well-cited paper on honeybee magnetoreception demonstrating that the original paper represented a false positive finding caused by incorrect estimates of probability. We also point out how good experimental design practices could have revealed the error prior to publication. Hopefully, this reanalysis will serve as a reminder of the importance of good experimental design in order to reduce the likelihood of publishing false positive results. [ABSTRACT FROM AUTHOR]

This document is a compilation of various scientific papers and preprints covering a wide range of topics, including protein folding, cell migration, machine learning, deep neural networks, neural scaling laws, representations and generalization in artificial and brain neural networks, and the neuron as a direct data-driven controller. The papers discuss different aspects of these subjects, providing a comprehensive overview of the current research in these fields. This document can be a valuable resource for library patrons conducting research on these topics, particularly in the fields of neuroscience and artificial intelligence. [Extracted from the article]

Understanding active matter has led to new perspectives on biophysics and non-equilibrium dynamics. However, the development of numerical tools for simulating active fluids capable of incorporating non-trivial boundaries or inclusions has lagged behind. Active particle-based methods, which typically excel at this, suffer from large density fluctuations that affect the dynamics of inclusions. To this end, we advance the Active-Nematic Multi-Particle Collision Dynamics algorithm, a particle-based method for simulating active nematics, by addressing the large density fluctuations that arise from activity. This paper introduces three activity formulations that mitigate the coupling between activity and local density. Local density fluctuations are decreased to a level comparable to the passive limit while retaining active nematic phenomenology and increasing the active turbulence regime four-fold in two dimensions. These developments extend the technique into a flexible tool for modeling active systems, including solutes and inclusions, with broad applications for the study of biophysical systems. Particle-based models of soft active matter are known to exhibit large density fluctuations, which may be problematic for considering homogeneous systems. Through considering the coupling of activity to local density, we reduce density fluctuations while retaining active turbulent dynamics. [ABSTRACT FROM AUTHOR]

Definition: This entry paper is an attempt to explain how the discrete nature of light (energy discreteness in the form of photons) constrains the light detection process all along the evolutionary path, in the not-fully-understood photoreceptive systems of unicellular microorganisms (nonimaging systems) and in the complex and well-known visual system of higher organisms (imaging systems). All these systems are perfect examples of the interplay between physics and biology, i.e., they are the perfect topic of research for biophysicists. The paper describes how photoreceptive and visual systems achieve the goal of photon counting, which information is conveyed by a finite number of photons, and which noise factors limit light-detecting processes. [ABSTRACT FROM AUTHOR]

Trapping diffusive particles at surfaces is a key step in many systems in chemical and biological physics. Trapping often occurs via reactive patches on the surface and/or the particle. The theory of boundary homogenization has been used in many prior works to estimate the effective trapping rate for such a system in the case that either (i) the surface is patchy and the particle is uniformly reactive or (ii) the particle is patchy and the surface is uniformly reactive. In this paper, we estimate the trapping rate for the case that the surface and the particle are both patchy. In particular, the particle diffuses translationally and rotationally and reacts with the surface when a patch on the particle contacts a patch on the surface. We first formulate a stochastic model and derive a five-dimensional partial differential equation describing the reaction time. We then use matched asymptotic analysis to derive the effective trapping rate, assuming that the patches are roughly evenly distributed and occupy a small fraction of the surface and the particle. This trapping rate involves the electrostatic capacitance of a four-dimensional duocylinder, which we compute using a kinetic Monte Carlo algorithm. We further use Brownian local time theory to derive a simple heuristic estimate of the trapping rate and show that it is remarkably close to the asymptotic estimate. Finally, we develop a kinetic Monte Carlo algorithm to simulate the full stochastic system and then use these simulations to confirm the accuracy of our trapping rate estimates and homogenization theory. [ABSTRACT FROM AUTHOR]

We examine the use of time series data, derived from Electric Cell-substrate Impedance Sensing (ECIS), to differentiate between standard mammalian cell cultures and those infected with a mycoplasma organism. With the goal of easy visualization and interpretation, we perform low-dimensional feature-based classification, extracting application-relevant features from the ECIS time courses. We can achieve very high classification accuracy using only two features, which depend on the cell line under examination. Initial results also show the existence of experimental variation between plates and suggest types of features that may prove more robust to such variation. Our paper is the first to perform a broad examination of ECIS time course features in the context of detecting contamination; to combine different types of features to achieve classification accuracy while preserving interpretability; and to describe and suggest possibilities for ameliorating plate-to-plate variation. [ABSTRACT FROM AUTHOR]

This research delves into a comprehensive exploration of exact solutions for the time-space fractional phi-four equation through the implementation of both the unified method and the modified Khater method. The Phi-four equation, rooted in the Klein-Gordon model, holds significance in diverse scientific realms, such as biological and nuclear physics, making it imperative to unravel its solutions. Leveraging a well-suited wave transformation, the governing equation is transformed into an ordinary differential equation, laying the groundwork for an in-depth analysis. The proposed methodologies yield a rich spectrum of solutions, encompassing trigonometric, hyperbolic, and rational forms. These solutions manifest as Kink, bright singular, dark, combo dark bright, periodic and singular periodic solutions, each characterized by explicit conditions defining their validity. The versatility and computational robustness of these methods establish a robust framework for soliton research. To provide a comprehensive assessment, a comparative analysis is conducted, contrasting the outcomes obtained through the proposed methodologies with those derived from earlier approaches. A key fact of this study is the visual representation of a subset of these solutions through carefully crafted graphical illustrations. Parameter values are judiciously selected to elucidate the nuanced characteristics of the solutions, enhancing our understanding of the model's physical behavior. It is noteworthy that all computations are meticulously executed with Mathematica software, underscoring the precision and computational efficiency integral to this research. The novelty of this paper lies in the identification of new solutions through the application of the unified and modified Khater methods. These solutions are not previously documented in existing literature. The visual depictions of dynamic behaviors through two and three-dimensional figures further contribute to the originality of our findings. [ABSTRACT FROM AUTHOR]

The European Biophysics Journal Prizes awarded at the European Biophysical Societies Association (EBSA) Congress in Stockholm in the Summer of 2023 recognised papers published in 2020 and 2021 which made use of multiple complementing experimental, theoretical and computational approaches. One of the winning papers addressed the specific role of arginine residues within antimicrobial and cell-penetrating peptides, in promoting membrane defect stabilisation and pore formation. The other winning paper described the influence of atomic force microscopy probe geometry on the measurement of surface deformability, assessed for investigation of the differing viscoelastic properties of non-malignant and cancerous cells. These papers showcase biophysical science; the importance of combining different experimental, modelling and molecular dynamics methods; and how researchers need to understand the theoretical basis and the limitations of the techniques they use. EBSA warmly congratulates the authors on their work and its subsequent recognition. Publication of these papers also demonstrates the ongoing commitment of the European Biophysics Journal to molecular scale and to systems biophysics, and to support of the international biophysical community. [ABSTRACT FROM AUTHOR]

Respiratory interactions with the heart have remained a challenging physiological phenomenon since their discovery more than two hundred and fifty years ago. In the course of translating the seminal publications of Carl Ludwig and his disciple Pavel Petrovich Einbrodt into English, we became aware of some under-appreciated aspects of their work that contain useful insights into the history of the phenomenon now called respiratory arrhythmia. Ludwig observed arrhythmic effects of respiratory movements in experiments on dogs and horses and published his findings in 1847. He subsequently undertook further work on this problem, together with Einbrodt. Already in 1847 Ludwig had mentioned an exciting observation on the possible role of mechanical factors of the respiratory movements on the action of the heart in a dog in whom he had artificially induced bouts of coughing. Einbrodt decided to systematically develop methods to increase or decrease the pressure of the air the animal had to breathe. He observed that this procedure led to a greater or lesser degree of compression or decompression of all the organs in the thoracic cavity without apparently causing harmful consequences during the time of its application. How the mechanical influence of breathing affects cardiac activity during respiratory arrhythmia has been the subject of scientific discussions and controversies over a period of more than 150 years and is still unresolved. Recent publications suggest that cardiac mechano-electrical coupling plays an important role in the emergence of cardio-respiratory interdependence. [ABSTRACT FROM AUTHOR]

The light-gated cation channel Channelrhodopsin-2 (ChR2), a retinylidene protein found in the eye-spot of Chlamydomonas reinhardtii, became an optogenetic tool to trigger neurophysiological responses by light and, thus, revolutionized spatio-temporal studies of such processes. The reaction mechanism still remains elusive but recent vibrational spectroscopic experiments started to resolve details of the associated structural changes during the photocycle. Large alterations in the polypeptide backbone were observed by FT-IR spectroscopy that precede and succeed the opening and closing of the channel, respectively. However, the molecular switch that controls gating is still unknown. Here, we present difference spectra of the D156E mutant of ChR2 and assign the observed vibrational bands to crucial hydrogen bonding changes of this residue in various intermediate states of the photoreaction. By comparison with spectra of wild-type ChR2 and the C128T mutant and correlation to electrophysiological studies, we propose the DC gate as a crucial hydrogen-bonding interaction between D156 and C128 which may represent the valve of the channel. [ABSTRACT FROM AUTHOR]

The introduction of time-resolved Fourier transform infrared (FT-IR) spectroscopy to biochemistry opened the possibility of monitoring the catalytic mechanism of proteins along their reaction pathways. The infrared approach is very fruitful, particularly in the application to membrane proteins where NMR and X-ray crystallography are challenged by the size and protein hydrophobicity, as well as by their limited time-resolution. Here, we summarize the principles and experimental realizations of time-resolved FT-IR spectroscopy developed in our group and compare with aspects emerging from other laboratories. Examples of applications to retinal proteins and energy transduction complexes are reviewed, which emphasize the impact of time-resolved FT-IR spectroscopy on the understanding of protein reactions on the level of single bonds. [ABSTRACT FROM AUTHOR]

Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes. [ABSTRACT FROM AUTHOR]

As we celebrate the 50th year of the American Association of Physicists in Medicine (AAPM), what better time to look back at our development as well as to look forward to the opportunities that lie ahead. Here the authors will review some of the achievements of the Education Council and show how the activities are helping to shape the future educational goals and opportunities of the AAPM and the medical physics profession. Much of the work of the Education Council is carried out by the various committees and subcommittees that make up the Council or have a liaison relationship with the Council. [ABSTRACT FROM AUTHOR]

A key biophysical process in biological systems, liquid–liquid phase separation (LLPS) is responsible for constructing membrane-less organelles and modulating cellular activities. The biophysical mechanisms underlying LLPS are explored in this paper, with an emphasis on multivalent interactions, entropy-driven processes, and how they affect cellular organization. We investigate the impact of external stimuli on phase behavior and clarify the physiological roles of biomolecular condensates, from stress response modulation to gene expression regulation. In addition, we study dysregulated LLPS in human disorders, providing information about possible therapeutic targets and approaches to innovative therapeutics. Through this interdisciplinary approach, we aim to improve our knowledge of LLPS and its effects on health and illness, opening the door to new therapeutic approaches that focus on the behavior of proteins and the structure of cells. [ABSTRACT FROM AUTHOR]

The anterolateral ligament (ALL) was first described in 1879 in the context of Segond fractures, which correlate with a 75–100% chance of an anterior cruciate ligament (ACL) tear or a 66–75% chance of a meniscal tear. The purpose of this paper is to provide an updated comprehensive review on the anterolateral ligament complex of the knee focusing on the: (1) anatomy of the ALL/ALC; (2) associated biomechanics/function; and (3) important surgical considerations in contemporary anterior cruciate ligament (ACL) reconstruction and total knee arthroplasty (TKA). A systematic review of studies on ALL was conducted on Pubmed/MEDLINE and Cochrane databases (May 7th, 2020 to February 1st, 2022), with 20 studies meeting inclusion/exclusion criteria. Studies meeting inclusion criteria were anatomical/biomechanical studies assessing ALL function, cadaveric and computer simulations, and comparative studies on surgical outcomes of ALLR (concomitant with ACL reconstruction). Eight studies were included and graded by MINOR and Newcastle–Ottawa scale to identify potential biases. The anatomy of the ALL is part of the anterolateral ligament complex (ALC), which includes the superficial/deep iliotibial band (including the Kaplan fiber system), iliopatellar band, ALL, and anterolateral capsule. Multiple biomechanical studies have characterized the ALC as a secondary passive stabilizer in resisting tibial internal rotation. Given the role of the ALC in resisting internal tibial rotation, lateral extra-articular procedures including ALL augmentation may be considered for chronic ACL tears, ACL revisions, and a high-grade pivot shift test. In the context of TKA, in the event of injury to the ALC, a more constrained implant or soft-tissue reconstruction may be necessary to restore appropriate knee stability. [ABSTRACT FROM AUTHOR]

Presented is a brief summary of recent developments of topics addressed by the reviews and original papers of this volume related to non-equilibrium phenomena in various (especially mesoscopic) systems, the foundations of quantum physics, quantum optics and related fields of physics including biophysics, cosmology, gravitation and astrophysics. [ABSTRACT FROM AUTHOR]

Biophysically detailed simulations of neuronal activity often rely on solving large systems of differential equations; in some models, these systems have tens of thousands of states per cell. Numerically solving these equations is computationally intensive and requires making assumptions about the initial cell states. Additional realism from incorporating more biological detail is achieved at the cost of increasingly more states, more computational resources, and more modeling assumptions. We show that for both a point and morphologically-detailed cell model, the presence and timing of future action potentials is probabilistically well-characterized by the relative timings of a moderate number of recent events alone. Knowledge of initial conditions or full synaptic input history is not required. While model time constants, etc. impact the specifics, we demonstrate that for both individual spikes and sustained cellular activity, the uncertainty in spike response decreases as the number of known input events increases, to the point of approximate determinism. Further, we show cellular model states are reconstructable from ongoing synaptic events, despite unknown initial conditions. We propose that a strictly event-based modeling framework is capable of representing the complexity of cellular dynamics of the differential-equations models with significantly less per-cell state variables, thus offering a pathway toward utilizing modern data-driven modeling to scale up to larger network models while preserving individual cellular biophysics. Author summary: There are 86 billion neurons in the human brain, each of which is a complex cell that responds to synaptic stimuli of other neurons with electrical signals. Neuroscientists have uncovered many of the biophysical mechanisms underlying the neuron's function and utilize them to create detailed simulations of neurons and neural networks. However, due to the complexity of the neuron, these simulations require extensive computational resources. In this paper, we present a new modeling framework that incorporates the discrete synaptic events of neurons with the detailed mechanistic modeling of their biophysics, using a strictly event-based protocol. We investigate the extent to which this new event-based framework behaves like the existing conductance-based modeling approach by measuring how much its future responses vary provided different numbers of past input stimuli. This framework is an entry point for integrating machine learning methods to assist in reducing the computational complexity of detailed neuron modeling. The goal of this work is to enable researchers to better integrate mechanistic understanding of cell biology into broader multiscale studies. [ABSTRACT FROM AUTHOR]

Deep brain stimulation (DBS) in thalamic reticular nucleus (TRN) neuron provides a novel treatment for drug-resistant epilepsy via the induced electrical field (EFs). However, the mechanisms underlying EF effects remain unclear. This paper investigated how EFs regulate low-threshold dendritic Ca2+ (dCa) response and thus contribute to the input–output relationship of TRN cell. Our results showed that EFs modulate firing modes differently in a neuronal state-dependent manner. At the depolarized state, EFs only regulate the spike timing of a somatic stimulus-evoked single action potential (AP) with less contribution in the regulation of dCa response but could induce the transition between a dendritic stimulus-evoked single AP and a tonic burst of APs via the moderate regulation of dCa response. At the hyperpolarized state, EFs have significant effects on the dCa response, which modulate the large dCa response-dependent burst discharge and even cause a transition from this type of burst discharge to a single AP with less dCa response. Moreover, EF effects on stimulation threshold of somatic spiking prominently depend on EF-regulated dCa responses and the onset time differences between the stimulus and EF give rise to the distinct effect in the EF regulation of dCa responses. Finally, the larger neuronal axial resistance tends to result in the dendritic stimulus-evoked dCa response independent of somatic state. Interestingly, in this case, the EF application could reproduce the similar somatic state-dependent dCa response to dendritic stimulus which occurs in the case of lower axial resistance. These results suggest that the influence of EF on neuronal activities depends on neuronal intrinsic properties, which provides insight into understanding how DBS in TRN neuron modulates epilepsy from the point of view of biophysics. [ABSTRACT FROM AUTHOR]

In this paper, a biophysical fractional diffusive cancer model with virotherapy is thoroughly analyzed and analytically simulated. The goal of this biophysical model is to represent both the dynamics of cancer development and the results of virotherapy, which uses viruses to target and destroy cancer cells. The Caputo sense is applied to the fractional derivatives. We look at the governing model's existence and uniqueness. For analytical solutions, the Laplace residual power series approach is used. The study investigates the model's dynamic behavior, shedding light on the development of cancer and the effects of virotherapy. The research advances our knowledge of cancer modeling and treatment options. Numerical simulations show the agreement between the analytical results and the related numerical solutions, proving the usefulness of the analytical solution. [ABSTRACT FROM AUTHOR]

This paper add new step information study ability of work on dopant Zink by 0.01% to nano crystal of NiFe3O4 that has good VSM signal on 33% Ni and 67% Fe to check ability to use it as a base on MRI Contrast Agent. BY using Hydrothermal technique  to prepare NiFexOy  this type of preparation results in cubic ferrites structure depending on the purity and condition of preparation. This paper will show some results of this material structure with dopant of Zinck this utility used contrast agent base in a medical physics Magnetisation properties study for super spinel ferrites. Data analyzing by use tow examination X-Ray diffraction Analysis and vibrating Sample Magnetometer. [ABSTRACT FROM AUTHOR]

Analysis of single cells after elasticity measurement may construct a linkage between biophysics and other cellular properties, e.g., cell signaling and genetics. This paper reports a microfluidic technology integrating trapping, elasticity measurement, and printing of single cells based on the precise regulation of pressure across an array of U-shaped traps. Both numerical and theoretical analyses revealed that the positive and negative pressure drop across each trap correspondingly contributed to the capture and release of single cells. Afterward, microbeads were employed to demonstrate the capabilities in rapid capturing of single beads. As the printing pressure increased from 0.64 to 3.03 kPa, all beads were released from traps one by one and dispensed into individual wells with an efficiency of 96%. Cell experiments demonstrated that all traps captured K562 cells within 15.25 ± 7.63 seconds. The single-cell trapping efficiency (75.86–95.31%) was proportional to the sample flow rate. Based on the protrusion of each trapped cell and the relevant pressure drop, the stiffness of passages 8 and 46 K562 cells was respectively determined as 171.15 ± 73.35 Pa and 13 959 ± 6328 Pa. The former was consistent with previous studies and the latter was extremely elevated, owing to the cell property variation during a long culture period. Finally, the single cells with known elasticity were deterministically printed into well plates with an efficiency of 92.62%. This technology is a powerful tool for both continuous single cell dispensing and innovatively enabling the relation of cell mechanics to biophysical properties using traditional equipment. [ABSTRACT FROM AUTHOR]

In this paper it is obtained, through variational methods and sub-supersolution arguments, existence and multiplicity of solutions for a nonhomogeneous problem which arise in several branches of science such as chemical reactions, biophysics and plasma physics. Under a general hypothesis it is proved an existence result and multiple solutions are obtained by considering an additional natural condition. [ABSTRACT FROM AUTHOR]

Advances in the graphics processing unit (GPU) development led to the opportunity for software developers to increase the execution speed for their programs by massive parallelization of the algorithms using GPU programming. NVIDIA company developed an arhitecture for parallel computing named Compute Unified Device Architecture (CUDA) which includes a set of CUDA instructions and the hardware for parallel computing. Computational Physics is an interdisciplinary field which is in continuous progress and which studies, develops and optimizes numerical algorithms and computational techniques for their application in solving various physics problems. Computational Physics has applicability in all sub-branches of physics and related fields such as: biophysics, astrophysics, plasma physics, biomechanics, fluid physics, etc. Moreover, with the evolution of technology in the last few decades, this relatively new field has helped to quickly obtain results in these fields, facilitating the connection between theoretical and experimental physics. In this paper, some of the latest researches and results obtained in computational physics by using GPU computing with CUDA architecture are reviewed. [ABSTRACT FROM AUTHOR]

[FeFe]-hydrogenases are gas-processing metalloenzymes that catalyze H2 oxidation and proton reduction (H2 release) in microorganisms. Their high turnover frequencies and lack of electrical overpotential in the hydrogen conversion reaction has inspired generations of biologists, chemists, and physicists to explore the inner workings of [FeFe]-hydrogenase. Here, we revisit 25 years of scientific literature on [FeFe]-hydrogenase and propose a personal account on 'must-read' research papers and review article that will allow interested scientists to follow the recent discussions on catalytic mechanism, O2 sensitivity, and the in vivo synthesis of the active site cofactor with its biologically uncommon ligands carbon monoxide and cyanide. Focused on—but not restricted to—structural biology and molecular biophysics, we highlight future directions that may inspire young investigators to pursue a career in the exciting and competitive field of [FeFe]-hydrogenase research. [ABSTRACT FROM AUTHOR]

The Cdv system is a protein machinery responsible for cell division in members of the TACK superphylum of archaea. The Cdv system presents many structural similarities to the eukaryotic ESCRT machinery, and it is presumed to act in a similar manner. The Cdv system has been found to be implied in a wide range of processes in the cells, such as division, vesicle budding, and virus release. The role of the CdvB paralogs is key in the division process, as became clear through recent developments in high-temperature live-cell imaging and super-resolution microscopy. In vitro experiments have shed light on the mutual interactions between CdvA, CdvC, and the various CdvB paralogs. The Cdv system is the protein machinery that performs cell division and other membrane-deforming processes in a subset of archaea. Evolutionarily, the system is closely related to the eukaryotic ESCRT machinery, with which it shares many structural and functional similarities. Since its first description 15 years ago, the understanding of the Cdv system progressed rather slowly, but recent discoveries sparked renewed interest and insights. The emerging physical picture appears to be that CdvA acts as a membrane anchor, CdvB as a scaffold that localizes division to the mid-cell position, CdvB1 and CvdB2 as the actual constriction machinery, and CdvC as the ATPase that detaches Cdv proteins from the membrane. This paper provides a comprehensive overview of the research done on Cdv and explains how this relatively understudied machinery acts to perform its cell-division function. Understanding of the Cdv system helps to better grasp the biophysics and evolution of archaea, and furthermore provides new opportunities for the bottom-up building of a divisome for synthetic cells. [ABSTRACT FROM AUTHOR]

• The pattern formation of morphogens is studied in geometrically-confined microtissues during early embryogenesis. • The microtissue consisted of human stem cells is modeled as a piece of biphasic poroelastic material. • The active contractility is fully-coupled with the reaction-diffusion of the morphogens through the poroelasticity. • Linear stability analysis is performed to determine ranges of parameters that leads to diffusion-induced instability. • A comprehensive parameter study, including the sizes and geometries of the tissues, is carried out in the paper. The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Mechanical cues, such as the cellular stresses and strains, have been found to dictate the pattern formation in human stem cell differentiation. As a result, the traditional reaction-diffusion models are modified by adding mechanically related terms to consider the role played by the mechanical cues during the very early stage of embryogenesis. However, these models either do not consider the activeness of the cellular tissues or neglect their poroelastic nature that biological tissues are made by both cells and interstitial fluid. Here we propose a modified reaction-diffusion model that couples with the active contraction of cellular tissues. The cellular tissue is modelled as a piece of biphasic poroelastic material, where mechanical forces naturally regulate the transport of chemical cues. Such chemical cues direct cell fate and hence yield certain types of pattern formations observed in previous experiments. [ABSTRACT FROM AUTHOR]

Markov state models have become popular in the computational biochemistry and biophysics communities as a technique for identifying stationary and kinetic information of protein dynamics from molecular dynamics simulation data. In this paper, we extend the applicability of automated Markov state modeling to simulation data of molecular self-assembly and aggregation by constructing collective coordinates from molecular descriptors that are invariant to permutations of molecular indexing. Understanding molecular self-assembly is of critical importance if we want to deepen our understanding of neurodegenerative diseases where the aggregation of misfolded or disordered proteins is thought to be the main culprit. As a proof of principle, we demonstrate our Markov state model technique on simulations of the KFFE peptide, a subsequence of Alzheimer's amyloid-β peptide and one of the smallest peptides known to aggregate into amyloid fibrils in vitro. We investigate the different stages of aggregation up to tetramerization and show that the Markov state models clearly map out the different aggregation pathways. Of note is that disordered and β-sheet oligomers do not interconvert, leading to separate pathways for their formation. This suggests that amyloid aggregation of KFFE occurs via ordered aggregates from the very beginning. The code developed here is freely available as a Jupyter notebook called TICAgg, which can be used for the automated analysis of any self-assembling molecular system, protein, or otherwise. [ABSTRACT FROM AUTHOR]

The FRagment Separator FRS at GSI is a versatile spectrometer and separator for experiments with relativistic in-flight separated short-lived exotic beams. One branch of the FRS is connected to the target hall where the bio-medical cave (Cave M) is located. Recently a joint activity between the experimental groups of the FRS and the biophysics at the GSI and Department of physics at LMU was started to perform biomedical experiments relevant for hadron therapy with positron emitting carbon and oxygen beams. This paper presents the new ion-optical mode and commissioning results of the FRS-Cave M branch where positron emitting 15O-ions were provided to the medical cave for the first time. An overall conversion efficiency of 2. 9 ± 0. 2 × 1 0 − 4 15O fragments per primary 16O ion accelerated in the synchrotron SIS18 was reached. [ABSTRACT FROM AUTHOR]

In this view point paper, we briefly summarize some of the clinical, biochemical and biophysical results obtained in our research on Relaxation Response. We also qualitatively describe the theoretical biophysical model that could link them. Our work points to a unified view of the human biological system activity, joining the dynamics ruling the interactions and correlations of the microscopic components to the knowledge of their specific individual properties in the effort of going beyond a purely atomistic approach. [ABSTRACT FROM AUTHOR]

Bacterial swarms are a highly-researched example of natural active matter. In particular, the interplay between biological interactions and the physics underlying the swarming dynamics is of both biological and physical interest. In this paper, we study mixed swarms of Bacillus subtilis and Pseudomonas aeruginosa. We find intricate interactions between the species, showing both cooperation and segregation across different spatial and temporal scales. On one hand, even though axenic colonies grow on disparate time scale, an order of magnitude apart, the two-species swarm together, forming a single, combined colony. However, the rapidly moving populations are locally segregated, with different characteristic speeds and lengths (or cluster sizes) that depend on the ratio between the species. Comparison with controlled mutant strains suggest that both the physical and known biological differences in species characteristics may not be enough to explain the segregation between the species in the mixed swarm. We hypothesize that the heterogeneous spatial distribution is due to some mechanism that enables bacteria to recognize their own kind, whose precise origin we could not identify. [ABSTRACT FROM AUTHOR]

This work explores fluctuations of potentiometric pH dynamics in environments with different configurations of geomagnetic fields. High-resolution pH measurements of test liquids are conducted in electromagnetically shielded and thermally stabilized conditions. External measurement environment in two laboratories is modulated by non-conducting/non-magnetic objects of organic and inorganic origins. Totally, 88 experiments in three groups have been conducted during 4 months. The affected pH dynamics at the level of 10−2-10−5pH is detected in 93.5%, 82.2% and 74.4% depending on dielectric permittivity of environmental objects. Reaction of potentiometric system has a typical delay of 30–180 minutes. Experiments in both laboratories demonstrated 19% difference of reproducibility rate caused by different background fluctuations. To explain the obtained results, the paper discusses the effects of the Earth's electric and magnetic fields in the form of magnetospheric Poynting vectors or spin-spin forces in geomagnetic field, which affects the productivity of ionic and free-radical reactions. Since the pH level of aqueous solutions controls various biochemical reactions, this mechanism can explain several biological effects with non-contact signal transmission observed in environmental biology and electromagnetic biophysics. [ABSTRACT FROM AUTHOR]

This paper presents the methods that have participated in the SHREC 2022 contest on protein–ligand binding site recognition. The prediction of protein- ligand binding regions is an active research domain in computational biophysics and structural biology and plays a relevant role for molecular docking and drug design. The goal of the contest is to assess the effectiveness of computational methods in recognizing ligand binding sites in a protein based on its geometrical structure. Performances of the segmentation algorithms are analyzed according to two evaluation scores describing the capacity of a putative pocket to contact a ligand and to pinpoint the correct binding region. Despite some methods perform remarkably, we show that simple non-machine-learning approaches remain very competitive against data-driven algorithms. In general, the task of pocket detection remains a challenging learning problem which suffers of intrinsic difficulties due to the lack of negative examples (data imbalance problem). [Display omitted] • A new contest for binding site detection in a protein. • Proteins are provided both as molecular surfaces and in anonymized PQR format. • Analysis of computational methods for recognizing ligand binding sites in a protein. • Analysis of the performances of the methods that participated in SHREC 2022. [ABSTRACT FROM AUTHOR]

Ervin Bauer (1890–1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper "The definition of living beings on the basis of their thermodynamic properties, and the fundamental biological principles that follow from it" published in Naturwissenschaften (1920) and the excerpts from his magnum opus "Theoretical Biology" (1935). These works became a bibliographical rarity. A complete English translation of "Theoretical Biology" is an important task for the future. [ABSTRACT FROM AUTHOR]

In this view point paper, we briefly summarize some of the clinical, biochemical and biophysical results obtained in our research on Relaxation Response. We also qualitatively describe the theoretical biophysical model that could link them. Our work points to a unified view of the human biological system activity, joining the dynamics ruling the interactions and correlations of the microscopic components to the knowledge of their specific individual properties in the effort of going beyond a purely atomistic approach. [ABSTRACT FROM AUTHOR]

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM's Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM's Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen's early Nobel prize winning experiments by using OpenMM's Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology. Author summary: The cell's most important pieces of machinery are large complexes of proteins often along with nucleic acids. From the ribosome, to CRISPR-Cas9, to transcription factors and DNA-wrangling proteins like the SMC-Kleisins, these complexes allow organisms to replicate and enable cells to respond to environmental cues. Computer simulation is a key technology that can be used to connect physical theories with biological reality. Unfortunately, the time and length scales accessible to molecular simulation have not kept pace with our ambition to study the cell's molecular factories. Many simulation codes also unfortunately remain effectively locked away from the user community who need to modify them as more of the underlying physics is learned. In this paper, we present OpenAWSEM and Open3SPN2, two new easy-to-use and easy to modify implementations of efficient and accurate coarse-grained protein and DNA simulation forcefields that can now be run hundreds of times faster than before, thereby making studies of large biomolecular machines more facile. [ABSTRACT FROM AUTHOR]

The great diversity of molecular processes in chemistry, physics, and biology exhibits universal property: they are controlled by powerful factor, angular momentum. Conservation of angular momentum (electron spin) is a fundamental and universal principle: all molecular processes are spin selective, they are allowed only for those spin states of reactants whose total spin is identical to that of products. Magnetic catalysis induced by magnetic interactions is a powerful and universal means to overcome spin prohibition and to control physical, chemical and biochemical processes. Contributing almost nothing in total energy, being negligibly small, magnetic interactions are the only ones which are able to change electron spin of reactants and switch over the processes between spin-allowed and spin-forbidden channels, controlling pathways and chemical reactivity in molecular processes. The main source of magnetic and electromagnetic effects in biological systems is now generally accepted and demonstrated in this paper to be radical pair mechanism which implies pairwise generation of radicals in biochemical reactions. This mechanism was convincingly established for enzymatic adenosine triphosphate (ATP) and desoxynucleic acid (DNA) synthesis by using catalyzing metal ions with magnetic nuclei (25Mg, 43Ca, 67Zn) and supported by magnetic field effects on these reactions. The mechanism, is shown to function in medicine as a medical remedy or technology (trans-cranial magnetic stimulation, nuclear magnetic control of the ATP synthesis in heart muscle, the killing of cancer cells by suppression of DNA synthesis). However, the majority of magnetic effects in biology remain to be irreproducible, contradictory, and enigmatic. Three sources of such a state are shown in this paper to be: the presence of paramagnetic metal ions as a component of enzymatic site or as an impurity in an uncontrollable amount; the property of the radical pair mechanism to function at a rather high concentration of catalyzing metal ions, when at least two ions enter into the catalytic site; and the kinetic restrictions, which imply compatibility of chemical and spin dynamics in radical pair. The purpose of the paper is to analyze the reliable sources of magnetic effects, to elucidate the reasons of their inconsistency, to show how and at what conditions magnetic effects exhibit themselves and how they may be controlled, switched on and off, taking into account not only biological and madical but some geophysical and environmental aspects as well. Image 1 [ABSTRACT FROM AUTHOR]

In Chinese philosophy, yin and yang ("dark‐bright," "negative‐positive") describe how seemingly opposite or contrary forces may actually be complementary, interconnected and interdependent. This paper provides this perspective on photodynamic and photothermal therapies, with a focus on the treatment of solid tumors. The relative strengths and weaknesses of each modality, both current and emerging, are considered with respect to the underlying biophysics, the required technologies, the biological effects, their translation into clinical practice and the realized or potential clinical outcomes. For each specific clinical application, one or the other modality may be clearly preferred, or both are effectively equivalent in terms of the various scientific/technological/practical/clinical trade‐offs involved. Alternatively, a combination may the best approach. Such combined approaches may be facilitated by the use of multifunctional nanoparticles. It is important to understand the many factors that go into the selection of the optimal approach and the objective of this paper is to provide guidance on this. [ABSTRACT FROM AUTHOR]

Earth system models (ESMs) have been developed to represent the role of terrestrial ecosystems on the energy, water, and carbon cycles. However, many ESMs still lack representation of within-ecosystem heterogeneity and diversity. In this paper, we present the Ecosystem Demography model version 2.2 (ED-2.2). In ED-2.2, the biophysical and physiological processes account for the horizontal and vertical heterogeneity of the ecosystem: the energy, water, and carbon cycles are solved separately for a series of vegetation cohorts (groups of individual plants of similar size and plant functional type) distributed across a series of spatially implicit patches (representing collections of micro-environments that have a similar disturbance history). We define the equations that describe the energy, water, and carbon cycles in terms of total energy, water, and carbon, which simplifies the differential equations and guarantees excellent conservation of these quantities in long-term simulation (< 0.1 % error over 50 years). We also show examples of ED-2.2 simulation results at single sites and across tropical South America. These results demonstrate the model's ability to characterize the variability of ecosystem structure, composition, and functioning both at stand and continental scales. A detailed model evaluation was conducted and is presented in a companion paper. Finally, we highlight some of the ongoing model developments designed to improve the model's accuracy and performance and to include processes hitherto not represented in the model. [ABSTRACT FROM AUTHOR]

The topological properties of DNA have long been a focal point in biophysics. In the 1970s, White proposed that the topology of closed DNA double helix follows White's formula: L k = W r + T w. However, there has been controversy in the calculation of DNA twisting number, partly due to discrepancies in the definition of torsion in differential geometry. In this paper, we delved into a detailed study of torsion, revealing that the calculation of DNA twisting number should use the curve's geodesic torsion. Furthermore, we found that the discrepancy in DNA twisting numbers calculated using different torsion is N. This study elucidated the impact of torsion on the calculation of DNA twisting numbers, aiming to resolve controversies in the calculation of DNA topology and provided accurate computational methods and theoretical foundations for related research. • Both as a spatial curve and as a curve lying on a surface, the DNA helix axis is taken into account during the calculation of the twisting number. The torsion derived from each perspective varies. • We have clarified that the torsion mentioned in Fuller's works should refer to the geodesic torsion of the surface where the DNA helix axis resides. • The twisting number computed from the torsion of a surface curve differs from that of a spatial curve by a specific numerical factor. [ABSTRACT FROM AUTHOR]

In this paper (Paper I) and a companion paper (Paper II), novel new algorithms and applications of the isokinetic ensemble as generated by Gauss' principle of least constraint, pioneered for use with molecular dynamics 20 years ago, are presented for biophysical, path integral, and Car-Parrinello based ab initio molecular dynamics. In Paper I, a new "extended system" version of the isokinetic equations of motion that overcomes the ergodicity problems inherent in the standard approach, is developed using a new theory of non-Hamiltonian phase space analysis [M. E. Tuckerman et al., Europhys. Lett. 45, 149 (1999); J. Chem. Phys. 115, 1678 (2001)]. Reversible multiple time step integrations schemes for the isokinetic methods, first presented by Zhang [J. Chem. Phys. 106, 6102 (1997)] are reviewed. Next, holonomic constraints are incorporated into the isokinetic methodology for use in fast efficient biomolecular simulation studies. Model and realistic examples are presented in order to evaluate, critically, the performance of the new isokinetic molecular dynamic schemes. Comparisons are made to the, now standard, canonical dynamics method, Nosé-Hoover chain dynamics [G. J. Martyna et al., J. Chem. Phys. 97, 2635 (1992)]. The new isokinetic techniques are found to yield more efficient sampling than the Nosé-Hoover chain method in both path integral molecular dynamics and biophysical molecular dynamics calculations. In Paper II, the use of isokinetic methods in Car-Parrinello based ab initio molecular dynamics calculations is presented. [ABSTRACT FROM AUTHOR]

The publishers of Physiological Measurement (PMEA), IOP Publishing, in association with the journal owners, the Institute of Physics and Engineering in Medicine (IPEM), jointly award an annual prize for the best paper published in PMEA during the previous year. The responsibility for deciding the ultimate winner falls to the Editorial and International Advisory boards of the journal. However, a shortlist of papers has to first be put together. Since a paper published early in the volume will have more exposure than one published later, it would be unfair to use download or citation statistics to judge papers. For this reason, the shortlist is constructed using the comments and ratings of our expert referees. For the 2009 award, 6 papers were considered. After the construction of the shortlist, it was then down to our board members to personally assess and rank the papers. This year, we have a clear and worthy winner. We have much pleasure in advising readers that the 2009 Martin Black award goes to Andy Adler et al for their paper on electrical impedance tomography. GREIT: a unified approach to 2D linear EIT reconstruction of lung images Andy Adler, John Arnold, Richard Bayford, Andrea Borsic, Brian Brown, Paul Dixon, Theo Faes, Inez Frerichs, Herve Gagnon, Yvo Garber, Bartlomiej Grychtol, Gunter Hahn, William Lionheart, Anjum Malik, Robert P Patterson, Janet Stocks, Andrew Tizzard, Norbert Weiler and Gerhard K Wolf 2009 Physiol. Meas. 30 S35-55 All of the shortlisted papers were of great merit, and the full top-6 is listed below (in alphabetical order). Richard Bayford Editor-in-Chief Jon Ruffle Publisher References Adler A, Arnold J H, Bayford R, Borsic A, Brown B, Dixon P, Faes T J C, Frerichs I, Gagnon H, Garber Y, Grychtol B, Hahn G, Lionheart W R B, Malik A, Patterson R P, Stocks J, Tizzard A, Weiler N and Wolf G K 2009 GREIT: a unified approach to 2D linear EIT reconstruction of lung images Physiol. Meas. 30 S35-55 Aelen P, Jurkov A, Aulanier A and Mintchev M P 2009 Pilot acute study of feedback-controlled retrograde peristalsis invoked by neural gastric electrical stimulation Physiol. Meas. 30 309-22 Borsic A, Halter R, Wan Y, Hartov A and Paulsen K D 2009 Sensitivity study and optimization of a 3D electric impedance tomography prostate probe Physiol. Meas. 30 S1-18 Kim K K, Kim J S, Lim Y G and Park K S 2009 The effect of missing RR-interval data on heart rate variability analysis in the frequency domain Physiol. Meas. 30 1039-50 Remme E W, Hoff L, Halvorsen P S, Naerum E, Skulstad H, Fleischer L A, Elle O J and Fosse E 2009 Validation of cardiac accelerometer sensor measurements Physiol. Meas. 30 1429-44 Wang L, Su S W, Celler B G, Chan G S H, Cheng T M and Savkin A V 2009 Assessing the human cardiovascular response to moderate exercise: feature extraction by support vector regression Physiol. Meas. 30 227-44 [ABSTRACT FROM AUTHOR]

Solitary waves have been well studied in various fields, including water waves, optical communications, plasmas, and biophysics. We present experimental results that a two-dimensional solitary wave, with its crest shaped like the letter "O," occurs around an island terrain in shallow water. We name it the O-soliton (a cylindrical-type soliton) in this paper. This is the first experimental observation of the O-soliton including both outward and inward propagation in shallow water. O-solitons are observed with stable and periodic occurrences under typical coastal conditions. A water column at its center is higher than eight times the initial mean wave height measured by six wave gauges arranged in a regular hexagon. A one-dimension solitary wave incurs a phase shift when it collides with the O-soliton. However, no phase shift is observed in the O-soliton itself. Furthermore, when it collapses to its center point, it remains in this state for a short period. This is analogous to the pausing of the wave crest during a head-on collision of solitary waves or the reflection of a solitary wave at a vertical wall. These results also enrich the general understanding of solitary waves, whose repeated occurrence suggests that they may naturally occur in the ocean, and motivate analogous studies in other fields of physics. [ABSTRACT FROM AUTHOR]

Systems of mutually coupled oscillators with delay coupling are of great interest for various applications in electronics, laser physics, biophysics, etc. Time delay usually originates from the finite speed of propagation of the coupling signal. In this paper, we present the results of detailed bifurcation analysis of two delay-coupled limit-cycle (Landau–Stuart) oscillators. First, we study the simplified case when the delay time is much smaller than the oscillation build-up time. When the coupling signal propagates between the two counterparts, it acquires a phase shift, which strongly affects the synchronization pattern. Depending on this phase shift, the system may demonstrate the behavior typical for either dissipative or conservative (reactive) coupling. We examine stability of the in-phase and anti-phase synchronous states and reveal the complicated pattern of the synchronization domains on the frequency mismatch—coupling strength parameter plane paying a special attention to the mechanisms of appearance and disappearance of the phase multistability. We demonstrate that taking into account reactive phase nonlinearity the coupling signal acquires an additional phase shift, which depends on the signal intensity. We also examine the more complicated case of finite delay time. The increase of the reactive nonlinearity parameter and the delay time leads to transformations of synchronization domains similar to those that occur when the phase shift increases. For the bifurcation analysis, we employ XPPAUT and DDEBifTool package and verify the results by direct numerical integration. [ABSTRACT FROM AUTHOR]

When a depolarizing event occurs across a cell membrane there is a remarkable change in its electrical properties. A complete depolarization event produces a considerably rapid increase in voltage that propagates longitudinally along the axon and is accompanied by changes in axial conductance. A dynamically changing magnetic field is associated with the passage of the action potential down the axon. Over 75 years of research has gone into the quantification of this phenomenon. To date, no unified model exist that resolves transmembrane polarization in a closed-form description. Here, a simple but formative description of propagated signaling phenomena in the membrane of an axon is presented in closed-form. The focus is on using both biophysics and mathematical methods for elucidating the fundamental mechanisms governing transmembrane polarization. The results presented demonstrate how to resolve electromagnetic and thermodynamic factors that govern transmembrane potential. Computational results are supported by well-established quantitative descriptions of propagated signaling phenomena in the membrane of an axon. The findings demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation function together in generating an action potential in a unified closed-form description. The work presented in this paper provides compelling evidence that three basic factors contribute to the propagated signaling in the membrane of an axon. It is anticipated this work will compel those in biophysics, physical biology, and in the computational neurosciences to probe deeper into the classical and quantum features of membrane magnetization and signaling. It is hoped that subsequent investigations of this sort will be advanced by the computational features of this model without having to resort to numerical methods of analysis. [ABSTRACT FROM AUTHOR]

Presents a list of papers presented at the Australian Biophysical Society Annual Meeting in November 2000, published in the March 2002 issue of 'European Biophysical Journal.'

First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Sherman Foo is first author on 'Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis', published in JCS. Sherman conducted the research described in this article while a PhD student in the labs of Snezhana Oliferenko (The Francis Crick Institute, London, UK, and Randall Centre for Cell and Molecular Biophysics, King's College London, UK) and Markus R. Wenk (Singapore Lipidomics Incubator, National University of Singapore). He is now a postdoc in the lab of Buzz Baum at Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK, where he is currently studying cellular organization of hyperthermophilic archaea, with a particular focus on the surface layer and cell cycle of Sulfolobus acidocaldarius. [ABSTRACT FROM AUTHOR]

First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Lilian Sluimer is first author on 'SKOR1 mediates FER kinase-dependent invasive growth of breast cancer cells', published in JCS. Lilian conducted the research described in this article while working on this research as a first-year master's student and continued working on this project as a research technician for a year in Patrick Derksen's lab atUMCUtrecht, The Netherlands. She is nowa PhD student in the lab of Anna Akhmanova at the Division of Cell Biology, Neurobiology and Biophysics, Utrecht University, The Netherlands, investigating the organization and dynamics of cytoskeletal microtubule networks in different cellular systems. [ABSTRACT FROM AUTHOR]