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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]

The role and importance of mechanical properties of cells and tissues in cellular function, development and disease has widely been acknowledged, however standard techniques currently used to assess them exhibit intrinsic limitations. Recently, Brillouin microscopy, a type of optical elastography, has emerged as a non-destructive, label- and contact-free method that can probe the viscoelastic properties of biological samples with diffraction-limited resolution in 3D. This led to increased attention amongst the biological and medical research communities, but it also sparked debates about the interpretation and relevance of the measured physical quantities. Here, we review this emerging technology by describing the underlying biophysical principles and discussing the interpretation of Brillouin spectra arising from heterogeneous biological matter. We further elaborate on the technique's limitations, as well as its potential for gaining insights in biology, in order to guide interested researchers from various fields.

A bibliometric analysis of TASK Quarterly in the years 1997-2021 in terms of various bibliometric indicators was performed to celebrate the 25th anniversary of the publication of the first issue of the journal. The number of publications and citations increased over the mentioned span of years. The leading countries in terms of the greatest number of papers published in TASK Quarterly are Poland, Italy, Germany, Ukraine, USA and Russia. Moreover, it is shown that international collaboration can result in a greater number of citations per publication. The average publication time in TASK Quarterly is 77 days, including the average submission-acceptance time (44 days) and the average acceptancepublication time (33 days). Based on the author's findings, it can be seen that although TASK Quarterly is a journal devoted mainly to physical and computer sciences, many publications also focus on the aspects related to mathematics, biomedical engineering and biophysics. CFD, molecular dynamics, the finite element method (FEM) and numerical simulations are the most frequently used keywords in articles published in TASK Quarterly. [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]

Course specific learning outcomes are an important tool to define the scope of a course and can be very helpful when designing experiments and assessments. With slight modification, these learning outcomes can serve as a guide when transitioning to the distance learning format especially in courses with a traditional lab. Here we present such an example for the biophysical chemistry course., (© 2020 International Union of Biochemistry and Molecular Biology.)

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]

This article examines economic redevelopment in a small city once dependent on the pulp and paper industry. In the wake of the industry's demise, biomass energy has emerged as the primary new forest-based industry there. I combine Freudenburg's “addictive economies” framework with a focus on place character to explore the relationship between historical patterns of resource control, contemporary forest conditions, and the shape of redevelopment in the study community. I demonstrate the continued applicability of Freudenburg and colleagues’ work on resource-dependent communities for understanding patterns of local change in the early 21st century, and extend his framework to show how addiction can involve not only dependence on a given resource-based industry, but also the changing characteristics of the resource base itself in a historical process of environmental degradation that can leave communities addicted to resources of particular, industrially produced types and conditions. [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]

Smarzewski carried out mechanical and microstructural tests of high-performance concretes possessing different levels of condensed silica fume used as replacements for cement [[2]] and evaluated the influence of polypropylene fibers on high-performance self-compacting concrete [[3]]. Prado et al. [[14]] carried out an experimental procedure using a commercial transient hot-wire device to measure the thermal conductivity of nanofluids. The study of materials has entailed several efforts by materials scientists to gain a deep understanding of their structural, mechanical, chemical, optical, magnetic and electronic properties and engineering applications. [Extracted from the article]

Remote Measurement Technologies (RMTs) could revolutionise management of chronic health conditions by providing real-time symptom tracking. However, the promise of RMTs relies on user engagement, which at present is variably reported in the field. This review aimed to synthesise the RMT literature to identify how and to what extent engagement is defined, measured, and reported, and to present recommendations for the standardisation of future work. Seven databases (Embase, MEDLINE and PsycINFO (via Ovid), PubMed, IEEE Xplore, Web of Science, and Cochrane Central Register of Controlled Trials) were searched in July 2020 for papers using RMT apps for symptom monitoring in adults with a health condition, prompting users to track at least three times during the study period. Data were synthesised using critical interpretive synthesis. A total of 76 papers met the inclusion criteria. Sixty five percent of papers did not include a definition of engagement. Thirty five percent included both a definition and measurement of engagement. Four synthetic constructs were developed for measuring engagement: (i) engagement with the research protocol, (ii) objective RMT engagement, (iii) subjective RMT engagement, and (iv) interactions between objective and subjective RMT engagement. The field is currently impeded by incoherent measures and a lack of consideration for engagement definitions. A process for implementing the reporting of engagement in study design is presented, alongside a framework for definition and measurement options available. Future work should consider engagement with RMTs as distinct from the wider eHealth literature, and measure objective versus subjective RMT engagement. Registration: This review has been registered on PROSPERO [CRD42020192652]. [ABSTRACT FROM AUTHOR]

In this paper the muscular activity will be treated from a physical point of view, considering the main physical parameters that can be quantified. A brief and simple theoretical treatment will be followed by some homeworks for students. The problems have a difficulty degree typical of an undergraduate class, and the arguments have been chosen just as examples straddling biology and physics. The goal of this work is to train biological area students to use and handle quantitative methods.

Mathematical models are indispensable for disentangling the interactions through which biological components work together to generate the forces and flows that position, mix, and distribute proteins, nutrients, and organelles within the cell. To illuminate the ever more specific questions studied at the edge of biological inquiry, such models inevitably become more complex. Solving, simulating, and learning from these more realistic models requires the development of new analytic techniques, numerical methods, and scalable software. In this review, we discuss some recent developments in tools for understanding how large numbers of cytoskeletal filaments, driven by molecular motors and interacting with the cytoplasm and other structures in their environment, generate fluid flows, instabilities, and material deformations which help drive crucial cellular processes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

There remains a strong movement for Introductory Physics for Life Sciences (IPLS) courses to better integrate physics and biology. Part of the challenge for IPLS educators is to introduce fundamental physical law while simultaneously establishing the relevance of physics to biological science. Life science relevant laboratory experiences are essential to the training of future biologists and health professionals. The physiology of neurotransmission can be especially challenging to life science majors, but may be somewhat clarified in the IPLS course by model circuit labs. A realistic axon model lab using rubber tubing and gelatin recently reported by Dyer highlights the motivational value of lab experiences bridging biophysics and neurophysiology. Time-independent and time-dependent circuit labs modeling passive spread of charge within an axon absent the action potential have been described. In this paper, we describe a progressive complex circuit lab sequence introducing students to Kirchhoff's rules, a model of the cell membrane resting potential, and a model representing key features of the action potential in an axon. In this context, "complex" describes a circuit that cannot be reduced to a single battery and resistor.

The importance of including concepts, examples, and techniques from mathematics and the physical and information sciences in biology courses to fulfill the need of today's undergraduates has been the principle motivation for developing interdisciplinary biology-focused courses. Although this movement started many years ago, developing and offering courses like biophysics is still new in many liberal arts colleges. Taking advantage of the experiences gained by introducing an interdisciplinary course, simply titled Biophysics, this paper was developed to present the adapted structure, challenges, and useful factors to further develop such a course in order to heighten students' retention of the material. (Contains 5 tables.)

Purpose: The purpose of this study is to develop a conceptual framework with related analysis methodologies that identifies the influence of social environment on an established cropping system. Design/Methodology/Approach: A stratified survey including 103 villages and 823 farmers was conducted in all districts of Haryana (India). Firstly, technical efficiency (TE) was modeled using biophysical data including grain yield, seeding rate, wheat varieties, tillage, sowing date, seed source, harvesting method and the application of fertilizer, herbicide and irrigation. The relationship between TE and social community factors such as farm size, farmer age, level of education and agricultural support programs was analyzed by regression tree. Findings: TE was lower with the farmers who only have education to a primary standard. Farmers with high TE scores were mostly between 35 and 40 years of age, and a higher TE association was common for farmers who use technical publications. Social individual factors such as farmers' views on the future of farming were also analyzed across different TE levels. Practical implications: Farmers with lower TE are an obvious target for production improvement, particularly given the understanding that the overall production yield gap is small in Haryana. Theoretical implications: Our conceptual framework shows a quantitative way to establish the socio-ecological linkage, and to identify the opportunities for changes in management with extension services leading to productivity improvement. Originality/Value: This paper provides a novel framework with detailed methodology to effectively identify the socio-economic factors that limit the biophysical production in an agricultural system.

Physical soil properties create lags between temperature change and corresponding soil responses, which obscure true Q10 values and other biophysical parameters such as depth of production. This study examines an inversion approach for estimating and depth of production (Zp) using physically based soil models, constrained by observed high-frequency surface fluxes and/or concentrations. Our inversion strategy uses a 1-D multi-layered soil model that simulates realistic temperature and gas diffusion. We tested inversion scenarios on synthetic data using a range of constraining parameters, time averaging techniques, mechanisms to improve computational efficiency, and various methods of incorporating real data into the model. Overall, we have found that with carefully constrained data, inversion was possible. While inversions using exclusively surface flux measurements could succeed, constraining the inversion using multiple shallow subsurface CO2 measurements proved to be most successful. Inversions constrained by these shallow measurements returned Q10 and Zp values with average errors of 1.85 and 0.16 % respectively. This work is a first step toward building a reliable framework for removing physical effects from high frequency soil CO2 data. Ultimately, we hope that this process will lead to better estimates of biophysical soil parameters and their variability on short timescales. [ABSTRACT FROM AUTHOR]

Carbon capture and storage (CCS) is a developing technology that seeks to mitigate against the impact of increasing anthropogenic carbon dioxide (CO2) production by capturing CO2 from large point source emitters. After capture the CO2 is compressed and transported to a reservoir where it is stored for geological time scales. Potential leakages from CCS projects, where stored CO2 migrates through the overlaying sediments, are likely to have severe implications on benthic and marine ecosystems. Nonetheless, prokaryotic response to elevated CO2 concentrations has been suggested as one of the first detectable warnings if a CO2 leakage should occur. Applying properties of prokaryotic communities (i.e. community composition and metabolic status) as a novel CO2 monitoring application is highly reliable within a multidisciplinary framework, where deviations from the baseline can easily be identified. In this paper we review current knowledge about the impact of CO2 leakages on marine sediments from a multidisciplinary-based monitoring perspective. We focus on aspects from the fields of biology, geophysics, and chemistry, and discuss a case study example. We argue the importance of an integrative multidisciplinary approach, incorporating biogeochemistry, geophysics, microbial ecology and modelling, with a particular emphasis on metagenomic techniques and novel bioinformatics, for future CCS monitoring. Within this framework, we consider that an effective CCS monitoring programme will ensure that large-scale leakages with potentially devastating effects for the overlaying ecosystem are avoided. Furthermore, the multidisciplinary approach suggested here for CCS monitoring is generic, and can be adapted to other systems of interest. [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]

Most future projections forecast significant and ongoing climate change during the 21st century, but with the severity of impacts dependent on efforts to restrain or reorganise human activity to limit carbon dioxide (CO2) emissions. A major sink for atmospheric CO2, and a key source of biological resources, the World Ocean is widely anticipated to undergo profound physical and -- via ocean acidification -- chemical changes as direct and indirect results of these emissions. Given strong biophysical coupling, the marine biota is also expected to experience strong changes in response to this anthropogenic forcing. Here we examine the large-scale response of ocean biogeochemistry to climate and acidification impacts during the 21st century for Representative Concentration Pathways (RCPs) 2.6 and 8.5 using an intermediate complexity global ecosystem model, Medusa--2.0. The primary impact of future change lies in stratification-led declines in the availability of key nutrients in surface waters, which in turn leads to a global decrease (1990s vs. 2090s) in ocean productivity (-6.3%). This impact has knock-on consequences for the abundances of the low trophic level biogeochemical actors modelled by Medusa--2.0 (-5.8%), and these would be expected to similarly impact higher trophic level elements such as fisheries. Related impacts are found in the flux of organic material to seafloor communities (-40.7% at 1000m), and in the volume of ocean suboxic zones (+12.5%). A sensitivity analysis removing an acidification feedback on calcification finds that change in this process significantly impacts benthic communities, suggesting that a better understanding of the OA-sensitivity of calcifying organisms, and their role in ballasting sinking organic carbon, may significantly improve forecasting of these ecosystems. For all processes, there is geographical variability in change, and changes are much more pronounced under RCP 8.5 than the RCP 2.6 scenario. [ABSTRACT FROM AUTHOR]

Humans and human communities influence--and are influenced by--the landscapes or ecosystems of which they are a part. The contemporary landscape which much of the world's population inhabits is a complex matrix of interrelated human and natural systems. The European Landscape Convention's comprehensive definition recognizes the importance of landscape but is deficient in classification frameworks and cohesive approaches to planning, particularly sustainable development. This paper provides a critical literature review for the term 'landscape'; it's evolving and iterative procedure synthesizes interdisciplinary perspectives of literature's varied theories, paradigms, frameworks and concepts. Results indicate the disciplines of Social Science and Environmental Science transcend the literature and current paradigms for the concept of 'landscape' still lack interrelated perspective and are generally poorly understood among disciplines. This literature review concludes that sustainable development within the European landscape requires an integrated spatial approach for applying the concept of 'landscape'. The context of the human-nature relationship within a socio-ecological production landscape (SEPL) allows the interactions of its interdependent components to be viewed comprehensively. This critical analysis grounds perspectives of landscape and assist students, practitioners, and researchers to interpret concepts of the term 'landscape' within multiple frameworks. This paper fills interdisciplinary gaps and provides the structural, spatial, and contextual considerations for further integrated research, theory, and planning in thinking about sustainable development within Europe's rapidly changing landscapes. [ABSTRACT FROM AUTHOR]

Driving is an everyday activity but also brings a substantial risk. Driver state monitoring is a potential method to alleviate such risk by detecting unsafe driver states. Monitoring systems can infer a driver's state based on physiological measurements, subjective report and/or performance. It is well-known that driver psychology, physiology and performance are affected by circadian rhythmicity independently from being affected by the psychological state. However, there is a paucity of research for the circadian effect on the interpretation of the driver state monitoring. This paper seeks to rectify this situation by reviewing the literature on the circadian effect on the physiological functions measured by the methods used in driver state monitoring. Systems tested in the laboratory as potential driver state monitoring and measures that are used to detect states are also considered. The findings suggest different circadian effects on electroencephalography, electrocardiography, electrooculography, electrodermal response, speech, event-related potential, electromyography, subjective report, blood pressure, facial expression, hormonal salivary content, body temperature, respiration, psychomotor performance, and body position. This study creates a theoretical basis for integrating studies about circadian rhythmicity into driver state monitoring. It shows the importance of circadian phase for the safety sciences, driver state monitoring, and systems design. [ABSTRACT FROM AUTHOR]

Josep Rizo is a Professor of Biophysics, Biochemistry and Pharmacology at the University of Texas Southwestern Medical Center, where he is Virginia Lazenby O'Hara Chair in Biochemistry. He is particularly interested in the study of the mechanisms of neurotransmitter release and intracellular membrane fusion using structural biology, a variety of biophysical techniques and reconstitution approaches. Jose has been a part of the FEBS Open Bio Editorial Board since 2021. In this interview, he shares his insights into developments in the field of neurotransmitter release, describes his move from Spain to the United States, and discusses how sometimes you need to use both logic and scientific hunches. [ABSTRACT FROM AUTHOR]

Even as we advance the frontiers of physics knowledge, our understanding of how this knowledge evolves remains at the descriptive levels of Popper and Kuhn. Using the American Physical Society (APS) publications data sets, we ask in this paper how new knowledge is built upon old knowledge. We do so by constructing year-to-year bibliographic coupling networks, and identify in them validated communities that represent different research fields. We then visualize their evolutionary relationships in the form of alluvial diagrams, and show how they remain intact through APS journal splits. Quantitatively, we see that most fields undergo weak Popperian mixing, and it is rare for a field to remain isolated/undergo strong mixing. The sizes of fields obey a simple linear growth with recombination. We can also reliably predict the merging between two fields, but not for the considerably more complex splitting. Finally, we report a case study of two fields that underwent repeated merging and splitting around 1995, and how these Kuhnian events are correlated with breakthroughs on Bose-Einstein condensation (BEC), quantum teleportation, and slow light. This impact showed up quantitatively in the citations of the BEC field as a larger proportion of references from during and shortly after these events. [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]

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]

The article focuses on the Nexus Land-Use model for articulating biophysical potential and economic dynamics for land-use. It offers a description of the biophysical features of the Nexus Land-Use model as well as details the economical principles ruling land-use changes and their parametrisations. The sensitivity of the area of extensive pastures to energy process and deforestation is illustrated.

This year, the first one as Editor-in-chief of AIMS Biophysics, comes to an end. This Editorial is devoted to summarize the main results of this year and the perspectives of the journal. Last but not least to the Thanks. [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]

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]

A better understanding of how environmental changes affect organic matter fluxes in Arctic marine ecosystems is sorely needed. Here, we combine mooring times-series, ship-based measurements and remote-sensing to assess the variability and forcing factors of vertical fluxes of particulate organic carbon (POC) across the Mackenzie Shelf in 2009. We developed a geospatial model of these fluxes to proceed to an integrative analysis of their biophysical determinants in summer. Flux data were obtained with sediment traps and via a regional empirical algorithm applied to particle size-distributions (17 classes from 0.08--4.2mm) measured by an Underwater Vision Profiler 5. Redundancy analyses and forward selection of abiotic/biotic parameters, linear trends, and spatial structures (i.e. principal coordinates of neighbor matrices, PCNM), were conducted to partition the variation of POC flux size-classes. Flux variability was explained at 69.5% by the addition of a linear temporal trend, 7 significant PCNM and 9 biophysical variables. The interaction of all these factors explained 27.8% of the variability. The first PCNM canonical axis (44.4% of spatial variance) reflected a shelf-basin gradient controlled by bottom depth and ice concentration (p < 0.01), but a complex assemblage of fine-to-broad scale patterns was also identified. Among bio-physical parameters, bacterial production and northeasterly wind (upwelling-avorable) were the two strongest explanatory variables (r² cum. = 0.37), suggesting that bacteria were associated with sinking material, which was itself partly linked to upwelling induced productivity. The second most important spatial structure corresponded actually to the two areas where shelf break upwelling is known to occur under easterlies. Copepod biomass was negatively correlated (p < 0.05) with vertical POC fluxes, implying that metazoans played a significant role in the regulation of export fluxes. The low fractal dimension of settling particles (1.26) and the high contribution (∼94%) of fast-sinking small aggregates (< 1mm; 20-30md-1) to the mass fluxes suggested that settling material across the region was overall fluffy, porous, and likely resulting from the aggregation of marine detritus, gel-like substances and ballast minerals. Our study demonstrates that vertical POC fluxes in Arctic shelf systems are spatially complex, sensitive to environmental forcings, and determined by both physicochemical mechanisms and food web functioning. In conclusion, we hypothesize that the incorporation of terrestrial matter into the Beaufort Sea food web could be catalyzed by bacteria via the incorporation of dissolved terrestrial carbon liberated through the photo-cleavage and/or hydrolysis of land-derived POC interweaved with marine aggregates. [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.'

This memorial issue is a collection of papers that showcase the diverse research interests of the late Professor King‐Chuen Lin (1953 – 2022) in the fields of physical chemistry, analytical chemistry, biophysics, and material chemistry. These papers have been contributed by Prof. Lin's friends, colleagues, and former group members. The global chemistry community deeply mourns the loss of Prof. Lin, and through this special issue, the invited contributors aim to honor his memory. [ABSTRACT FROM AUTHOR]

The degree of DNA compaction in various regions of the cell nucleus determines whether the corresponding genes should be expressed and other crucial cellular processes, such as DNA replication and repair, should occur. Therefore, the development of approaches to the experimental assessment of DNA compactness in cell nuclei, as well as its indicator, dynamic disorder which determines the degree of thermal fluctuation in the position and mutual orientation of molecular fragments, is highly relevant. In this paper, using single-stranded guanine and cytosine oligonucleotides, as well as their double-stranded combination as an example, it is shown that dynamic disorder in DNA can be assessed based on low-frequency Raman scattering (RS) spectroscopy data. For the first time, Raman spectra of oligonucleotides have been measured over a wide frequency range, including the low-frequency (10–200 cm ) and high-frequency (200–2000 cm ) regions. It was found that the low-frequency Raman intensity is maximal in single-stranded oligocytosine and minimal in the double-stranded oligonucleotide, which is in full agreement with the magnitude of dynamic disorder estimated from molecular dynamics simulations. The obtained results indicate the promising application of low-frequency Raman spectroscopy for assessing dynamic disorder and DNA compactness. The use of such a technique is expected to contribute to the understanding of key cellular processes and the physical mechanisms that underlie them, which is necessary for the development of advanced methods in molecular biophysics and cell biology. [ABSTRACT FROM AUTHOR]

Professionals in the environmental domain require cognitive interdisciplinary skills to be able to develop sustainable solutions to environmental problems. We demonstrate that education in environmental systems analysis allows for the development of these skills. We identify three components of cognitive interdisciplinary skills: (1) the ability to understand environmental issues in a holistic way, taking into account the interplay of social and biophysical dynamics; (2) the ability to connect both the analysis of environmental problems and the devising of solutions with relevant disciplinary knowledge and methodologies; and (3) the ability to reflect on the role of scientific research in solving societal problems. Environmental systems analysis provides tools, methods, and models to assist in framing complex environmental issues in a holistic way and facilitates the integration of disciplines. Systems analysis also supports reflection by making students aware that a system always represents a simplified model and a particular perspective. Through the analysis of a collection of bachelor of science students' "reflection papers", we identify two major challenges in teaching these cognitive skills: (1) to train students to not just follow a systematic approach but acquire a systemic view and (2) to train students to be reflexive about systems analysis and the role of science. We recommend that training in cognitive skills starts early in a study program.

This paper describes theory and experiments, taken from biophysics and physiological measurements, to illustrate the technique of signal averaging. In the process, students are introduced to the basic concepts of signal processing, such as digital filtering, Fourier transformation, baseline correction, pink and Gaussian noise, and the cross- and autocorrelation functions. From these computations, the students estimate physically interesting parameters such as the pulse rate and blood flow velocity. They also learn about some of the pitfalls encountered in quantifying the signal and noise components for a meaningful computation of the signal-to-noise ratio. (Contains 14 figures.)

The northern terrestrial net ecosystem carbon balance (NECB) is contingent on inputs from vegetation gross primary productivity (GPP) to offset ecosystem respiration (Reco) of carbon dioxide (CO2) and methane (CH4) emissions, but an effective framework to monitor the regional Arctic NECB is lacking. We modified a terrestrial carbon flux (TCF) model developed for satellite remote sensing applications to estimate peatland and tundra CO2 and CH4 fluxes over a pan-Arctic network of eddy covariance (EC) flux tower sites. The TCF model estimates GPP, CO2 and CH4 emissions using either in-situ or remote sensing based climate data as input. TCF simulations driven using in-situ data explained > 70% of the r² variability in 8 day cumulative EC measured fluxes. Model simulations using coarser satellite (MODIS) and reanalysis (MERRA) data as inputs also reproduced the variability in the EC measured fluxes relatively well for GPP (r² =0.75), Reco (r² =0.71), net ecosystem CO2 exchange (NEE, r² =0.62) and CH4 emissions (r² =0.75). Although the estimated annual CH4 emissions were small (< 18 gCm-2 yr-1) relative to Reco (> 180 gCm-2 yr-1), they reduced the across-site NECB by 23% and contributed to a global warming potential of approximately 165-128 gCO2eqm-2 yr-1 when considered over a 100 yr time span. This model evaluation indicates a strong potential for using the TCF model approach to document landscape scale variability in CO2 and CH4 fluxes, and to estimate the NECB for northern peatland and tundra ecosystems. [ABSTRACT FROM AUTHOR]