Biophysical Reviews: a transition in the journal

This Editorial for Volume 16 Issue 2 first describes the issue contents before describing some upcoming events within Biophysical Reviews and concludies with an announcement on the transition of Chief Editors thanks to the outgoing Chief Editor.

Equations describing semi-confluent cell growth (I) Analytical approximations

A set of differential equations with analytical solutions are presented that can quantitatively account for variable degrees of contact inhibition on cell growth in two- and three-dimensional cultures. The developed equations can be used for comparative purposes when assessing contribution of higher-order effects, such as culture geometry and nutrient depletion, on mean cell growth rate. These equations also offer experimentalists the opportunity to characterize cell culture experiments using a single reductive parameter.

Principal Accompaniment in Australian Faith-Based Schools: A Salutogenesis Approach

A program designed to provide accompaniment reflects a salutogenesis emphasis aimed at sustaining the professional well-being of experienced principals. A mixed methods pilot study focused on participant (N = 12) orientation, principles of accompaniment, mission-aligned processes, leadership agency, structured conversations, and nominated outcomes. Data were collected over twelve months at three stages using online survey. Australian Catholic principals reported a positive orientation experience, professional well-being, the comprehensiveness of the program, and the manageability of its implementation. Discussion confirmed design elements contributed to the wholistic nature of accompaniment linking body, mind, and spirit in conversational processes and the transformative effects of these exchanges on professional practice and well-being.

Biophysical reviews Special issue call: The 21st IUPAB Congress 2024 Kyoto Japan

This commentary describes an open call for submissions to the upcoming Biophysical Reviews' Special Issue: The 21st IUPAB Congress 2024 Kyoto Japan. The submission deadline is July 1st of 2024. Interested parties are requested to make contact with the Special Issue editors prior to submission.

Biophysical Reviews: peering into 2024

After introducing the winner of this year's Michèle Auger Award for Young Scientists' Independent Research, this Editorial for Volume 16 Issue 1 then describes the Issue contents. The Editorial concludes by providing a look into what lies ahead for 2024.

Simulating biological surface dynamics in high-speed atomic force microscopy experiments

High-speed atomic force microscopy (HSAFM) is an important tool for studying the dynamic behavior of large biomolecular assemblies at surfaces. However, unlike light microscopy techniques, which visualize each point in the field of view at the same time, in HSAFM, the surface is literally imaged pixel-by-pixel with a variable extent of time separation existing between recordings made at one pixel and all others within the surface image. Such "temporal asynchronicity" in the recording of the spatial information can introduce distortions into the image when the surface components move at a rate comparable to that at which the surface is imaged. This Letter describes recently released software developments that are able to predict the likely form of these distortions and estimate confidence levels when assigning the identity of observed structures. These described approaches may facilitate both the design and optimization of future HSAFM experimental protocols. Further to this, they may assist in the interpretation of results from already published HSAFM studies.

Biophysical Reviews: A goodbye to 2023

This Editorial for the IUPAB Biophysical Reviews journal (2023 volume 15 issue 6) first provides an overview of the contents of this "Regular Issue featuring an Issue Focus on the Computational Biophysics of Atomic Force Microscopy" before going on to highlight some of the notable work published in the journal throughout 2023. Highlights of the current Issue include the contributed review article by Antonio Benedetto, winner of the 2023 Michèle Auger Award for Young Scientists' Independent Research, the latest installment of the "Biophysical Reviews Top 5 Series" authored by Angela Dulhunty, and an Issue Focus on the topic of computational aspects of atomic force microscopy generated from an IUPAB-sponsored workshop held in 2022.

Computational biophysics of atomic force microscopy-an IUPAB-sponsored workshop

Atomic Force Microscopy (AFM) is a structural determination technique that involves 'prodding' surfaces with a nanometer sized needle with concomitant measurement of the resisting force. Due to its ability to interrogate the nanometer-to-micrometer size range, AFM is especially suited to the structural analysis of everything from biopolymers to cells and, as such, has become an important biophysical method. As AFM was only invented in 1986 it is relatively less scientifically developed than other structural techniques, such as NMR, X-ray crystallography and electron microscopy, that have a longer history of usage. In September of 2022 the first workshop of its kind was held to examine modern computational methods useful for simulating and analysing bioAFM experiments. Sponsored by a small IUPAB workshop grant, the three day meeting was of the hybrid (joint online /in person) type and had presenting participants based in Australia, UK, Finland, Thailand, South Korea, Vietnam and Japan. Each invited speaker was asked to deliver a lecture composed of half educational material (pitched at the level of an advanced postgraduate student) and half cutting edge research material (gathered from their own studies). IUPAB funds were used to invite young researchers (postgraduate students and early career scientists) from both within Japan and countries in the near asian region who had an interest in learning about the theoretical and experimental basis of the AFM technique. This Editorial describes the workshop and introduces the written contributions from the invited lecturers.

Biophysical Reviews' "Meet the Editors Series": a profile of Damien Hall

This piece introduces Damien Hall, Chief Editor of the Biophysical Reviews journal since 2019. Currently working as an Assistant Professor at Kanazawa University, the author describes his association with the journal along with some parts of his family history and academic journey.

HSAFM-MIREBA - Methodology for Inferring REsolution in biological applications

Due to a lack of requirement for any direct labelling of the target molecule, high speed atomic force microscopy (HS-AFM) is a potentially powerful procedure for the assessment of biological processes involving macromolecules. When the sample is static the AFM device can be purposefully setup to recover high-resolution information about the feature in question. However, when the feature to be studied moves an appreciable amount during the course of the measurement, the obtained image will be blurred. Encountering such blurred observations prompts the experimenter to sacrifice higher resolution images for higher scanning speeds by tuning available experimental parameters (such as the scanned image area, the image pixel size, the resonance frequency of the cantilever and/or the diameter of the AFM tip). The present work describes a software tool, HSAFM-MIREBA (High Speed Atomic Force Microscopy - Methodology for Inferring REsolution in Biological Applications) that allows for pre-experimental optimization of such parameters through iterative rounds of simulation of both the dynamic surface process and the HS-AFM measurement (based on the particular set of governing parameters). A representative set of five dynamic biological processes that describe a range of diffusive and directed motions (which can themselves be tuned by altering characteristic governing parameter sets) are provided.

Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD

To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer-promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds to chromatin for minutes, decompacts chromatin structure and increases enhancer dynamics. We also uncovered a rare fast-diffusing state of enhancers and found that NuRD restricts the time spent in this state. Hi-C and Cut&Run experiments revealed that NuRD modulates enhancer-promoter interactions in active chromatin, allowing them to contact each other over longer distances. Furthermore, NuRD leads to a marked redistribution of CTCF and, in particular, cohesin. We propose that NuRD promotes a decondensed chromatin environment, where enhancers and promoters can contact each other over longer distances, and where the resetting of enhancer-promoter interactions brought about by the fast decondensed chromatin motions is reduced, leading to more stable, long-lived enhancer-promoter relationships.

MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission

The single-celled baker's yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool (Monitoring Induction and Loss of prions in Cells; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging.

Posterior Fossa Horns in Hurler Syndrome: Prevalence and Regression

Posterior fossa "horns" caused by internal hypertrophy of the occipitomastoid sutures are one of the more recently defined cranial abnormalities described in mucopolysaccharidoses, especially in Hurler Syndrome. However, details of this finding, including the development and natural history, are not well-understood. Two hundred eighty-six brain MR imaging studies of 61 patients with mucopolysaccharidosis I-Hurler syndrome treated at single institution between 1996 and 2015 were studied. Posterior fossa horn height was measured as the perpendicular distance from the tip of the horn to the expected curvature of the occipital inner table. Fifty-seven of the 61 patients (93.4%) had evidence of posterior fossa horns on at least one occasion. The initial average height of the right horn was 4.5 mm, and the left horn, 4.7 mm. Most of the posterior horns regressed before transplantation in our cohort, though the exact age was variable among the patients. Nearly all patients in our cohort had posterior fossa horns, and these horns regressed with age. The regression of the horns frequently started before transplantation. This trend has not been previously described, and it may suggest unknown effects of mucopolysaccharidosis on skull development.

Biophysical Reviews: a call for nominations to the 2024 Michéle Auger Award

This editorial for volume 15 issue 3 first provides a brief introduction to the issue contents before then going on to open the call for nominations to the 2024 Michéle Auger Award for Young Scientists' Independent Research-the journal's single award.

Editors' Roundup: June 2023

This commentary article represents the latest edition of the Biophysical Reviews 'Editors' Roundup' Series - a platform made available to the editorial board members of any journal with a genuine interest in promoting biophysical content. Each journal associated editor is able to submit a short description of up to five articles recently appearing in their journals with an explanation of why these articles are of interest. This edition (Vol. 15 Issue 3 June 2023) carries contributions from editorial members associated with Biophysics and Physicobiology (Biophysical Society of Japan), Biophysics (Russian Academy of Sciences), Cell Biochemistry and Biophysics (Springer), and Biophysical Reviews (IUPAB-International Union for Pure and Applied Biophysics).

Editors' roundup: April 2023

The IUPAB Biophysical Reviews journal provides a regular forum, known as the "Editors' Roundup," that is available to editorial board members of any biophysics-related journal to contribute a personal recommendation of articles appearing within their publications. This latest Issue of the Editors' Roundup carries recommendations from editorial board members associated with the following journals, Cell Biochemistry and Biophysics, Biophysics, and the Biophysical Reviews journal.

Biophysical Reviews: And the winner is …

This Editorial (Vol. 15 Issue 2-Regular Issue) first announces the winner of the 2023 Michèle Auger Award for Young Scientists' Independent Research before then going on to describe the contents of the current Issue. The Editorial closes with a discussion of the pros and cons of writing in the formulation of scientific ideas.

Biophysical Reviews Issue Focus call: Computational biophysics of atomic force microscopy

This Commentary describes an open call for submissions to an Issue Focus of the IUPAB Biophysical Reviews journal on the topic of the, 'Computational biophysics of atomic force microscopy'. The Issue Focus will be published in Volume 15 Issue 6 of Biophysical Reviews in late December of 2023. The submission deadline is September 1st of 2023. Interested parties are requested to contact the Special Issue Editors prior to submission.

Biophysical Reviews: Turning the page from 2022 to 2023

This Editorial (vol. 15 issue 1-Regular Issue featuring an Issue Focus on the "100th Anniversary of Har Gobind Khorana") first describes the issue contents before providing both, a look back at some journal highlights from 2022, and a look forward to what we can expect from 2023. The Editorial closes with a roundup of new journal access features and an acknowledgement of those supporting the journal.

Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday

Receiving his initial training jointly in theoretical and applied physics at the University of Tokyo, Professor Haruki Nakamura has had a long and eventful scientific career, along the way helping to shape the way that biophysics is carried out in Japan. Concentrating his research efforts on the simulation of protein structure and function, he has, over his career arc, acted as director of the Institute for Protein Research (Osaka, Japan), director of the Protein Data Bank of Japan (PDBj), president of the Biophysical Society of Japan (BSJ), president of the Protein Science Society of Japan (PSSJ), and group leader and professor of Bioinformatics and Computational Structural Biology at Osaka University. In 2022, Prof. Haruki Nakamura turned 70 years old, and to mark this occasion, his scientific colleagues from around the world have combined their efforts to produce this Festschrift Issue of the IUPAB Biophysical Reviews journal around the theme of the computational biophysics and structural biology of proteins.

Correction to: Biophysical Reviews: Publishing short and critical reviews written by key figures in the field

[This corrects the article DOI: 10.1007/s12551-022-01009-6.].

Editors' roundup: October 2022

This commentary constitutes the October edition of the 'Editors' roundup'-a multi-author omnibus of personal recommendations to interesting biophysics-related articles contributed by members of the editorial boards of leading international biophysics journals. The present commentary contains contributions from Progress in Biochemistry and Biophysics (an official journal of the Biophysical Society of China), European Biophysics Journal (the official journal of the European Biophysical Societies Association), Biophysical Reviews (the official IUPAB journal), and Biophysics (an official journal of the Russian Academy of Sciences). This edition of the Editors' Roundup also contains a new section from an editor at large who has provided selections from a number of journals on a single thematic topic.

Biophysical Reviews: Publishing short and critical reviews written by key figures in the field

This Editorial for Issue 5 (Vol. 14 2022) of Biophysical Reviews begins with a short note of commemoration for the journal's founding chief editor Jean Garnier (1929-2022) who sadly passed away this month. Following this is a precis of the current Issue contents that begins with an introduction of the prizewinning article by Assoc. Prof. Miho Yanagisawa, winner of the 2022 Michèle Auger Award for Young Scientists' Independent Research. This Editorial concludes with a brief and somewhat subjective discussion of what features do and don't, help to make for a 'good journal'.

Biophysical reviews: call for nominations for the 2023 Michèle Auger Award

This Editorial for Issue 3 (Vol. 14 2022) of Biophysical Reviews first describes the Issue's contents (five commentaries/editorials within the front matter and seven review/letter articles appearing within the main body) before going on to discuss a number of matters of potential importance to the journal and its readers. Amongst this second tranche of content is the opening of the call for nominations for the 2023 Michèle Auger Award for Young Scientists' Independent Research.

Biophysical Reviews: focusing on an issue

This Issue of Biophysical Reviews (Volume 14, Issue 2) presents a new feature known as an 'Issue Focus' - a contiguous thematic block of five articles placed within a regular Issue format. The current 'Issue Focus' is concerned with the recent developments in Costa Rican biophysical science. The regular aspect of this Issue consists of a 'Meet the Editor' piece by Sabrina Leslie, the first instalment of an ongoing Commentary feature known as the 'Editors' Roundup', and five disparate review articles covering a variety of topics.

Improving the Quality of Paediatric ECG Interpretation

Aims Our aim was to complete an audit loop and identify whether implementing a paediatric ECG checklist improved the documentation and therefore the quality of paediatric ECG interpretation. We designed a paediatric ECG and education proforma in a Paediatric Emergency Department and incorporated it into daily practice. Methods We audited the medical records of children presenting with clinical indications for ECG. We included 40 records before and 40 records after the introduction of a paediatric ECG interpretation checklist. Results We assessed 10 items of documentation of which 8 related to the wave-form. Recording of these ranged from 0-65% before and from 95-100% after the checklist. Conclusion An intervention to introduce a paediatric ECG checklist, including education proforma, demonstrated significant improvement in the interpretation and documentation of a paediatric ECG. We recommend the use of this checklist in primary care and hospital settings.

Biophysical Reviews: from the umbra of 2020-2021 into the antumbra of 2022

This sub-Editorial for Volume 14 Issue 1 (2022) first makes comment on the current issue and then describes matters of interest related to the journal’s activities in 2022—chief among which are (i.) the announcement of the winner of the 2022 Michèle Auger Award for Young Scientists’ Independent Research, (ii.) an outline of this year’s finalized Special Issue (SI) lineup, (iii.) a description of a new production service offered by Springer to those submitting to the Biophysical Reviews journal, and (iv.) an introduction of newly appointed members of the Biophysical Reviews’ Editorial Board.

Biophysical Reviews- 2021, the year that was

The current issue (volume 13 issue 6, 2021) is a Special Issue jointly dedicated to scientific content presented at the 20th triennial IUPAB Congress that was held in conjunction with both the 45th Annual Meeting of the Brazilian Biophysical Society (Sociedade Brasileira de Biofísica - SBBf) and the 50th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (Sociedade Brasileira de Bioquímica e Biologia Molecular - SBBq). In addition to describing the scientific and nonscientific content arising from the meeting this sub-editorial also provides a look back at some of the high points for Biophysical Reviews in the year 2021 before going on to describe a number of matters of interest to readers of the journal in relation to the coming year of 2022.

Biophysical reviews-providing an effective critique

This Editorial for Volume 13, Issue 4 of Biophysical Reviews begins with an introduction to the invited Review contributed by the 2021 winner of "The Michèle Auger Award for Young Scientists' Independent Research" (Assoc. Prof. Jorge Alegre-Cebollada). After providing a short summary of the other articles contained within the Issue, we discuss some additional matters important to the journal and its readers. In particular, this Editorial describes ongoing preparations for the upcoming IUPAB World Congress (October 4th-8th); it introduces two new Executive Editors from the UK and Spain; it describes the journal's placement in the latest SCIMago journal rankings, and it explains a new feature of the journal-"The Biophysical Reviews Historical Top Five". This piece closes with some thoughts about what might constitute a constructive critique of a manuscript.

Biophysical Reviews-A call to young biophysicists

This Editorial for Volume 13, Issue 3 of Biophysical Reviews begins with a summary of the Issue contents. This is then followed by a discussion of some additional matters important to the journal. In particular, this Editorial offers some thoughts as to what constitutes a good scientific Commentary before announcing the call for nominations for the 'The 2022 Michèle Auger Award for Young Scientists' Independent Research'.

Biophysical Reviews: slowly getting back to 'normal'?

Run by the International Union for Pure and Applied Biophysics (IUPAB) and published by Springer Nature, Biophysical Reviews is an international journal dedicated to publishing topical review articles in the areas of (i) biology-related physics, (ii) structural biology, and (iii) molecular biology. This Editorial for Volume 13, Issue 2 of Biophysical Reviews provides a brief summary of the contents of the current Issue and then describes some matters important to the journal for 2021.

Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19

After several months of "lockdown" as the sole answer to the COVID-19 pandemic, balancing the re-opening of society against the implementation of non-pharmaceutical measures needed for minimizing interpersonal contacts has become important. Here, we present a stochastic model that examines this problem. In our model, people are allowed to move between discrete positions on a one-dimensional grid with viral infection possible when two people are collocated at the same site. Our model features three sets of adjustable parameters, which characterize (i) viral transmission, (ii) viral detection, and (iii) degree of personal mobility, and as such, it is able to provide a qualitative assessment of the potential for second-wave infection outbreaks based on the timing, extent, and pattern of the lockdown relaxation strategies. Our results suggest that a full lockdown will yield the lowest number of infections (as anticipated) but we also found that when personal mobility exceeded a critical level, infections increased, quickly reaching a plateau that depended solely on the population density. Confinement was not effective if not accompanied by a detection/quarantine capacity surpassing 40% of the symptomatic patients. Finally, taking action to ensure a viral transmission probability of less than 0.4, which, in real life, may mean actions such as social distancing or mask-wearing, could be as effective as a soft lockdown.

Biophysical Reviews: 2020-looking back, going forward

After first describing the issue contents (Biophysical Reviews-Volume 12 Issue 6), this Editorial goes on to provide a short round-up of the activities of the journal in 2020. Directly following this Editorial are two obituaries marking the recent deaths of Prof. Fumio Oosawa (Japan) and Dr. Herbert Tabor (USA)-two major figures in Biophysical/Biochemical science from the last 100 years.

A simple method for modeling amyloid kinetics featuring position biased fiber breakage

A mathematical model of amyloid fiber formation is described that is able to simply specify different rates of fiber breakage at internal versus end regions. This Note presents the derivation of the relevant equations and provides results showing the dramatic effects of position biased fiber breakage on the kinetics of amyloid growth.

Biophysical Reviews: a Q1 ranked journal in biophysics and structural biology

This Editorial for Biophysical Reviews (Volume 12, Issue 5) begins with a description of the two feature articles. The first being the latest in the "Meet the Editors Series" describing Rosangela Itri-the Biophysical Reviews Executive Editor responsible for the South American region. The second feature article is by Alexandra Zidovska, the inaugural winner of the 2020 "Michèle Auger Award for Young Scientists' Independent Research." Next highlighted are the Issue contents, which consist of five Commentaries/Letters and eleven Reviews. Finally, we conclude with a description of Biophysical Reviews' ascension within the world's major journal rankings index (Elsevier, Scimago)-becoming 12th overall (out of 156) within the biophysics category and receiving the coveted Q1 rating in both biophysics and structural biology sections.

Biophysics of human anatomy and physiology-a Special Issue in honor of Prof. Cristobal dos Remedios on the occasion of his 80th birthday

In 2001, Cristobal dos Remedios was made Professor of Anatomy (now emeritus) within Australia’s highest-ranked university (University of Sydney). For the majority of his career, he has examined the biomechanics and biophysics of human muscle contraction. To coincide with the occasion of his 80^th birthday, this Special Issue has commissioned a collection of review articles from experts exploring biophysical subjects within the general areas of human anatomy and physiology. After introducing the scope and contents of the Issue, we provide a short scientific biography, placing his scientific achievements within the context of the course of his life’s developments.

Biophysical Reviews-Quantitative analysis of biological phenomenon

This Editorial first describes the articles constituting the current Issue (Volume 12 Issue 3). It then goes on to outline the formal invitation procedure for those interested in submitting a review article to the journal. The Editorial concludes by describing the nomination process for the 2021 Michèle Auger Award for Young Scientists' Independent Research.

Biophysical Reviews' national biophysical society partnership program

This Special Issue is focused on the Biophysical Society of Japan. It represents the first in a series tasked with introducing an individual national biophysical society to the wider biophysical community. In this Editorial for Volume 12 Issue 2, I first outline the nature and goals of this program before going on to describe the contents of the Special Issue that relate to the activities organized by the Biophysical Society of Japan and the scope of the research performed by its members.

A new decade for Biophysical Reviews and a look into the future of biophysics

This Editorial for Volume 12 Issue 1 first describes the contents of the current issue before informing on a few of the developments occurring in Biophysical Reviews during 2020. Notable items include the announcement of the (i) inaugural winner of the Michèle Auger Award for Young Scientists' Independent Research and (ii) lineup of Special Issue topics for 2020. This Editorial concludes with a short forward-looking discussion piece on the future of biophysics as an increasingly important and vital sub-discipline of modern scientific research.

On the nature of the optimal form of the holdase-type chaperone stress response

The holdase paradigm of chaperone action involves preferential binding by the chaperone to the unfolded protein state, thereby preventing it from either, associating with other unstable proteins (to form large dysfunctional aggregates), or being degraded by the proteolytic machinery of the cell/organism. In this paper, we examine the necessary physical constraints imposed upon the holdase chaperone response in a cell-like environment and use these limitations to comment on the likely nature of the optimal form of chaperone response in vivo.