Biophysical reviews最新文献

{"title":"A contemporary systematic review on deterministic numerical simulations of light propagation in head tissues.","authors":"Filipa Fernandes, Nuno Sousa, Filipe S Silva, Óscar Carvalho, Susana O Catarino","doi":"10.1007/s12551-025-01403-w","DOIUrl":"10.1007/s12551-025-01403-w","url":null,"abstract":"<p><p>Understanding how light interacts with the head's tissues is relevant for several biomedical applications. Since in vivo studies involve ethical considerations, numerical simulations have become a recognised alternative method for studying light propagation in biological tissue. Although Monte Carlo methods are the gold standard for these studies, deterministic simulations are becoming more common due to their lower computational cost. Thus, this document reviews articles published after 2010, containing deterministic numerical simulations of light propagation (visible to infrared wavelengths) in human head tissues, to define how these methods are implemented and whether they are a viable alternative to the stochastic Monte Carlo algorithms. Most of the selected articles included a 3D simulation, using Finite Element Methods (FEM) to solve the Diffusion Equation (DE), with Robin boundary conditions, and considering the tissues as horizontal rectangular layers, to improve imaging techniques' algorithms. Regarding target areas, there is an almost identical number of records studying the brain as a whole or dividing it into grey and white matter, while more studies consider the scalp and skull as individual layers instead of grouping them. The cerebrospinal fluid (CSF) was included in more than half of the studies, confirming that it is possible to simulate this tissue using the DE, if the optical parameters are adequate. Some of the challenges identified in the reported simulations are the variations in the optical properties of tissues (reduced scattering and absorption coefficients) and oversimplifications of the geometric models, which raise the question of whether using subject-specific data could improve the outcomes of light-based diagnosis and therapies. Although Monte Carlo methods are still the most commonly used for the simulation of optical properties, all the reviewed works reached comprehensive results, with most of them showing that deterministic numerical simulations can be an efficient and relatively accurate alternative to the time-consuming Monte Carlo methods.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s12551-025-01403-w.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"18 1","pages":"57-82"},"PeriodicalIF":5.0,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13031484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147572525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ian Cormack Palmer Smith.","authors":"Lawrence J Berliner","doi":"10.1007/s12551-025-01389-5","DOIUrl":"https://doi.org/10.1007/s12551-025-01389-5","url":null,"abstract":"<p><p>Ian was a dear friend, mentor, and colleague, who introduced me to the world of international science and collaborators. I knew his family very well and we met frequently over the years, mostly professionally. He was a shining light in Canadian science and a leader in several areas of magnetic resonance. My commentary, however, highlights his mentoring me to the world of international travel and collaborations.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 6","pages":"1669-1670"},"PeriodicalIF":3.7,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12957663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147364065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparing cryo-EM structures of the vertebrate cardiac muscle thick filament.","authors":"Roger Craig, Debabrata Dutta, Natalia A Koubassova, Andrey K Tsaturyan, Raúl Padrón","doi":"10.1007/s12551-025-01393-9","DOIUrl":"10.1007/s12551-025-01393-9","url":null,"abstract":"<p><p>The thick filaments of muscle carry the myosin motors that generate contraction by interacting with actin filaments. Despite decades of research, an atomic model of the vertebrate striated muscle thick filament has been lacking. Three cryo-EM thick filament structures from cardiac muscle have now been reported, revealing the organization of myosin heads in interacting-heads motifs (IHMs) on the thick filament surface, and a complex arrangement of myosin tails, titin, and myosin-binding protein C (MyBP-C) in the filament backbone. The three studies are complementary, coming from two species (mouse and human), two techniques (cryo-electron tomography and single particle cryo-EM), and from muscles treated or untreated with the myosin-stabilizing drug mavacamten. The structures are remarkably similar, agreeing on most elements of molecular organization but differing on the degree of stability of the IHMs and the organization of MyBP-C. The differences arise from the different techniques used and the observation of filaments within, or isolated from, the filament lattice.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":" ","pages":""},"PeriodicalIF":5.0,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13089571/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147721609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Life and career of Ian C. P. Smith.","authors":"Angela M Gronenborn, Erick J Dufourc, John E Baenziger, Shirley Schreier","doi":"10.1007/s12551-025-01399-3","DOIUrl":"https://doi.org/10.1007/s12551-025-01399-3","url":null,"abstract":"<p><p>Ian C. P. Smith was a pioneer in the application of magnetic resonance techniques to biological systems.  He was also an outstanding leader and mentor.  Through his dazzling personality, Ian inspired the world of biophysics.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 6","pages":"1661-1663"},"PeriodicalIF":3.7,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12957665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147364017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Astrocyte morphology: complex or trivial?","authors":"Anna Kriuchechnikova, Anastasia Soldatova, Alisa Tiaglik, Yong Tang, Alexey Brazhe","doi":"10.1007/s12551-025-01402-x","DOIUrl":"https://doi.org/10.1007/s12551-025-01402-x","url":null,"abstract":"<p><p>Astrocyte morphology, a key element of CNS function, emerges from a dynamic interplay of molecular cues, intercellular interactions, and physical constraints. It is often referred to as \"complex\" and \"dynamic.\" This review synthesizes current picture of how astrocyte morphogenesis is shaped at different levels from cell adhesion and molecular cues to overarching cell lineage and anatomical placement. We review how motile astrocyte leaflets actively participate in synaptic plasticity through structural dynamics that regulate neurotransmission. Conversely, pathological disruptions in these local mechanisms, from leaflets to endfeet, cascade to macroscale morphological changes linked to dysfunctional synaptic regulation, excitability, and metabolism. Next, we review mathematical approaches to model and analyze branching morphologies with a focus on astrocytes, but also making incursions to adjacent fields, regarding morphologies of neurons, other glial cells, or mitochondrial networks. Despite significant advances, open remain fundamental questions regarding the principles governing this apparent structural complexity: the balance between stochastic and regulated growth, the physiology-based optimality of morphology, and the functional significance of tiling. Furthermore, the transition from physiological to pathological extent of structural motility in conditions like depression and neurodegeneration requires further research. We argue that resolving these questions necessitates the broader adoption of quantitative analytical frameworks based on graph theory and applied topology. Rapid progress in open-source computational tools, including deep learning approaches, promises an imminent breakthrough in understanding astrocyte morphology in CNS health and disease.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"18 2","pages":"477-497"},"PeriodicalIF":5.0,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13272703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148276110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A quest for greater thermodynamic rigour in the quantitative characterization of protein self-association by direct assessment of sedimentation equilibrium distributions.","authors":"Donald J Winzor, Peter R Wills","doi":"10.1007/s12551-025-01371-1","DOIUrl":"10.1007/s12551-025-01371-1","url":null,"abstract":"<p><p>This review summarizes research designed to enhance thermodynamic rigour in the quantitative characterization of protein self-association by direct analysis of sedimentation equilibrium distributions. The effects of thermodynamic nonideality have been incorporated into analytical approaches that not only afford experimental delineation of the monomer thermodynamic activity throughout a sedimentation equilibrium distribution but also take into account the composition dependence of species activity coefficients that arises from their consideration on the statistical-mechanical basis of excluded volume. Allowance for thermodynamic nonideality in terms of nearest-neighbor interactions should suffice for that iterative procedure. Attempts to eliminate the need for iterative analysis by expressing total protein concentration as a virial expansion in monomer activity have met with only limited success. The relevance of these scientific developments to their incorporation into the currently used numerical simulation approaches for the characterization of protein self-association by sedimentation equilibrium is also discussed.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"18 2","pages":"281-305"},"PeriodicalIF":5.0,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13272738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148276042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic signatures of galactosemia in magnetic resonance.","authors":"Calin Deleanu, Natalia Uşurelu, Daniela Blăniță, Alina Nicolescu","doi":"10.1007/s12551-025-01400-z","DOIUrl":"https://doi.org/10.1007/s12551-025-01400-z","url":null,"abstract":"<p><p>The paper explores the information provided by various magnetic resonance (MR) techniques in the diagnosis of galactosemia. Galactosemia (GA) is an autosomal recessive inborn error of metabolism, included in the category disorders of carbohydrate metabolism. In this disorder, the body is unable to metabolize galactose, leading to the accumulation of toxic intermediates like galactose-1-phosphate, galactitol, and galactonate. The information provided by magnetic resonance imaging (MRI), localized nuclear magnetic resonance spectroscopy (MRS), and non-localized nuclear magnetic resonance (NMR) is complementary both in terms of data supplied and organ/body fluid targeted. In spite of this complementarity, we found that these MR techniques have never been jointly applied in the diagnosis of GA.</p><p><strong>Graphical abstract: </strong></p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 6","pages":"1795-1806"},"PeriodicalIF":3.7,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12957755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147364026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ian C. P. Smith-a Romanian perspective.","authors":"Alina Nicolescu, Calin Deleanu","doi":"10.1007/s12551-025-01401-y","DOIUrl":"https://doi.org/10.1007/s12551-025-01401-y","url":null,"abstract":"<p><p>Ian C. P. Smith had a special connection with Romania that started with his first visit as a student in 1964. This connection continued throughout Ian's career and led directly to the development of a strong NMR spectroscopy-based medical diagnosis group in the country. The authors benefitted from Ian's connections to Romania for almost two decades. They are proud to extend his legacy in the field of NMR metabolomics.</p><p><strong>Graphical abstract: </strong></p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 6","pages":"1675-1677"},"PeriodicalIF":3.7,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12957754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147364010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Daily profile of COVID-19 infections in Europe - a biophysical perspective.","authors":"Derek Marsh","doi":"10.1007/s12551-025-01383-x","DOIUrl":"10.1007/s12551-025-01383-x","url":null,"abstract":"<p><p>Progression of the European COVID-19 pandemic is monitored using daily cases and associated deaths, reported in Italy, Germany and England. Weekly periodicity in reporting is filtered out with a moving average over a 7-day window. This reveals underlying stages of exponential growth and decay, and changes in response to preventative interventions. Exponential rate constants <math><msub><mi>r</mi> <mi>t</mi></msub> </math> , combined with different serial-interval distributions, yield estimates for the basic reproduction number R₀ and instantaneous R _<i>t</i> , and characterize the emergence of successive dominant viral variants. Rates of testing are discussed in detail, and corrected for. COVID-associated deaths are linked with daily cases, and fatality/case ratios (cfr) used to estimate the extent of under-reporting in the early stages. Reproduction numbers, R₀ and R _<i>t</i> , provide estimates of vaccine coverage required to reach population-level immunity, and subsequent modifications needed during the vaccination programme. Hence, we obtain a straightforward integrated description of the pandemic that is essentially biophysical.</p><p><strong>Graphical abstract: </strong></p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 6","pages":"1717-1734"},"PeriodicalIF":5.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12957723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147363926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lipid-dependent uncoupling of agonist binding and channel gating in the nicotinic acetylcholine receptor.","authors":"Deepansh Mody, Toka O K Hussein, John E Baenziger","doi":"10.1007/s12551-025-01397-5","DOIUrl":"https://doi.org/10.1007/s12551-025-01397-5","url":null,"abstract":"<p><p>The prototypic muscle-type nicotinic acetylcholine receptor (nAChR) from <i>Torpedo</i> displays exquisite functional sensitivity to its lipid environment. A defining feature of lipid-nAChR interactions is that in the absence of both neutral and anionic lipids, the nAChR adopts a conformation that binds agonist, but does not undergo agonist-induced conformational transitions-the so-called lipid-dependent uncoupled state. Here, we review the evidence supporting the existence of this non-canonical lipid-dependent uncoupled conformation. We highlight structural and functional measurements that shed light on the mechanisms by which lipids influence the activity of the nAChR, and other pentameric ligand-gated ion channels, leading to a plausible model for lipid-dependent uncoupling. Finally, we describe new structural and molecular dynamics simulation data showing the existence of both cholesterol and anionic lipid binding sites on the nAChR and highlight current research aimed at understanding whether lipid-binding to these sites allosterically influences the ability of the nAChR to undergo agonist-induced conformational transitions.</p>","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 6","pages":"1763-1779"},"PeriodicalIF":3.7,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12957688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147364020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}