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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]

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

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

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]

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

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

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

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

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

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.'

In Brazil, the CNPq (National Council for Scientific and Technological Development) provides grants, funds and fellowships to productive scientists to support their investigations. They are ranked and categorized into four hierarchical levels ranging from PQ 1A (the highest) to PQ 1D (the lowest). Few studies, however, report and analyse scientific productivity in different sub-fields of Biomedical Sciences (BS), e.g., Biochemistry, Pharmacology, Biophysics and Physiology. In fact, systematic comparisons of productivity among the PQ 1 categories within the above sub-fields are lacking in the literature. Here, the scientific productivity of 323 investigators receiving PQ 1 fellowships (A to D levels) in these sub-fields of BS was investigated. The Scopus database was used to compile the total number of articles, citations, h-index values and authorship positions (first-, co- or last-listed author) in the most cited papers by researchers granted CNPq fellowships. We found that researchers from Pharmacology had the best performance for all of the parameters analysed, followed by those in Biochemistry. There was great variability in scientific productivity within the PQ 1A level in all of the sub-fields of BS, but not within the other levels (1B, 1C and 1D). Analysis of the most cited papers of PQ 1(A–D) researchers in Pharmacology revealed that the citations of researchers in the 1C and 1D levels were associated with publications with their senior supervisors, whereas those in the 1B level were less connected with their supervisors in comparison to those in 1A. Taken together, these findings suggest that the scientific performance of PQ 1A researchers in BS is not homogenous. In our opinion, parameters such as the most cited papers without the involvement of Ph.D. and/or post-doctoral supervisors should be used to make decisions regarding any given researcher's fellowship award level. [ABSTRACT FROM AUTHOR]

Dear Editors, I am writing to add my voice to those making I BLANCO-80 i contributions to the I Journal of Membrane Biology i to celebrate the birthday of Professor Stephen H. White of the University of California-Irvine and his long career of discovery in membrane biophysics. Papers from this era included no less than 5 on alkane-bilayer interactions (White [29]; White et al. [30]; Jacobs and White [13], [14]; King et al. [17]). This period of his career culminated in the classic Wiener and White paper on the dynamics structure of lipid bilayers (Wiener and White [36]). [Extracted from the article]

In this paper, we introduce a special device, in which the topological rejection effect in the study of biomacromolecule translocation competes with the entropic tensile force. The expected results for the translocation of the polymer chain given by these two different theories do not coincide with each other, so we call this problem the "translocation paradox". The dynamics of the polymer chain and the preference translocation in such device are studied using computer simulation method. Surprisingly, these results do not completely satisfy all these hypothesis. We provide a plausible explanation which coincides our simulation results perfectly. Meanwhile, this explanation provides a possible solution to the design of translocation device in biophysics field. [ABSTRACT FROM AUTHOR]

In this paper, we reject commonly accepted views on fundamentality in science, either based on bottom-up construction or top-down reduction to isolate the alleged fundamental entities. We do not introduce any new scientific methodology, but rather describe the current scientific methodology and show how it entails an inherent search for foundations of science. This is achieved by phrasing (minimal sets of) metaphysical assumptions into falsifiable statements and define as fundamental those that survive empirical tests. The ones that are falsified are rejected, and the corresponding philosophical concept is demolished as a prejudice. Furthermore, we show the application of this criterion in concrete examples of the search for fundamentality in quantum physics and biophysics. [ABSTRACT FROM AUTHOR]

INTRODUCTION BY ANA-NICOLETA BONDAR, BIOPHYSICS SECTION HEAD EDITOR: This issue of the Journal of Membrane Biology inaugurates Up-and-Coming Scientist, in which investigators at early career stages are invited to present recent research in the broad context of their discipline. We inaugurate Up-and-Coming Scientist with the essay by Dr. Elena Lesca of the ETH Zürich and the Paul Scherrer Institut, Switzerland. Dr. Lesca has completed her doctoral degree at the Technical University München, Germany, in 2014, and pursued postdoctoral research at the ETH Zürich and Paul Scherrer Institut, where she is Senior Assistant since 2019. Two recent papers by Dr. Lesca et al. (references 33 and 39) have used X-ray crystallography and experimental biophysics approaches to shed light on the mechanism of action of a membrane receptor from the G Protein-Coupled Receptor (GPCR) family, Jumping Spider Rhodopsin-1 (JSR-1). JSR-1 is a visual rhodopsin activated upon absorption of light by its covalently bound retinal chromophore. Unlike the better-understood bovine rhodopsin GPCR, which is monostable, JSR-1 is bistable (i.e., in JSR-1 the Schiff base that binds retinal to the protein stays protonated throughout the reaction cycle), and absorption of a second photon resets the retinal ligand to the resting state configuration. In her essay, Dr. Lesca discusses the implications of her work on JSR-1 and, more broadly, GPCR research, for state-of-the-art applications in optogenetics and drug design. [ABSTRACT FROM AUTHOR]

The following paper presents the history of the Climate and Human Health Commission at the International Society of Biometeorology after more than one decade since its creation. A brief history of the origins of the human biometeorology is revealed through some of the main research topics and publications of the founders of the society in this field. Secondly, it is presented as a brief review of the activities of the commission in the last 10 years, based on the reports that have periodically been submitted by members of the commission to the Bulletin of the society. A summary of the topics of interest on human biometeorology and the most frequent research topics are also described. Thirdly, the need of adapting human biometeorology contents, methods and techniques to a changing world is articulated according to some of the new environmental threats in the XXI century. Finally, a list of future actions and research lines collected through a form from members of the commission is presented. The paper concludes with the existence of great challenge for human biometeorology in order to transform biometeorological knowledge into specific services to improve the wellbeing of human beings. [ABSTRACT FROM AUTHOR]

A compact, portable and improved blood flow measurement system for an extracorporeal circuit having a rotating permanent magnetic excitation scheme is described in this paper. The system consists of a set of permanent magnets rotating near blood or any conductive fluid to create high-intensity alternating magnetic field in it and inducing a sinusoidal varying voltage across the column of fluid. The induced voltage signal is acquired, conditioned and processed to determine its flow rate. Performance analysis shows that a sensitivity of more than 250 mV/lpm can be obtained, which is more than five times higher than conventional flow measurement systems. Choice of rotating permanent magnet instead of an electromagnetic core generates alternate magnetic field of smooth sinusoidal nature which in turn reduces switching and interference noises. These results in reduction in complex electronic circuitry required for processing the signal to a great extent and enable the flow measuring device to be much less costlier, portable and light weight. The signal remains steady even with changes in environmental conditions and has an accuracy of greater than 95%. This paper also describes the construction details of the prototype, the factors affecting sensitivity and detailed performance analysis at various operating conditions. [ABSTRACT FROM AUTHOR]

Biophysics has been either an independent discipline or an element of another discipline in the United States, but it has always been recognized as a stand-alone discipline in the People's Republic of China (PRC) since 1949. To inquire into this apparent divergence, this paper investigates the formational history of biophysics in China by examining the early institutional history of one of the best-known and prestigious science and technology universities in the PRC, the University of Science and Technology of China (USTC). By showing how the university and its biophysics program co-evolved with national priorities from the school's founding in 1958 to the eve of the Cultural Revolution in 1966, the purpose of this paper is to assess the development of a scientific discipline in the context of national demands and institutional politics. Specific materials for analysis include the school's admission policies, curricula, students' dissertations, and research program. To further contextualize the institutional setting of Chinese biophysics, this paper begins with a general history of proto-biophysical institutions in China during the Nationalist-Communist transitional years. This paper could be of interest to historians wanting to know more about the origin of the biophysics profession in China, and in particular how research areas that constitute biophysics changed in tandem with socio-political contingencies. [ABSTRACT FROM AUTHOR]

The development of the DNA theory of inheritance culminated in the publication of the molecular structure of DNA 60 years ago. This paper describes this development, beginning with the discovery of DNA as a chemical substance by Friedrich Miescher in 1869, followed by its basic chemical analysis and demonstration of its participation in the structure of chromosomes. Subsequently it was discovered by Oswald Avery in 1944 that DNA was the genetic material, and then Erwin Chargaff showed that the proportions of the bases included in the structure of DNA followed a certain law. These findings, in association with the biophysical studies of Maurice Wilkins and Rosalind Franklin with Raymond Gosling, led James Watson and Francis Crick to the discovery of the double-helical structure of DNA in 1953. The paper ends with a short description of the development of the DNA theory of inheritance after the discovery of the double helix. [ABSTRACT FROM AUTHOR]

Cardiopulmonary resuscitation (CPR) is used widely to rescue cardiac arrest patients, yet some physiological aspects of the procedure remain poorly understood. We conducted this study to characterize the dynamic mechanical properties of the thorax during CPR in a swine model. This is an important step toward determining optimal CPR chest compression mechanics with the goals of improving the fidelity of CPR simulation manikins and ideally chest compression delivery in real-life resuscitations. This paper presents a novel nonlinear model of the thorax that captures the complex behavior of the chest during CPR. The proposed model consists of nonlinear elasticity and damping properties along with frequency dependent hysteresis. An optimization technique was used to estimate the model coefficients for force-compression using data collected from experiments conducted on swine. To track clinically relevant, time-dependent changes of the chest's properties, the data was divided into two time periods, from 1 to 10 min (early) and greater than 10 min (late) after starting CPR. The results showed excellent agreement between the actual and the estimated forces, and energy dissipation due to viscous damping in the late stages of CPR was higher when compared to the earlier stages. These findings provide insight into improving chest compression mechanics during CPR, and may provide the basis for developing CPR simulation manikins that more accurately represent the complex real world changes that occur in the chest during CPR. [ABSTRACT FROM AUTHOR]

Organisms not only respond to their environment but also influence the availability of resources and change environmental conditions. Hence, the impacts of organisms on their environment shape the selective regimes that drive, on ecological time scales, the assembly of ecological communities and, on evolutionary time scales, diversification. Recent studies have drawn attention to the fact that feedbacks between organisms and the environment can prevent or induce catastrophic transitions in ecosystem states and argue that climate change increases the likelihood of such catastrophic regime shifts. Ecologists have very limited ability to predict the likelihood of such regime shifts or the properties of the ecosystems that assemble after such collapses. This is because ecology does not have a theory of ecosystem assembly, nor does it have an established way of translating such a theory into models capable of predicting future ecosystem states. Without knowing these potential endpoints, we cannot develop strategies for coercing ecosystems into desired states, severely constraining our capacity to mitigate climate change and climate change impacts. This paper outlines a roadmap for developing a theory of terrestrial ecosystem assembly. Recent progress in dynamic global vegetation modelling and community assembly provides a useful foundation for a theory of ecosystem assembly. Environmental filtering and limiting similarity are key principles, but to be useful, they need to be linked to resource consumption and environmental modulation, and be more strongly constrained by biophysics and the trade-offs defined by biophysical principles. Such a theory recognises that ecological and evolutionary history ensures that many different ecosystem assemblies are possible at any given point in space and time. [ABSTRACT FROM AUTHOR]

Knowledge regarding the 3D structure of a protein provides useful information about the protein's functional properties. Particularly, structural similarity between proteins can be used as a good predictor of functional similarity. One method that uses the 3D geometrical structure of proteins in order to compare them is the similarity value (SV). In this paper, we introduce a new definition of the SV measure for comparing two proteins. To this end, we consider the mass of the protein's atoms and concentrate on the number of protein's atoms to be compared. This defines a new measure, called the weighted similarity value (WSV), adding physical properties to geometrical properties. We also show that our results are in good agreement with the results obtained by TM-SCORE and DALILITE. WSV can be of use in protein classification and in drug discovery. [ABSTRACT FROM AUTHOR]

A growing number of laboratory and clinical studies over the past 10 years have shown that low-level laser stimulation (633 or 670 nm) at extremely low power densities (about 0.15 mW/cm(2)), when administered through a particular emission mode, is capable of eliciting significant biological effects. Studies on cell cultures and animal models as well as clinical trials give support to a novel therapeutic modality, which may be referred to as ultra low level laser therapy (ULLLT). In cultured neural cells, pulsed irradiation (670 nm, 0.45 mJ/cm(2)) has shown to stimulate NGF-induced neurite elongation and to protect cells against oxidative stress. In rats, anti-edema and anti-hyperalgesia effects following ULLL irradiation were found. Clinical studies have reported beneficial effects (also revealed through sonography) in the treatment of musculoskeletal disorders. The present paper reviews the existing experimental evidence available on ULLLT. Furthermore, the puzzling issue of the biophysical mechanisms that lie at the basis of the method is explored and some hypotheses are proposed. Besides presenting the state-of-the-art about this novel photobiostimulation therapy, the present paper aims to open up an interdisciplinary discussion and stimulate new research on this subject. [ABSTRACT FROM AUTHOR]

Fracture mechanics concepts are applied to gain some understanding of the hierarchical nanocomposite structures of hard biological tissues such as bone, tooth and shells. At the most elementary level of structural hierarchy, bone and bone-like materials exhibit a generic structure on the nanometer length scale consisting of hard mineral platelets arranged in a parallel staggered pattern in a soft protein matrix. The discussions in this paper are organized around the following questions: (1) The length scale question: why is nanoscale important to biological materials? (2) The stiffness question: how does nature create a stiff composite containing a high volume fraction of a soft material? (3) The toughness question: how does nature build a tough composite containing a high volume fraction of a brittle material? (4) The strength question: how does nature balance the widely different strengths of protein and mineral? (5) The optimization question: Can the generic nanostructure of bone and bone-like materials be understood from a structural optimization point of view? If so, what is being optimized? What is the objective function? (6) The buckling question: how does nature prevent the slender mineral platelets in bone from buckling under compression? (7) The hierarchy question: why does nature always design hierarchical structures? What is the role of structural hierarchy? A complete analysis of these questions taking into account the full biological complexities is far beyond the scope of this paper. The intention here is only to illustrate some of the basic mechanical design principles of bone-like materials using simple analytical and numerical models. With this objective in mind, the length scale question is addressed based on the principle of flaw tolerance which, in analogy with related concepts in fracture mechanics, indicates that the nanometer size makes the normally brittle mineral crystals insensitive to cracks-like flaws. Below a critical size on the nanometer length scale, the mineral crystals fail no longer by propagation of pre-existing cracks, but by uniform rupture near their limiting strength. The robust design of bone-like materials against brittle fracture provides an interesting analogy between Darwinian competition for survivability and engineering design for notch insensitivity. The follow-up analysis with respect to the questions on stiffness, strength, toughness, stability and optimization of the biological nanostructure provides further insights into the basic design principles of bone and bone-like materials. The staggered nanostructure is shown to be an optimized structure with the hard mineral crystals providing structural rigidity and the soft protein matrix dissipating fracture energy. Finally, the question on structural hierarchy is discussed via a model hierarchical material consisting of multiple levels of self-similar composite structures mimicking the nanostructure of bone. We show that the resulting “fractal bone”, a model hierarchical material with different properties at different length scales, can be designed to tolerate crack-like flaws of multiple length scales. [ABSTRACT FROM AUTHOR]

The article presents information for the contributors of the journal "Khimiko Farmatsevticheskii Zhurnal". The papers submitted to the journal should reflect new, previously unreported investigations performed at the modern scientific and technological level and advanced commercial experience, in the fields of molecular biology and biochemistry. Papers presenting the results of experiments on the synthesis of new compounds and their characterization should contain separate chemical and biological experimental parts. Papers presenting new medicinal products should provide data on the chemical and physical properties; molecular and structural formulas; main results of the biological tests and clinical investigations.

This paper presents a novel hybrid medical stent device. This hybrid stent device formed by fractal mesh structures provides a flow-diverting effect and stent-assisted coil embolization. Flow-diverter stents decrease blood flow into an aneurysm to prevent its rupture. In general, the mesh size of a flow-diverter stent needs to be small enough to prevent blood flow into the aneurysm. Conventional flow-diverter stents are not available for stent-assisted coil embolization, which is an effective method for aneurysm occlusion, because the mesh size is too small to insert a micro-catheter for coil embolization. The proposed hybrid stent device is capable of stent-assisted coil embolization while simultaneously providing a flow-diverting effect. The fractal stent device is composed of mesh structures with fine and rough mesh areas. The rough mesh area can be used to insert a micro-catheter for stent-assisted coil embolization. Flow-diverting effects of two fractal stent designs were composed to three commercially available stent designs. Flow-diverting effects were analyzed using computational fluid dynamics (CFD) analysis and particle image velocimetry (PIV) experiment. Based on the CFD and PIV results, the fractal stent devices reduce the flow velocity inside an aneurism just as much as the commercially available flow-diverting stents while allowing stent-assisted coil embolization. [ABSTRACT FROM AUTHOR]

The leaf area index (LAI) is a key biophysical parameter that determines the state of plant growth. A global LAI has been routinely produced by the Moderate Resolution Imaging Spectro-radiometer (MODIS) and Advanced Very High Resolution Radiometer (AVHRR). However, the MODIS and AVHRR LAI products cannot be synchronized with the same spatial and temporal resolution. The LAI features are not discernible when a global LAI product is implemented at the regional scale because it has low resolution and different land cover types. To obtain high spatial and temporal resolution of LAI products, an empirical model based on the pixel scale was developed. The approach to generate a long (multi-decade) time series of a 1-km spatial resolution LAI normally integrates both AVHRR and MODIS datasets for different land cover types. In this paper, a regression-based model for generating a vegetation LAI was developed using the AVHRR Global Inventory Modelling and Mapping Studies Normalized Difference Vegetation Index (NDVI), MODIS LAI and land cover as input data; the model was evaluated by using relevant data from the same period data from 2000 to 2006. The results of this method show a good consistency in LAI values retrieved from the AVHRR NDVI and MODIS LAI. This simple method has no specific-limited data requirements and can provide improved spatial and temporal resolution in a region without ground data. [ABSTRACT FROM AUTHOR]

The results reported in the papers on protein crystallography entering this issue were obtained with the aid of synchrotrons. B.K. Vainshtein was a pioneer of protein crystallography in Russia: he organized a protein crystallography laboratory at the Institute of Crystallography of the USSR Academy of Sciences in 1958 (now the Federal Scientific Research Centre (FSRC) "Crystallography and Photonics" of the Russian Academy of Sciences (RAS)). X-ray diffraction analysis of proteins (or protein crystallography), which was originated in the 1950s, holds the leading position until now. [Extracted from the article]

Combining ASIC and multiple microsensors low-power wireless electronic capsule was developed for the long-term monitoring of the entire human gastro-intestinal (GI) tract. To meet the system requirements, several low-power designs were used in the wireless electronic capsule. The capsule measured 11×22 mm including batteries (45mAh). The capsule system’s lifetime was 233 h, and it could meet the requirements of almost all clinical applications. A wireless electronic capsule, portable data recorder, and workstation comprised the human GI physiological parameters monitoring system. In this paper, this system was used in a clinical trial to compare colon peristaltic pressure between patients with constipation and healthy people. [ABSTRACT FROM AUTHOR]

Estimating the behavior of a network of neurons requires accurate models of the individual neurons along with accurate characterizations of the connections among them. Whereas for a single cell, measurements of the intracellular voltage are technically feasible and sufficient to characterize a useful model of its behavior, making sufficient numbers of simultaneous intracellular measurements to characterize even small networks is infeasible. This paper builds on prior work on single neurons to explore whether knowledge of the time of spiking of neurons in a network, once the nodes (neurons) have been characterized biophysically, can provide enough information to usefully constrain the functional architecture of the network: the existence of synaptic links among neurons and their strength. Using standardized voltage and synaptic gating variable waveforms associated with a spike, we demonstrate that the functional architecture of a small network of model neurons can be established. [ABSTRACT FROM AUTHOR]

Purpose: The primary objective of this study is to investigate the content of biologically active compounds producing an antioxidant effect in Plantago maxima and their influence on main mechanisms of dietary obesity development. Methods: Biologically active compounds in P. maxima were tested using paper chromatography. In in vivo experiment, high-fat-fed Wistar rats obtained P. maxima water extract for 3 months. Morphometric parameters, weight gain, serum adipokines, and cytokines, as well as oxidative stress biomarkers in rats' tissues were evaluated. Gut microflora was also examined. Results: Plantago maxima leaves used in the experiment contained significant amount of flavonoids, iridoids, phenol carboxylic acids, and tannins and ascorbic acid. Our in vivo experiment data demonstrate that P. maxima water extract prevents excessive adiposity in a diet-induced model. P. maxima consumption reduced serum leptin (twofold), macrophage chemoattractant protein-1 (sevenfold), tumor-necrosis factor-α (25 %), and interleukine-6 (26 %) levels. P. maxima water extract decreased adipose tissue oxidative stress biomarkers in rats fed a high-fat diet. In addition, increased bacterial growth in the diet-induced obesity model was reversed by the P. maxima extract treatment. Conclusion: Plantago maxima water extract possessed antiadipogenic, antidiabetic, antiinflammatory, antioxidant activity, and normalized gut microflora in a rat model of diet-induced excessive adiposity due to a high content of biologically active compounds. [ABSTRACT FROM AUTHOR]

Background: Alpine ski racing is a popular international winter sport that is complex and challenging from physical, technical, and tactical perspectives. Despite the vast amount of scientific literature focusing on this sport, including topical reviews on physiology, ski-snow friction, and injuries, no review has yet addressed the biomechanics of elite alpine ski racers and which factors influence performance. In World Cup events, winning margins are often mere fractions of a second and biomechanics may well be a determining factor in podium place finishes. Objective: The aim of this paper was to systematically review the scientific literature to identify the biomechanical factors that influence the performance of elite alpine ski racers, with an emphasis on slalom, giant slalom, super-G, and downhill events. Methods: Four electronic databases were searched using relevant medical subject headings and key words, with an additional manual search of reference lists, relevant journals, and key authors in the field. Articles were included if they addressed human biomechanics, elite alpine skiing, and performance. Only original research articles published in peer-reviewed journals and in the English language were reviewed. Articles that focused on skiing disciplines other than the four of primary interest were excluded (e.g., mogul, ski-cross and freestyle skiing). The articles subsequently included for review were quality assessed using a modified version of a validated quality assessment checklist. Data on the study population, design, location, and findings relating biomechanics to performance in alpine ski racers were extracted from each article using a standard data extraction form. Results: A total of 12 articles met the inclusion criteria, were reviewed, and scored an average of 69 ± 13 % (range 40-89 %) upon quality assessment. Five of the studies focused on giant slalom, four on slalom, and three on downhill disciplines, although these latter three articles were also relevant to super-G events. Investigations on speed skiing (i.e., downhill and super-G) primarily examined the effect of aerodynamic drag on performance, whereas the others examined turn characteristics, energetic principles, technical and tactical skills, and individual traits of high-performing skiers. The range of biomechanical factors reported to influence performance included energy dissipation and conservation, aerodynamic drag and frictional forces, ground reaction force, turn radius, and trajectory of the skis and/or centre of mass. The biomechanical differences between turn techniques, inter-dependency of turns, and abilities of individuals were also identified as influential factors in skiing performance. In the case of slalom and giant slalom events, performance could be enhanced by steering the skis in such a manner to reduce the ski-snow friction and thereby energy dissipated. This was accomplished by earlier initiation of turns, longer path length and trajectory, earlier and smoother application of ground reaction forces, and carving (rather than skidding). During speed skiing, minimizing the exposed frontal area and positioning the arms close to the body were shown to reduce the energy loss due to aerodynamic drag and thereby decrease run times. In actual races, a consistently good performance (i.e., fast time) on different sections of the course, terrains, and snow conditions was a characteristic feature of winners during technical events because these skiers could maximize gains from their individual strengths and minimize losses from their respective weaknesses. Limitations: Most of the articles reviewed were limited to investigating a relatively small sample size, which is a usual limitation in research on elite athletes. Of further concern was the low number of females studied, representing less than 4 % of all the subjects examined in the articles reviewed. In addition, although overall run time is the ultimate measure of performance in alpine ski racing, several other measures of instantaneous performance were also employed to compare skiers, including the aerodynamic drag coefficient, velocity, section time, time lost per change in elevation, and mechanical energy behaviours, which makes cross-study inferences problematic. Moreover, most studies examined performance through a limited number of gates (i.e., 2-4 gates), presumably because the most commonly used measurement systems can only capture small volumes on a ski field with a reasonable accuracy for positional data. Whether the biomechanical measures defining high instantaneous performance can be maintained throughout an entire race course remains to be determined for both male and female skiers. Conclusions: Effective alpine skiing performance involves the efficient use of potential energy, the ability to minimize ski-snow friction and aerodynamic drag, maintain high velocities, and choose the optimal trajectory. Individual tactics and techniques should also be considered in both training and competition. To achieve better run times, consistency in performance across numerous sections and varied terrains should be emphasized over excellence in individual sections and specific conditions. [ABSTRACT FROM AUTHOR]

Sharks detect their prey using an extremely sensitive electrosensory system that is capable of distinguishing weak external stimuli from a relatively strong background noise generated by the animal itself. Experiments indicate that part of the shark's hindbrain, the dorsal octavolateralis nucleus (DON), is responsible for extracting the external stimulus using an adaptive filter mechanism to suppress signals correlated with the shark's breathing motion. The DON's principal neuron integrates input from afferents as well as many thousands of parallel fibres transmitting, inter alia, breathing-correlated motor command signals. There are a number of models in the literature, studying how this adaptive filtering mechanisms occurs, but most of them are based on a spike-train model approach. This paper presents a biophysically based computational simulation which demonstrates a mechanism for adaptive noise filtering in the DON. A spatial model of the neuron uses the Hodgkin-Huxley equations to simulate the propagation of action potentials along the dendrites. Synaptic inputs are modelled by applied currents at various positions along the dendrites, whose input conductances are varied according to a simple learning rule. Simulation results show that the model is able to demonstrate adaptive filtering in agreement with previous experimental and modelling studies. Furthermore, the spatial nature of the model does not greatly affect its learning properties, and in its present form is effectively equivalent to an isopotential model which does not incorporate a spatial element. [ABSTRACT FROM AUTHOR]

To date, scientific investigations into the biomechanical aspects of cricket fast bowling techniques have predominantly focused on identifying the mechanical factors that may predispose fast bowlers to lower back injury with a relative paucity of research being conducted on the technical features that underpin proficient fast bowling performance. In this review paper, we critique the scientific literature examining fast bowling performance. We argue that, although many published investigations have provided some useful insights into the biomechanical factors that contribute to a high ball release speed and, to a lesser extent, bowling accuracy, this research has not made a substantive contribution to knowledge enhancement and has only had a very minor influence on coaching practice. To significantly enhance understanding of cricket fast bowling techniques and, therefore, have greater impact on practice, we recommend that future scientific research adopts an interdisciplinary focus, integrating biomechanical measurements with the analytical tools and concepts of dynamical systems motor control theory. The use of qualitative (topological) analysis techniques, in particular, promises to increase understanding of the coordinative movement patterns that define 'technique' in cricket fast bowling and potentially help distinguish between functional and dysfunctional aspects of technique for individual fast bowlers. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

In this paper we introduce two models of stochastic processes driven by Brownian motion and fractional Brownian motion subordinated with tempered α-stable waiting times. By using a new integro-differential operator we obtain the generalized Fokker-Planck type equations associated with these subordinated stochastic processes. [ABSTRACT FROM AUTHOR]

Viscoelastic support has been previously established as a valuable modeling ingredient to represent the effect of surrounding tissues and organs in a fluid-structure vascular model. In this paper, we propose a complete methodological chain for the identification of the corresponding boundary support parameters, using patient image data. We consider distance maps of model to image contours as the discrepancy driving the data assimilation approach, which then relies on a combination of (1) state estimation based on the so-called SDF filtering method, designed within the realm of Luenberger observers and well adapted to handling measurements provided by image sequences, and (2) parameter estimation based on a reduced-order UKF filtering method which has no need for tangent operator computations and features natural parallelism to a high degree. Implementation issues are discussed, and we show that the resulting computational effectiveness of the complete estimation chain is comparable to that of a direct simulation. Furthermore, we demonstrate the use of this framework in a realistic application case involving hemodynamics in the thoracic aorta. The estimation of the boundary support parameters proves successful, in particular in that direct modeling simulations based on the estimated parameters are more accurate than with a previous manual expert calibration. This paves the way for complete patient-specific fluid-structure vascular modeling in which all types of available measurements could be used to estimate additional uncertain parameters of biophysical and clinical relevance. [ABSTRACT FROM AUTHOR]

From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed capsid proteins having thicknesses between 2 nm and 4 nm. To investigate whether, in addition to the fairly conserved geometry, capsid proteins show similarities in the way they interact with one another, we examined the shapes of the capsids in detail. We classified them numerically according to their similarity to sphere and icosahedron and an interpolating set of shapes in between, all of them obtained from the theory of elasticity of shells. In order to make a unique and straightforward connection between an idealized, numerically calculated shape of an elastic shell and a capsid, we devised a special shape fitting procedure, the outcome of which is the idealized elastic shape fitting the capsid best. Using such a procedure we performed statistical analysis of a series of virus shapes and we found similarities between the capsid elastic properties of even very different viruses. As we explain in the paper, there are both structural and functional reasons for the convergence of protein sizes and capsid elastic properties. Our work presents a specific quantitative scheme to estimate relatedness between different proteins based on the details of the (quaternary) shape they form (capsid). As such, it may provide an information complementary to the one obtained from the studies of other types of protein similarity, such as the overall composition of structural elements, topology of the folded protein backbone, and sequence similarity. [ABSTRACT FROM AUTHOR]

Small Footprint LiDAR (Light Detection And Ranging) has been proposed as an effective tool for measuring detailed biophysical characteristics of forests over broad spatial scales. However, by itself LiDAR yields only a sample of the true 3D structure of a forest. In order to extract useful forestry relevant information, this data must be interpreted using mathematical models and computer algorithms that infer or estimate specific forest metrics. For these outputs to be useful, algorithms must be validated and/or calibrated using a sub-sample of 'known' metrics measured using more detailed, reliable methods such as field sampling. In this paper we describe a novel method for delineating and deriving metrics of individual trees from LiDAR data based on watershed segmentation. Because of the costs involved with collecting both LiDAR data and field samples for validation, we use synthetic LiDAR data to validate and assess the accuracy of our algorithm. This synthetic LiDAR data is generated using a simple geometric model of Loblolly pine ( Pinus taeda) trees and a simulation of LiDAR sampling. Our results suggest that point densities greater than 2 and preferably greater than 4 points per m2 are necessary to obtain accurate forest inventory data from Loblolly pine stands. However the results also demonstrate that the detection errors (i.e. the accuracy and biases of the algorithm) are intrinsically related to the structural characteristics of the forest being measured. We argue that experiments with synthetic data are directly useful to forest managers to guide the design of operational forest inventory studies. In addition, we argue that the development of LiDAR simulation models and experiments with the data they generate represents a fundamental and useful approach to designing, improving and exploring the accuracy and efficiency of LiDAR algorithms. [ABSTRACT FROM AUTHOR]

The main contribution of this paper is to use homogenization techniques to compute diffusion coefficients from experimental images of microbial biofilms. Our approach requires the analysis of several experimental spatial structures of biofilms in order to derive from them a Representative Volume Element (RVE). Then, we apply a suitable numerical procedure to the RVE to derive the diffusion coefficients. We show that diffusion coefficients significantly vary with the biofilm structure. These results suggest that microbial biofilm structures can favour nutrient access in some cases. [ABSTRACT FROM AUTHOR]

Molecules of dissolved substance in many homochiral solutions are arranged in linear associations forming chiral strings (with length to diameter proportion of 10-10), which leads to solidification of the solution into anisometric gel. This paper describes the formation of the string system in aqueous solution of amino acid phenylalanine, formation of individual strings, weaving of thin strings into thick ones, successive alteration of the solution chirality sign with transition to new levels of the association organization. It seems that biological media are anisometric fluids containing chiral molecular associations and strings, or anisometric gels. [ABSTRACT FROM AUTHOR]

This paper describes a proposed biophysical mechanism of a novel diagnostic method for cancer detection developed recently by Vedruccio. The diagnostic method is based on frequency selective absorption of electromagnetic waves by malignant tumors. Cancer is connected with mitochondrial malfunction (the Warburg effect) suggesting disrupted physical mechanisms. In addition to decreased energy conversion and nonutilized energy efflux, mitochondrial malfunction is accompanied by other negative effects in the cell. Diminished proton space charge layer and the static electric field around the outer membrane result in a lowered ordering level of cellular water and increased damping of microtubule-based cellular elastoelectrical vibration states. These changes manifest themselves in a dip in the amplitude of the signal with the fundamental frequency of the nonlinear microwave oscillator-the core of the diagnostic device-when coupled to the investigated cancerous tissue via the near-field. The dip is not present in the case of healthy tissue. [ABSTRACT FROM AUTHOR]

For the understanding of radiation action in humans, a synergistic approach of experiments and quantitative modeling of working hypotheses is necessary. A large set of experimental data at the single-cell level are available, and biophysical modeling of radiation action has so far mostly concentrated on the first phases of radiation interaction with the biomolecules, and later biochemical stages including DNA breakage, repair, and the formation of chromosomal aberrations. The models can be extended to cell killing and transformation, but so far still using a single-cell (clonal expansion) approach. On the contrary, new experimental evidence points to the microenvironment and the tissue level as a critical radiation target for late effects, and to epigenetic and signaling mechanisms as mediators of radiation damage. This higher structural level is generally ignored in modeling, owing to its complexity and to the lack of experimental data. In this paper we will highlight the requirements for specific experimental approaches targeting the tissue/microenvironment level and the most promising available experimental models. [ABSTRACT FROM AUTHOR]

The investigation of very complex dynamical systems like the human metabolism requires the comprehension of important subsystems. The present paper deals with energy supply chains as subsystems of the metabolism on the molecular, cellular, and individual levels. We form a mathematical model of ordinary differential equations and we show fundamental properties by Fourier techniques. The results are supported by a transition from a system of ordinary differential equations to a partial differential equation, namely, a transport equation. In particular, the behavior of supply chains with dominant pull components is discussed. A special focus lies on the role of buffer compartments. [ABSTRACT FROM AUTHOR]

This paper explains the biophysical principles which, according to us, govern the Proteus mirabilis swarm phenomenon. Then, this explanation is translated into a mathematical model, essentially based on partial differential equations. This model is then implemented using numerical methods of the finite volume type in order to make simulations. The simulations show most of the characteristics which are observed in situ and in particular the terrace generation. [ABSTRACT FROM AUTHOR]

In this paper we demonstrate a quantitative way to measure the membrane potential of live cells by dielectric spectroscopy. We also show that the values of the membrane potential obtained using our technique are in good agreement with those obtained using traditional methods—voltage-sensitive dyes. The membrane potential is determined by fitting the experimental dielectric dispersion curves with the dispersion curves obtained from a theoretical model. Variations in the membrane potential were induced by modifying the concentration of potassium chloride in the solution of the cell suspension in the presence of valinomycin. For exemplification of the method, E. coli was chosen for our experiments. [ABSTRACT FROM AUTHOR]

Information about several papers discusses at a conference on molecule biophysics is presented. The conference covers an emerging discipline in which the behaviors of individual macromolecules are measured with a variety of biophysical techniques including optical trapping, atomic force microscopy, fluorescense microscopy and magnetic tweezers. single-molecule techniques have been used to study transcription by prokaryotic RNA polymerase with which transcription is initiated in bacteria.

Communications Physics is 2 years old. To celebrate, we look back at our achievements and put together a collection of our editors' favourite papers. We will renew this collection over the months to share with our community what we like the most. [ABSTRACT FROM AUTHOR]