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Relevant bibliographies by topics / Biophysical transition

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Academic literature on the topic 'Biophysical transition'

Author: Grafiati

Published: 31 August 2024

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Journal articles on the topic "Biophysical transition"

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Van Dyke, Chris. "Boxing daze – using state-and-transition models to explore the evolution of socio-biophysical landscapes." Progress in Physical Geography: Earth and Environment 39, no. 5 (May 17, 2015): 594–621. http://dx.doi.org/10.1177/0309133315581700.

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Critical physical geography (CPG) proposes to bridge the lingering gap between human and physical geographers. To rejuvenate conversations among different corners of the discipline about the possibility of trans-disciplinary collaboration, CPG must provide unique epistemological, methodological, and conceptual frameworks that human and physical geographers alike will find appealing, relevant, and timely. These should help them perceptively characterize, narrate, and anticipate changes in socio-biophysical landscapes. This paper outlines a conceptual framework that can be harnessed in future CPG studies and reflects on what it means to be a critical geographer. To solve the epistemological dilemmas confronting CPG, this paper demonstrates that state-and-transition models (STMs) can provide a unifying framework to address questions about socio-biophysical landscape evolution. Originally developed to account for nonlinear dynamics in rangeland ecosystems, STMs have been used to analyze a variety of ecological, geomorphic, and hydrological transitions in complex biophysical landscapes. STMs have epistemological commonalities with explanatory frameworks pioneered by political ecologists, and while thus far they have been used to account for complex biophysical dynamics, they can be expanded to accommodate critical investigations of the social dynamics underpinning landscape change. By foregrounding the transitional dynamics of socio-biophysical landscape – a theme that has interested physical and critical human geographers – STMs establish a conceptual space in which to holistically interpret the interacting drivers that underwrite socio-biophysical landscape change.

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Larson, Ben T., Teresa Ruiz-Herrero, Stacey Lee, Sanjay Kumar, L. Mahadevan, and Nicole King. "Biophysical principles of choanoflagellate self-organization." Proceedings of the National Academy of Sciences 117, no. 3 (January 2, 2020): 1303–11. http://dx.doi.org/10.1073/pnas.1909447117.

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Inspired by the patterns of multicellularity in choanoflagellates, the closest living relatives of animals, we quantify the biophysical processes underlying the morphogenesis of rosette colonies in the choanoflagellate Salpingoeca rosetta. We find that rosettes reproducibly transition from an early stage of 2-dimensional (2D) growth to a later stage of 3D growth, despite the underlying variability of the cell lineages. Our perturbative experiments demonstrate the fundamental importance of a basally secreted extracellular matrix (ECM) for rosette morphogenesis and show that the interaction of the ECM with cells in the colony physically constrains the packing of proliferating cells and, thus, controls colony shape. Simulations of a biophysically inspired model that accounts for the size and shape of the individual cells, the fraction of ECM, and its stiffness relative to that of the cells suffices to explain our observations and yields a morphospace consistent with observations across a range of multicellular choanoflagellate colonies. Overall, our biophysical perspective on rosette development complements previous genetic perspectives and, thus, helps illuminate the interplay between cell biology and physics in regulating morphogenesis.

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UEMURA, Sotaro. "Importance of Research Field Transition with Biophysical Standpoint." Seibutsu Butsuri 52, no. 2 (2012): 096–97. http://dx.doi.org/10.2142/biophys.52.096.

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Oelschlaeger, Max. "Ecosemiotics and the sustainability transition." Sign Systems Studies 29, no. 1 (December 31, 2001): 219–36. http://dx.doi.org/10.12697/sss.2001.29.1.14.

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The emerging epistemic community of ecosemioticians and the multidisciplinary field of inquiry known as ecosemiotics offer a radical and relevant approach to so-called global environmental crisis. There are no environmental fixes within the dominant code, since that code overdetermines the future, thereby perpetuating ecologically untenable cultural forms. The possibility of a sustainability transition (the attempt to overcome destitution and avoid ecocatastrophe) becomes real when mediated by and through ecosemiotics. In short, reflexive awareness of humankind's linguisticality is a necessary condition for transforming ecologically maladaptive cultural forms. As a multidisciplinary, interdisciplinary research program integrating the human and natural sciences, ecosemiotic inquiry closes the gap between biophysical ecology and human ecology. A provisional outline of a pragmatic theory of ecoserniotics attempts to describe the processes by which adaptive cultural changes might be facilitated and points toward substantive content areas that constitute sites for further research. Ecosemiotic inquiry frames cultural codes as these shape and reproduce the ongoing stream of individual and societal choices that shape distinctively human existence in a larger context of biophysical realities that drive natural selection. However, while ecosemiotics is a necessary condition for the sustainability transition, it is not a sufficient condition.

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Olson, Donald B. "Biophysical dynamics of western transition zones: a preliminary synthesis." Fisheries Oceanography 10, no. 2 (June 2001): 133–50. http://dx.doi.org/10.1046/j.1365-2419.2001.00161.x.

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Fernandez, Fernando R., Jordan D. T. Engbers, and Ray W. Turner. "Firing Dynamics of Cerebellar Purkinje Cells." Journal of Neurophysiology 98, no. 1 (July 2007): 278–94. http://dx.doi.org/10.1152/jn.00306.2007.

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Knowledge of intrinsic neuronal firing dynamics is a critical first step to establishing an accurate biophysical model of any neuron. In this study we examined cerebellar Purkinje cells to determine the bifurcations likely to underlie firing dynamics within a biophysically realistic and experimentally supported model. We show that Purkinje cell dynamics are consistent with a system undergoing a saddle-node bifurcation of fixed points in the transition from rest to firing and a saddle homoclinic bifurcation from firing to rest. Our analyses account for numerous observed Purkinje cell firing properties that include bistability, plateau potentials, specific aspects of the frequency–current ( F– I) relationship, first spike latency, and the ability for climbing fiber input to induce state transitions in the bistable regime. We also experimentally confirm new properties predicted from our model and analysis that include the presence of a depolarizing afterpotential (DAP), the ability to fire at low frequencies (<50 Hz) and with a high gain in the F– I relationship, and a bistable region limited to low-frequency firing. Purkinje cell dynamics, including bistability, prove to arise from numerous biophysical factors that include the DAP, fast refractory dynamics, and a long membrane time constant. A hyperpolarizing activated cation current ( IH) is shown not to be directly involved in establishing bistable dynamics but rather reduces the range for bistability. A combined electrophysiological and modeling approach thus accounts for several properties of Purkinje cells, providing a firm basis from which to assess Purkinje cell output patterns.

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Singh, Simron Jit, and Clemens M. Grünbühel. "Environmental relations and biophysical transition: the case of trinket island." Geografiska Annaler: Series B, Human Geography 85, no. 4 (December 2003): 191–208. http://dx.doi.org/10.1111/j.0435-3684.2003.00142.x.

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Lu, Yi, Amdrea K. Brown, Juewen Liu, Jing Li, and Peter J. Bruesehoff. "Biochemical and biophysical study of transition metal ion-dependent DNAzymes." Journal of Inorganic Biochemistry 96, no. 1 (July 2003): 182. http://dx.doi.org/10.1016/s0162-0134(03)80695-5.

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Tesloianu, Nicolae Dan, Lucian Dobreci, Vlad Ghizdovat, Andrei Zala, Adrian Valentin Cotirlet, Alina Gavrilut, Maricel Agop, et al. "Multifractality through Non-Markovian Stochastic Processes in the Scale Relativity Theory. Acute Arterial Occlusions as Scale Transitions." Entropy 23, no. 4 (April 9, 2021): 444. http://dx.doi.org/10.3390/e23040444.

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By assimilating biological systems, both structural and functional, into multifractal objects, their behavior can be described in the framework of the scale relativity theory, in any of its forms (standard form in Nottale’s sense and/or the form of the multifractal theory of motion). By operating in the context of the multifractal theory of motion, based on multifractalization through non-Markovian stochastic processes, the main results of Nottale’s theory can be generalized (specific momentum conservation laws, both at differentiable and non-differentiable resolution scales, specific momentum conservation law associated with the differentiable–non-differentiable scale transition, etc.). In such a context, all results are explicated through analyzing biological processes, such as acute arterial occlusions as scale transitions. Thus, we show through a biophysical multifractal model that the blocking of the lumen of a healthy artery can happen as a result of the “stopping effect” associated with the differentiable-non-differentiable scale transition. We consider that blood entities move on continuous but non-differentiable (multifractal) curves. We determine the biophysical parameters that characterize the blood flow as a Bingham-type rheological fluid through a normal arterial structure assimilated with a horizontal “pipe” with circular symmetry. Our model has been validated based on experimental clinical data.

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Lima, Igor, Ambuja Navalkar, Samir K. Maji, Jerson L. Silva, Guilherme A. P. de Oliveira, and Elio A. Cino. "Biophysical characterization of p53 core domain aggregates." Biochemical Journal 477, no. 1 (January 8, 2020): 111–20. http://dx.doi.org/10.1042/bcj20190778.

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Aggregation is the cause of numerous protein conformation diseases. A common facet of these maladies is the transition of a protein from its functional native state into higher order forms, such as oligomers and amyloid fibrils. p53 is an essential tumor suppressor that is prone to such conformational transitions, resulting in its compromised ability to avert cancer. This work explores the biophysical properties of early-, mid-, and late-stage p53 core domain (p53C) aggregates. Atomistic and coarse-grained molecular dynamics (MD) simulations suggest that early- and mid-stage p53C aggregates have a polymorphic topology of antiparallel and parallel β-sheets that localize to the core amyloidogenic sequence. Both topologies involve similar extents of interstrand mainchain hydrogen bonding, while sidechain interactions could play a role in regulating strand orientation. The free energy difference between the antiparallel and parallel states was within statistical uncertainty. Negative stain electron microscopy of mature fibrils shows a wide distribution of fiber widths, indicating that polymorphism may extend to the quaternary structure level. Circular dichroism of the fibrils was indicative of β-sheet rich structures in atypical conformations. The Raman spectrum of aggregated p53C was consistent with a mixture of arranged β-sheets and heterogeneous structural elements, which is compatible with the MD findings of an ordered β-sheet nucleus flanked by disordered structure. Structural polymorphism is a common property of amyloids; however, because certain polymorphs of the same protein can be more harmful than others, going forward it will be pertinent to establish correlations between p53C aggregate structure and pathology.

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Dissertations / Theses on the topic "Biophysical transition"

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Colledge, Vicki Louise. "Stuructural and biophysical investigations of bacillus subtillis transition-state regulators." Thesis, University of York, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.535053.

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Valba, Olga. "Statistical analysis of networks and biophysical systems of complex architecture." Phd thesis, Université Paris Sud - Paris XI, 2013. http://tel.archives-ouvertes.fr/tel-00919606.

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Complex organization is found in many biological systems. For example, biopolymers could possess very hierarchic structure, which provides their functional peculiarity. Understating such, complex organization allows describing biological phenomena and predicting molecule functions. Besides, we can try to characterize the specific phenomenon by some probabilistic quantities (variances, means, etc), assuming the primary biopolymer structure to be randomly formed according to some statistical distribution. Such a formulation is oriented toward evolutionary problems.Artificially constructed biological network is another common object of statistical physics with rich functional properties. A behavior of cells is a consequence of complex interactions between its numerous components, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes, allowing them to respond and to adapt to changing environment. Recent theoretical advances allow us to describe cellular network structure using graph concepts to reveal the principal organizational features shared with numerous non-biological networks.The aim of this thesis is to develop bunch of methods for studying statistical and dynamic objects of complex architecture and, in particular, scale-free structures, which have no characteristic spatial and/or time scale. For such systems, the use of standard mathematical methods, relying on the average behavior of the whole system, is often incorrect or useless, while a detailed many-body description is almost hopeless because of the combinatorial complexity of the problem. Here we focus on two problems.The first part addresses to statistical analysis of random biopolymers. Apart from the evolutionary context, our studies cover more general problems of planar topology appeared in description of various systems, ranging from gauge theory to biophysics. We investigate analytically and numerically a phase transition of a generic planar matching problem, from the regime, where almost all the vertices are paired, to the situation, where a finite fraction of them remains unmatched.The second part of this work focus on statistical properties of networks. We demonstrate the possibility to define co-expression gene clusters within a network context from their specific motif distribution signatures. We also show how a method based on the shortest path function (SPF) can be applied to gene interactions sub-networks of co-expression gene clusters, to efficiently predict novel regulatory transcription factors (TFs). The biological significance of this method by applying it on groups of genes with a shared regulatory locus, found by genetic genomics, is presented. Finally, we discuss formation of stable patters of motifs in networks under selective evolution in context of creation of islands of "superfamilies".

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Nauseef, Jones Trevor. "An investigation of the molecular and biophysical properties of metastatic cells." Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/3150.

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Prostate cancer presents a significant paradox: it is very common, yet rarely fatal. To wit, the prostate is the most common non-skin tissue for cancer diagnosis in men in the United States. Despite its high incidence, fatal malignancy occurs in only a small fraction of diagnosed men. The fatal cases are characteristically defined by distant spread in the body, also known as metastasis. In order to metastasize a cancer cell must complete several sequential steps. These include degradation of and invasion through the epithelial basement membrane, typically through the loss of static intracellular adhesions with fellow epithelial cells; entrance into the blood stream (intravasation); survival within circulation; exit from the blood stream upon arrival at a new tissue (extravasation); and survival and colonization at the secondary site. At the time of diagnosis, it is not currently possible to accurately predict future metastasis and thereby clinicians cannot delineate those men at high risk for fatal disease from the vast majority of men who are likely to experience an indolent disease course. Consequently, we examined the behavior of cancer cells in several steps of the metastatic cascade. In doing so, we uncovered both molecular and biophysical characteristics of cancer cells that may facilitate successful metastatic dissemination and tumor outgrowth. Epithelial-to-mesenchymal transition (EMT) is physiological process of transdifferentiation that is normally initiated during vertebrate development, but has recently been implicated in tumor development, progression, and metastases. The EMT program results in dramatic changes, including the exchange of epithelial for mesenchymal markers, altered cellular morphology, and gain of motility. EMT-like cellular alterations have been implicated most strongly in the metastasis steps of invasion and survival of cells at primary tumors sites. How EMT-like changes may facilitate survival and growth in the microenvironment of a micrometastatic niche has been less clearly elucidated. Consequently, we evaluated how EMT-like changes may affect the survival and subsequent outgrowth of prostate cancer cell lines following restrictive growth conditions. We observed that EMT-like cells as compared to their more epithelial counterparts displayed enhanced maintenance of their proliferative potential following extended culture in nutrient restriction. This phenotype depended on an EMT-associated increase in autophagy. Notably, the post-stress outgrowth phenotype could be conferred through a paracrine signaling mechanism that may involve autophagy-derived exosome-like extracellular vesicles. These studies demonstrated that EMT-like cells have a resistance to nutrient restriction through enhanced autophagy and may have uncovered a novel autophagy-dependent exosomal secretion pathway. Metastatic efficiency is thought to be strongly limited by the destruction of circulating tumor cells by the hemodynamic shear forces within the vasculature. However, such a persistent belief has little appropriate published experimental evidence. We developed an in vitro assay to expose cells to fluid shear stress (FSS). By monitoring the viability of the cells, we determined that transformed cells had a highly conserved ability to resist even very high FSS. The mechanism depended on the capacity to patch membrane defects, extracellular calcium, and a dynamic cytoskeleton. We also observed a stiffening of cancer cell membranes after exposure to FSS. Taken together, these studies expand the understanding of how cancer cells survive in circulation and indicate that metastatic efficiency is less limited by hemodynamic forces than previously thought. The steps of hematogenous metastasis between intravasation and extravasation necessitate the existence of circulating tumor cells (CTCs). Collection, enumeration, and study of CTCs have the potential to serve as a "liquid biopsy" of the metastatic cascade. In prostate cancer, the enumeration of CTCs by detection of the expression of epithelial markers has displayed limited clinical utility. We hypothesized that the prognostic value of CTC number may be enhanced by detection of cells which have undergone the pro-metastatic EMT-like program. We developed a flow cytometry-based experimental assay for enumeration of CTCs using epithelial (EpCAM) and mesenchymal-like (N-cadherin) surface proteins. We detected from prostatectomy patients before and after surgery events expressing EpCAM, N-cadherin, and both. However, the detection of background events from healthy control subjects was unacceptably high. These studies support the idea of mesenchymal-like tumor cells in circulation, but will require further assay development for reliable conclusions to be drawn. In sum, the work described above has provided descriptive and mechanistic insight to molecular and biophysical properties that may facilitate prostate cancer metastasis. It is our hope that these data will result in the development of relevant preventative, diagnostic, and therapeutic clinical strategies for prostate cancer.

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Leekumjorn, Sukit. "Molecular Dynamics Simulations for the Study of Biophysical Processes on Biological Membranes." Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/29180.

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Phospholipid bilayers constitute the primary structural element of biological membranes, and as such, they play a central role in biochemical and biophysical processes at the cellular level, including cell protection, intercellular interactions, trans-membrane transport, cell morphology, and protein function, to name a few. The properties of phospholipid bilayers are thus of great interest from both experimental and theoretical standpoints. Although experiments have provided much of the macroscopic functions and properties of biological membranes, insight into specific mechanisms at the molecular level are seldom accessible by conventional methods. To obtain a better understanding of biochemical and biophysical processes at the molecular level involving phospholipid bilayers, we apply molecular simulation methods to investigate the complexity of the membrane matrix using atomistic models. Here, we discuss three specific biological processes that are associated with biological membranes: 1) membrane stabilization, 2) membrane phase behavior, and 3) fatty acid-induced toxicity in cell membranes. For membrane stabilization, molecular dynamics studies were performed for mixed phospholipid bilayers containing two of the most prevalent phospholipids (phosphatidylcholine and phosphatidylethanolamime) in biological membranes. We presented structural and dynamics properties of these systems, as well as the effect of stabilizing agents, such as trehalose, on their properties. Furthermore, we performed a comprehensive analysis of the phase transition of lipid bilayers and investigated the interactions of stabilizing agents (glucose or trehalose) with lipid bilayers under dehydrated conditions to understand the mechanisms for preservation of cellular systems. For membrane phase behavior, a comprehensive study of the structural properties of saturated and monounsaturated lipid bilayers near the main phase transition were investigated using molecular dynamics simulations. In this study, we demonstrated that atomistic simulations are capable of capturing the phase transformation process of lipid bilayers, providing a valuable set of molecular and structural information at and near its transition state. Lastly, the third study investigated the mechanism for fatty acid-induced toxicity by integrating in vitro and in silico experiments to reveal the biophysical interactions of saturated fatty acid (palmitate) with the cellular membranes and the role of trehalose and unsaturated fatty acids (oleate and linoleate) in preventing changes to the membrane structure. Knowledge gained from this study is essential in the prevention and treatment of obesity-associated cirrhosis diseases.
Ph. D.

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Wang, Yin 1951. "Influences of membrane biophysical properties on the Metarhodopsin I to Metarhodopsin II transition in visual excitation." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282520.

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Current biophysical studies of membrane proteins are centered on the relation of their structures to key biological functions of membranes in terms of lipid-protein interactions. The conformational transition of rhodopsin from Metarhodopsin I to Metarhodopsin II (Meta I-Meta II) is the triggering event for the visual process. Meta II is the activated form of the visual receptor and binds a signal transducing G protein (transducin), followed by two amplification stages which lead to generation of a visual nerve impulse. Herein, flash photolysis and surface plasmon resonance (SPR) spectroscopy techniques have been used to monitor the Meta I-Meta II transition of rhodopsin in various membrane recombinants. The flash photolysis experiments clearly show a substantial shift to the left of the Meta I-Meta II equilibrium for rhodopsin in egg phosphatidylcholine recombinant membranes. Investigation of the influences on rhodopsin function by non-lamellar forming lipids reveals a characteristic relationship between the Gibbs free energy change for the Meta I-Meta II equilibrium of rhodopsin and the intrinsic curvature of the lipid bilayer. Complementary SPR studies suggest a protrusion of the protein at the activated Meta II state which may be associated with exposure of recognition sites for the signal transducing G protein on the cytoplasmic surface of rhodopsin. All the experimental results obtained here are consistent with the hypothesis of a new flexible surface biomembrane model. The Meta II state is favored by a negative spontaneous curvature of the bilayer, corresponding to an imbalance of the lateral forces within the polar head groups and acyl chains. The mean curvature of membrane bilayer in the Meta II state reflects the small spontaneous curvature of the lipid bilayer in the vicinity of protein. Relief of the lipid curvature frustration in the Meta II state energetically couples the lipids to the photoexcitation of rhodopsin. Consideration of the various energetic contributions suggests the bilayer curvature free energy provides a reservoir of work in the modulation of rhodopsin function in the visual process. These studies that biophysical properties of the liquid-crystalline lipid bilayer are important in relation to protein function and may be relevant to the biomedical investigations of visual dysfunction.

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Stam, Carson A. "Using Biophysical Geospatial and Remotely Sensed Data to Classify Ecological Sites and States." DigitalCommons@USU, 2012. https://digitalcommons.usu.edu/etd/1389.

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Monitoring and identifying the state of rangelands on a landscape scale can be a time consuming process. In this thesis, remote sensing imagery has been used to show how the process of classifying different ecological sites and states can be done on a per pixel basis for a large landscape. Twenty-seven years' worth of remotely sensed imagery was collected, atmospherically corrected, and radiometrically normalized. Several vegetation indices were extracted from the imagery along with derivatives from a digital elevation model. Dominant vegetation components from five major ecological sites in Rich County, Utah, were chosen for study. The vegetation components were Aspen, Douglas-fir, Utah juniper, mountain big sagebrush, and Wyoming big sagebrush. Training sites were extracted from within map units with a majority of one of the five ecological sites. A Random Forests decision tree model was developed using an attribute table populated with spectral biophysical variables derived from the training sites. The overall out-of-bag accuracy for the Random Forests model was 97.2%. The model was then applied to the predictor spectral and biophysical variables to spatially map the five major vegetation components for all of Rich County. Each vegetation class had greater than 90% accuracies except for Utah juniper at 81%. This process is further explained in chapter 2. As a follow-on effort, we attempted to classify vegetation ecological states within a single ecological site (Wyoming big sagebrush). This was done using field data collected by previous studies as training data for all five ecological states documented for our chosen ecological site. A Maximum Likelihood classifier was applied to four years of Landsat 5 Thematic Mapper imagery to map each ecological state to pixels coincident to the map units correlated to the Wyoming big sagebrush ecological site. We used the Mahalanobis distance metric as an indicator of pixel membership to the Wyoming big sagebrush ecological site. Overall classification accuracy for the different ecological states was 64.7% for pixels with low Mahalanobis distance and less than 25% for higher distances.

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Drew, Elliot Dudley. "Biophysical and computational characterisation of the disorder-to-order structural transition of the small hydrophilic endoplasmic-reticulum associated protein, SHERP." Thesis, Birkbeck (University of London), 2018. http://bbktheses.da.ulcc.ac.uk/366/.

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This thesis explores the disorder-to-order structural transition of the small hydrophilic endoplasmic reticulum associated protein (SHERP). SHERP has been shown to be essential to the life cycle of Leishmania major, a parasite responsible for leishmaniasis which kills tens of thousands every year. The protein is almost entirely disordered in solution, but undergoes a dramatic increase in helicity upon binding to anionic lipids or detergents. Although the ordered structure of SHERP had previously been solved by solution nuclear magnetic resonance spectroscopy in the presence of sodium dodecyl sulphate (SDS), both the nature of the disordered ensemble of the protein and the organisation of the SHERP/detergent complex were unknown. Using a combination of synchrotron radiation circular dichroism spectroscopy (SRCD), small angle X-ray scattering (SAXS) and molecular dynamics (MD), several projects were carried out exploring the disorder-to-order structural transition of SHERP in the presence of SDS. The effectiveness of sequence-based predictors to estimate the effect of single mutants was explored, with a number of mutants expressed and characterised by SRCD and MD. A mutant, the "permutant", was designed with the aim of decreasing the disorder of the protein in solution while maintaining amino acid composition, by introduction of multiple potential i → i4 salt bridges created by permutations of the wild-type sequence. Molecular dynamics simulations of the wild-type and "permutant" construct found a dramatic increase in salt bridge formation, and in vitro characterisation of the "permutant" construct showed it had significantly greater helical character than the wild-type in the absence of SDS. The disordered ensemble of SHERP was characterised by replica exchange MD, SRCD and SAXS. Good agreement was found between simulation and experiment, with a predominantly unfolded ensemble deficient in secondary structure described by our results. The changes that occur upon SHERP binding to SDS were also characterised. MD simulation of the SHERP-SDS complex showed that the protein bound among the head-groups of the SDS micelle, and the helical content and helix-turn-helix structure was retained. It also allowed identification of several cationic side-chains which formed stabilising salt bridges with the sulphates of SDS. The complex was then characterised in vitro, by SAXS and CD spectroscopy. The addition of the protein led to a doubling in micelle length, with multiple SHERP molecules found to bind to the anionic head-groups in the shell of the micelle. The residues identified during the MD simulation were substituted with alanine to make a series of mutants with increasing negative charge. Significant decreases in helicity, micelle length and the numbers of protein bound occurred as negative charge increased, possibly caused by decreased affinity of the protein for the micelle causing less protein molecules to bind per micelle, leading to a decreased chance of stabilising protein-protein interactions resulting in partial folding of the protein. These results demonstrate the importance of charge-charge interactions in the disorder-to-order structural transition of SHERP, and provide structural context for future functional work on this protein.

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Kettner, Claudia, Angela Köppl, and Sigrid Stagl. "List of well-being indicators." European Commission, bmwfw, 2012. http://epub.wu.ac.at/4714/1/WWWforEurope_WPS_no002_MS30.pdf.

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This milestone presents a pool of available indicators and indicator systems which go beyond the narrow concepts of national economic accounts as well as a structuring of the indicators and indices according to central areas of well-being. The milestone builds the basis for Task 202.2, where a subset of indicators will be selected based on different theoretical frameworks, e.g. services / functionings, needs. Some of the indicators will be included in the macro-economic models in order to account for key dimensions of sustainability.
Series: WWWforEurope

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Kettner, Claudia, Angela Köppl, and Sigrid Stagl. "Towards an operational measurement of socio-ecological performance." European Commission, bmwfw, 2014. http://epub.wu.ac.at/4718/1/WWWforEurope_WPS_no052_MS29.pdf.

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Questioning GDP as dominant indicator for economic performance has become commonplace. For economists economic policy always aims for a broader array of goals (like income, employment, price stability, trade balance) alongside income, with income being the priority objective. The Stiglitz-Sen-Fitoussi Commission argued for extending and adapting key variables of macroeconomic analysis. International organisations such as the EC, OECD, Eurostat and UN have proposed extended arrays of macroeconomic indicators (see 'Beyond GDP', 'Compendium of wellbeing indicators', 'GDP and Beyond', 'Green Economy', 'Green Growth', 'Measuring Progress of Societies'). Despite these high profile efforts, few wellbeing and environmental variables are in use in macroeconomic models. The reasons for the low uptake of socio-ecological indicators in macroeconomic models range from path dependencies in modelling, technical limitations, indicator lists being long and unworkable, choices of indicators appearing ad hoc and poor data availability. In this paper we review key approaches and identify a limited list of candidate variables and - as much as possible - offer data sources.
Series: WWWforEurope

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Stelzl, Lukas Sebastian. "Studying marcomolecular transitions by NMR and computer simulations." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6e4bbe06-fc58-471b-a932-d940fe78b9a5.

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Macromolecular transitions such as conformational changes and protein-protein association underlie many biological processes. Conformational changes in the N-terminal domain of the transmembrane protein DsbD (nDsbD) were studied by NMR and molecular dynamics (MD) simulations. nDsbD supplies reductant to biosynthetic pathways in the oxidising periplasm of Gram-negative bacteria after receiving reductant from the C-terminal domain of DsbD (cDsbD). Reductant transfer in the DsbD pathway happens via protein-protein association and subsequent thiol-disulphide exchange reactions. The cap loop shields the active-site cysteines in nDsbD from non-cognate oxidation, but needs to open when nDsbD bind its interaction partners. The loop was rigid in MD simulations of reduced nDsbD. More complicated dynamics were observed for oxidised nDsbD, as the disulphide bond introduces frustration which led to loop opening in some trajectories. The simulations of oxidised and reduced nDsbD agreed well with previous NMR spin-relaxation and residual dipolar coupling measurements as well as chemical shift-based torsion angle predictions. NMR relaxation dispersion experiments revealed that the cap loop of oxidised nDsbD exchanges between a major and a minor conformation. The differences in their conformational dynamics may explain why oxidised nDsbD binds its physiological partner cDsbD much tighter than reduced nDsbD. The redox-state dependent interaction between cDsbD and nDsbD is thought to enhance turnover. NMR relaxation dispersion experiments gave insight into the kinetics of the redox-state dependent interaction. MD simulations identified dynamic encounter complexes in the association of nDsbD with cDsbD. The mechanism of the conformational changes in the transport cycle of LacY were also investigated. LacY switches between periplasmic open and cytoplasmic open conformations to transport sugars across the cell membrane. Two mechanisms have been proposed for the conformational change, a rocker-switch mechanism based on rigid body motions and an “airlock” like mechanism in which the transporter would switch conformation via a fully occluded structure. In MD simulations using the novel dynamics importance sampling approach such a fully occluded structure was found. The simulations argued against a strict “rocker-switch” mechanism.

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Books on the topic "Biophysical transition"

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Csiszar, Susan A. The role of water in structural transitions of biophysical systems. 2005.

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Csiszar, Susan A. The role of water in structural transitions of biophysical systems. 2005, 2005.

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Csiszar, Susan A. The role of water in structural transitions of biophysical systems. 2005.

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(Translator), S. L. Schnur, ed. The Physics of Phase Transitions: Concepts and Applications (Advanced Texts in Physics). 2nd ed. Springer, 2006.

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Leblond, Jacques, Paul H. E. Meijer, and Pierre Papon. The Physics of Phase Transitions. Springer, 2002.

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Schnur, S. L., Paul H. E. Meijer, Jacques Leblond, and Pierre Papon. Physics of Phase Transitions: Concepts and Applications. Springer London, Limited, 2013.

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Roldán, Édgar. Irreversibility and Dissipation in Microscopic Systems. Springer, 2014.

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Irreversibility and Dissipation in Microscopic Systems. Springer, 2014.

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Book chapters on the topic "Biophysical transition"

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Lubchenco, Jane, and Peter M. Haugan. "The Ocean Transition: What to Learn from System Transitions." In The Blue Compendium, 445–83. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-16277-0_12.

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AbstractThe ocean is the ultimate commons. Sustainability narratives now recognise what science continues to demonstrate—that ecosystems on land, rivers, deltas, estuaries and the ocean are intrinsically linked (Mathews et al. 2019). There is a growing consensus that the prosperity and well-being of humanity depends on the health of the ocean environment, including the ocean-climate nexus (OECD 2016; IPCC 2019). Critical indicators reveal that business as usual is going to result in the collapse of key biophysical ocean functions, with major implications for the global economy and societies (IPCC 2019). Science has demonstrated that these close systemic interlinkages in and among ecological, economic and social systems require solutions which are responsive and flexible, robust yet elastic (SDG 2019).

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Möbius, Klaus, and Daniella Goldfarb. "High-Field/High-Frequency Electron Paramagnetic Resonance Involving Single- and Multiple-Transition Schemes." In Biophysical Techniques in Photosynthesis, 267–304. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-8250-4_14.

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Nellaepalli, Sreedhar, Ottó Zsiros, László Kovács, Yadavalli Venkateswarlu, Mekala Nageswara Rao, Prasanna Mohanty, and Rajagopal Subramanyam. "State Transition Mechanism in Arabidopsis Thaliana: Biophysical and Proteomic Studies." In Advanced Topics in Science and Technology in China, 398–401. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-32034-7_83.

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Chudyk, Ewa. "Differential Transition State Stabilization - Nonempirical Analysis." In Encyclopedia of Biophysics, 459–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_251.

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Stoll, Stefan. "Simulation of Transition-Metal EPR Spectra." In Encyclopedia of Biophysics, 2316–19. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_650.

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Rodger, Alison. "Absorption Spectroscopy and Transition Polarizations: Pictorial Description." In Encyclopedia of Biophysics, 29. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_782.

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Koynova, Rumiana, and Boris Tenchov. "Phase Transitions and Phase Behavior of Lipids." In Encyclopedia of Biophysics, 1841–54. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_542.

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Wormell, Paul. "Absorption Spectroscopy: Relationship of Transition Type to Molecular Structure." In Encyclopedia of Biophysics, 1–4. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-642-35943-9_781-1.

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Rodger, Alison. "Absorption Spectroscopy, the Beer-Lambert Law, and Transition Polarizations." In Encyclopedia of Biophysics, 1–2. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-642-35943-9_782-1.

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Wormell, Paul. "Absorption Spectroscopy: Relationship of Transition Type to Molecular Structure." In Encyclopedia of Biophysics, 35–38. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_781.

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Conference papers on the topic "Biophysical transition"

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Galpayage Dona, Kalpani Nisansala Udeni, Jia Liu, Yuhao Qiang, E. Du, and A. W. C. Lau. "Electrical Equivalent Circuit Model of Sickle Cell." In ASME 2017 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/imece2017-70677.

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Mature red blood cell (RBC) consists of cytoplasm, mainly normal hemoglobin (HbA) within a plasma membrane. In sickle cell disease, abnormal sickle hemoglobin (HbS) molecule polymerizes and forms into rigid fibers at low oxygen tension, which contributes to variation in the biophysical properties of sickle cells from healthy RBCs. This paper presents an electrical equivalent circuit (EEC) model of sickle cell that considers the phase transition of oxy-HbS solution to deoxy-HbS polymers. Briefly, we model the oxy-HbS solution following healthy RBCs using a resistor and deoxy-HbS fibers as a capacitor. To validate the model, electrical impedance measurements of cell suspensions for normal RBCs and sickle cells are performed, using a multi-channel lock in amplifier in the frequency range of 1 kHz to 10 MHz in a customized microfluidic chamber. Quantitative measurements of the classical components of EEC model are extracted using the developed EEC sickle cell model, allowing us to better understand the biophysics of cell sickling event in sickle cell disease.

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Shun, Ozaki, Shima Okada, Masanobu Manno, Yusuke Sakaue, and Masaaki Makikawa. "Non-Contact Sleep Stage Estimation Using Wireless Millimetre-Wave Sensor." In AHFE 2023 Hawaii Edition. AHFE International, 2023. http://dx.doi.org/10.54941/ahfe1004388.

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Insufficient sleep quality has significant physical and mental health impacts on humans. However, measuring sleep quality requires a Polysomnography (PSG) test at a clinical site, which requires specialised knowledge. This study used a wireless millimetre-wave, non-contact biophysical information detection sensor to estimate sleep depth. This sensor can obtain body movements and respiratory rates from millimetre-wave fluctuations. We calculated several parameters from the respiration and body movement data obtained from these sensors and applied machine learning to create a model for estimating sleep depth. In addition, we applied the sleep stage probability obtained in advance from the sleep stages of all the experimental subjects using simple PSG as one of the sleep stage estimation parameters. The actual sleep stage was obtained using a simple PSG as a reference for machine learning. The experimental subjects were 15 healthy adults, and measurements were taken over 1–3 nights. Because some of the wireless millimetre-wave sensors did not work correctly and the first night of measurement did not provide normal sleep owing to the first-night effect, we excluded some data. Finally, nine sets of data were used for training. Sleep depth was classified into four stages: waking (W), rem (R), light (L), and deep (D). The sensitivities of this machine-learning model for each sleep depth were 51.1% (W), 27.6% (R), 81.0% (L), and 47.8% (D), and the correct response rates were 73.7% (W), 53.3% (R), 59.8% (L), and 64.3% (D). The overall accuracy is 60.5%. In the future, we will implement hidden Markov state transition probabilities in the state probabilities. In addition, sensors can detect heartbeats to improve the accuracy of sleep-depth estimation.

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Sychev, Alexander V., Roman N. Belenkov, Dmitry N. Ukolov, Artem V. Budaev, Anastasia I. Lavrova, and Eugene B. Postnikov. "Revealing kinetics of chemical transitions in colorimetric indicators of microorganisms growth based on photometric data from a portable microbiological analyser." In Computational Biophysics and Nanobiophotonics, edited by Boris N. Khlebtsov and Dmitry E. Postnov. SPIE, 2022. http://dx.doi.org/10.1117/12.2625794.

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Ivanova, N. A., Alexander S. Rubanov, Alexei L. Tolstik, and A. V. Chaley. "Transition to chaos in an interferometer with amplitude-phase nonlinearity." In ICONO '98: Laser Spectroscopy and Optical Diagnostics--Novel Trends and Applications in Laser Chemistry, Biophysics, and Biomedicine, edited by Sergei S. Chesnokov, Valerii P. Kandidov, and Nikolai I. Koroteev. SPIE, 1999. http://dx.doi.org/10.1117/12.340060.

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Baranov, D. V., A. A. Egorov, Evgeny M. Zolotov, and Konstantin K. Svidzinsky. "Step-height and step-transition measurements with the heterodyne differential interferometer." In ICONO '98: Laser Spectroscopy and Optical Diagnostics--Novel Trends and Applications in Laser Chemistry, Biophysics, and Biomedicine, edited by Anatoli V. Andreev, Sergei N. Bagayev, Anatoliy S. Chirkin, and Vladimir I. Denisov. SPIE, 1999. http://dx.doi.org/10.1117/12.340150.

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Isaeva, E. A., Anna A. Isaeva, A. V. Pantyukov, and D. A. Zimnyakov. "Spatially resolved speckle-correlometry of sol-gel transition." In Saratov Fall Meeting 2017: Fifth International Symposium on Optics and Biophotonics: Laser Physics and Photonics XIX; Computational Biophysics and Analysis of Biomedical Data IV, edited by Vladimir L. Derbov and Dmitry E. Postnov. SPIE, 2018. http://dx.doi.org/10.1117/12.2315148.

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Anikeev, S. V., V. N. Kuliasov, V. B. Morozov, A. N. Olenin, and V. G. Tunkin. "Population and nonlinear polarization coherent changes on Raman transition due to two-photon pulse excitation." In ICONO '98: Laser Spectroscopy and Optical Diagnostics--Novel Trends and Applications in Laser Chemistry, Biophysics, and Biomedicine, edited by Konstantin N. Drabovich, V. I. Emelyanova, and Vladimir A. Makarov. SPIE, 1999. http://dx.doi.org/10.1117/12.342336.

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Emel'yanov, Vladimir I., and V. A. Fedotov. "Roughening phase transition and surface local field increase under the action of powerful laser radiation on solids." In ICONO '98: Laser Spectroscopy and Optical Diagnostics--Novel Trends and Applications in Laser Chemistry, Biophysics, and Biomedicine, edited by Konstantin N. Drabovich, V. I. Emelyanova, and Vladimir A. Makarov. SPIE, 1999. http://dx.doi.org/10.1117/12.342364.

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Zimnyakov, Dmitry A., Sergej Yuvchenko, Anna Isaeva, Elena Isaeva, and Tatiana Samorodina. "Evolution of the scattering anisotropy of aged foams in the wet-to-dry transition." In Saratov Fall Meeting 2017: Fifth International Symposium on Optics and Biophotonics: Laser Physics and Photonics XIX; Computational Biophysics and Analysis of Biomedical Data IV, edited by Vladimir L. Derbov and Dmitry E. Postnov. SPIE, 2018. http://dx.doi.org/10.1117/12.2311474.

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Schering, Jan, Sander Keemink, and Johannes Textor. "Fitting stochastic lattice models using approximate gradients." In 38th ECMS International Conference on Modelling and Simulation. ECMS, 2024. http://dx.doi.org/10.7148/2024-0366.

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Stochastic lattice models (sLMs) are computational tools for simulating spatiotemporal dynamics in physics, computational biology, chemistry, ecology, and other fields. Despite their widespread use, it is challenging to fit sLMs to data, as their likelihood function is commonly intractable and the models non-differentiable. The adjacent field of agent-based modelling (ABM), faced with similar challenges, has recently introduced an approach to approximate gradients in network-controlled ABMs via reparameterization tricks. This approach enables efficient gradient-based optimization with automatic differentiation (AD), which allows for a directed local search of suitable parameters rather than estimation via black-box sampling. In this study, we investigate the feasibility of using similar reparameterization tricks to fit sLMs through backpropagation of approximate gradients. We consider three common scenarios: fitting to single-state transitions, fitting to trajectories, and identification of stable lattice configurations. We demonstrate that all tasks can be solved by AD using three example sLMs from sociology, biophysics, and physical chemistry. Our results show that AD via approximate gradients is a promising method to fit sLMs to data for a wide variety of models and tasks.

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Reports on the topic "Biophysical transition"

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Thoma, David. Landscape phenology, vegetation condition, and relations with climate at Capitol Reef National Park, 2000–2019. Edited by Alice Wondrak Biel. National Park Service, March 2023. http://dx.doi.org/10.36967/2297289.

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Quantitatively linking satellite observations of vegetation condition and climate data over time provides insight to climate influences on primary production, phenology (timing of growth), and sensitivity of vegetation to weather and longer-term patterns of weather referred to as climate. This in turn provides a basis for understanding potential climate impacts to vegetation—and the potential to anticipate cascading ecological effects, such as impacts to forage, habitat, fire potential, and erosion, as climate changes in the future. This report provides baseline information about vegetation production and condition over time at Capitol Reef National Park (NP), as derived from satellite remote sensing. Its objective is to demonstrate methods of analysis, share findings, and document historic climate exposure and sensitivity of vegetation to weather and climate as a driver of vegetation change. This report represents a quantitative foundation of vegetation–climate relationships on an annual timestep. The methods can be modified to finer temporal resolution and other spatial scales if further analyses are needed to inform park planning and management. The knowledge provided in this report can inform vulnerability assessments for Climate Smart Conservation planning by park managers. Patterns of pivot points and responses can serve as a guide to anticipate what, where, when, and why vegetation change may occur. For this analysis, vegetation alliance groups were derived from vegetation-map polygons (Von Loh et al. 2007) by lumping vegetation types expected to respond similarly to climate. Relationships between vegetation production and phenology were evaluated for each alliance map unit larger than a satellite pixel (~300 × 300 m). We used a water-balance model to characterize the climate experienced by plants. Water balance translates temperature and precipitation into more biophysically relevant climate metrics, such as soil moisture and drought stress, that are often more strongly correlated with vegetation condition than temperature or precipitation are. By accounting for the interactions between temperature, precipitation, and site characteristics, water balance helps make regional climate assessments relevant to local scales. The results provide a foundation for interpreting weather and climate as a driver of changes in primary production over a 20-year period at the polygon and alliance-group scale. Additionally, they demonstrate how vegetation type and site characteristics, such as soil properties, slope, and aspect, interact with climate at local scales to determine trends in vegetation condition. This report quantitatively defines critical water needs of vegetation and identifies which alliance types, in which locations, may be most susceptible to climate-change impacts in the future. Finally, this report explains how findings can be used in the Climate Smart Conservation framework, with scenario planning, to help manage park resources through transitions imposed by climate change.

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Thoma, David. Landscape phenology, vegetation condition, and relations with climate at Canyonlands National Park, 2000–2019. Edited by Alice Wondrak Biel. National Park Service, June 2023. http://dx.doi.org/10.36967/2299619.

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Quantitatively linking satellite observations of vegetation condition and climate data over time provides insight to climate influences on primary production, phenology (timing of growth), and sensitivity of vegetation to weather and longer-term patterns of weather referred to as climate. This in turn provides a basis for understanding potential climate impacts to vegetation—and the potential to anticipate cascading ecological effects—such as impacts to forage, habitat, fire potential, and erosion—as climate changes in the future. This report provides baseline information about vegetation production and condition over time at Canyonlands National Park (NP), as derived from satellite remote sensing. Its objective is to demonstrate methods of analysis, share findings, and document historic climate exposure and sensitivity of vegetation to weather and climate as a driver of vegetation change. This report represents a quantitative foundation of vegetation–climate relationships on an annual timestep. The methods can be modified to finer temporal resolution and other spatial scales if further analyses are needed to inform park planning and management. The knowledge provided in this report can inform vulnerability assessments for Climate Smart Conservation planning by park managers. Patterns of pivot points and responses can serve as a guide to anticipate what, where, when, and why vegetation change may occur. For this analysis, vegetation alliance groups were derived from vegetation-map polygons (Von Loh et al. 2007) by lumping vegetation types expected to respond similarly to climate. Relationships between vegetation production and phenology were evaluated for each alliance map unit larger than a satellite pixel (~300 × 300 m). We used a water-balance model to characterize the climate experienced by plants. Water balance translates temperature and precipitation into more biophysically relevant climate metrics, such as soil moisture and drought stress, that are often more strongly correlated with vegetation condition than temperature or precipitation are. By accounting for the interactions between temperature, precipitation, and site characteristics, water balance helps make regional climate assessments relevant to local scales. The results provide a foundation for interpreting weather and climate as a driver of changes in primary production over a 20-year period at the polygon and alliance-group scale. Additionally, they demonstrate how vegetation type and site characteristics, such as soil properties, slope, and aspect, interact with climate at local scales to determine trends in vegetation condition. This report quantitatively defines critical water needs of vegetation and identifies which alliance types, in which locations, may be most susceptible to climate-change impacts in the future. Finally, this report explains how findings can be used in the Climate Smart Conservation framework, with scenario planning, to help manage park resources through transitions imposed by climate change.

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