Simple molecules as complex systems.
Ontology highlight
ABSTRACT:
SUBMITTER: Furtenbacher T
PROVIDER: S-EPMC3983599 | biostudies-other | 2014
REPOSITORIES: biostudies-other
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Project description:Molecular logic gates (MLGs) are compounds that can solve Boolean logic operations to give an answer (OUTPUT) upon receiving a stimulus (INPUT). These derivatives can be used as biological sensors and are promising substitutes for the present logic gates. Although MLGs with complex molecular structures have been reported, they often show stability problems. To address this problem, we describe herein six stable pseudo-hemiindigo-derived MLGs capable of solving complex logic operations. MLGs 7, 8, 9, and 10 can solve a complex logic operation connecting 4 logic gates using 2 different wavelengths (445 nm and 400 nm) and the presence of p-TsOH and triethylamine (TEA) as inputs; MLG 11 solves a complex logic operation connecting 3 logic gates and uses 3 inputs, one wavelength of 445 nm and the presence of p-TsOH and TEA; and MLG 12 can only solve one logic operation (INH) and uses only the presence of p-TsOH and TEA as an input. Each operating method of the MLGs was evaluated with several techniques; proton interactions with MLGs were screened with NMR by titrating with p-TsOH, the photochemical properties were examined with absorption ultraviolet-visible (UV-Vis) spectroscopy, and the isomerization dynamics were examined with NMR using the two wavelengths for isomerization (photostationary isomer). The results indicate that the pseudo-hemiindigo-derived MLGs described herein can be applied as multiplexers or data selectors that are necessary for the transient flow of information for biological and computer systems. Finally, to design different MLGs and a system that can treat more information as complex logic gates (demultiplexers), two and three MLGs were mixed in different experiments. In both cases, four inputs were employed (445 nm, 400 nm, p-TsOH and TEA), yielding more outputs. Detailed information about the system dynamics was obtained from NMR experiments.
| S-EPMC9034006 | biostudies-literature
Project description:Over the past three decades, carbon nanotubes and fullerenes have become remarkable objects for starting the implementation of new models and technologies in different branches of science. To a great extent, this is defined by the unique electronic and spatial properties of nanocavities due to the ramified ?-electron systems. This provides an opportunity for the formation of endohedral complexes containing non-covalently bonded atoms or molecules inside fullerenes and nanotubes. The guest species are exposed to the force field of the nanocavity, which can be described as a combination of electronic and steric requirements. Its action significantly changes conformational properties of even relatively simple molecules, including ethane and its analogs, as well as compounds with C-O, C-S, B-B, B-O, B-N, N-N, Al-Al, Si-Si and Ge-Ge bonds. Besides that, the cavity of the host molecule dramatically alters the stereochemical characteristics of cyclic and heterocyclic systems, affects the energy of pyramidal nitrogen inversion in amines, changes the relative stability of cis and trans isomers and, in the case of chiral nanotubes, strongly influences the properties of R- and S- enantiomers. The present review aims at primary compilation of such unusual stereochemical effects and initial evaluation of the nature of the force field inside nanotubes and fullerenes.
| S-EPMC7287839 | biostudies-literature
Project description:BackgroundEnsuring patients benefit from the latest medical and technical advances remains a major challenge, with rational-linear and reductionist approaches to translating evidence into practice proving inefficient and ineffective. Complexity thinking, which emphasises interconnectedness and unpredictability, offers insights to inform evidence translation theories and strategies. Drawing on detailed insights into complex micro-systems, this research aimed to advance empirical and theoretical understanding of the reality of making and sustaining improvements in complex healthcare systems.MethodsUsing analytical auto-ethnography, including documentary analysis and literature review, we assimilated learning from 5 years of observation of 22 evidence translation projects (UK). We used a grounded theory approach to develop substantive theory and a conceptual framework. Results were interpreted using complexity theory and 'simple rules' were identified reflecting the practical strategies that enhanced project progress.ResultsThe framework for Successful Healthcare Improvement From Translating Evidence in complex systems (SHIFT-Evidence) positions the challenge of evidence translation within the dynamic context of the health system. SHIFT-Evidence is summarised by three strategic principles, namely (1) 'act scientifically and pragmatically' - knowledge of existing evidence needs to be combined with knowledge of the unique initial conditions of a system, and interventions need to adapt as the complex system responds and learning emerges about unpredictable effects; (2) 'embrace complexity' - evidence-based interventions only work if related practices and processes of care within the complex system are functional, and evidence-translation efforts need to identify and address any problems with usual care, recognising that this typically includes a range of interdependent parts of the system; and (3) 'engage and empower' - evidence translation and system navigation requires commitment and insights from staff and patients with experience of the local system, and changes need to align with their motivations and concerns. Twelve associated 'simple rules' are presented to provide actionable guidance to support evidence translation and improvement in complex systems.ConclusionBy recognising how agency, interconnectedness and unpredictability influences evidence translation in complex systems, SHIFT-Evidence provides a tool to guide practice and research. The 'simple rules' have potential to provide a common platform for academics, practitioners, patients and policymakers to collaborate when intervening to achieve improvements in healthcare.
| S-EPMC6009041 | biostudies-literature
Project description:Simple temporal models that ignore the spatial nature of interactions and track only changes in mean quantities, such as global densities, are typically used under the unrealistic assumption that individuals are well mixed. These so-called mean-field models are often considered overly simplified, given the ample evidence for distributed interactions and spatial heterogeneity over broad ranges of scales. Here, we present one reason why such simple population models may work even when mass-action assumptions do not hold: spatial structure is present but it relates to global densities in a special way. With an individual-based predator-prey model that is spatial and stochastic, and whose mean-field counterpart is the classic Lotka-Volterra model, we show that the global densities and densities of pairs (or spatial covariances) establish a bi-power law at the stationary state and also in their transient approach to this state. This relationship implies that the dynamics of global densities can be written simply as a function of those densities alone without invoking pairs (or higher order moments). The exponents of the bi-power law for the predation rate exhibit a remarkable robustness to changes in model parameters. Evidence is presented for a connection of our findings to the existence of a critical phase transition in the dynamics of the spatial system. We discuss the application of similar modified mean-field equations to other ecological systems for which similar transitions have been described, both in models and empirical data.Electronic supplementary material The online version of this article (doi:10.1007/s12080-011-0116-2) contains supplementary material, which is available to authorized users.
| S-EPMC4270435 | biostudies-literature
Project description:BackgroundPhysiologic signals, such as cardiac interbeat intervals, exhibit complex fluctuations. However, capturing important dynamical properties, including nonstationarities may not be feasible from conventional time series graphical representations.MethodsWe introduce a simple-to-implement visualisation method, termed dynamical density delay mapping ("D3-Map" technique) that provides an animated representation of a system's dynamics. The method is based on a generalization of conventional two-dimensional (2D) Poincaré plots, which are scatter plots where each data point, x(n), in a time series is plotted against the adjacent one, x(n?+?1). First, we divide the original time series, x(n) (n?=?1,…, N), into a sequence of segments (windows). Next, for each segment, a three-dimensional (3D) Poincaré surface plot of x(n), x(n?+?1), h[x(n),x(n?+?1)] is generated, in which the third dimension, h, represents the relative frequency of occurrence of each (x(n),x(n?+?1)) point. This 3D Poincaré surface is then chromatised by mapping the relative frequency h values onto a colour scheme. We also generate a colourised 2D contour plot from each time series segment using the same colourmap scheme as for the 3D Poincaré surface. Finally, the original time series graph, the colourised 3D Poincaré surface plot, and its projection as a colourised 2D contour map for each segment, are animated to create the full "D3-Map."ResultsWe first exemplify the D3-Map method using the cardiac interbeat interval time series from a healthy subject during sleeping hours. The animations uncover complex dynamical changes, such as transitions between states, and the relative amount of time the system spends in each state. We also illustrate the utility of the method in detecting hidden temporal patterns in the heart rate dynamics of a patient with atrial fibrillation. The videos, as well as the source code, are made publicly available.ConclusionsAnimations based on density delay maps provide a new way of visualising dynamical properties of complex systems not apparent in time series graphs or standard Poincaré plot representations. Trainees in a variety of fields may find the animations useful as illustrations of fundamental but challenging concepts, such as nonstationarity and multistability. For investigators, the method may facilitate data exploration.
| S-EPMC3899032 | biostudies-literature
Project description:The potential of genomic DNA is realized when new modalities are invented that manipulate large DNAs with minimal breakage or loss of sample. Here, we describe a polydimethylsiloxane-polycarbonate membrane device to remove small molecules from a sample while retaining large DNAs. Dialysis rates dramatically change as DNA size in kb (M) increases and DNA dimensions become comparable to pore size, and chain characteristics go from rod-like to Gaussian. Consequently, we describe empirical rates of dialysis, R, as a function of M as falling into two regimes: DNAs ≤ 1 kb show R(M) ∼e - t/τ M (t = time, τM = time constant), while DNAs ≥1.65 kb slowly passage with R(M) ∼M -1.68; such partitioning potentiates single-molecule imaging.
| S-EPMC6494463 | biostudies-literature
Project description:BackgroundEvidence translation and improvement research indicate that healthcare contexts are complex systems, characterized by uncertainty and surprise, which often defy orchestrated intervention attempts. This article reflects on the implications of complexity on attempts to translate evidence, and on a newly published framework for Successful Healthcare Improvements From Translating Evidence in complex systems (SHIFT-Evidence).DiscussionSHIFT-Evidence positions the challenge of evidence translation within the complex and evolving context of healthcare, and recognizes the wider issues practitioners routinely face. It is empirically grounded, and designed to be comprehensive, practically relevant and actionable. SHIFT-evidence is summarized by three principles designed to be intuitive and memorable: 'act scientifically and pragmatically'; 'embrace complexity'; and 'engage and empower'. Common challenges and strategies to overcome them are summarized in 12 'simple rules' that provide actionable guidance.ConclusionSHIFT-Evidence provides a practical tool to guide practice and research of evidence translation and improvement within complex dynamic healthcare settings. Implications are that improvement initiatives and research study designs need to take into account the unique initial conditions in each local setting; conduct needs to respond to unpredictable effects and address dependent problems; and evaluation needs to be sensitive to evolving priorities and the emergent range of activities required to achieve improvement.
| S-EPMC6464098 | biostudies-literature
Project description:Transmembrane helical segments (TMs) can be classified into two groups of so-called 'simple' and 'complex' TMs. Whereas the first group represents mere hydrophobic anchors with an overrepresentation of aliphatic hydrophobic residues that are likely attributed to convergent evolution in many cases, the complex ones embody ancestral information and tend to have structural and functional roles beyond just membrane immersion. Hence, the sequence homology concept is not applicable on simple TMs. In practice, these simple TMs can attract statistically significant but evolutionarily unrelated hits during similarity searches (whether through BLAST- or HMM-based approaches). This is especially problematic for membrane proteins that contain both globular segments and TMs. As such, we have developed the transmembrane helix: simple or complex (TMSOC) webserver for the identification of simple and complex TMs. By masking simple TM segments in seed sequences prior to sequence similarity searches, the false-discovery rate decreases without sacrificing sensitivity. Therefore, TMSOC is a novel and necessary sequence analytic tool for both the experimentalists and the computational biology community working on membrane proteins. It is freely accessible at http://tmsoc.bii.a-star.edu.sg or available for download.
| S-EPMC3394259 | biostudies-literature
Project description:Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats, often 100-400 bp in length, found on every chromosome, typically in one location within heterochromatin. Drosophila melanogaster is unusual in that the heterochromatin contains many families of mostly short (5-12 bp) tandem repeats, none of which appears to be present at all centromeres, and none of which is found only at centromeres. Although centromere sequences from a minichromosome have been identified and candidate centromere sequences have been proposed, the DNA sequences at native Drosophila centromeres remain unknown. Here we use native chromatin immunoprecipitation to identify the centromeric sequences bound by the foundational kinetochore protein cenH3, known in vertebrates as CENP-A. In D. melanogaster, these sequences include a few families of 5-bp and 10-bp repeats, but in closely related D. simulans, a partially overlapping set of short repeats and more complex repeats comprise the centromeres. The results suggest that a recent expansion of short repeats is replacing more complex centromeric repeats in the melanogaster subgroup of Drosophila.
2018-01-08 | GSE105100 | GEO
Project description:Silks are biodegradable, biocompatible, self-assembling proteins that can also be tailored via genetic engineering to contain specific chemical features, offering utility for drug and gene delivery. Silkworm silk has been used in biomedical sutures for decades and has recently achieved Food and Drug Administration approval for expanded biomaterials device utility. With the diversity and control of size, structure and chemistry, modified or recombinant silk proteins can be designed and utilized in various biomedical application, such as for the delivery of bioactive molecules. This review focuses on the biosynthesis and applications of silk-based multi-block copolymer systems and related silk protein drug delivery systems. The utility of these systems for the delivery of small molecule drugs, proteins and genes is reviewed.
| S-EPMC2901564 | biostudies-literature