scholarly journals Sequential Diffusion Spectra as a Tool for Studying Time-Dependent Translational Molecular Dynamics: A Cement Hydration Study

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 68
Author(s):  
Igor Serša
Keyword(s):  
Molecular Dynamics ◽  
Porous Structure ◽  
Time Scales ◽  
Cement Hydration ◽  
Pulse Sequence ◽  
Spin Echo ◽  
Model Parameters ◽  
Signal Attenuation ◽  
Wide Range ◽  
Novel Method

The translational molecular dynamics in porous materials are affected by the presence of the porous structure that presents an obstacle for diffusing molecules in longer time scales, but not as much in shorter time scales. The characteristic time scales have equivalent frequency ranges of molecular dynamics, where longer time scales correspond to lower frequencies while the shorter time scales correspond to higher frequencies of molecular dynamics. In this study, a novel method for direct measurement of diffusion at a given frequency of translational molecular dynamics is exploited to measure the diffusion spectra, i.e., distribution of diffusion in a wide range of frequencies. This method utilizes NMR modulated gradient spin-echo (MGSE) pulse sequence to measure the signal attenuation during the train of spin-echoes formed in the presence of a constant gradient. From attenuation, the diffusion coefficient at the frequency equal to the inverse double inter-echo time is calculated. The method was employed to study the white cement hydration process by the sequential acquisition of the diffusion spectra. The measured spectra were also analyzed by the diffusion spectra model to obtain the time-dependence of the best-fit model parameters. The presented method can also be applied to study other similar systems with the time evolution of porous structure.

Protein dynamics from NMR

1998 ◽  
Vol 76 (2-3) ◽  
pp. 145-152 ◽  
Author(s):  
Lewis E Kay
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Protein Dynamics ◽  
Time Scales ◽  
Spin Relaxation ◽  
Biological Systems ◽  
Multidimensional Nmr ◽  
The Past ◽  
Wide Range ◽  
Nmr Methods

The past several years have seen the development of a significant number of new multidimensional NMR methods for the study of molecular dynamics spanning a wide range of time scales. Applications involving a large number of different biological systems have emerged and correlations with function have been established. Unique insights are obtained that are not available from structure alone, indicating the importance of dynamics studies for understanding function.Key words: NMR spin relaxation, protein dynamics, protein structure.

scholarly journals Catchment classification: hydrological analysis of catchment behavior through process-based modeling along a climate gradient

2011 ◽  
Vol 15 (11) ◽  
pp. 3411-3430 ◽  
Author(s):  
G. Carrillo ◽  
P. A. Troch ◽  
M. Sivapalan ◽  
T. Wagener ◽  
C. Harman ◽  
...  
Keyword(s):  
Time Scales ◽  
Climate Model ◽  
Model Parameters ◽  
Hydrologic Response ◽  
Dimensionless Numbers ◽  
Landscape Features ◽  
Climate Gradient ◽  
Catchment Characteristics ◽  
Wide Range ◽  
Parameter Values

Abstract. Catchment classification is an efficient method to synthesize our understanding of how climate variability and catchment characteristics interact to define hydrological response. One way to accomplish catchment classification is to empirically relate climate and catchment characteristics to hydrologic behavior and to quantify the skill of predicting hydrologic response based on the combination of climate and catchment characteristics. Here we present results using an alternative approach that uses our current level of hydrological understanding, expressed in the form of a process-based model, to interrogate how climate and catchment characteristics interact to produce observed hydrologic response. The model uses topographic, geomorphologic, soil and vegetation information at the catchment scale and conditions parameter values using readily available data on precipitation, temperature and streamflow. It is applicable to a wide range of catchments in different climate settings. We have developed a step-by-step procedure to analyze the observed hydrologic response and to assign parameter values related to specific components of the model. We applied this procedure to 12 catchments across a climate gradient east of the Rocky Mountains, USA. We show that the model is capable of reproducing the observed hydrologic behavior measured through hydrologic signatures chosen at different temporal scales. Next, we analyze the dominant time scales of catchment response and their dimensionless ratios with respect to climate and observable landscape features in an attempt to explain hydrologic partitioning. We find that only a limited number of model parameters can be related to observable landscape features. However, several climate-model time scales, and the associated dimensionless numbers, show scaling relationships with respect to the investigated hydrological signatures (runoff coefficient, baseflow index, and slope of the flow duration curve). Moreover, some dimensionless numbers vary systematically across the climate gradient, possibly as a result of systematic co-variation of climate, vegetation and soil related time scales. If such co-variation can be shown to be robust across many catchments along different climate gradients, it opens perspective for model parameterization in ungauged catchments as well as prediction of hydrologic response in a rapidly changing environment.

scholarly journals Catchment classification: hydrological analysis of catchment behavior through process-based modeling along a climate gradient

2011 ◽  
Vol 8 (3) ◽  
pp. 4583-4640 ◽  
Author(s):  
G. Carrillo ◽  
P. A. Troch ◽  
M. Sivapalan ◽  
T. Wagener ◽  
C. Harman ◽  
...  
Keyword(s):  
Time Scales ◽  
Climate Model ◽  
Model Parameters ◽  
Hydrologic Response ◽  
Catchment Scale ◽  
Landscape Features ◽  
Climate Gradient ◽  
Catchment Characteristics ◽  
Wide Range ◽  
Parameter Values

Abstract. Catchment classification is an efficient method to synthesize our understanding of how climate variability and catchment characteristics interact to define hydrological response. One way to accomplish catchment classification is to empirically relate climate and catchment characteristics to hydrologic behavior and to quantify the skill of predicting hydrologic response based on the combination of climate and catchment characteristics. Since there are important subsurface properties that cannot be readily measured, the skill of classification reflects (the lack of) the amount of cross-correlation between observable landscape features and unobservable subsurface features. The resulting empirical approach is also strongly controlled by the dataset used, and therefore lacks the power to generalize beyond the heterogeneity of characteristics found in the dataset. An alternative approach, that can partially alleviate the above-mentioned issue of observability, uses our current level of hydrological understanding, expressed in the form of a process-based model, to interrogate how climate and catchment characteristics interact to produce the observed hydrologic response. In this paper we present a general method of hydrologic analysis by means of a process-based model to support a bottom-up catchment classification system complementary to top-down classification methods. The model uses topographic, geomorphologic, soil and vegetation information at the catchment scale and conditions parameter values using readily available data on precipitation, temperature and streamflow. It is applicable to a wide range of catchments in different climate settings. We have developed a step-by-step procedure to analyze the observed hydrologic response and to assign parameter values related to specific components of the model. We applied this procedure to 12 catchments across a climate gradient east of the Rocky Mountains, USA. We show that the model is capable of reproducing the observed hydrologic behavior measured through hydrologic signatures chosen at different temporal scales. Next, we analyze the dominant time scales of catchment response and their dimensionless ratios with respect to climate and observable landscape features in an attempt to explain hydrologic partitioning. We find that only a limited number of model parameters can be related to observable landscape features. However, several climate-model time scales, and the associated dimensionless numbers, show scaling relationships with respect to the investigated hydrological signatures (runoff coefficient, baseflow index, and slope of the flow duration curve). Moreover, our analysis revealed systematic co-variation of climate, vegetation and soil related time scales along the climate gradient. If such co-variation can be shown to be robust across many catchments along different climate gradients, it opens perspective for model parameterization in ungauged catchments as well as prediction of hydrologic response in a rapidly changing environment.

3D MRI of the Ankle: A Concise State-of-the-Art Review

2021 ◽  
Vol 25 (03) ◽  
pp. 514-526
Author(s):  
Benjamin Fritz ◽  
Jan Fritz ◽  
Reto Sutter
Keyword(s):  
Pulse Sequence ◽  
Spin Echo ◽  
Pulse Sequences ◽  
Acquisition Time ◽  
Slice Thickness ◽  
3D Mri ◽  
Partial Volume ◽  
Partial Volume Effects ◽  
Wide Range ◽  
Volume Effects

AbstractMagnetic resonance imaging (MRI) is a powerful imaging modality for visualizing a wide range of ankle disorders that affect ligaments, tendons, and articular cartilage. Standard two-dimensional (2D) fast spin-echo (FSE) and turbo spin-echo (TSE) pulse sequences offer high signal-to-noise and contrast-to-noise ratios, but slice thickness limitations create partial volume effects. Modern three-dimensional (3D) FSE/TSE pulse sequences with isotropic voxel dimensions can achieve higher spatial resolution and similar contrast resolutions in ≤ 5 minutes of acquisition time. Advanced acceleration schemes have reduced the blurring effects of 3D FSE/TSE pulse sequences by affording shorter echo train lengths. The ability for thin-slice partitions and multiplanar reformation capabilities eliminate relevant partial volume effects and render modern 3D FSE/TSE pulse sequences excellently suited for MRI visualization of several oblique and curved structures around the ankle. Clinical efficiency gains can be achieved by replacing two or three 2D FSE/TSE sequences within an ankle protocol with a single isotropic 3D FSE/TSE pulse sequence. In this article, we review technical pulse sequence properties for 3D MRI of the ankle, discuss practical considerations for clinical implementation and achieving the highest image quality, compare diagnostic performance metrics of 2D and 3D MRI for major ankle structures, and illustrate a broad spectrum of ankle abnormalities.

Variable Precision Depth Encoding for 3D Range Geometry Compression

2020 ◽  
Vol 2020 (17) ◽  
pp. 34-1-34-7
Author(s):  
Matthew G. Finley ◽  
Tyler Bell
Keyword(s):  
Normal Distribution ◽  
Arbitrary Distribution ◽  
File Size ◽  
Geometry Compression ◽  
Variable Precision ◽  
Wide Range ◽  
Novel Method ◽  
Encoding Method ◽  
Rgb Image ◽  
Color Channels

This paper presents a novel method for accurately encoding 3D range geometry within the color channels of a 2D RGB image that allows the encoding frequency—and therefore the encoding precision—to be uniquely determined for each coordinate. The proposed method can thus be used to balance between encoding precision and file size by encoding geometry along a normal distribution; encoding more precisely where the density of data is high and less precisely where the density is low. Alternative distributions may be followed to produce encodings optimized for specific applications. In general, the nature of the proposed encoding method is such that the precision of each point can be freely controlled or derived from an arbitrary distribution, ideally enabling this method for use within a wide range of applications.

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Proton Release ◽  
Intrinsic Resistance ◽  
Constant Ph ◽  
Wide Range ◽  
Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

Expressing the Self

2018 ◽  
Keyword(s):  
Philosophy Of Mind ◽  
The Self ◽  
Epistemic Status ◽  
First Person ◽  
Semantic Categories ◽  
Wide Range ◽  
Person Reference ◽  
De Se ◽  
Novel Method ◽  
Cultural Pragmatics

This book addresses different linguistic and philosophical aspects of referring to the self in a wide range of languages from different language families, including Amharic, English, French, Japanese, Korean, Mandarin, Newari (Sino-Tibetan), Polish, Tariana (Arawak), and Thai. In the domain of speaking about oneself, languages use a myriad of expressions that cut across grammatical and semantic categories, as well as a wide variety of constructions. Languages of Southeast and East Asia famously employ a great number of terms for first-person reference to signal honorification. The number and mixed properties of these terms make them debatable candidates for pronounhood, with many grammar-driven classifications opting to classify them with nouns. Some languages make use of egophors or logophors, and many exhibit an interaction between expressing the self and expressing evidentiality qua the epistemic status of information held from the ego perspective. The volume’s focus on expressing the self, however, is not directly motivated by an interest in the grammar or lexicon, but instead stems from philosophical discussions of the special status of thoughts about oneself, known as de se thoughts. It is this interdisciplinary understanding of expressing the self that underlies this volume, comprising philosophy of mind at one end of the spectrum and cross-cultural pragmatics of self-expression at the other. This unprecedented juxtaposition results in a novel method of approaching de se and de se expressions, in which research methods from linguistics and philosophy inform each other. The importance of this interdisciplinary perspective on expressing the self cannot be overemphasized. Crucially, the volume also demonstrates that linguistic research on first-person reference makes a valuable contribution to research on the self tout court, by exploring the ways in which the self is expressed, and thereby adding to the insights gained through philosophy, psychology, and cognitive science.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals Antifungal Activity of Propyl Disulfide from Neem (Azadirachta indica) in Vapor and Agar Diffusion Assays against Anthracnose Pathogens (Colletotrichum gloeosporioides and Colletotrichum acutatum) in Mango Fruit

2021 ◽  
Vol 9 (4) ◽  
pp. 839
Author(s):  
Muhammad Rafiullah Khan ◽  
Vanee Chonhenchob ◽  
Chongxing Huang ◽  
Panitee Suwanamornlert
Keyword(s):  
Antifungal Activity ◽  
Mycelial Growth ◽  
Colletotrichum Gloeosporioides ◽  
Colletotrichum Acutatum ◽  
Model Parameters ◽  
Pathogenicity Test ◽  
Agar Diffusion ◽  
Wide Range ◽  
Significant Difference ◽  
Diffusion Assay

Microorganisms causing anthracnose diseases have a medium to a high level of resistance to the existing fungicides. This study aimed to investigate neem plant extract (propyl disulfide, PD) as an alternative to the current fungicides against mango’s anthracnose. Microorganisms were isolated from decayed mango and identified as Colletotrichum gloeosporioides and Colletotrichum acutatum. Next, a pathogenicity test was conducted and after fulfilling Koch’s postulates, fungi were reisolated from these symptomatic fruits and we thus obtained pure cultures. Then, different concentrations of PD were used against these fungi in vapor and agar diffusion assays. Ethanol and distilled water were served as control treatments. PD significantly (p ≤ 0.05) inhibited more of the mycelial growth of these fungi than both controls. The antifungal activity of PD increased with increasing concentrations. The vapor diffusion assay was more effective in inhibiting the mycelial growth of these fungi than the agar diffusion assay. A good fit (R2, 0.950) of the experimental data in the Gompertz growth model and a significant difference in the model parameters, i.e., lag phase (λ), stationary phase (A) and mycelial growth rate, further showed the antifungal efficacy of PD. Therefore, PD could be the best antimicrobial compound against a wide range of microorganisms.

scholarly journals A Reinforcement Learning Framework for Spiking Networks with Dynamic Synapses

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Karim El-Laithy ◽  
Martin Bogdan
Keyword(s):  
Reinforcement Learning ◽  
Spike Timing ◽  
Neural Representation ◽  
Model Parameters ◽  
Learning Framework ◽  
Reference Target ◽  
Wide Range ◽  
Spiking Network ◽  
Dynamic Synapses ◽  
Exclusive Or

An integration of both the Hebbian-based and reinforcement learning (RL) rules is presented for dynamic synapses. The proposed framework permits the Hebbian rule to update the hidden synaptic model parameters regulating the synaptic response rather than the synaptic weights. This is performed using both the value and the sign of the temporal difference in the reward signal after each trial. Applying this framework, a spiking network with spike-timing-dependent synapses is tested to learn the exclusive-OR computation on a temporally coded basis. Reward values are calculated with the distance between the output spike train of the network and a reference target one. Results show that the network is able to capture the required dynamics and that the proposed framework can reveal indeed an integrated version of Hebbian and RL. The proposed framework is tractable and less computationally expensive. The framework is applicable to a wide class of synaptic models and is not restricted to the used neural representation. This generality, along with the reported results, supports adopting the introduced approach to benefit from the biologically plausible synaptic models in a wide range of intuitive signal processing.

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