Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 8.728
Filtrar
1.
Zhongguo Zhong Yao Za Zhi ; 47(7): 1776-1789, 2022 Apr.
Artigo em Chinês | MEDLINE | ID: mdl-35534248

RESUMO

The potential quality markers(Q-markers) of Polygoni Perfoliati Herba were studied based on analytic hierarchy process(AHP)-entropy weight method(EWM), network pharmacology, and spectrum-effect relationship analysis. The AHP-EWM was used for quantitative identification of the Q-markers. To be specific, AHP was applied for the weight analysis of the validity, testability, and specificity of the first-level indexes, and EWM for the analysis of the second-level indexes supported by literature and experimental data. Based on literature and network pharmacology, the validity analysis was to study the component-target-disease-efficacy network, and select the components with the strongest correlation with the efficacy of clearing heat and removing toxin, diuresis and alleviating edema, and relieving cough. For the testability analysis, the high performance liquid chromatography(HPLC) and literature research were used to determine the 10 components in Polygoni Perfoliati Herba, and the fingerprints of Polygoni Perfoliati Herba were established at the same time. The specificity analysis was based on the statistics of the number of plants in which the components existed. Thereby, the 11 compounds: quercetin, oleanolic acid, ellagic acid, gallic acid, kaempferol, rutin, esculetin, quercetin-3-O-glucuronide, ursolic acid, protocatechuic acid, and ferulic acid, were identified as potential Q-markers. The 11 compounds were identified to have high anti-inflammatory activity, indicating that the 11 Q-markers may be the functional material basis. The result in this study is expected to serve as a reference for the quality control of Polygoni Perfoliati Herba.


Assuntos
Medicamentos de Ervas Chinesas , Processo de Hierarquia Analítica , Cromatografia Líquida de Alta Pressão , Medicamentos de Ervas Chinesas/farmacologia , Entropia , Quercetina
2.
PLoS One ; 17(5): e0268158, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35522688

RESUMO

In the problem of multiple attributes group decision making (MAGDM), the probabilistic linguistic term sets (PLTSs) is an useful tool which can be more flexible and accurate to express the evaluation information of decision makers (DMs). However, due to the lack of time or knowledge, DMs tend to provide the evaluation information by incomplete PLTSs (InPLTSs) which contain missing information. The process to estimate the missing information of InPLTSs is essential, which is called the normalization of InPLTSs. By analyzing the previous methods, the existing defect is that the original uncertainty information of InPLTS can be hardly retained after normalizing. Moreover, the literature that considers the normalization method from perspective of entropy change is absent. Thus, to overcome the shortcoming and fill the research blank, we propose two optimization models based on minimum entropy change of InPLTSs, which can remain the original uncertainty information of InPLTSs to the greatest extent. Inspired by entropy measure of PLTSs, the novel concepts related to entropy measure of InPLTS are developed. In addition, based on the novel normalization method, a decision model is constructed to solve the MAGDM problem. To verify the feasibility and superiority of the proposed method and model, a case about the selection of five-star scenic spots is given and we conduct to have comparative analysis with other methods.


Assuntos
Tomada de Decisões , Lógica Fuzzy , Entropia , Linguística/métodos , Incerteza
3.
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi ; 39(2): 311-319, 2022 Apr 25.
Artigo em Chinês | MEDLINE | ID: mdl-35523552

RESUMO

Heart sound signal is a kind of physiological signal with nonlinear and nonstationary features. In order to improve the accuracy and efficiency of the phonocardiogram (PCG) classification, a new method was proposed by means of support vector machine (SVM) in which the complete ensemble empirical modal decomposition with adaptive noise (CEEMDAN) permutation entropy was as the eigenvector of heart sound signal. Firstly, the PCG was decomposed by CEEMDAN into a number of intrinsic mode functions (IMFs) from high to low frequency. Secondly, the IMFs were sifted according to the correlation coefficient, energy factor and signal-to-noise ratio. Then the instantaneous frequency was extracted by Hilbert transform, and its permutation entropy was constituted into eigenvector. Finally, the accuracy of the method was verified by using a hundred PCG samples selected from the 2016 PhysioNet/CinC Challenge. The results showed that the accuracy rate of the proposed method could reach up to 87%. In comparison with the traditional EMD and EEMD permutation entropy methods, the accuracy rate was increased by 18%-24%, which demonstrates the efficiency of the proposed method.


Assuntos
Ruídos Cardíacos , Máquina de Vetores de Suporte , Entropia , Processamento de Sinais Assistido por Computador , Razão Sinal-Ruído
4.
J Chem Phys ; 156(17): 174114, 2022 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-35525642

RESUMO

Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces-base stacking, counterion-induced backbone self-interactions, and base pairing-via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach.


Assuntos
Ácidos Nucleicos , Simulação por Computador , Entropia , Conformação de Ácido Nucleico , Ácidos Nucleicos/química , Física , Termodinâmica
5.
Comput Intell Neurosci ; 2022: 4558839, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35502359

RESUMO

A method based on a computational intelligence information model is proposed to study the visualization of large data packages. Since the CAIM algorithm only considers the distribution of the largest number of classes in an interval, it offers an optimization method and simultaneously determines the appropriate stopping conditions to avoid overcrowding. The effectiveness of the improved algorithm has been experimentally proven. Methods of character reduction and weight determination are used to reduce the index and weight, establishing a large packaging information system. Experimental results show that the improved algorithm in this article produces more classification rules than the CAIM algorithm, because the discrete intervals created by the CAIM algorithm are relatively simple, but the classification rules are few, but less than the number of CAIM algorithms. Classification rules are generated by entropy-based sampling algorithms. This can make the classification rules simple and universal, and it is clear that the optimal sampling algorithm is more accurate than the CAIM algorithm.


Assuntos
Inteligência Artificial , Visualização de Dados , Algoritmos , Big Data , Entropia
6.
Sci Rep ; 12(1): 7389, 2022 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-35513477

RESUMO

Hypsarrhythmia is a specific chaotic morphology, present in the interictal period of the electroencephalogram (EEG) signal in patients with West Syndrome (WS), a severe form of childhood epilepsy and that, recently, was also identified in the examinations of patients with Zika Virus Congenital Syndrome (ZVCS). This innovative work proposes the development of a computational methodology for analysis and differentiation, based on the time-frequency domain, between the chaotic pattern of WS and ZVCS hypsarrhythmia. The EEG signal time-frequency analysis is carried out from the Continuous Wavelet Transform (CWT). Four joint moments-joint mean-[Formula: see text], joint variance-[Formula: see text], joint skewness-[Formula: see text], and joint kurtosis-[Formula: see text]-and four entropy measurements-Shannon, Log Energy, Norm, and Sure-are obtained from the CWT to compose the representative feature vector of the EEG hypsarrhythmic signals under analysis. The performance of eight classical types of machine learning algorithms are verified in classification using the k-fold cross validation and leave-one-patient-out cross validation methods. Discrimination results provided 78.08% accuracy, 85.55% sensitivity, 73.21% specificity, and AUC = 0.89 for the ANN classifier.


Assuntos
Espasmos Infantis , Infecção por Zika virus , Zika virus , Algoritmos , Eletroencefalografia/métodos , Entropia , Humanos , Processamento de Sinais Assistido por Computador , Máquina de Vetores de Suporte , Síndrome , Análise de Ondaletas , Infecção por Zika virus/complicações
7.
Philos Ethics Humanit Med ; 17(1): 9, 2022 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-35505377

RESUMO

Ethics is an unconventional field of research for a surgeon, as ethics in surgery owns several specificities and surgery is considered an aggressive specialty. Therefore, the interest of research in medical ethics is sometimes unclear.In this short essay, we discussed the interest of research in medical ethics using a comparison to thermodynamics and mainly, entropy. During the transformation of a figure from one state to another, some energy is released or absorbed; yet, a part of this energy is wasted because of "unordered" (and unsuccessful) reactions: it is Entropy.This "wasted energy" exists in Medical practice and justifies research in Medical ethics.


Assuntos
Ética Médica , Entropia , Termodinâmica
8.
Sci Prog ; 105(2): 368504221096000, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35491727

RESUMO

In this research, the electro-osmotic effects are highlighted for a blood-based hybrid nanofluid flow across an artery infected with multiple stenosis. The artery has permeable walls together with slip boundary effects. The slip and permeable boundary conditions model the more realistic blood flow problems. The governing equations of the problem are converted into non-dimensional form by introducing adequate dimensionless variables and acquired the exact solutions. The detailed study of heat transfer is given by Joule heating and viscous dissipation effects. The disorder of fluid flow is investigated by the mathematical study of entropy generation. Analytically attained solutions are examined graphically for both symmetric and non-symmetric shapes of stenosis. Streamlines are analyzed for varying values of flow rate Q and electro-osmotic parameter m. The flow velocity has smallest values on the axis of channel and gets higher value near the boundary walls. The temperature profile delineates opposite behavior to the velocity, and it is parabolic in nature. The velocity reduces towards the non-uniform stenosis except for electroosmotic parameter m. The temperature has larger magnitude in the case of anti-symmetric stenosis. Moreover, the stability of velocity solution is also analyzed.


Assuntos
Hemodinâmica , Nanopartículas , Artérias , Constrição Patológica , Entropia , Humanos
9.
JACC Cardiovasc Imaging ; 15(5): 783-792, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35512951

RESUMO

OBJECTIVES: The authors investigated the incremental prognostic value of entropy, a novel measure of myocardial tissue heterogeneity by cardiac magnetic resonance (CMR) imaging in patients presenting with ventricular arrhythmias (VAs). BACKGROUND: CMR can characterize myocardial areas serving as arrhythmogenic substrate. METHODS: Consecutive patients undergoing CMR imaging for VAs were followed for major adverse cardiac events (MACEs) defined by all-cause death, incident VAs requiring therapy, or heart failure hospitalization. Entropy was derived from the probability distribution of pixel signal intensities of the left ventricular (LV) myocardium. RESULTS: A total of 583 patients (age 54 ± 15 years, female 39%, left ventricular ejection fraction [LVEF] 54 ± 13%) were followed for a median of 4.4 years and experienced 141 MACEs. Entropy showed strong unadjusted association with MACE (HR: 1.88; 95% CI: 1.63-2.17; P < 0.001). In a multivariable model including LVEF, QRS duration, late gadolinium enhancement, and presenting arrhythmia, entropy maintained independent association with MACE (HR: 1.61; 95% CI: 1.32-1.96; P < 0.001). Entropy was further significantly associated with MACE in patients without myocardial scar (HR: 2.43; 95% CI: 1.55-3.82; P < 0.001) and in those presenting with nonsustained VAs (HR: 2.16; 95% CI: 1.43-3.25; P < 0.001). Addition of LV entropy to the baseline multivariable model significantly improved model performance (C-statistic improvement: 0.725 to 0.754; P = 0.003) and risk reclassification. CONCLUSIONS: In patients with VAs, CMR-assessed LV entropy was independently associated with MACE and provided incremental prognostic value, on top of LVEF and late gadolinium enhancement. LV entropy assessment may help risk stratification in patients with absence of myocardial scar or with nonsustained VAs.


Assuntos
Gadolínio , Função Ventricular Esquerda , Adulto , Idoso , Arritmias Cardíacas , Cicatriz/complicações , Meios de Contraste , Entropia , Feminino , Humanos , Imagem Cinética por Ressonância Magnética , Pessoa de Meia-Idade , Miocárdio , Valor Preditivo dos Testes , Prognóstico , Volume Sistólico
10.
Int J Mol Sci ; 23(8)2022 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-35456917

RESUMO

Attempts to find and quantify the supposed low entropy of organisms and its preservation are revised. The absolute entropy of the mixed components of non-living biomass (approximately -1.6 × 103 J K-1 L-1) is the reference to which other entropy decreases would be ascribed to life. The compartmentation of metabolites and the departure from the equilibrium of metabolic reactions account for reductions in entropy of 1 and 40-50 J K-1 L-1, respectively, and, though small, are distinctive features of living tissues. DNA and proteins do not supply significant decreases in thermodynamic entropy, but their low informational entropy is relevant for life and its evolution. No other living feature contributes significantly to the low entropy associated with life. The photosynthetic conversion of radiant energy to biomass energy accounts for most entropy (2.8 × 105 J K-1 carbon kg-1) produced by living beings. The comparatively very low entropy produced in other processes (approximately 4.8 × 102 J K-1 L-1 day-1 in the human body) must be rapidly exported outside as heat to preserve low entropy decreases due to compartmentation and non-equilibrium metabolism. Enzymes and genes are described, whose control minimizes the rate of production of entropy and could explain selective pressures in biological evolution and the rapid proliferation of cancer cells.


Assuntos
Fenômenos Bioquímicos , Biologia , Biomassa , Entropia , Humanos , Termodinâmica
11.
Sensors (Basel) ; 22(8)2022 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-35458900

RESUMO

In general, one may have access to a handful of labeled normal and defect datasets. Most unlabeled datasets contain normal samples because the defect samples occurred rarely. Thus, the majority of approaches for anomaly detection are formed as unsupervised problems. Most of the previous methods have typically chosen an autoencoder to extract the common characteristics of the unlabeled dataset, assumed as normal characteristics, and determine the unsuccessfully reconstructed area as the defect area in an image. However, we could waste the ground truth data if we leave them unused. In addition, a suitable choice of threshold value is needed for anomaly segmentation. In our study, we propose a semi-supervised setting to make use of both unlabeled and labeled samples and the network is trained to segment out defect regions automatically. We first train an autoencoder network to reconstruct defect-free images from an unlabeled dataset, mostly containing normal samples. Then, a difference map between the input and the reconstructed image is calculated and feeds along with the corresponding input image into the subsequent segmentation module. We share the ground truth for both kinds of input and train the network with binary cross-entropy loss. Additional difference images can also increase stability during training. Finally, we show extensive experimental results to prove that, with help from a handful of ground-truth segmentation maps, the result is improved overall by 3.83%.


Assuntos
Processamento de Imagem Assistida por Computador , Aprendizado de Máquina Supervisionado , Entropia , Processamento de Imagem Assistida por Computador/métodos
12.
Sensors (Basel) ; 22(8)2022 Apr 13.
Artigo em Inglês | MEDLINE | ID: mdl-35458965

RESUMO

In recent years, a number of new research papers have emerged on the application of neural networks in affective computing. One of the newest trends observed is the utilization of graph neural networks (GNNs) to recognize emotions. The study presented in the paper follows this trend. Within the work, GraphSleepNet (a GNN for classifying the stages of sleep) was adjusted for emotion recognition and validated for this purpose. The key assumption of the validation was to analyze its correctness for the Circumplex model to further analyze the solution for emotion recognition in the Ekman modal. The novelty of this research is not only the utilization of a GNN network with GraphSleepNet architecture for emotion recognition, but also the analysis of the potential of emotion recognition based on differential entropy features in the Ekman model with a neutral state and a special focus on continuous emotion recognition during the performance of an activity The GNN was validated against the AMIGOS dataset. The research shows how the use of various modalities influences the correctness of the recognition of basic emotions and the neutral state. Moreover, the correctness of the recognition of basic emotions is validated for two configurations of the GNN. The results show numerous interesting observations for Ekman's model while the accuracy of the Circumplex model is similar to the baseline methods.


Assuntos
Emoções , Redes Neurais de Computação , Entropia , Modalidades de Fisioterapia , Reconhecimento Psicológico
13.
Sci Rep ; 12(1): 6618, 2022 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-35459282

RESUMO

5 kinds of genuine medicinal materials, including Diding (Latin name: Corydalis bungeana Turcz), Purslane (Latin name: Portulaca oleracea L.), straw sandal board (Latin name: Hoya carnosa (L.f.) R. Br), June snow (Latin name: Serissa japonica (Thunb.) Thunb.), pine vine rattan (Latin name: Lycopodiastrum casuarinoides (Spring) Holub. [Lycopodium casuarinoides Spring]), were selected as the research objects. The combustion heat, thermo gravimetric parameters, and fat content, calcium content, trace element content, ash content of 5 kinds of genuine medicinal materials were measured. The combustion heat, differential thermal gravimetric analysis, fat content, calcium content, trace elements content, and ash content of 5 kinds of genuine medicinal materials were used to build a systematic multi-index evaluation system by gray pattern recognition and grey correlation coefficient cluster analysis, which can make up for the gaps in this area and provide scientific basis and research significance for the study of genuine medicinal materials quality. The results showed that the order of combustion heat of 5 kinds of genuine medicinal materials, including Diding, Purslane, straw sandal board, June snow, pine vine rattan, was Diding > June snow > straw sandal board > Purslane > pine vine rattan, the order of fat content (%) of 5 kinds of genuine medicinal materials was straw sandal board > Diding > pine vine rattan > June snow > Purslane, the order of calcium content (%) was pine vine rattan > June snow > Purslane > straw sandal board > Diding, the order of ash content was June snow > Purslane > straw sandal board > pine vine rattan > Diding. From the analysis of thermogravimetric analysis results and thermogravimetric combustion stability, the order of combustion stability of 5 kinds of genuine medicinal materials was June snow > pine Vine rattan > straw sandal board > Diding > Portulaca oleracea. The order of the content of 12 trace elements in 5 kinds of genuine medicinal materials, in terms of trace element content, June snow contains the highest trace elements in all samples. According to combustion heat, combustibility (combustion stability of genuine medicinal materials), fat, calcium, ash, trace element content, the comprehensive evaluation results of multi-index analysis constructed by gray correlation degree, gray correlation coefficient factor analysis, and gray hierarchical cluster analysis showed that the comprehensive evaluation multi-index order of 5 genuine medicinal materials, including Diding, Purslane, straw sandal board, June snow and pine vine rattan, was June snow > straw sandal board > Diding > Purslane > pine vine rattan. Therefore, the comprehensive evaluation results of the quality of genuine medicinal materials selected in this study were June snow the best, followed by straw sandal board. This research has important theoretical and practical significance for the multi-index measurement and comprehensive evaluation of genuine medicinal materials, and can provide scientific basis and research significance for the research of multi-index quality control of genuine medicinal material.


Assuntos
Portulaca , Oligoelementos , Cálcio , Análise por Conglomerados , Entropia
14.
Phys Chem Chem Phys ; 24(17): 9904-9920, 2022 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-35416820

RESUMO

Accurate prediction of binding affinity is a primary objective in structure-based drug discovery. A free energy perturbation (FEP) method based on molecular dynamics simulation shows great promise for protein-ligand binding affinity predictions. However, accurate calculation of binding affinity for allosteric inhibitors remains unknown and elusive, which hampers the discovery of allosteric inhibitors. Allosteric inhibitors exhibit several significant advantages over orthosteric inhibitors including higher specificity and lower side effects. Allosteric inhibitors against SHP2 are thought to be beneficial not only for diseases related to metabolism, but also for cancer, which make SHP2 a potential drug target. However, high structural sensitivity makes structural optimization of SHP2 allosteric inhibitors face challenges. Herein, we calculated the absolute binding free energy of SHP2 allosteric inhibitors using the FEP method by employing different λ-windows/simulation time sampling strategies. A simulation run with 32 λ-windows/64 ps sampling strategy delivered an excellent correlation (r = 0.96) and an unprecedented low mean absolute error of 0.5 kcal mol-1 between predicted binding free energies and experimental ones, outperforming the MM/PBSA method. Our study demonstrates the possibility to accurately calculate the absolute binding free energy of allosteric inhibitors using FEP, which offers exciting prospects for the discovery of more effective allosteric inhibitors.


Assuntos
Simulação de Dinâmica Molecular , Entropia , Ligantes , Ligação Proteica , Termodinâmica
15.
J Chem Theory Comput ; 18(4): 2642-2656, 2022 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-35363478

RESUMO

Atomistic molecular dynamics simulations represent an established technique for investigation of RNA structural dynamics. Despite continuous development, contemporary RNA simulations still suffer from suboptimal accuracy of empirical potentials (force fields, ffs) and sampling limitations. Development of efficient enhanced sampling techniques is important for two reasons. First, they allow us to overcome the sampling limitations, and second, they can be used to quantify ff imbalances provided they reach a sufficient convergence. Here, we study two RNA tetraloops (TLs), namely the GAGA and UUCG motifs. We perform extensive folding simulations and calculate folding free energies (ΔGfold°) with the aim to compare different enhanced sampling techniques and to test several modifications of the nonbonded terms extending the AMBER OL3 RNA ff. We demonstrate that replica-exchange solute tempering (REST2) simulations with 12-16 replicas do not show any sign of convergence even when extended to a timescale of 120 µs per replica. However, the combination of REST2 with well-tempered metadynamics (ST-MetaD) achieves good convergence on a timescale of 5-10 µs per replica, improving the sampling efficiency by at least 2 orders of magnitude. Effects of ff modifications on ΔGfold° energies were initially explored by the reweighting approach and then validated by new simulations. We tested several manually prepared variants of the gHBfix potential which improve stability of the native state of both TLs by ∼2 kcal/mol. This is sufficient to conveniently stabilize the folded GAGA TL while the UUCG TL still remains under-stabilized. Appropriate adjustment of van der Waals parameters for C-H···O5' base-phosphate interaction may further stabilize the native states of both TLs by ∼0.6 kcal/mol.


Assuntos
Simulação de Dinâmica Molecular , RNA , Entropia , RNA/química
16.
PLoS One ; 17(4): e0266618, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35446844

RESUMO

BACKGROUND: Identifying differentially expressed genes between experimental conditions is still the gold-standard approach to interpret transcriptomic profiles. Alternative approaches based on diversity measures have been proposed to complement the interpretation of such datasets but are only used marginally. METHODS: Here, we reinvestigated diversity measures, which are commonly used in ecology, to characterize mice pregnancy microenvironments based on a public transcriptome dataset. Mainly, we evaluated the Tsallis entropy function to explore the potential of a collection of diversity measures for capturing relevant molecular event information. RESULTS: We demonstrate that the Tsallis entropy function provides additional information compared to the traditional diversity indices, such as the Shannon and Simpson indices. Depending on the relative importance given to the most abundant transcripts based on the Tsallis entropy function parameter, our approach allows appreciating the impact of biological stimulus on the inter-individual variability of groups of samples. Moreover, we propose a strategy for reducing the complexity of transcriptome datasets using a maximation of the beta diversity. CONCLUSIONS: We highlight that a diversity-based analysis is suitable for capturing complex molecular events occurring during physiological events. Therefore, we recommend their use through the Tsallis entropy function to analyze transcriptomics data in addition to differential expression analyses.


Assuntos
Ecologia , Transcriptoma , Animais , Entropia , Camundongos
17.
J Phys Chem Lett ; 13(15): 3507-3509, 2022 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-35443779

RESUMO

The importance of the nonexistence of a unit for equilibrium constants is well-recognized by the chemistry community. However, it is still common to encounter the use of equilibrium constants with units in recent chemistry education papers, which may mislead students and even instructors. This is mainly due to the lack of studies on the representation of the derivations of equilibrium constants in a logical manner. We hope that the explanations provided in this Viewpoint will help to clarify this issue.


Assuntos
Entropia , Humanos
18.
J Chem Theory Comput ; 18(5): 3017-3026, 2022 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-35420428

RESUMO

As a fundamental property of all fluids, diffusion plays myriad roles in both science and our daily lives. Diffusive properties of many liquids including water have been extensively studied both experimentally and theoretically, while for transition metal ions, there exist significant experimental data that have not been extensively studied theoretically. Hence, high-confidence predictions for challenging systems like radioactive ions that are biohazardous cannot be reliably generated. In this work, a workflow named ISAIAH (Ion Simulation using AMBER for dIffusion Action when Hydrated) was designed to accurately simulate the diffusion coefficients of 15 monoatomic ions with charges varying from -1 to +3 in four water models. As the results indicate, good agreement with experimental values was achieved, leading us to select 239Pu4+ (for which no experimental data are available) as a candidate ion to make a theoretical prediction of its diffusion coefficient in water. Among all the force field parameter sets, the ones parametrized using an augmented 12-6-4 Lennard-Jones (LJ) potential showed lower average unsigned errors (AUE) for ions of various radii and electron configurations relative to some 12-6 LJ parameters. This observation agrees well with the fact that diffusion is affected by both the hydration free energy (HFE) and the ion-oxygen distance (IOD) between solute and solvent molecules, both of which are handled well by the 12-6-4 model.


Assuntos
Água , Entropia , Íons , Solventes , Termodinâmica
19.
J Phys Chem A ; 126(16): 2609-2617, 2022 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-35420821

RESUMO

A fragmentation approach referred to as a simple overlapping region method for force matching (SORForM) is presented. SORForM is designed to enable efficient computation of quantum mechanical (QM) forces for large molecules and is validated in the framework of adaptive force matching (AFM) to develop solute models in water. The SORForM method divides a molecule into overlapping QM regions with each region containing a gradient zone and a buffer zone. The buffer zone ensures that the atoms in the gradient zone have their surroundings unchanged with fragmentation. The performance of the method is validated with mefenamic acid and linalyl acetate by comparing the hydration free energies of AFM models developed with and without SORForM. The AFM hydration free energies are also compared with that of the experiments. The models developed with B3LYP-D3(BJ) and def2-TZVP are in excellent agreement with experiments. Our work shows that PBE-D3(BJ) provides less satisfactory results when compared to B3LYP-D3(BJ). The def2-TZVP basis set is found to greatly improve the agreement with experiments when compared to a double-zeta quality basis set.


Assuntos
Simulação de Dinâmica Molecular , Teoria Quântica , Entropia , Termodinâmica , Água
20.
J Biol Phys ; 48(2): 129-150, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35445347

RESUMO

Pseudoknotted RNA molecules play important biological roles that depend on their folded structure. To understand the underlying principles that determine their thermodynamics and folding/unfolding mechanisms, we carried out a study on a variant of the mouse mammary tumor virus pseudoknotted RNA (VPK), a widely studied model system for RNA pseudoknots. Our method is based on a coarse-grained discrete-state model and the algorithm of PK3D (pseudoknot structure predictor in three-dimensional space), with RNA loops explicitly constructed and their conformational entropic effects incorporated. Our loop entropy calculations are validated by accurately capturing previously measured melting temperatures of RNA hairpins with varying loop lengths. For each of the hairpins that constitutes the VPK, we identified alternative conformations that are more stable than the hairpin structures at low temperatures and predicted their populations at different temperatures. Our predictions were validated by thermodynamic experiments on these hairpins. We further computed the heat capacity profiles of VPK, which are in excellent agreement with available experimental data. Notably, our model provides detailed information on the unfolding mechanisms of pseudoknotted RNA. Analysis of the distribution of base-pairing probability of VPK reveals a cooperative unfolding mechanism instead of a simple sequential unfolding of first one stem and then the other. Specifically, we find a simultaneous "loosening" of both stems as the temperature is raised, whereby both stems become partially melted and co-exist during the unfolding process.


Assuntos
Vírus do Tumor Mamário do Camundongo , RNA , Animais , Entropia , Vírus do Tumor Mamário do Camundongo/genética , Camundongos , Conformação de Ácido Nucleico , RNA/química , Termodinâmica
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...