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https://www.readbyqxmd.com/read/28340406/a-local-adjustment-strategy-for-the-initialization-of-dynamic-causal-modelling-to-infer-effective-connectivity-in-brain-epileptic-structures
#1
Wentao Xiang, Ahmad Karfoul, Huazhong Shu, Régine Le Bouquin Jeannès
This paper addresses the question of effective connectivity in the human cerebral cortex in the context of epilepsy. Among model based approaches to infer brain connectivity, spectral Dynamic Causal Modelling is a conventional technique for which we propose an alternative to estimate cross spectral density. The proposed strategy we investigated tackles the sub-estimation of the free energy using the well-known variational Expectation-Maximization algorithm highly sensitive to the initialization of the parameters vector by a permanent local adjustment of the initialization process...
March 7, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28339597/compositional-differences-in-multi-species-biofilms-formed-on-various-orthodontic-adhesives
#2
Jung-Sub An, Kyungsun Kim, Soha Cho, Bum-Soon Lim, Sug-Joon Ahn
Objectives: To investigate the aspects of multi-species biofilm formation on various orthodontic adhesives with different surface characteristics. Methods: Multi-species biofilms using 13 bacterial species were grown on the surfaces of composite, compomer, and resin-modified glass-ionomer cement (RMGI). The changes in Streptococcus mutans (Sm), Streptococcus sobrinus (Ss), Porphyromonas gingivalis (Pg), Aggregatibacter actinomycetemcomitans (Aa), and total bacteria were determined at day 1 (T1) and day 4 (T2) using real-time polymerase chain reaction...
January 25, 2017: European Journal of Orthodontics
https://www.readbyqxmd.com/read/28334976/a-sensitivity-analysis-of-rna-folding-nearest-neighbor-parameters-identifies-a-subset-of-free-energy-parameters-with-the-greatest-impact-on-rna-secondary-structure-prediction
#3
Jeffrey Zuber, Hongying Sun, Xiaoju Zhang, Iain McFadyen, David H Mathews
Nearest neighbor parameters for estimating the folding energy changes of RNA secondary structures are used in structure prediction and analysis. Despite their widespread application, a comprehensive analysis of the impact of each parameter on the precision of calculations had not been conducted. To identify the parameters with greatest impact, a sensitivity analysis was performed on the 291 parameters that compose the 2004 version of the free energy nearest neighbor rules. Perturbed parameter sets were generated by perturbing each parameter independently...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334819/comparative-analyses-of-the-thermodynamic-rna-binding-signatures-of-different-types-of-rna-recognition-motifs
#4
Brighton Samatanga, Antoine Cléry, Pierre Barraud, Frédéric H-T Allain, Ilian Jelesarov
RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334186/rnascclust-clustering-rna-sequences-using-structure-conservation-and-graph-based-motifs
#5
Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen
Motivation: Clustering RNA sequences with common secondary structure is an essential step towards studying RNA function. Whereas structural RNA alignment strategies typically identify common structure for orthologous structured RNAs, clustering seeks to group paralogous RNAs based on structural similarities. However, existing approaches for clustering paralogous RNAs, do not take the compensatory base pair changes obtained from structure conservation in orthologous sequences into account...
February 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28332812/hierarchical-nico2s4-nife-ldh-heterostructures-supported-on-nickel-foam-for-enhanced-overall-water-splitting-activity
#6
Jia Liu, Jinsong Wang, Bao Zhang, Yunjun Ruan, Lin Lv, Xiao Ji, Kui Xu, Ling Miao, Jianjun Jiang
Low cost and high efficient bifunctional electrocatalysts for the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER) are intensively investigated for overall water splitting. Herein, we combined experimental researches with first-principles calculations based on density functional theory (DFT) to engineer the NiCo2S4@NiFe LDH heterostructures interface for enhancing overall water splitting activity. The DFT calculations exhibit a strong interaction and charge transfer between NiCo2S4 and NiFe LDH, which change the interfacial electronic structure and surface reactivity...
March 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28330366/phase-behaviour-of-quasicrystal-forming-systems-of-core-corona-particles
#7
Harini Pattabhiraman, Marjolein Dijkstra
Using Monte Carlo simulations and free-energy calculations, we study the phase behaviour of a two-dimensional system of particles interacting with a hard core of diameter σHD and a repulsive square shoulder potential. The interest in this system lies in the formation of quasicrystals of different symmetries at specific square-shoulder widths δ as previously reported by Dotera et al. [Nature 506, 208 (2014)]. However, an insight into other possible periodic phases formed in these systems and the thermodynamic stability of both the periodic and quasicrystal phases is yet to be addressed...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28330356/grand-canonical-electronic-density-functional-theory-algorithms-and-applications-to-electrochemistry
#8
Ravishankar Sundararaman, William A Goddard, Tomas A Arias
First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28330345/coexistence-of-low-and-high-overlap-phases-in-a-supercooled-liquid-an-integral-equation-investigation
#9
Jean-Marc Bomont, Giorgio Pastore, Jean-Pierre Hansen
The pair structure, free energy, and configurational overlap order parameter Q of an annealed system of two weakly coupled replicas of a supercooled "soft sphere" fluid are determined by solving the hypernetted-chain (HNC) and self-consistent Rogers-Young (RY) integral equations over a wide range of thermodynamic conditions ρ (number-density), T (temperature), and inter-replicas couplings ε12. Analysis of the resulting effective (or Landau) potential W(ρ,T; Q) and of its derivative with respect to Q confirms the existence of a "precursor transition" between weak and strong overlap phases below a critical temperature Tc well above the temperature To of the "ideal glass" transition observed in the limit ε12→0...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28330339/the-attachment-of-%C3%AE-synuclein-to-a-fiber-a-coarse-grain-approach
#10
Ioana M Ilie, Wouter K den Otter, Wim J Briels
We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28330175/exploration-of-the-binding-modes-of-l-asparaginase-complexed-with-its-amino-acid-substrates-by-molecular-docking-dynamics-and-simulation
#11
Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-glutamine (L-Gln) deamination plays crucial role in ALL treatment. Role of Erwinaze(®) (L-asparaginase from Erwinia chrysanthemi) in regulation of L-Asn and L-Gln has been confirmed by the experimental studies. Therapeutic research against ALL remained elusive with the lack of structural information on Erwinaze(®) enzyme. In this present study, homology model of the Erwinaze(®) was developed using MODELLER and the same was validated by various quality indexing tools...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330153/an-evaluation-of-the-major-factors-influencing-the-removal-of-copper-ions-using-the-egg-shell-dromaius-novaehollandiae-chitosan-agaricus-bisporus-composite
#12
R K Anantha, S Kota
Rapid industrialisation, technological development, urbanization and increase in population in the recent past coupled with unplanned and unscientific disposal methods led to increased heavy metal levels in water. Realizing the need for development of eco-friendly and cost effective methods, the present investigation was done for the adsorptive removal of copper from aqueous solutions with Dromaius novaehollandiae eggshell and chitosan composite. By one variable at a time method, the optimum contact time was found to be 60 min with an adsorbent dosage of 8 g/L at pH 6, initial adsorbate concentration of 20 mg/L and temperature 30 °C...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327752/umbrella-sampling-molecular-dynamics-simulations-reveal-concerted-ion-movement-through-g-quadruplex-dna-channels
#13
Parisa Akhshi, Gang Wu
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28326770/creating-a-homeodomain-with-high-stability-and-dna-binding-affinity-by-sequence-averaging
#14
Katherine W Tripp, Matt Sternke, Ananya Majumdar, Doug Barrick
There is considerable interest in generating proteins with both high stability and high activity for biomedical and industrial purposes. One approach that has been used successfully to increase the stability of linear repeat proteins is consensus design. It is unclear the extent over which the consensus design approach can be used to produce folded and hyperstable proteins, and importantly, whether such stabilized proteins would retain function. Here we extend the consensus strategy to design a globular protein...
March 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28324756/na-ion-batteries-based-on-the-inorganic-bn-nanocluster-anodes-dft-studies
#15
K Nejati, A Hosseinian, A Bekhradnia, E Vessally, L Edjlali
It has been recently indicated that the Li-ion batteries may be replaced by Na-ion batteries because of their low safety, high cost, and low-temperature performance, and lack of the Li mineral reserves. Here, using density functional theory calculations, we studied the potential application of B12N12 nanoclusters as anode in Na-ion batteries. Our calculations indicate that the adsorption energy of Na(+) and Na are about -23.4 and -1.4kcal/mol, respectively, and the pristine BN cage to improve suffers from a low cell voltage (∼0...
March 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28322561/accuracy-of-substrate-selection-by-enzymes-is-controlled-by-kinetic-discrimination
#16
Kinshuk Banerjee, Anatoly B Kolomeisky, Oleg A Igoshin
Enzymes have the remarkable ability to select the correct substrate from the pool of chemically similar molecules. The accuracy of such a selection is determined by differences in the free energy profiles for the right and wrong reaction pathways. Here, we investigate what features of the free energy landscape govern the variation and minimization of selectivity error. It is generally believed that minimal error is affected by both kinetic (activation barrier heights) and thermodynamic (binding stability) factors...
March 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28321247/investigations-on-binding-pattern-of-kinase-inhibitors-with-ppar%C3%AE-molecular-docking-molecular-dynamic-simulations-and-free-energy-calculation-studies
#17
Mohit Mazumder, Prija Ponnan, Umashankar Das, Samudrala Gourinath, Haseeb Ahmad Khan, Jian Yang, Meena Kishore Sakharkar
Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential target for the treatment of several disorders. In view of several FDA approved kinase inhibitors, in the current study, we have investigated the interaction of selected kinase inhibitors with PPARγ using computational modeling, docking, and molecular dynamics simulations (MDS). The docked conformations and MDS studies suggest that the selected KIs interact with PPARγ in the ligand binding domain (LBD) with high positive predictive values...
2017: PPAR Research
https://www.readbyqxmd.com/read/28320932/data-based-modeling-of-drug-penetration-relates-human-skin-barrier-function-to-the-interplay-of-diffusivity-and-free-energy-profiles
#18
Robert Schulz, Kenji Yamamoto, André Klossek, Roman Flesch, Stefan Hönzke, Fiorenza Rancan, Annika Vogt, Ulrike Blume-Peytavi, Sarah Hedtrich, Monika Schäfer-Korting, Eckart Rühl, Roland R Netz
Based on experimental concentration depth profiles of the antiinflammatory drug dexamethasone in human skin, we model the time-dependent drug penetration by the 1D general diffusion equation that accounts for spatial variations in the diffusivity and free energy. For this, we numerically invert the diffusion equation and thereby obtain the diffusivity and the free-energy profiles of the drug as a function of skin depth without further model assumptions. As the only input, drug concentration profiles derived from X-ray microscopy at three consecutive times are used...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28319868/synthesis-characterization-of-amide-substituted-dexibuprofen-derivatives-and-their-spectral-voltammetric-and-docking-investigations-for-dna-binding-interactions
#19
Nasima Arshad, Muhammad Zafran, Zaman Ashraf, Fouzia Perveen
Three amide derivatives - methyl-2-[2-(4-isobutylphenyl)propanamido]propanoate (Dex-2), methyl 2-[2-(4-isobutylphenyl) propanamido]-3-phenylpropanoate (Dex-3) and methyl 2-[2-(4-isobutylphenyl)-propanamido]-4-methylpentanoate (Dex-4) of dexibuprofen (Dex-1) 2-(4-isobutylphenyl)propanoic acid were synthesized and conformed for structures by physical data and spectral analysis. Further, all the compounds were studied for their binding with ds.DNA through experimental (UV-visible/and fluorescence spectroscopy, cyclic voltammetry) and theoretical (molecular docking) techniques...
March 3, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28319781/systematic-study-of-imidazoles-inhibiting-ido1-via-the-integration-of-molecular-mechanics-and-quantum-mechanics-calculations
#20
Yi Zou, Fang Wang, Yan Wang, Wenjie Guo, Yihua Zhang, Qiang Xu, Yisheng Lai
Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations...
March 14, 2017: European Journal of Medicinal Chemistry
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