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PubMed Journals Articles About "Molecular Dynamics Simulation Cellulose Ethylenediamine Complex Crystal Models" - Page: 5 RSS

22:57 EST 23rd February 2020 | BioPortfolio

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Showing "Molecular Dynamics Simulation Cellulose Ethylenediamine Complex Crystal Models" PubMed Articles 101–125 of 31,000+

Choices and trade-offs in inference with infectious disease models.

Inference using mathematical models of infectious disease dynamics can be an invaluable tool for the interpretation and analysis of epidemiological data. However, researchers wishing to use this tool are faced with a choice of models and model types, simulation methods, inference methods and software packages. Given the multitude of options, it can be challenging to decide on the best approach. Here, we delineate the choices and trade-offs involved in deciding on an approach for inference, and discuss aspec...


Low cost, easy-to-replicate myringotomy tube insertion simulation model.

Simulation is an established part of modern surgical education. Several training centers have proposed different simulation models for myringotomy tube (MT) placement and validated their effectiveness in medical student and resident training. None is widely used. Early models were simple tubes that lacked important microsurgical elements. Newer simulators are more comprehensive, but are difficult and expensive to build. We present a MT placement simulator that is low cost, easy to construct with basic power...

Molecular dynamics simulation of strengthening dependence on precipitate Cr composition in Fe-15at.%Cr alloy.

Molecular Dynamics simulation was employed to study precipitate composition dependence on strengthening. Edge dislocation interaction with pure, 80at.%, and 60at.% Cr precipitates of different sizes in a matrix of Fe-15at.%Cr was investigated. The precipitates were found to be relatively hard. This is evident from the absence of shearing mechanism after the dislocation has bypassed them, the formation of an Orowan-like dislocation shape, and comparatively higher stress values. Precipitates with higher Cr co...


The effect of calcium binding on the unfolding force of mutated and healthy titin I10 domain: A steered molecular dynamics simulation study.

Titin plays an important role in eccentric contraction by creating elastic property in the sarcomere. It can restore muscle to its rest length by stretching and increasing its length. Titin's structure is made of 244 domains. Due to its position, the I10 domain can be subjected to a mutation which leads to Arrhythmogenic cardiomyopathy. Furthermore, the calcium ion has an important role in muscle contractions by binding to some domains like I10 in titin and accordingly creating changes in the unfolding forc...

Insight into the antimicrobial mechanism of action of β-amino acid derivatives from molecular dynamics simulation: dancing the can-can at the membrane surface.

The development of antimicrobial agents that target and selectively disrupt biofilms is a pressing issue since, so far, no antibiotics have been developed that achieve this effectively. Previous experimental work has found a promising set of antibacterial peptides: β-amino acid derivatives, relatively small molecules with common structural elements composed of a polar head group and two non-polar hydrocarbon arms. In order to develop insight into possible mechanisms of action of these novel antibacterial a...

Numerical simulation on electrostatic alignment control of cellulose nano-fibrils in flow.

The alighment process of the cellulose nano-fibrils (CNFs) in an alternating electric field and elongational flow is numerically simulated for the fabrication of strong cellulose filaments. The order parameter of CNFs in the flow channel is evaluated by solving the Smoluchowski equation for the orientation distribution function of the CNFs. The results show that CNF alignment in the electric field is enhanced with applied voltage because the electrostatic torque is dominant over the Brownian rotation. An op...

Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study.

The replica exchange molecular dynamics (REMD) simulation is demonstrated to readily predict the conformations of the macrocyclic drug lorlatinib, as validated by solution NMR studies. In aqueous solution, lorlatinib adopts a conformer identical to its target bound structure. This conformer is stabilized by an extensive hydrogen bond network to the solvents. In chloroform, lorlatinib populates two conformers with the second one being less polar, which may contribute to lorlatinib's ability to cross cell mem...

On the reaction mechanism of an endoperoxide ring formation by fumitremorgin B endoperoxidase. The right arrangement makes a difference.

Fumitremorgin B endoperoxidase (FtmF) belongs to 2-oxoglutarate dependent dioxygenases and catalyzes an unusual oxidative reaction of endoperoxide formation at the final stage of biosynthesis of verruculogen - a mycotoxin produced by Aspergillus and Penicillinum strains. The published crystal structure of FtmF (PDB: 4ZON), which is of overall good quality, contains a model of the substrate bound in the active site, which, however, has very low occupancy and its conformation does not comply with the small mo...

Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model.

We extend the framework for polarizable force fields to include the case where the electrostatic multipoles are not determined by a variational minimization of the electrostatic energy. Such models formally require that the polarization response is calculated for all electrostatic variables for all possible geometrical perturbations in order to obtain the energy gradient required for performing molecular dynamics simulations.By making use of a Lagrange formalism, however, this computational demanding task c...

Statistics and Dynamics of Polymer Melt in Neutral Diblock Copolymer Single-Crystal Platelets.

Polymer single-crystal (SC) platelets of poly(butylene oxide)--poly(lactic acid) (PBO--PLLA) of a well-defined shape, size, and grafting density have been fabricated and embedded into PBO melt for the study of the statistics and dynamics of the host polymers. The colloidal liquid-crystalline order of SCs above a threshold concentration of ∼2.2 vol % provides a confining environment for the molten PBO. Meanwhile, the peculiar type-A characteristics of PBO allow us to simultaneously probe the dielectric cha...

Current status of simulation and training models in microsurgery: A systematic review.

With the prolific uptake of simulation-based training courses, this systematic review aims to identify the available microsurgical simulation and training models, their status of validation, associated studies, and levels of evidence (LoE) for each training model, thereby establishing a level of recommendation (LoR). MEDLINE, Embase, and the Cochrane Library databases were searched for English language articles, describing microsurgery simulators and/or validation studies. All studies were assessed for LoE,...

A mean-field approach to the dynamics of networks of complex neurons, from nonlinear Integrate-and-Fire to Hodgkin-Huxley models.

We present a mean field formalism to predict the collective dynamics of large networks of conductance-based interacting spiking neurons. We apply this formalism to several neuronal models, from the simplest Adaptive Exponential Integrate-and-Fire model to the more complex Hodgkin-Huxley and Morris-Lecar models. We show that these mean-field models are capable to correctly predict the spontaneous activity of both excitatory and inhibitory neurons in asynchronous irregular regimes typical of cortical dynamics...

Network analyses to quantify effects of host movement in multilevel disease transmission models using foot and mouth disease in Cameroon as a case study.

The dynamics of infectious diseases are greatly influenced by the movement of both susceptible and infected hosts. To accurately represent disease dynamics among a mobile host population, detailed movement models have been coupled with disease transmission models. However, a number of different host movement models have been proposed, each with their own set of assumptions and results that differ from the other models. Here, we compare two movement models coupled to the same disease transmission model using...

Molecular dynamics simulation and QM/MM calculation reveal the selectivity mechanism of type I 1/2 kinase inhibitors: the effect of intramolecular H-bonds and conformational restriction for improved selectivity.

Understanding the selectivity mechanisms of inhibitors towards highly similar proteins is extremely important work on the way to a new drug. Here, we aim to reveal the selectivity mechanisms of type I 1/2 kinase inhibitors towards p21-activated kinase (PAK4) and mitogen-activated protein kinase kinase kinase 14 (MAP3K14, NIK). PAK4, belonging to the serine/threonine protein kinases, is involved in cell signaling pathways and controls cellular functions and has received attention as an attractive drug target...

The Fidelity of Cancer Cells in PDX Models: Characteristics, Mechanism and Clinical Significance.

Patient-derived xenograft (PDX) models are widely used as preclinical cancer models and are considered better than cell culture models in recapitulating the histological features, molecular characteristics and intratumoral heterogeneity (ITH) of human tumors. While the PDX model is commonly accepted for use in drug discovery and other translational studies, a growing body of evidence has suggested its limitations. Recently, the fidelity of cancer cells within a PDX has been has been questioned, which may im...

The electronic structure and physicochemical property of boron nitridene.

Inspired by searching new forms of Boron Nitride (BN) compounds, the electronic structure and physicochemical property of a graphyne-like BN compound was explored by density functional theory with cluster models as well as periodic models. This graphyne-like BN compound is named Boron Nitridene in this work, based on geometry and bond order analysis as its B-N linking units take on double bond characteristics. Different cluster models of Boron Nitridene-x (x = 1-5) were constructed. Results show that th...

Water Activity from Equilibrium MD Simulations and Kirkwood-Buff Theory.

Water activity and related thermodynamic properties are calculated for several aqueous solutions using equilibrium molecular dynamics in conjunction with the recent extension of the Kirkwood-Buff (KB) theory for closed systems. The general applicability of this method is evaluated on aqueous mixtures of ethanol, glyoxal, malonic acid, and NaCl, which represent different types of condensed-phase interactions. Solution microstructures are analyzed using KB integrals and cluster analysis to identify molecular ...

Correlation between mobility and the hydrogen bonding network of water at an electrified-graphite electrode using molecular dynamics simulation.

Focusing on the electric double layer formed at aqueous solution/graphite electrode interfaces, we investigated the relationship between the mobility of interfacial water and its hydrogen bonding networks by using molecular dynamics simulations. We focused on the mobility of the first hydration layer constructed nearest to the electrode. The mobility was determined by calculating the diffusion coefficient which showed an opposite trend to that of the applied potential polarity. The mobility decreased upon p...

FMOxFMO: Elucidating Excitonic Interactions in the Fenna-Matthews-Olson Complex with the Fragment Molecular Orbital Method.

In order to study Förster resonance energy transfer (FRET), the fragment molecular orbital (FMO) method is extended to compute electronic couplings between local excitations via the transition excited state density and transition dipole models, enabling efficient calculations of nonlocal excitations in a large molecular system and overcoming the previous limitation of being able to compute only local excitations. The results of these simple but accurate models are validated against full quantum calculation...

Effect of Sugars on the Real-Time Adsorption of Expansin on Cellulose.

Biological pretreatment is a safe and environmentally friendly method for disrupting recalcitrant lignocellulose structures. Expansin and expansin-like proteins are used to open up the cellulose structure and display significant synergism when mixed with cellulases that catalyze the breakdown of (hemi)cellulose into sugars. However, the adsorption behavior of expansin in the presence of sugar products is yet unknown. In this work, we monitored the effects of various sugars on the real-time adsorption of ex...

Ultrasonic waves effect on S-shaped β-amyloids conformational dynamics by non-equilibrium molecular dynamics.

Ultrasound-based technologies are widely adopted in the clinical practice. Recently, the ultrasound stable cavitation has been proposed as a strategy to destabilize amyloid aggregates in Alzheimer disease. However, the molecular mechanisms driving ultrasound-induced amyloid destabilization are not fully clarified yet. Here, molecular dynamics is applied to investigate in silico the conformational dynamics induced by ultrasound stable cavitation on S-shaped Aβ1-42 amyloid fibrils, which has been highlighted...

Aggregation behaviors of thermo-responsive methylcellulose in water: A molecular dynamics simulation study.

The aggregation behaviors of methylcellulose (MC) in aqueous solution were investigated using all-atom molecular dynamic simulations (MD). The interactions between MC chains and water molecules at different temperatures were investigated by a series of MD analyses, such as the solvent accessible surface area, number of hydrogen bonds, radial distribution functions and the interaction energies. Constant temperature simulations and heating simulations of MC aqueous solution were carried out in this work. In t...

Computational investigation of a ternary model of SnoN-SMAD3-SMAD4 complex.

The transforming growth factor β (TGFβ) plays an essential role in the regulation of cellular processes such as cell proliferation, migration, differentiation, and apoptosis by association with SMAD transcriptional factors that are regulated by the transcriptional regulator SnoN. The crystal structure of SnoN-SMAD4 reveals that SnoN can adopt two binding modes, the open and closed forms, at the interfaces of SMAD4 subunits. Accumulating evidence indicates that SnoN can interact with both SMAD3 and SMAD4 t...

Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches.

Thermal conductivity of Deoxyribonucleic acid molecules is important for nanotechnology applications. Theoretical simulations based on simple models predict thermal conductivity for these molecular structures.

Mind the last spike - firing rate models for mesoscopic populations of spiking neurons.

The dominant modeling framework for understanding cortical computations are heuristic firing rate models. Despite their success, these models fall short to capture spike synchronization effects, to link to biophysical parameters and to describe finite-size fluctuations. In this opinion article, we propose that the refractory density method (RDM), also known as age-structured population dynamics or quasi-renewal theory, yields a powerful theoretical framework to build rate-based models for mesoscopic neural ...


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