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PubMed Journals Articles About "Molecular Dynamics Simulation Cellulose Ethylenediamine Complex Crystal Models" RSS

11:17 EST 17th January 2020 | BioPortfolio

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Showing "Molecular Dynamics Simulation Cellulose Ethylenediamine Complex Crystal Models" PubMed Articles 1–25 of 31,000+

Molecular Dynamics Simulation of Cellulose I-Ethylenediamine Complex Crystal Models.

Cellulose I fibrils swell on exposure to ethylenediamine (EDA), which forms the cellulose I-EDA complex. These are regarded as host materials with guest intercalation. The present study reports molecular dynamics (MD) simulations of cellulose I-EDA crystal models with finite fiber to reproduce desorption of EDA molecules. The force field parameters for EDA were improved. Part of the EDA molecules was desorbed only from the surfaces of the crystal models, not from their interiors. The EDA molecules diffused ...


Interfacial Adhesion of Polylactic Acid on Cellulose Surface: A Molecular Dynamics Study.

Interfacial bonding and adhesion mechanisms are important in determining the final properties of the polymer composite. Molecular dynamics (MD) simulations have been used to characterize the interfacial structure and adhesion behavior of crystalline cellulose planes in contact with polylactic acid. The structure of the PLA at the interface exhibits a shape that can accommodate the structure of the cellulose surface. The adhesion between the PLA and the cellulose surface is affected by the polarity of the fu...

Molecular Dynamics Simulations of Crystal Nucleation from Solution at Constant Chemical Potential.

A widely spread method of crystal preparation is to precipitate it from a supersaturated solution. In such a process, control of solution concentration is of paramount importance. The nucleation process, polymorph selection, and crystal habits depend crucially on this thermodynamic parameter. When performing molecular dynamics simulations with a fixed number of molecules in the canonical ensemble, crystal growth is accompanied by a decrease in the solution concentration. This modification of the thermodynam...


Analysis of crystallization phenomenon in Indian honey using molecular dynamics simulations and artificial neural network.

Molecular dynamics simulation was performed on sugar profile and moisture content-based mixture systems of six Indian honey samples. Comparative studies were performed to understand the interactive effects of fructose, glucose, sucrose, maltose and water on crystallization. All simulations led to formation of stable crystal but with different interaction energies. Post-simulation analysis showed that Fructose:Glucose of 1.18 formed the most stable crystal with highest van der Waals and electrostatic interac...

Uncovering the action of ethanol controlled crystallization of 3,4-bis(3-nitrofurazan-4-yl)furoxan crystal: A molecular dynamics study.

A computational strategy in consideration of attachment energy, temperature, solubility and supersaturation unravels details of the solvent effect on the crystal morphology. The crystal morphologies were predicted by the advanced screw dislocation growth model. This research sheds much light on the crystal growth mechanisms with the example of 3,4-bis(3-nitrofurazan-4-yl)furoxan (DNTF) in ethanol. The solvation model based on the experiment situation was established into periodic supercell. Molecular dynami...

Artificial Intelligence Approach To Investigate the Longevity Drug.

Longevity is a very important and interesting topic, and has been demonstrated to be related to longevity. We combined network pharmacology, machine learning, deep learning, and molecular dynamics (MD) simulation to investigate potent lead drugs. Related protein insulin-like growth factor 1 receptor (IGF1R) and insulin receptor (IR) were docked with the traditional Chinese medicine (TCM) database to screen out several novel candidates. Besides, nine different machine learning algorithms were performed to b...

cryo_fit: Democratization of Flexible Fitting for Cryo-EM.

Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit,...

Theoretical investigation into the influence of molar ratio on mixture system: α, γ, δ-HMX molecules coexisting with β-HMX crystal.

Molecular dynamics (MD) simulation was conducted to research the effect of molar ratios for α/β-HMX, γ/β-HMX, and δ/β-HMX(octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) mixture systems on thermal stability, sensitivity, and mechanical properties of explosives, and the computing models were established by Materials Studio (MS). The binding energies, the maximum trigger bond length (L), cohesive energy density as well as mechanical properties of the mixture systems and the pure β-HMX crystal were ob...

Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation.

Biomolecular crowding affects the biophysical and biochemical behavior of macro- molecules when compared to the dilute environment in experiments on isolated proteins. Computational modeling and simulation are useful tools to study how crowding affects the structural dynamics and biological properties of macromolecules. As computational power increased, modeling and simulating large scale all-atom explicit solvent models of the prokaryote cytoplasm has now become possible. In this work, we build an atomisti...

Controlled On-Off Switching of Tight Binding Hydrogen Bonds between Model Cell Membranes and Acetylated Cellulose Surfaces.

Controlling interactions between cellulose-based materials and membranes of living cells is critical in medicine and biotechnology in, for example, wound dressing, tissue engineering, haemodialysis membranes and drug transport. Cellulose acetylation is one of the widely used approaches to tune those interactions. Surprisingly, however, the detailed interactions of acetylated cellulose and membranes have thus far not been characterized. Using atomistic molecular dynamics (MD) simulations, we show that the ke...

Molecular Dynamics Simulations Insight into Interfacial Stability and Fluidity Properties of Microemulsions.

Whereas the interfacial properties of microemulsions have been extensively studied in both experimental and simulation research, the molecular mechanisms of stability and fluidity about microemulsion are still poorly understood. Herein, we report a molecular dynamics simulation study to elaborate motion of emulsion droplet involving dichain surfactant Aerosol OT (AOT) and its dynamics evolution at the oil-water interface. By varying the concentrations of AOT, we show that the interfacial thickness and emuls...

Temperature-dependence of the dielectric relaxation of water using non-polarizable water models.

Key physical and chemical properties of aqueous fluids are determined by the structure and dynamics of the hydrogen bond network of water but we lack adequate models for the linkages between hydrogen bonding and aqueous chemistry, particularly in non-ambient conditions or in confinement. Dielectric relaxation spectroscopy (DRS) provides a sensitive approach for probing water dynamics but sound interpretation of DRS data requires molecular simulation and associated computational methods capable of accurately...

Prospects for Declarative Mathematical Modeling of Complex Biological Systems.

Declarative modeling uses symbolic expressions to represent models. With such expressions, one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation program, in a general-purpose programming language. Examples of such computations on models include model analysis, relatively general-purpose model reduction maps, and the initial phases of model implementation, all of which should preserve or approximate the mathemati...

Exploring the different environments effect of piperine via combined crystallographic, QM/MM and molecular dynamics simulation study.

Piperine is a pungent alkaloid, largely present in the skin of pepper. It is the most active component of pepper and being used as a medicine in many Asian countries. The effect of piperine on memory impairment and neurodegeneration in Alzheimer's disease model has been investigated. In the present study, we aim to investigate the effect of piperine molecule in different environments (crystal and active site of proteins) from crystallography, molecular docking, QM/MM based charge density analysis and molecu...

Molecular mobility of Terfenadine: investigation by Dielectric Relaxation Spectroscopy and Molecular Dynamics simulation.

The molecular mobility of an amorphous active pharmaceutical ingredient, Terfenadine, was carefully investigated by Dielectric Relaxation Spectroscopy and Molecular Dynamics simulation for the first time. Comprehensive characterisation on a wide frequency (10-10 Hz) and temperature (300 K) range highlights the fragile nature of this good glass-former (m = 112) and the relatively large non-exponentiality of the main relaxation (β = 0.53 ± 0.01). In the glassy state, a particularly broad secondary relaxatio...

Enhancing thermostability of a psychrophilic alpha-amylase by the structural energy optimization in the trajectories of molecular dynamics simulations.

The cold-adapted alpha-amylase (PHA) from Pseudoalteromonas Haloplanktis is a psychrophilic enzyme which demonstrates high activity at low temperatures, but poor thermostability. Most of the method only employed the crystal structure to design the target protein. However, the trajectory of protein molecular dynamics (MD) simulation contained clues about the protein stability. In this study, we combined MD simulation and energy optimization methods to design mutations located at non-conserved residues. Two s...

Structural prediction, whole exome sequencing and molecular dynamics simulation confirms p.G118D somatic mutation of PIK3CA as functionally important in breast cancer patients.

To understand the structural and functional importance of PIK3CA somatic mutations, whole exome sequencing, molecular dynamics simulation techniques in combination with in silico prediction algorithms such as SIFT, PolyPhen, Provean and CADD were employed. Twenty out of eighty missense somatic mutations in PIK3CA gene were found to be pathogenic by all the four algorithms. Most recurrent mutations found were known hotspot PIK3CA mutations with known clinical significance like p.E545 K, p.E545A, p.E545 G...

Modeling antimalarial and antihuman African trypanosomiasis compounds: a ligand- and structure-based approaches.

This study examines the interaction of 137 antimalarial and antihuman African trypanosomiasis compounds [bis(2-aminoimidazolines), bisguanidinediphenyls and polyamines] on three different in vitro assays (Trypanosoma brucei rhodesiense (T.b.r.), Plasmodium falciparum (P.f.) and cytotoxicity-L6 cells). ΔT values, wherever available, were also examined for the considered ligands. Eight DNA-ligand complexes and one DNA structure without ligand were selected from protein data bank (PDB) based on the structural...

Anisotropic Thermal Expansion as the Source of Macroscopic and Molecular Scale Motion in Phosphorescent Amphidynamic Crystals.

The structural origin of multiscale phenomena, with physical manifestations ranging from the molecular to the macroscopic scale, remains largely undocumented.  Here we report the discovery of a crystalline molecular rotor with rotationally-modulated triplet emission that displays macroscopic dynamics in the form of crystal moving and/or jumping, also known as salient effects. Crystals of molecular rotor 2 with a central 1,4-diethynyl-2,3-difluorophenylene rotator linked to two gold(I) nodes, which crystali...

Facile treatment to fine-tune cellulose crystals in cellulose-silk biocomposites through hydrogen peroxide.

The modulation of structural fibrous protein and polysaccharide biopolymers for the design of biomaterials is still relatively challenging due to the non-trivial nature of the transformation from a biopolymer's native state to a more usable form. To gain insight into the nature of the molecular interaction between silk and cellulose chains, we characterized the structural, thermal and morphological properties of silk-cellulose biocomposites regenerated from the ionic liquid, 1-ethyl-3-methylimidazolium acet...

The effect of dimerization on the activation and conformational dynamics of adenosine A receptor.

The adenosine A1 receptor (A1R) is one of four adenosine receptors in humans, which are involved in the function of the cardiovascular, respiratory and central nervous systems. Experimental results indicate that A1R can form a homodimer and that the protomer-protomer interaction in the A1R dimer is related to certain pharmacological characteristics of A1R activation. In this work, we performed docking, metadynamics simulation, conventional molecular dynamics simulations, Gaussian-accelerated molecular dynam...

Spontaneous Crystallization of a Supercooled Lennard-Jones Liquid: Molecular Dynamics Simulation.

The paper presents the results of molecular dynamics (MD) simulation of the kinetics of spontaneous crystallization of supercooled Lennard-Jones (LJ) liquid. In the study of nucleation the mean lifetime method, direct forward flux sampling and the seeding approach were used. The nucleation rate, the number of particles in a critical nucleus, the diffusion coefficient of nuclei in the space of their sizes, and some other parameters have been determined. Calculations have been made along four isobars in the r...

Car-Parrinello Monitor for more robust Born-Oppenheimer molecular dynamics.

Born-Oppenheimer molecular dynamics (BOMD) is a promising simulation method for exploring the possible reaction pathways of a chemical system, but one significant challenge is the increased difficulty of converging the self-consistent field (SCF) calculation that often accompanies the breaking and forming of chemical bonds. To address this challenge, we developed an enhancement to the BOMD simulation method called the Car-Parrinello monitor (CPMonitor) that uses Car-Parrinello molecular dynamics (CPMD) to r...

Simulation of the nanosecond-pulse laser damage of KDP surface by the smoothed particle hydrodynamics method.

We present a simulation method to reproduce the damage crater formation and particle ejection phenomena observed in the laser-induced surface damage process of potassium dihydrogen phosphate (KDP) crystals. Based on the smoothed particle hydrodynamics method, which is commonly used for solving shock and blast problems, equivalent explosion simulation models of the laser-induced damage process have been established. Moreover, laser damage experiments combined with time-resolved techniques are performed on KD...

Novel preclinical PET geometrical concept using a monolithic scintillator crystal offering concurrent enhancement in spatial resolution and detection sensitivity: a simulation study.

We propose a small-animal PET scanner design combining two sets of monolithic crystals with two different thicknesses. The detectors with thinner crystals serve for high resolution imaging while the thicker crystals retain the detection efficiency. Two small-animal PET models based on 10 and 12 detector blocks made of monolithic LYSO crystals were implemented in the GEANT4 Monte Carlo toolkit. In each of these models, half of the detector blocks consisted of a crystal thickness of 10 mm whereas the second h...


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