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# MD simulation

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#1
S Sahmani, A M Fattahi
New ceramic materials containing nanoscaled crystalline phases create a main object of scientific interest due to their attractive advantages such as biocompatibility. Zirconia as a transparent glass ceramic is one of the most useful binary oxides in a wide range of applications. In the present study, a new size-dependent plate model is constructed to predict the nonlinear axial instability characteristics of zirconia nanosheets under axial compressive load. To accomplish this end, the nonlocal continuum elasticity of Eringen is incorporated to a refined exponential shear deformation plate theory...
April 27, 2017: Journal of Molecular Graphics & Modelling
#2
Minhua Zhang, Lihang Chen, Huaming Yang, Jing Ma
Combining molecular dynamics (MD) and quantum chemistry (QM) simulation, the association mechanism of acetic acid systems were examined. DFT method was proposed to compare the hydrogen-bonding energy of variable acetic acid dimers, and definitely provided the stable dimers configuration. Geometry parameters of dimers were also obtained by QM calculations, which were taken as the characteristic criteria for further MD analysis. Proportion of different acetic acid dimers in gas phase was obtained by Radial distribution function (RDF) analysis, and cyclic dimer with two O=c-Hoacid hydrogen bonds was demonstrated as the most stable structure...
May 26, 2017: Journal of Physical Chemistry. A
#3
Richard J Alsop, Alexander Dhaliwal, Maikel C Rheinstadter
Curcumin is the main ingredient of turmeric, a common Indian spice. Curcumin shows a broad spectrum of effects, including anti-Alzheimer's and anti-oxidant properties. An interaction between curcumin and lipid membranes has been speculated as the root-cause, and the molecule is often proposed to protect' the bilayer. However, the detailed molecular mechanism of this protection is disputed. There is evidence that curcumin either a) lies flat on the bilayer and provides a carpet' for protection by forming a steric barrier, or b) inserts into the membrane and stiffens tails, thereby protecting against peptide insertion...
May 26, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
#4
Sandra Hoppe, Yong Li, Lyudmila V Moskaleva, Stefan Müller
Gold has many unique properties, some of which continue to be uncovered, such as the rich chemistry of gold at the nanoscale. In this study, gold surprises us again by the unusual stability of one-dimensional gold oxide structures on the surface of gold, which enhances in the presence of silver impurities. We employ first-principles calculations to investigate the surface segregation of silver in the presence of atomic-oxygen adsorbates arranged in chains on the Au(321) surface. Such 1D oxide chains have previously been suggested as the most stable form of adsorbed oxygen on gold...
May 26, 2017: Physical Chemistry Chemical Physics: PCCP
#5
Xi Wu, Pei-Hsun Wei, Xiao Zhu, Mary J Wirth, Arun Bhunia, Ganesan Narsimhan
Antimicrobial peptides (AMPs) have the ability to penetrate the cell membrane, form pores which eventually lead to cell death. Immobilization of AMP on nanoparticles can play a major role in antimicrobial materials, biosensors for pathogen detection and in food safety. The minimum inhibitory concentration (MIC) of free Cecropin P1 (CP1, sequence SWLSTAKKLENSAKKRLSEGIAIAIQGGPR) and adsorbed on silica nanoparticle against E. coli O157:H7 EDL933 were 0.78μg/ml. This was found to be consistent with preservation of α-helical secondary structure of CP1 upon adsorption as indicated by circular dichroism (CD)...
May 17, 2017: Colloids and Surfaces. B, Biointerfaces
#6
Safaa Sader, Jun Cai, Anna C G Muller, Chun Wu
Fexofenadine, a potent antagonist to human histamine 1 (H1) receptor, is a non-sedative third generation antihistamine that is widely used to treat various human allergic conditions such as allergic rhinitis, conjunctivitis and atopic dermatitis. Encouragingly, it's been successfully used to treat canine atopic dermatitis, this supports the notion that it might have a great potential for treating other canine allergic conditions and other mammal pets such as dog. Regrettably, while there is a myriad of studies conducted on the interactions of antihistamines with human H1 receptor, the similar studies on non-human pet H1 are considerably scarce...
May 17, 2017: Journal of Molecular Graphics & Modelling
#7
Daniel R Moberg, Shelby C Straight, Christopher Knight, Francesco Paesani
An unambiguous assignment of the vibrational spectra of ice Ih remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice Ih in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal...
May 26, 2017: Journal of Physical Chemistry Letters
#8
Janet S Anderson, Griselda Hernandez, David M LeMaster
Protein molecular dynamics interpretation of the standard R1, R2 and heteronuclear NOE relaxation measurements has typically been limited to a single S(2) order parameter which is often insufficient to characterize the rich content of these NMR experiments. In the absence of exchange linebroadening, an optimized reduced spectral density analysis of these measurements can yield spectral density values at three distinct frequencies. Surprisingly, these three discrete spectral density values have proven to be sufficient for a Larmor frequency-selective order parameter analysis of the 223 methine and methylene H-C bonds of the B3 domain of Protein G (GB3) to accurately back-calculate the entire curve of the corresponding bond vector autocorrelation functions upon which the NMR relaxation behavior depends...
May 25, 2017: Journal of Chemical Theory and Computation
#9
S Roy Kimura, Haipeng Hu, Anatoly M Ruvinsky, Woody B Sherman, Angelo D Favia
In recent years, molecular dynamics simulations of proteins in explicit mixed-solvents have been applied to various problems in protein biophysics and drug discovery, including protein folding, protein surface characterization, fragment screening, allostery, and druggability assessment. In this study, we perform a systematic study on how mixtures of organic solvent probes in water can reveal cryptic ligand binding pockets that are not evident in crystal structures of apo proteins. We examine a diverse set of eight PDB proteins that show pocket opening induced by ligand binding and investigate whether solvent MD simulations on the apo structures can induce the binding site observed in the holo structures...
May 24, 2017: Journal of Chemical Information and Modeling
#10
José Javier Burgos-Mármol, Óscar Álvarez-Machancoses, Alessandro Patti
Due to their central role in industrial formulations spanning from food packaging to smart coatings, polymer nanocomposites have been the object of a remarkable attention over the last two decades. Incorporating nanoparticles (NPs) to a polymer matrix modifies the conformation and mobility of the polymer chains at the NP-polymer interface and can potentially provide materials with enhanced properties as compared to pristine polymers. To this end, it is crucial to predict and control the ability of NPs to diffuse and achieve a good dispersion in the polymer matrix...
May 24, 2017: Journal of Physical Chemistry. B
#11
Hamed Akbarzadeh, Mohsen Abbaspour, Esmat Mehrjouei
In this study, we investigated the heating process for pure (Rh55 and Cu55), single dopant (Rh1Cu54 and Rh54Cu), core@shell (Rh13@Cu42 and Cu13@Rh42), and alloy (Rh13Cu42, Rh42Cu13) nanoclusters in two structures (cuboctahedral and icosahedral) from 0 to 2000 K using molecular dynamics (MD) simulations. Our aim was to investigate the effects of composition and chemical arrangement on the kinetic and thermodynamic stability of Rh-Cu bimetallic nanoalloys. Our results indicated that Cu55, Ir55, Rh1Cu54, Rh54Cu, and Cu13@Rh42 in the cuboctahedral and icosahedral structures and Rh42Cu13 in the icosahedral structure did not experience any transformation with the exception of melting...
May 24, 2017: Physical Chemistry Chemical Physics: PCCP
#12
R Grüber, J Aranda, A Bellili, I Tuñón, E Dumont
DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol(-1) and sometimes inexistent, and of the exergonicities...
May 24, 2017: Physical Chemistry Chemical Physics: PCCP
#13
Ramesh Itteboina, Srilata Ballu, Sree Kanth Sivan, Vijjulatha Manga
Janus kinase 1 (JAK 1) belongs to the JAK family of intracellular nonreceptor tyrosine kinase. JAK-signal transducer and activator of transcription (JAK-STAT) pathway mediate signaling by cytokines, which control survival, proliferation and differentiation of a variety of cells. Three-dimensional quantitative structure activity relationship (3 D-QSAR), molecular docking and molecular dynamics (MD) methods was carried out on a dataset of Janus kinase 1(JAK 1) inhibitors. Ligands were constructed and docked into the active site of protein using GLIDE 5...
May 24, 2017: Journal of Receptor and Signal Transduction Research
#14
REVIEW
Anna Bochicchio, Sandra Jordaan, Valeria Losasso, Shivan Chetty, Rodrigo Casasnovas Perera, Emiliano Ippoliti, Stefan Barth, Paolo Carloni
Targeted human cytolytic fusion proteins (hCFPs) are humanized immunotoxins for selective treatment of different diseases including cancer. They are composed of a ligand specifically binding to target cells genetically linked to a human apoptosis-inducing enzyme. hCFPs target cancer cells via an antibody or derivative (scFv) specifically binding to e.g., tumor associated antigens (TAAs). After internalization and translocation of the enzyme from endocytosed endosomes, the human enzymes introduced into the cytosol are efficiently inducing apoptosis...
February 17, 2017: Biomedicines
#15
Xuezheng Cao, Holger Merlitz, Chen-Xu Wu
Controlling the nanoparticle (NP) diffusion in polymers is a prerequisite to obtain polymer nanocomposites (PNCs) with desired dynamical and rheological properties, and to achieve targeted delivery of nanomedicine in biological systems. Here we determinate the suppression mechanism of direct NP-polymer attraction to hamper the NP mobility in adsorbing polymers, and then quantify the dependence of the effective viscosity \eta_{eff} felt by the NP on the adsorption duration \tau_{ads} of polymers on the NP, using scaling theory analysis and molecular dynamics (MD) simulations...
May 23, 2017: Journal of Physical Chemistry Letters
#16
Denitsa Yordanova, Eric Ritter, Thomas Gerlach, Jan-Hendrik Jensen, Irina Smirnova, Sven Jakobtorweihen
The partition equilibria of solutes between micelles and an aqueous phase is a key factor in many applications. Depending on the task, many micelle-solute combinations are possible. Therefore, theoretical methods to predict the partition behavior in micellar systems are needed. Here, two predictive methods are evaluated and compared. First, it is shown how molecular dynamics simulations (MD) with the umbrella sampling method can be used to calculate free energy profiles in micellar systems. The second applied method is an extension of the COSMO-RS theory to anisotropic systems termed COSMOmic...
May 23, 2017: Journal of Physical Chemistry. B
#17
Naoki Sakashita, Hiroshi C Watanabe, Takuya Ikeda, Keisuke Saito, Hiroshi Ishikita
The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region...
May 23, 2017: Biochemistry
#18
Jonathan Maiangwa, Mohd Shukuri Mohamad Ali, Abu Bakar Salleh, Raja Noor Zaliha Raja Abd Rahman, Yahaya M Normi, Fairolniza Mohd Shariff, Thean Chor Leow
The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%...
2017: PeerJ
#19
Charles M Stevens, Kaveh Rayani, Gurpreet Singh, Bairam Lotfalisalmasi, D Peter Tieleman, Glen F Tibbits
Cardiac troponin C (cTnC) is the regulatory protein that initiates cardiac contraction in response to Ca(2+) TnC binding Ca(2+) initiates a cascade of protein-protein interactions that begins with the opening of the N-terminal domain of cTnC, followed by cTnC binding the Troponin I switch peptide (TnISW). We have evaluated, through isothermal titration calorimetry (ITC) and MD simulation, the effect of several clinically relevant mutations (A8V, L29Q, A31S, L48Q, Q50R and C84Y) on the Ca(2+) affinity, structural dynamics, and calculated interaction strengths between cTnC and each of Ca(2+) and TnISW Surprisingly the Ca(2+) affinity measured by ITC was only significantly affected by half of these mutations, with the exceptions of the L48Q, Q50R and C84Y mutants, which had an affinity 10-fold, 3-fold and 3-fold higher than wild-type, respectively...
May 22, 2017: Journal of Biological Chemistry
#20
Hem Moktan, Donghua H Zhou
The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
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