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molecular dynamics

Jasmin Milzetti, Divya Nayar, Nico F A van der Vegt
The computation of Kirkwood-Buff integrals (KBIs) using molecular simulations of closed systems is challenging due to finite system-size effects. One of the problems involves the incorrect asymptotic behavior of the radial distribution function. Corrections to rectify such effects have been proposed in the literature. This study reports a systematic comparison of the proposed corrections (as given by Ganguly et al. J. Chem. Theory Comput. 2013, 9, 1347-1355 and Krueger et al. J. Phys. Chem. Lett. 2013, 4, 4-7) to assess the asymptotic behavior of the RDFs, the KBIs as well as the estimation of thermodynamic quantities for ideal urea--water and non-ideal modified-urea--water mixtures using molecular dynamics simulations...
January 17, 2018: Journal of Physical Chemistry. B
Varnavas D Mouchlis, Yuan Chen, J Andrew McCammon, Edward A Dennis
We demonstrate that lipidomics coupled with molecular dynamics reveals unique phospholipase A2 specificity toward membrane phospholipid substrates. We discovered unexpected head-group and acyl-chain specificity for three-major human phospholipases A2. These differences between each enzyme's specificity coupled with molecular dynamicsbased structural and binding studies revealed unique active site and interfacial surface binding moieties for each enzyme that explains the observed specificity at a hitherto inaccessible structural level...
January 17, 2018: Journal of the American Chemical Society
Jordan Muscatello, Enrique Chacón, Pedro Tarazona, Fernando Bresme
The interfacial thermal resistance determines condensation-evaporation processes and thermal transport across material-fluid interfaces. Despite its importance in transport processes, the interfacial structure responsible for the thermal resistance is still unknown. By combining nonequilibrium molecular dynamics simulations and interfacial analyses that remove the interfacial thermal fluctuations we show that the thermal resistance of liquid-vapor interfaces is connected to a low density fluid layer that is adsorbed at the liquid surface...
July 28, 2017: Physical Review Letters
Yu V Arkhipov, A Askaruly, A E Davletov, D Yu Dubovtsev, Z Donkó, P Hartmann, I Korolov, L Conde, I M Tkachenko
Dynamic characteristics of strongly coupled classical one-component Coulomb and Yukawa plasmas are obtained within the nonperturbative model-free moment approach without any data input from simulations so that the dynamic structure factor (DSF) satisfies the first three nonvanishing sum rules automatically. The DSF, dispersion, decay, sound speed, and other characteristics of the collective modes are determined using exclusively the static structure factor calculated from various theoretical approaches including the hypernetted chain approximation...
July 28, 2017: Physical Review Letters
T Marchenko, G Goldsztejn, K Jänkälä, O Travnikova, L Journel, R Guillemin, N Sisourat, D Céolin, M Žitnik, M Kavčič, K Bučar, A Mihelič, B Cunha de Miranda, I Ismail, A F Lago, F Gel'mukhanov, R Püttner, M N Piancastelli, M Simon
A combination of resonant inelastic x-ray scattering and resonant Auger spectroscopy provides complementary information on the dynamic response of resonantly excited molecules. This is exemplified for CH_{3}I, for which we reconstruct the potential energy surface of the dissociative I 3d^{-2} double-core-hole state and determine its lifetime. The proposed method holds a strong potential for monitoring the hard x-ray induced electron and nuclear dynamic response of core-excited molecules containing heavy elements, where ab initio calculations of potential energy surfaces and lifetimes remain challenging...
September 29, 2017: Physical Review Letters
Chuanlong Lin, Xue Yong, John S Tse, Jesse S Smith, Stanislav V Sinogeikin, Curtis Kenney-Benson, Guoyin Shen
We report the results of in situ structural characterization of the amorphization of crystalline ice Ih under compression and the relaxation of high-density amorphous (HDA) ice under decompression at temperatures between 96 and 160 K by synchrotron x-ray diffraction. The results show that ice Ih transforms to an intermediate crystalline phase at 100 K prior to complete amorphization, which is supported by molecular dynamics calculations. The phase transition pathways show clear temperature dependence: direct amorphization without an intermediate phase is observed at 133 K, while at 145 K a direct Ih-to-IX transformation is observed; decompression of HDA shows a transition to low-density amorphous ice at 96 K and ∼1  Pa, to ice Ic at 135 K and to ice IX at 145 K...
September 29, 2017: Physical Review Letters
C A Brackley, J Johnson, D Michieletto, A N Morozov, M Nicodemi, P R Cook, D Marenduzzo
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site...
September 29, 2017: Physical Review Letters
Wilbert J Smit, Fujie Tang, M Alejandra Sánchez, Ellen H G Backus, Limei Xu, Taisuke Hasegawa, Mischa Bonn, Huib J Bakker, Yuki Nagata
Phase-resolved sum-frequency generation measurements combined with molecular dynamics simulations are employed to study the effect of temperature on the molecular arrangement of water on the basal face of ice. The topmost monolayer, interrogated through its nonhydrogen-bonded, free O-H stretch peak, exhibits a maximum in surface H-bond density around 200 K. This maximum results from two competing effects: above 200 K, thermal fluctuations cause the breaking of H bonds; below 200 K, the formation of bulklike crystalline interfacial structures leads to H-bond breaking...
September 29, 2017: Physical Review Letters
Meng Shen, Honghao Li, Monica Olvera de la Cruz
Surface polarization in ion-containing heterogeneous dielectric media such as cell media and emulsions is determined by and determines the positions of the ions. We compute the surface polarization self-consistently as the ions move and analyze their effects on the interactions between electro-neutral, ion-containing droplets using coarse-grained molecular dynamics simulations based on the true energy functional. For water droplets immersed in oil, the interdroplet interaction is attractive, and the surface polarization makes the major contribution...
September 29, 2017: Physical Review Letters
Saumyak Mukherjee, Sayantan Mondal, Ashish Anilrao Deshmukh, Balasubramanian Gopal, Biman Bagchi
Self-assembly of proteins often gives rise to interesting quasi-stable structures that serve important biological purposes. Insulin hexamer is such an assembly. While monomer is the biologically active form of insulin, hexamer serves as the storehouse of the hormone. The hexamer also prevents the formation of higher order aggregates. While several studies explored the role of bivalent metal ions like Zn2+, Ca2+ etc. in the stabilization of the hexameric form, the role of water molecules has been ignored. We combine molecular dynamics simulations, quantum calculations and X-ray analyses to discover that a team of approximately ten water molecules confined inside a barrel-shaped nano-cavity at the center of insulin hexamer is one of the major causes that account for the unusual stability of the biomolecular assembly...
January 17, 2018: Journal of Physical Chemistry. B
Ari Hardianto, Fei Liu, Shoba Ranganathan
(-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with little selectivity. While PKA is known as a tumour promoter, PKC isozymes can be tumour promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood...
January 17, 2018: Journal of Chemical Information and Modeling
Yong-Guang Jia, Jiahong Jin, Sa Liu, Li Ren, Juntao Luo, X X Zhu
Poly(vinyl alcohol) (PVA) is a cytocompatible synthetic polymer and has been commonly used to prepare hydrogels. Bile acids and β-cyclodextrin are both natural compounds and they form stable host-guest inclusion complexes. They are attached covalently onto a low molecular weight PVA separately. Self-healing hydrogels can be easily formed by mixing the aqueous solutions of these PVA based polymers. The mechanical properties of the hydrogels can be tuned by varying the molar fractions of bile acid units on PVA...
January 17, 2018: Biomacromolecules
Qi Zhang, Zhihao Han, Ji Tao, Wancun Zhang, Ping Li, Liping Tang, Yueqing Gu
Targeting COX-2 for molecular imaging is an attractive approach applicable for its overexpression in inflammation and many malignancies. Herein, for monitoring COX-2, we synthesize a specific COX-2 probe CMP, based on celecoxib and a water-soluble near-infrared dye MPA. Its high affinity for binding to COX-2 is verified by molecular docking, dynamics simulation and inhibition assay. At cellular level, CMP selectively accumulates in cytoplasm of COX-2-positive cells. In vivo assays, probe guided-imaging in inflamed or cancerous tissues confirms that CMP can bind to the locally endogenic COX-2 and exhibit intense fluorescence...
January 17, 2018: Journal of Biophotonics
Huynh Minh Hung, Tran Dieu Hang, Minh Tho Nguyen
Hepatitis C virus (HCV), known as the leading cause of liver cirrhosis, viral hepatitis and hepatocellular carcinoma, has been affecting more than 150 million people globally. The HCV non-structure 3 (NS3) protease protein domain plays a key role in HCV replication and pathogenesis; and is currently a primary target for HCV antiviral therapy. Through unbiased molecular dynamics simulations which take advantage of the novel highly mobile membrane mimetic model, we constructed the membrane-bound state of the protein domain at the atomic level...
January 17, 2018: Proteins
Stefano Della Longa, Alessandro Arcovito
Antagonists of the nociceptin receptor (NOP) are raising interest for their possible clinical use as antidepressant drugs. Recently, the structure of NOP in complex with some piperidine-based antagonists has been revealed by X-ray crystallography. In this study, a multi-flexible docking (MF-docking) procedure, i.e. docking to multiple receptor conformations extracted by preliminary molecular dynamics trajectories, together with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have been carried out to provide the binding mode of two novel NOP antagonists, one of them selective (BTRX-246040, formerly named LY-2940094) and one non selective (AT-076), i...
January 16, 2018: Journal of Computer-aided Molecular Design
Naisheng Jiang, Mani Sen, Wenduo Zeng, Zhizhao Chen, Justin M Cheung, Yuma Morimitsu, Maya K Endoh, Tadanori Koga, Masafumi Fukuto, Guangcui Yuan, Sushil K Satija, Jan-Michael Y Carrillo, Bobby G Sumpter
Here we report a link between the interfacial structure and adhesive property of homopolymer chains physically adsorbed (i.e., via physisorption) onto solids. Polyethylene oxide (PEO) was used as a model and two different chain conformations of the adsorbed polymer were created on silicon substrates via the well-established Guiselin's approach: "flattened chains" which lie flat on the solid and are densely packed, and "loosely adsorbed polymer chains" which form bridges jointing up nearby empty sites on the solid surface and cover the flattened chains...
January 17, 2018: Soft Matter
Xiaojie Chen, D Peter Tieleman, Qing Liang
The interactions between nanoparticles and lipid bilayers are critical in applications of nanoparticles in nanomedicine, cell imaging, toxicology, and elsewhere. Here, we investigate the interactions between nanoparticles coated with neutral and/or charged ligands and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. Both penetration and adsorption processes as well as the final distribution of the nanoparticles can be readily modulated by varying the ligand density and the surface charge of the nanoparticles...
January 17, 2018: Nanoscale
Christos Davatzikos, Saima Rathore, Spyridon Bakas, Sarthak Pati, Mark Bergman, Ratheesh Kalarot, Patmaa Sridharan, Aimilia Gastounioti, Nariman Jahani, Eric Cohen, Hamed Akbari, Birkan Tunc, Jimit Doshi, Drew Parker, Michael Hsieh, Aristeidis Sotiras, Hongming Li, Yangming Ou, Robert K Doot, Michel Bilello, Yong Fan, Russell T Shinohara, Paul Yushkevich, Ragini Verma, Despina Kontos
The growth of multiparametric imaging protocols has paved the way for quantitative imaging phenotypes that predict treatment response and clinical outcome, reflect underlying cancer molecular characteristics and spatiotemporal heterogeneity, and can guide personalized treatment planning. This growth has underlined the need for efficient quantitative analytics to derive high-dimensional imaging signatures of diagnostic and predictive value in this emerging era of integrated precision diagnostics. This paper presents cancer imaging phenomics toolkit (CaPTk), a new and dynamically growing software platform for analysis of radiographic images of cancer, currently focusing on brain, breast, and lung cancer...
January 2018: Journal of Medical Imaging
Ronald D Hills
Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues...
2018: PeerJ
Pinki Dey, Arnab Bhattacherjee
Recent experiments suggest that cellular crowding facilitates the target search dynamics of proteins on DNA, the mechanism of which is not yet known. By using large scale computer simulations, we show that two competing factors, namely the width of the depletion layer that separates the crowder cloud from the DNA molecule and the degree of protein-crowder crosstalk, act in harmony to affect the target search dynamics of proteins. The impacts vary from nonspecific to specific target search regime. During a nonspecific search, dynamics of a protein is only minimally affected, whereas, a significantly different behaviour is observed when the protein starts forming a specific protein-DNA complex...
January 16, 2018: Scientific Reports
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