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# molecular dynamics

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https://www.readbyqxmd.com/read/28732284/field-free-molecular-orientation-by-delayed-elliptically-polarised-laser%C3%A2-pulses
#1
Anjali Maan, Ashish Tyagi, Vinod Prasad
A theoretical model of NAREX (non-adiabatic rotational excitation) and field-free molecular orientation by a short specific elliptically polarised laser pulses (EPLPs) driving a polar molecule is presented. By choosing the proper value of elliptically polarised field parameters, efficient field-free orientation could be achieved. It is demonstrated that NAREX can be controlled by various laser parameters, out of which pulse shape plays the most significant role. The effect of elliptic parameter on the rotational excitation and orientation dynamics is also under concern...
July 13, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28732267/understanding-the-holobiont-the-interdependence-of-plants-and-their-microbiome
#2
REVIEW
Carmen Sánchez-Cañizares, Beatriz Jorrín, Philip S Poole, Andrzej Tkacz
The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system...
July 18, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28732163/diamines-can-initiate-new-particle-formation-in-the-atmosphere
#3
Jonas Elm, Monica Passananti, Theo Kurtén, Hanna Vehkamaki
Recent experimental evidence suggests that diamines can enhance atmospheric new particle formation more efficiently compared to monoamines such as dimethylamine. Here we investigate the molecular interactions between sulfuric acid (sa) and the di- amine putrescine (put) using computational methods. The molecular structure of up to four sulfuric acid molecules and up to four putrescine molecules were obtained at the ωB97X-D/6-31++G(d,p) level of theory. We utilized a domain local pair natural orbital coupled cluster method - DLPNO-CCSD(T)/aug-cc-pVTZ - to obtain highly accurate binding energies of the clusters...
July 21, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28732041/understanding-russell-s-viper-venom-factor-v-activator-s-substrate-specificity-by-surface-plasmon-resonance-and-in-silico-studies
#4
Pradeep K Yadav, Christian B Antonyraj, Syed Ibrahim Basheer Ahamed, Sistla Srinivas
Blood coagulation factor V (FV) is activated either by Factor X or thrombin, cleaving at three different sites viz., Site I (Arg709-Ser710), site II (Arg1018-Thr1019), and site III (Arg1545-Ser1546). Russell's viper venom factor V activator (RVV-V) is a thrombin-like serine proteinase that activates FV with selective, single cleavage at site III. A long lasting effort is being pending in understanding the 'selective' binding specificity of the RVV-V towards site III. Here, we present the binding kinetic study of RVV-V with two designed peptides corresponding to the regions from site I (Gln699-Asn713) and site II (1008Lys-Pro1022), respectively, that include 15 amino acids...
2017: PloS One
https://www.readbyqxmd.com/read/28732011/proteomics-analysis-reveals-a-dynamic-diurnal-pattern-of-photosynthesis-related-pathways-in-maize-leaves
#5
Dan Feng, Yanwei Wang, Tiegang Lu, Zhiguo Zhang, Xiao Han
Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions...
2017: PloS One
https://www.readbyqxmd.com/read/28732007/a-data-driven-modeling-approach-to-identify-disease-specific-multi-organ-networks-driving-physiological-dysregulation
#6
Warren D Anderson, Danielle DeCicco, James S Schwaber, Rajanikanth Vadigepalli
Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension). We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28731776/predicting-flory-huggins-%C3%AF-from-simulations
#7
Wenlin Zhang, Enrique D Gomez, Scott T Milner
We introduce a method, based on a novel thermodynamic integration scheme, to extract the Flory-Huggins χ parameter as small as 10^{-3}kT for polymer blends from molecular dynamics (MD) simulations. We obtain χ for the archetypical coarse-grained model of nonpolar polymer blends: flexible bead-spring chains with different Lennard-Jones interactions between A and B monomers. Using these χ values and a lattice version of self-consistent field theory (SCFT), we predict the shape of planar interfaces for phase-separated binary blends...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28731759/single-molecule-investigation-of-energy-dynamics-in-a-coupled-plasmon-exciton-system
#8
Hiroshi Imada, Kuniyuki Miwa, Miyabi Imai-Imada, Shota Kawahara, Kensuke Kimura, Yousoo Kim
We investigate the near-field interaction between an isolated free-base phthalocyanine molecule and a plasmon localized in the gap between an NaCl-covered Ag(111) surface and the tip apex of a scanning tunneling microscope. When the tip is located in the close proximity of the molecule, asymmetric dips emerge in the broad luminescence spectrum of the plasmon generated by the tunneling current. The origin of the dips is explained by energy transfer between the plasmon and molecular excitons and a quantum mechanical interference effect, where molecular vibrations provide additional degrees of freedom in the dynamic process...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28731742/semiclassical-divide-and-conquer-method-for-spectroscopic-calculations-of-high-dimensional-molecular-systems
#9
Michele Ceotto, Giovanni Di Liberto, Riccardo Conte
A new semiclassical "divide-and-conquer" method is presented with the aim of demonstrating that quantum dynamics simulations of high dimensional molecular systems are doable. The method is first tested by calculating the quantum vibrational power spectra of water, methane, and benzene-three molecules of increasing dimensionality for which benchmark quantum results are available-and then applied to C_{60}, a system characterized by 174 vibrational degrees of freedom. Results show that the approach can accurately account for quantum anharmonicities, purely quantum features like overtones, and the removal of degeneracy when the molecular symmetry is broken...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28731734/determining-potentials-of-zero-charge-of-metal-electrodes-versus-the-standard-hydrogen-electrode-from-density-functional-theory-based-molecular-dynamics
#10
Jiabo Le, Marcella Iannuzzi, Angel Cuesta, Jun Cheng
We develop a computationally efficient scheme to determine the potentials of zero charge (PZC) of metal-water interfaces with respect to the standard hydrogen electrode. We calculate the PZC of Pt(111), Au(111), Pd(111) and Ag(111) at a good accuracy using this scheme. Moreover, we find that the interface dipole potentials are almost entirely caused by charge transfer from water to the surfaces, the magnitude of which depends on the bonding strength between water and the metals, while water orientation hardly contributes at the PZC conditions...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28731710/computational-calorimetry-of-pnipam-cononsolvency-in-water-methanol-mixtures
#11
Cahit Dalgicdir, Francisco Rodriguez-Ropero, Nico F A van der Vegt
We revisit the mechanism for cononsolvency of PNIPAM in water/methanol mixtures. Using extensive molecular dynamics simulations we calculate the calorimetric enthalpy of the PNIPAM collapse transition and observe a unique fingerprint of PNIPAM cononsolvency which is analysed in terms of microscopic interactions. We find that polymer hydration is the determining factor for PNIPAM collapse in the cononsolvency regime. In particular, it is shown that methanol frustrates the ability of water to form hydrogen bonds with the amide proton and therefore causes polymer collapse...
July 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28731705/reversible-self-assembly-of-degradable-polymersomes-with-upper-critical-solution-temperature-in-water
#12
Thomas Wolf, Timo Rheinberger, Johanna Simon, Frederik R Wurm
Temperature-induced self-assembly of block copolymers allows the formation of smart nanodimensional structures. Mostly, non-degradable LCST segments are applied to prepare such dynamic aggregates. However, degradable UCST block copolymers that would allow the swelling or disassembly at elevated temperatures with eventual backbone hydrolysis have not been reported to date. We present the first well-defined degradable poly(phosphonate)s with adjustable UCST. The organocatalytic anionic ring-opening copolymerization of 2-alkyl-2-oxo-1,3,2-dioxaphospholanes provided functional polymers with excellent control over molecular weight and copolymer composition...
July 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28731702/drude-polarizable-force-field-for-molecular-dynamics-simulations-of-saturated-and-unsaturated-zwitterionic-lipids
#13
Hui Li, Janamejaya Chowdhary, Lei Huang, Xibing He, Alexander D MacKerell, Benoît Roux
Additive force fields are designed to account for induced electronic polarization in a mean-field average way using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations...
July 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28731696/tuning-nonradiative-lifetimes-via-molecular-aggregation
#14
Alan Celestino, Alexander Eisfeld
We show that molecular aggregation can strongly influence the nonradiative decay (NRD) lifetime of an electronic excitation. As a demonstrative example, we consider a transition-dipole-dipole-interacting dimer whose monomers have harmonic potential energy surfaces (PESs). Depending on the position of the NRD channel ($q_{\rm nr}$), we find that the NRD lifetime ($\tau_{\rm nr}^{\rm dim}$) can exhibit a completely different dependence on the intermolecular-interaction strength. We observe that (i) for $q_{\rm nr}$ near the Franck-Condon region, $\tau_{\rm nr}^{\rm dim}$ increases with the interaction strength; (ii) for $q_{\rm nr}$ near the minimum of the monomer excited PES, the intermolecular interaction has little influence on $\tau_{\rm nr}^{\rm dim}$; (iii) for $q_{\rm nr}$ near the classical turning point of the monomer nuclear dynamics, on the other side of the minimum, $\tau_{\rm nr}^{\rm dim}$ decreases with the interaction strength...
July 21, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28731695/how-rhodopsin-tunes-the-equilibrium-between-protonated-and-deprotonated-forms-of-the-retinal-chromophore
#15
Siri Camee van Keulen, Alicia Solano, Ursula Rothlisberger
Rhodopsin is a photoactive G-protein-coupled receptor (GPCR) that converts dim light into a signal for the brain, leading to eyesight. Full activation of this GPCR is achieved after passing through several steps of the protein's photoactivation pathway. Key events of rhodopsin activation are the initial cis-trans photoisomerisation of the covalently bound retinal moiety followed by conformational rearrangements and deprotonation of the chromophore's protonated Schiff base (PSB), which ultimately lead to full activation in the meta II state...
July 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28731682/cold-adaptation-of-triosephosphate-isomerase
#16
Johan Åqvist
The main problem for enzymes from psychrophilic species, that need to work near the freezing point of liquid water, is the exponential decay of reaction rates as the temperature is lowered. Cold-adapted enzymes have solved this problem by shifting the activation enthalpy-entropy balance for the catalyzed reaction compared to their mesophilic orthologs. To understand the structural basis of this universal feature it is necessary to examine pairs of such orthologous enzymes, with known 3D structures, at the microscopic level...
July 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28731353/altering-dna-programmable-colloidal-crystallization-paths-by-modulating-particle-repulsion
#17
Mary X Wang, Jeffrey D Brodin, Jaime A Millan, Soyoung E Seo, Martin Girard, Monica Olvera de la Cruz, Byeongdu Lee, Chad A Mirkin
Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior...
July 21, 2017: Nano Letters
https://www.readbyqxmd.com/read/28731148/molecular-genetics-and-targeted-therapy-of-wnt-related-human-diseases-review
#18
Masuko Katoh, Masaru Katoh
Canonical WNT signaling through Frizzled and LRP5/6 receptors is transduced to the WNT/β-catenin and WNT/stabilization of proteins (STOP) signaling cascades to regulate cell fate and proliferation, whereas non-canonical WNT signaling through Frizzled or ROR receptors is transduced to the WNT/planar cell polarity (PCP), WNT/G protein-coupled receptor (GPCR) and WNT/receptor tyrosine kinase (RTK) signaling cascades to regulate cytoskeletal dynamics and directional cell movement. WNT/β-catenin signaling cascade crosstalks with RTK/SRK and GPCR-cAMP-PKA signaling cascades to regulate β-catenin phosphorylation and β-catenin-dependent transcription...
July 19, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28731083/mutable-polyelectrolyte-tube-arrays-mesoscale-modeling-and-lateral-force-microscopy
#19
Steven W Cranford, Lin Han, Christine Ortiz, Markus J Buehler
In this study, the pH-dependent friction of layer-by-layer assemblies of poly(allylamine hydrochloride) and poly(acrylic acid) (PAH/PAA) are quantified for microtube array structures via experimental and simulated lateral force microscopy (LFM). A novel coarse-grain tube model is developed, utilizing a molecular dynamics (MD) framework with a Hertzian soft contact potential (such that F ∼ δ(3/2)) to allow the efficient dynamic simulation of 3D arrays consisting of hundreds of tubes at micrometer length scales...
July 21, 2017: Soft Matter
https://www.readbyqxmd.com/read/28730431/protocols-for-molecular-dynamics-simulations-of-rna-nanostructures
#20
Taejin Kim, Wojciech K Kasprzak, Bruce A Shapiro
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package...
2017: Methods in Molecular Biology
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