1,720,989 research outputs found
Effects Of Spherical Fullerene Nanoparticles On A Dipalmitoyl Phosphatidylcholine Lipid Monolayer: A Coarse Grain Molecular Dynamics Approach
No full textThe effect of carbon-based nanoparticles (CNPs) on biological systems is currently of great concern. Yet, few experimental techniques are capable of directly imaging and probing the energetics of such nano-bio systems. Here, we use coarse grain molecular dynamics simulations to study spherical fullerene molecules interacting with dipalmitoyl phosphatidylcholine (DPPC) lipid membranes. Using free energy calculations we show that all the tested fullerene molecules can spontaneously diffuse into both a lipid bilayer and a lipid monolayer. In addition, we establish that large fullerene molecules tend to partition preferentially into bilayers, which affects the lipid monolayer-to-bilayer transition during the respiration cycle. Our results identify a possible CNP perturbation to the function of the pulmonary monolayer membrane and suggest a potential pathway for CNP entry into the body through lung inhalation
Nested Sampling of Isobaric Phase Space for the Direct Evaluation of the Isothermal-Isobaric Partition Function of Atomic Systems
No full textarticle figures in both high-res and PowerPoint formats available at publisher's website.Nested Sampling (NS) is a powerful athermal statistical mechanical sampling technique that directly calculates the partition function, and hence gives access to all thermodynamic quantities in absolute terms, including absolute free energies and absolute entropies. NS has been used predominately to compute the canonical (NVT) partition function. Although NS has recently been used to obtain the isothermal-isobaric (NPT) partition function of the hard sphere model, a general approach to the computation of the NPT partition function has yet to be developed. Here, we describe an isobaric NS (IBNS) method which allows for the computation of the NPT partition function of any atomic system. We demonstrate IBNS on two finite Lennard-Jones systems and confirm the results through comparison to parallel tempering Monte Carlo. Temperature-entropy plots are constructed as well as a simple pressure-temperature phase diagram for each system. We further demonstrate IBNS by computing part of the pressure-temperature phase diagram of a Lennard-Jones system under periodic boundary conditions
A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation
No full textA new method is proposed to estimate the bending rigidity of lipid membranes from molecular dynamics simulations. An external cylindrical guiding potential is used to impose a sinusoidal deformation to a planar membrane. The bending rigidity is obtained from the mean force acting on the cylinder by calibrating against a discretized Helfrich model that accounts for thermal fluctuations of the membrane surface. The method has been successfully applied to a dimyristoyl phosphatidylcholine bilayer simulated with a coarse-grained model. A well-converged bending rigidity was obtained for the tension-free membrane and showed reasonable agreement with that obtained from the height fluctuation spectrum."This work is supported by JSPS KAKENHI Grant No. 23350014, the Next Generation Super Computing Project, TCCI/CMSI in the Strategic Programs for Innovative Research, MEXT, Japan, and HPCI Systems Research Projects (Project ID hp120093).
Modifying the Electronic Properties of Single-Walled Carbon Nanotubes using Designed Surfactant Peptides
No full textThe electronic properties of carbon nanotubes can be altered significantly by modifying the nanotube surface. In this study, single-walled carbon nanotubes (SWCNTs) were functionalized noncovalently using designed surfactant peptides, and the resultant SWCNT electronic properties were investigated. These peptides have a common amino acid sequence of X(Valine) 5(Lysine) 2, where X indicates an aromatic amino acid containing either an electron-donating or electron-withdrawing functional group (i.e. p-amino-phenylalanine or p-cyano-phenylalanine). Circular dichroism spectra showed that the surfactant peptides primarily have random coil structures in an aqueous medium, both alone and in the presence of SWCNTs, simplifying analysis of the peptide/SWCNT interaction. The ability of the surfactant peptides to disperse individual SWCNTs in solution was verified using atomic force microscopy and ultraviolet-visible-near-infrared spectroscopy. The electronic properties of the surfactant peptide/SWCNT composites were examined using the observed nanotube Raman tangential band shifts and the observed additional features near the Fermi level in the scanning tunneling spectroscopy dI/dV spectra. The results revealed that SWCNTs functionalized with surfactant peptides containing electron-donor or electron-acceptor functional groups showed n-doped or p-doped altered electronic properties, respectively. This work unveils a facile and versatile approach to modify the intrinsic electronic properties of SWCNTs using a simple peptide structure, which is easily adaptable to obtain peptide/SWCNT composites for the design of tunable nanoscale electronic devices
Towards an Understanding of Structure-Nonlinearity Relationships in Triarylamine-based Push-Pull Electro-Optic Chromophores: The Influence of Substituent and Molecular Conformation on Molecular Hyperpolarizabilities
No full textIncludes supplementary material.We calculated the second-order hyperpolarizability (beta) of a series of triarylamine (TAA) based donor-bridge-acceptor (D-π-A) push-pull type nonlinear optical (NLO) chromophores with different electron donor moieties and the same thiophene π-bridge and dicyanovinyl electron acceptor using a time-dependent Hartree-Fock (TDHF) approach within the software package MOPAC 2012. NLO chromophores with various quantities and positions of methoxy groups in the TAA donor moiety were investigated. The relationship between NLO properties and the electronic or geometric structures of the TAA donor subunit is discussed through the calculation results. Both substituent and conformational effects affect the delocalization of the nitrogen lone pair into the aryl rings, leading to a dramatic influence on the nonlinear optical properties. Introduction of methoxy groups at the ortho positions of the TAA moiety has a larger influence on the molecular hyperpolarizability and dipole moment than the introduction of methoxy group at the para or meta positions. Our calculation results demonstrate how to improve the NLO properties of TAA based chromophores while meeting practical device requirements
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Molecular Dynamics Simulations to Study Molecular Interactions at Biologically and Mechanically Important Surfaces
No full textIn this dissertation molecular dynamics computer simulations (MD) were used to explore
molecular scale behavior in order to interpret experimental results and guide challenging
experimental work. In Chapters 2, 3 and 4 MD simulations were utilized to study a new
immunointeractive surface approach to induce titanium implant osseointegration, using the
constructive inflammatory effects of high mobility group box 1 (HMGB1) protein. First, in
Chapter 2 the protein, ion and water interactions with the rutile (110) TiO2 surface induced
by surface hydroxylation were investigated. In an aqueous environment, we show the direct
binding of HMGB1 to the TiO2 surface regardless of its hydroxylation state, which causes
structural changes to the protein, thereby affecting its biological function. Hence, to find a
compromise between stable adsorption and preservation of protein activity in Chapter 3 we
study the advantages of dicationic imidazolium-based ionic liquids (IonLs) containing amino
acid anions to serve as a vehicle for delivering proteins on the surface of TiO2 implants. A
strongly bound well structured IonL coating formed on the TiO2 surface effectively blocking
HMGB1 from direct adsorption on the implant. Additionally, the protein is immobilized
due to IonL cations and anions which bind to oppositely charged amino acids on the protein
surface. In order to account for the different biological roles of HMGB1, the different HMGB1
isoforms were studied in Chapter 4. Once the IonL/HMGB1 coating on the TiO2 surface
comes into contact with water, the protein release mechanism and the integrity of its receptor
binding sites were investigated.
Imidazolium based IonLs are becoming increasingly popular not only in bioengineering but
also in many other fields due to their promising properties. Because of the large number of
cation and anion combinations available, it is not feasible to experimentally measure IonL
properties over a wide range of composition and operating conditions. Therefore, fast and
reliable methods such as molecular modeling tools are needed to acquire these properties.
However, to validate and tune the molecular modeling approach some experimental data is
required. Therefore, in Chapter 5 by combining experiments with molecular modeling we
explore the properties of a series of IonLs.
In Chapter 6, we used MD simulations to study vapor condensation which is an area with
a wide range of industrial applications. We provide molecular insight into the condensation
mechanism as a function of surface wettability using surfaces chemisorbed with alkanethiol
self-assembled monolayers. By changing the alkanethiol head group chemistry, the surface
wettability was tuned and the role of surface wettability on the rate of water condensation was studied. We show that decreasing surface hydrophobicity significantly increases
the electrostatic forces between water molecules and the surface, thus increasing the water
condensation rate. We also provide connections with other microscopic and macroscopic
interfacial characterizations.
In Chapter 7, we used MD simulations to link experimentally observed anion sensing, specifically towards nitrate, nitrite, iodide, and thiocyanate by polyvinylpyrrolidone (PVP) polymer, to anion interactions on the polymer surface and concomitant changes in the polymer
aggregation state. Supporting the experimental observations, our results suggest that anions associating most strongly to the surface of PVP quench its fluorescence to the greatest
extent
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