2,724 research outputs found
Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains
No full textWe propose the first model of a polypeptide chain based on a hybrid-particle field approach. The intramolecular potential is built on a two-bead coarse grain mapping for each amino acid. We employ a combined potential for the bending and the torsional degrees of freedom that ensures the stabilization of secondary structure elements in the conformational space of the polypeptide. The electrostatic dipoles associated with the peptide bonds of the main chain are reconstructed by a topological procedure. The intermolecular interactions comprising both the solute and the explicit solvent are treated by a density functional-based mean-field potential. Molecular dynamics simulations on a series of test systems show how the model here introduced is able to capture all the main features of polypeptides. In particular, homopolymers of different lengths yield a complex folding phase diagram, covering from the collapsed to swollen state. Moreover, simulations on models of a four-helix bundle and of an alpha + beta peptide evidence how the collapse of the hydrophobic core drives the appearance of both folded motifs and the stabilization of tertiary or quaternary assemblies. Finally, the polypeptide model is able to structurally respond to the environmental changes caused by the presence of a lipid bilayer
Excited state properties of liquid water
No full textIn this paper, we give an overview of the state of the art in calculations of the electronic band structure and absorption spectra of water. After an introduction to the main theoretical and computational schemes used, we present results for the electronic and optical excitations of water. We focus mainly on liquid water, but spectroscopic properties of ice and vapor phase are also described. The applicability and the accuracy of first-principles methods are discussed, and results are critically presented. © 2009 IOP Publishing Ltd
Introduction to Clinical Methods in Communication Disorders
No full textThis is the second edition of Introduction to Clinical Methods in Communication Disorders which originally published in 2002. Like the first edition, this textbook guides SLPs through the entire clinical experience, including the process of assessment using a variety of instruments, sampling of communicative behaviors, and planning and implementing interventions. The chapters provide introductory and background information and also address current issues such as multiculturalism and technological advances. The book discusses a wide range of clinical approaches (pull out, consultation, collaboration) in a variety of settings (hospitals, schools, etc.) and shows how they apply across communication disorders. Based on standards mandated by ASHA, this second edition serves as an essential start to mastering the science and art of clinical practice --Amazon.
Contents: Introduction to clinical practice in communication disorders / Rhea Paul, Paul W. Cascella -- Ethical and professional practices / Paul W. Cascella -- Principles of assessment / Marianne Kennedy -- Assessment of the speech mechanism / G. Robert Buckendorf, Allyson Goodwyn-Craine -- Communication sampling procedures / Rhea Paul, John Tetnowski, Ellen Reuler -- Communication intervention: principles and procedures / Froma Roth, Rhea Paul -- Evidence based decision making in communication intervention / Marc E. Fey, Laura M. Justice -- Interviewing, counseling, and clinical communication / Kevin M. McNamara -- Public policies affecting clinical practice / Nickola W. Nelson, Yvette D. Hyter, Michele A. Anderson -- Clinical service delivery and work settings / Paul W. Cascella, Mary H. Purdy, James J. Dempsey -- Issues of cultural and linguistic diversity / Brian Goldstein, Aquiles Iglesias -- Assistive technology in communication disorders / Melanie Fried-Oken -- Family centered practice / Denise LaPrade Rini, Jane Hindenlang
Toward chemically resolved computer simulations of dynamics and remodeling of biological membranes
No full textCellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries of the cells, they are involved in a wide range of biological functions, associated with both their structural and the dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel–liquid phase transitions, change of aggregation structure, formation of microtubules, or rupture into vesicles. All of these processes are dependent on a delicate interplay between intermolecular forces, molecular crowding, and entropy, and their understanding requires approaches that are able to capture and rationalize the details of all of the involved interactions. Molecular dynamics-based computational models at atom-level resolution are, in principle, the best way to perform such investigations. Unfortunately, the relevant spatial and time dimensionalities involved in membrane remodeling phenomena would require computational costs that are today unaffordable on a routinely basis. Such hurdles can be removed by coarse-graining the representations of the individual molecular components of the systems. This procedure anyway reduces the possibility of describing the chemical variations in the lipid mixtures composing biological membranes. New hybrid particle field multiscale approaches offer today a promising alternative to the more traditional particle-based simulations methods. By combining chemically distinguishable molecular representations with mesoscale-based computationally affordable potentials, they appear as one of the most promising ways to keep an accurate description of the chemical complexity of biological membranes and, at the same time, cover the required scales to describe remodeling events
Intramolecular structural parameters are key modulators of the gel-liquid transition in coarse grained simulations of DPPC and DOPC lipid bilayers
No full textThe capability of coarse-grained models based on the MARTINI mapping to reproduce the gel-liquid phase transition in saturated and unsaturated model lipids was investigated. We found that the model is able to reproduce a lower critical temperature for 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) with respect to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). Nonetheless, the appearance of a gel phase for DOPC is strictly dependent on the intramolecular parameters chosen to model its molecular structure. In particular, we show that the bending angle at the coarse-grained bead corresponding to the unsaturated carbon-carbon bond acts as an order parameter determining the temperature of the phase transition. Structural analysis of the molecular dynamics simulations runs evidences that in the gel phase, the packing of the lipophilic tails of DOPC assume a different conformation than in the liquid phase. In the latter phase, the DOPC geometry resembles that of the relaxed free molecule. DPPC:DOPC mixtures show a single phase transition temperature, indicating that the observation of a phase separation between the two lipids requires the simulation of systems with sizes much larger than the ones used here
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