Molecular Dynamics Simulation Of Water Near Structured Hydrophobic Surfaces

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Molecular Dynamics Simulation of Water Near Structured Hydrophobic Surfaces

Author : Sandeep Pal
Publisher :
ISBN 13 :
Total Pages : 138 pages
Book Rating : 4.:/5 (232 download)

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Book Synopsis Molecular Dynamics Simulation of Water Near Structured Hydrophobic Surfaces by : Sandeep Pal

Download or read book Molecular Dynamics Simulation of Water Near Structured Hydrophobic Surfaces written by Sandeep Pal and published by . This book was released on 2005 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: The main focus of the thesis is to study the enhancement in the hydrophobicity of an already hydrophobic surface by creating surface structuring on the surface of the crystal. The local structuring and the free energy of interfacial water at the crystal/water interface is analysed by molecular dynamics simulation. An alkane crystal has been taken as the parent model for a hydrophobic surface. Surface structuring were created by either indenting pits on the surface of the crystal or by raising a protrusion on the surface of the crystal. Around all structures the water density was lower and the number of contacts between water and the surface of the crystal decreased due to surface structuring. The difference in the free energy of hydration between planar surface and the structured surface also revealed the increase in the hydrophobicity of the already hydrophobic crystal. Finally a study on the hydrophobicity of a perfluoro-n-alkane crystal is discussed in the final chapter. A qualitative comparison of the water structuring near an alkane and a perfluoro-n-alkane crystal show a higher htdrophobicity in case of a perfluoro-n-alkane crystal than an alkane crystal.

Structures and Dynamics of Interfacial Water

Author : Duanyun Cao
Publisher : Springer Nature
ISBN 13 : 9811969213
Total Pages : 149 pages
Book Rating : 4.8/5 (119 download)

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Book Synopsis Structures and Dynamics of Interfacial Water by : Duanyun Cao

Download or read book Structures and Dynamics of Interfacial Water written by Duanyun Cao and published by Springer Nature. This book was released on 2023-03-14 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis highlights the study into the structures and dynamics of interfacial water, which is a cutting edge issue in condensed matter physics. Using the first principles calculation, classical molecular dynamics simulation and the simulation of atomic force microscopy (AFM), combined with the experimental results of AFM, the book systematically studies interfacial water at the atomic scale, especially the structure and growth mechanism of two-dimensional ice on hydrophobic Au (111) surface, the structure and the interconversion of the Eigen/Zundel hydrated proton on the Au(111) and Pt(111) surfaces, the microstructure and the hydration effect of the diffusion of ion hydrates on NaCl surface. This book displays the atomic scale information about the interaction between water and surface, and achieves many innovative results. Furthermore, the research methods included in this book can be further extended to study the more complex interfacial systems.

Molecular Simulation of Adsorption at Solid-aqueous Interfaces

Author : Travis Gerard Trudeau
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (858 download)

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Book Synopsis Molecular Simulation of Adsorption at Solid-aqueous Interfaces by : Travis Gerard Trudeau

Download or read book Molecular Simulation of Adsorption at Solid-aqueous Interfaces written by Travis Gerard Trudeau and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The structure of liquid water and adsorbed leucine at solid surfaces of tunable hydrophobicity has been examined by molecular dynamics simulation. The results have been used to extend models of water ordering at superhydrophobic surfaces to create a general model of density-dependent ordering of water and adsorbates at hydrophobic interfaces. In this model, interfacial water structures can be classified according to two hydrophobic regimes, a non-wetting structure and a semi-wetting structure, distinguished by the orientation of interfacial water molecules. We propose that the emergence of the wetting-type order is strongly dependent on the density profile across the interfacial region. Leucine adsorbed at the same surfaces also shows two patterns of adsorption, distinguished by the proportion of time the molecule adopts an orientation parallel to the surface. These patterns correspond to the non-wetting and semi-wetting regimes of water and also arise from the density structure of water in the interfacial region.

Innovations in Biomolecular Modeling and Simulations

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
ISBN 13 : 1849735042
Total Pages : 381 pages
Book Rating : 4.8/5 (497 download)

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Book Synopsis Innovations in Biomolecular Modeling and Simulations by : Tamar Schlick

Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012-05-24 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Interfacial and Confined Water

Author : Ivan Brovchenko
Publisher : Elsevier
ISBN 13 : 0080558178
Total Pages : 317 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis Interfacial and Confined Water by : Ivan Brovchenko

Download or read book Interfacial and Confined Water written by Ivan Brovchenko and published by Elsevier. This book was released on 2008-06-03 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: Water in the proximity of a surface (interfacial water) is abundant on the earth. It is involved in various physical and chemical processes and crucial for biological function. Despite numerous studies of interfacial water, systematic analysis of its properties is missing in scientific literature. This book is a first comprehensive review of experimental and simulation studies of water in various confining environments, such as hydrophilic and hydrophobic surfaces, surfaces of biomolecules, porous media, etc. Systematic analysis of interfacial and confined water is based on the firm physical ground, which accounts for variety of the thermodynamic states of water near the surface, surface phase transitions, surface critical behaviour, effect of confinement on the bulk and surface phase transitions of water, clustering and formation of a spanning hydrogen-bonded water network via percolation transition. This allows distinguishing between universal features, common for all fluids, and some specific water properties, related to intermolecular hydrogen bonds. Special attention is paid to the properties of hydration water, which covers biomolecules and enables their biological activity. This book provides readers with basic information on interfacial and confined water, which will be useful for scientists and engineers working in the fields of bioscienses, nanociences and nanotechnologies. Comprehensive review and analysis of interfacial and confined water Updates and informs practitioners and students on all the latest developments in the field Written by leading scholars and industry experts

Water and Peptide Structure at Hydrophobic and Hydrophilic Surfaces

Author : Sandra Roy
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (858 download)

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Book Synopsis Water and Peptide Structure at Hydrophobic and Hydrophilic Surfaces by : Sandra Roy

Download or read book Water and Peptide Structure at Hydrophobic and Hydrophilic Surfaces written by Sandra Roy and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In order to better understand the interfacial peptide-water interaction, molecular dynamics simulations were made for both water, and an amphipathic peptide, LKa14, adsorbed at hy- drophobic and hydrophilic surfaces. Structural and orientational analyses were performed on both systems. Vibrational mode frequency and oscillator coupling were analyzed for the interfacial water. When looking at the peptide, DFT (density functional theory) ab initio calculations were performed to obtain the non linear vibrational information of the different side chains conformers. Non linear vibrational spectra derived from these results were simulated for both interfacial water and adsorbed peptide. The sum frequency vibrational spectra obtained were correlated to the orientation analysis results. Comparison with literature results were made for both spectral and orientational analysis. The results obtained of water at hydrophilic surfaces lead us to conclude that the absence of signal in the 3700 cm?1 region is due to a cancellation of strongly opposite oriented water layers rather than the absence of O?H oscillators at this vibrational frequency region. The hydrophobic and water-air simulation resulted in surprisingly strong similarity but with difference in the depth of those features. When analyzing the structure of LKa14, results showed that it retained an? helix conformation preference in bulk and adsorbedon surfaces. The hydrophobic surface results lead us to conclude a strong orientation of the leucine side chain towards the interface. Results from the adsorption of LKa14 at the hydrophilic surface proved that the adsorption process takes longer than for the hydrophobic surface. Due to results of water and peptide adsorption, we propose that the time scale of the adsorption process for peptide interaction with hydrophilic surface is partially due to the multiple, strongly orientated, water layers.

Molecular Simulation on Cement-Based Materials

Author : Dongshuai Hou
Publisher : Springer Nature
ISBN 13 : 9811387117
Total Pages : 197 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Molecular Simulation on Cement-Based Materials by : Dongshuai Hou

Download or read book Molecular Simulation on Cement-Based Materials written by Dongshuai Hou and published by Springer Nature. This book was released on 2019-09-26 with total page 197 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a number of studies on the molecular dynamics of cement-based materials. It introduces a practical molecular model of cement-hydrate, delineates the relationship between molecular structure and nanoscale properties, reveals the transport mechanism of cement-hydrate, and provides useful methods for material design. Based on the molecular model presented here, the book subsequently sheds light on nanotechnology applications in the design of construction and building materials. As such, it offers a valuable asset for researchers, scientists, and engineers in the field of construction and building materials.

Water in Biomaterials Surface Science

Author : Marco Morra
Publisher : John Wiley & Sons
ISBN 13 : 9780471490418
Total Pages : 422 pages
Book Rating : 4.4/5 (94 download)

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Book Synopsis Water in Biomaterials Surface Science by : Marco Morra

Download or read book Water in Biomaterials Surface Science written by Marco Morra and published by John Wiley & Sons. This book was released on 2001-08-30 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt: Theorie, Analytik, Praxis: Dieser Band behandelt alle wesentlichen Aspekte eines relativ jungen Forschungsgebietes, das sich mit Wechselwirkungen an Grenzflächen zwischen biologischen Materialien (u.a. Polysacchariden, Polyethylenoxid, Proteinen, Kohlenhydraten) und Wasser beschäftigt. Diskutiert werden Konsequenzen für Biotechnologie, Medizin und für die Herstellung von Beschichtungen.

Water in Biological and Chemical Processes

Author : Biman Bagchi
Publisher : Cambridge University Press
ISBN 13 : 1107037298
Total Pages : 383 pages
Book Rating : 4.1/5 (7 download)

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Book Synopsis Water in Biological and Chemical Processes by : Biman Bagchi

Download or read book Water in Biological and Chemical Processes written by Biman Bagchi and published by Cambridge University Press. This book was released on 2013-11-14 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: A unified overview of the dynamical properties of water and its unique and diverse role in biological and chemical processes.

Hydration Processes in Biology

Author : Marie-Claire Bellissent-Funel
Publisher : IOS Press
ISBN 13 : 9789051994391
Total Pages : 456 pages
Book Rating : 4.9/5 (943 download)

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Book Synopsis Hydration Processes in Biology by : Marie-Claire Bellissent-Funel

Download or read book Hydration Processes in Biology written by Marie-Claire Bellissent-Funel and published by IOS Press. This book was released on 1999 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interaction of water at organic surfaces or interfaces is of fundamental and technological interest and importance in chemistry, physics and biology. Progress towards an in-depth, molecular interpretation of the structure and dynamics of interfacial water needs a range of novel experimental and simulation techniques. We are now reaching the stage at which we understand, at the molecular level, the mutual perturbation at a macromolecule/water interface. The aims of this book are to provide with a comprehensive background to the properties of bulk water at the microscopic level and with a substantial account of the theoretical and experimental contributions which have been done to understand the role of water in various systems from some model systems to the more complex ones such as the biological systems.

Comprehensive Biophysics

Author :
Publisher : Academic Press
ISBN 13 : 0080957188
Total Pages : 3533 pages
Book Rating : 4.0/5 (89 download)

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Book Synopsis Comprehensive Biophysics by :

Download or read book Comprehensive Biophysics written by and published by Academic Press. This book was released on 2012-04-12 with total page 3533 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysics is a rapidly-evolving interdisciplinary science that applies theories and methods of the physical sciences to questions of biology. Biophysics encompasses many disciplines, including physics, chemistry, mathematics, biology, biochemistry, medicine, pharmacology, physiology, and neuroscience, and it is essential that scientists working in these varied fields are able to understand each other's research. Comprehensive Biophysics, Nine Volume Set will help bridge that communication gap. Written by a team of researchers at the forefront of their respective fields, under the guidance of Chief Editor Edward Egelman, Comprehensive Biophysics, Nine Volume Set provides definitive introductions to a broad array of topics, uniting different areas of biophysics research - from the physical techniques for studying macromolecular structure to protein folding, muscle and molecular motors, cell biophysics, bioenergetics and more. The result is this comprehensive scientific resource - a valuable tool both for helping researchers come to grips quickly with material from related biophysics fields outside their areas of expertise, and for reinforcing their existing knowledge. Biophysical research today encompasses many areas of biology. These studies do not necessarily share a unique identifying factor. This work unites the different areas of research and allows users, regardless of their background, to navigate through the most essential concepts with ease, saving them time and vastly improving their understanding The field of biophysics counts several journals that are directly and indirectly concerned with the field. There is no reference work that encompasses the entire field and unites the different areas of research through deep foundational reviews. Comprehensive Biophysics fills this vacuum, being a definitive work on biophysics. It will help users apply context to the diverse journal literature offering, and aid them in identifying areas for further research Chief Editor Edward Egelman (E-I-C, Biophysical Journal) has assembled an impressive, world-class team of Volume Editors and Contributing Authors. Each chapter has been painstakingly reviewed and checked for consistent high quality. The result is an authoritative overview which ties the literature together and provides the user with a reliable background information and citation resource

Effects of Confinement on Water Structure and Dynamics and on Proton Transport

Author : Pussana Hirunsit
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (69 download)

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Book Synopsis Effects of Confinement on Water Structure and Dynamics and on Proton Transport by : Pussana Hirunsit

Download or read book Effects of Confinement on Water Structure and Dynamics and on Proton Transport written by Pussana Hirunsit and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Classical molecular dynamics (MD) simulations are performed to study structural and dynamic properties of water confined within graphite surfaces. The surfaces are separated at distances varying between 7 and 14.5 Å and the water density is held constant at 1g/cc. Results at 298 K show the formation of a well-ordered structure constituted by water layers parallel to the graphite surfaces. The water molecules in the layers in contact with the surface have a tendency to orient their dipole parallel to the surface. Such ice-like structures may have different structural and dynamic properties than those of ice. The calculated mean square displacement reveals that the mobilities of the confined water at a separation of 8 Å become similar to that of low-temperature water (213 K) at the same density, although the structures of water are very different. The temperature at which the mobility of water confined at the separation of 7 Å would become similar to that of bulk low-temperature water was found to be 373K. With respect to the dynamics of confined water, a significant blue shift is observed in the intermolecular vibrational modes associated with the O···O···O bending and O···O stretching of molecules linked by hydrogen bonds. The analysis of the geometry of water clusters confined between two graphite surfaces has been performed using ab initio methods. The ab initio calculations yield two preferential orientations of water molecules which are; 1) one O-H bond points to the surface and the other is parallel; 2) both O-H bonds are parallel to the surface. These orientations agree with those found in our MD simulation results. The calculated energy barriers for proton transfer of the confined H3O-(H2O) complexes between two graphite model surfaces suggest that the confinement enhances the proton transfer at the separation 6-14.5 Å. When the confinement is high, at a separation of 4 Å, the barrier energies are extremely large. The confinement does not enhance proton transfer when the H3O-(H2O) complexes are located further from the surfaces by more than 8 Å. As a result, the barrier energies start to increase at the separation of 20 Å.

Water: Molecular Structure And Properties

Author : Xiao-feng Pang
Publisher : World Scientific
ISBN 13 : 9814440442
Total Pages : 491 pages
Book Rating : 4.8/5 (144 download)

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Book Synopsis Water: Molecular Structure And Properties by : Xiao-feng Pang

Download or read book Water: Molecular Structure And Properties written by Xiao-feng Pang and published by World Scientific. This book was released on 2014-01-03 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a broad and complete introductions to the molecular structure, novel and anomalous properties, nonlinear excitations, soliton motions, magnetization, and biological effects of water. These subjects are described by both experimental results and theoretical analyses. These contents are very interesting and helpful to elucidate and explain the problem of “what is on earth water”. This book contains the research results of the author and plenty of scientists in recent decades.“Water: Molecular Structure and Properties” is self-contained and unified in presentation. It may be used as an advanced textbook by graduate students and even ambitious undergraduates in Physics and Biology. It is also suitable for the researchers and engineers in Physics, Biology and water science.

Molecular Modeling

Author : Hans-Dieter Höltje
Publisher : John Wiley & Sons
ISBN 13 : 3527614761
Total Pages : 206 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Molecular Modeling by : Hans-Dieter Höltje

Download or read book Molecular Modeling written by Hans-Dieter Höltje and published by John Wiley & Sons. This book was released on 2008-07-11 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by experienced experts in molecular modeling, this books describes the basics to the extent that is necessary if one wants to be able to reliably judge the results from molecular modeling calculations. Its main objective is the description of the various pitfalls to be avoided. Without unnecessary overhead it leads the reader from simple calculations on small molecules to the modeling of proteins and other relevant biomolecules. A textbook for beginners as well as an invaluable reference for all those dealing with molecular modeling in their daily work!

Surfaces and Interfaces of Biomimetic Superhydrophobic Materials

Author : Zhiguang Guo
Publisher : John Wiley & Sons
ISBN 13 : 3527342648
Total Pages : 398 pages
Book Rating : 4.5/5 (273 download)

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Book Synopsis Surfaces and Interfaces of Biomimetic Superhydrophobic Materials by : Zhiguang Guo

Download or read book Surfaces and Interfaces of Biomimetic Superhydrophobic Materials written by Zhiguang Guo and published by John Wiley & Sons. This book was released on 2017-12-26 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive and systematic treatment that focuses on surfaces and interfaces phenomena inhabited in biomimetic superhydrophobic materials, offering new fundamentals and novel insights. As such, this new book covers the natural surfaces, fundamentals, fabrication methods and exciting applications of superhydrophobic materials, with particular attention paid to the smart surfaces that can show switchable and reversible water wettability under external stimuli, such as pH, temperature, light, solvents, and electric fields. It also includes recent theoretical advances of superhydrophobic surfaces with regard to the wetting process, and some promising breakthroughs to promote this theory. As a result, materials scientists, physicists, physical chemists, chemical engineers, and biochemists will benefit greatly from a deeper understanding of this topic.

Molecular Modeling for the Design of Novel Performance Chemicals and Materials

Author : Beena Rai
Publisher : CRC Press
ISBN 13 : 1439840792
Total Pages : 398 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Molecular Modeling for the Design of Novel Performance Chemicals and Materials by : Beena Rai

Download or read book Molecular Modeling for the Design of Novel Performance Chemicals and Materials written by Beena Rai and published by CRC Press. This book was released on 2012-03-23 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular modeling (MM) tools offer significant benefits in the design of industrial chemical plants and material processing operations. While the role of MM in biological fields is well established, in most cases MM works as an accessory in novel products/materials development rather than a tool for direct innovation. As a result, MM engineers and

Microscale and Nanoscale Heat Transfer

Author : Mourad Rebay
Publisher : CRC Press
ISBN 13 : 1498736319
Total Pages : 499 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Microscale and Nanoscale Heat Transfer by : Mourad Rebay

Download or read book Microscale and Nanoscale Heat Transfer written by Mourad Rebay and published by CRC Press. This book was released on 2016-01-06 with total page 499 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microscale and Nanoscale Heat Transfer: Analysis, Design, and Applications features contributions from prominent researchers in the field of micro- and nanoscale heat transfer and associated technologies and offers a complete understanding of thermal transport in nano-materials and devices. Nanofluids can be used as working fluids in thermal system