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Molecular Simulations Of The Interaction Of Penetration Enhancing Molecules With Lipid Bilayers
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Book Synopsis Molecular Simulations of the Interaction of Penetration Enhancing Molecules with Lipid Bilayers by : Rebecca Notman
Download or read book Molecular Simulations of the Interaction of Penetration Enhancing Molecules with Lipid Bilayers written by Rebecca Notman and published by . This book was released on 2007 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Dynamics Simulation Studies of Interaction of Amphiphilic Molecules with Lipid Bilayers by : Jieqiong Lin
Download or read book Molecular Dynamics Simulation Studies of Interaction of Amphiphilic Molecules with Lipid Bilayers written by Jieqiong Lin and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Percutaneous Penetration Enhancers Chemical Methods in Penetration Enhancement by : Nina Dragicevic
Download or read book Percutaneous Penetration Enhancers Chemical Methods in Penetration Enhancement written by Nina Dragicevic and published by Springer. This book was released on 2016-01-05 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: Percutaneous Penetration Enhancers in a mini-series format comprising five volumes, represents the most comprehensive reference on enhancement methods – both well established and recently introduced – in the field of dermal/transdermal drug delivery. In detail the broad range of both chemical and physical methods used to enhance the skin delivery of drugs is described. All aspects of drug delivery and measurement of penetration are covered and the latest findings are provided on skin structure and function, mathematics in skin permeation and modern analytical techniques adapted to assess and measure penetration. In offering a detailed description of the methods currently in use for penetration enhancement, this book will be of value for researchers, pharmaceutical scientists, practitioners and also students.
Book Synopsis Biological Membranes by : Kenneth M. Merz
Download or read book Biological Membranes written by Kenneth M. Merz and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interface between a living cell and the surrounding world plays a critical role in numerous complex biological processes. Sperm/egg fusion, virus/cell fusion, exocytosis, endocytosis, and ion permeation are a few examples of processes involving membranes. In recent years, powerful tools such as X-ray crystal lography, electron microscopy, nuclear magnetic resonance, and infra-red and Raman spectroscopy have been developed to characterize the structure and dy namics of biomembranes. Despite this progress, many of the factors responsible for the function of biomembranes are still not well understood. The membrane is a very complicated supramolecular liquid-crystalline structure that is largely composed of lipids, forming a bilayer, to which proteins and other biomolecules are anchored. Often, the lipid bilayer environment is pictured as a hydropho bic structureless slab providing a thermodynamic driving force to partition the amino acids of a membrane protein according to their solubility. However, much of the molecular complexity of the phospholipid bilayer environment is ignored in such a simplified view. It is likely that the atomic details of the polar head group region and the transition from the bulk water to the hydrophobic core of the membrane are important. An understanding of the factors responsible for the function of biomembranes thus requires a better characterization at the molec ular level of how proteins interact with lipid molecules, of how lipids affect protein structure and of how lipid molecules might regulate protein function.
Book Synopsis Peptide-Lipid Interactions by : Sidney A. Simon
Download or read book Peptide-Lipid Interactions written by Sidney A. Simon and published by Academic Press. This book was released on 2002-11-13 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a comprehensive overview of peptide-lipid interactions by leading researchers. The first part covers theoretical concepts, experimental considerations, and thermodynamics. The second part presents new results obtained through site-directed EPR, electron microscopy, NMR, isothermal calorimetry, and fluorescence quenching. The final part covers problems of biological interest, including signal transduction, membrane transport, fusion, and adhesion. Key Features * world-renowned experts * state-of-the-art experimental methods * monolayers, bilayers, biological membranes * theoretical aspects and computer simulations * rafts * synaptic transmission * membrane fusion * signal transduction
Book Synopsis Molecular Dynamic Simulations of the Interaction of Natural Compounds with Lipid Bilayer Membranes by : Gabin Fabre
Download or read book Molecular Dynamic Simulations of the Interaction of Natural Compounds with Lipid Bilayer Membranes written by Gabin Fabre and published by . This book was released on 2012 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt: Based on the structures of natural molecules, many new derivatives are continuously synthetized to enhance therapeutic. To understand the mechanism of action of these compounds, one of the key steps is the capacity to incorporate/cross lipid bilayer membranes. Molecular dynamics (MD) has recently appeared as a powerful tool to rationalize these interactions at the molecular level. Here we report on two different types of derivatives. The first class concerns antioxidants. One of the most important oxidative processes in the organism is lipid peroxidation in cell membrane. To efficiently stop lipid peroxidation, potential antioxidants have to (i) scavenge free radicals and (ii) incorporate inside the membrane. Lipocarbazole exhibits an efficient antioxidant activity against lipid peroxidation in vitro, which can be correlated to its actual position and orientation inside the membrane. The second class concerns antibacterials. Plantazolicin A exhibits antibacterial activity against Gram+ strains. In order to understand this activity (i) the 3D re-arrangement and (ii) its interaction with bacterial membrane must be fully understood. Using a model of lipid bilayer membrane, the capacity of this compound to form pores is evaluated here.
Book Synopsis Molecular Dynamics Simulation by : J. M. Haile
Download or read book Molecular Dynamics Simulation written by J. M. Haile and published by Wiley-Interscience. This book was released on 1997-03-14 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Provides a lot of reading pleasure and many new insights." -Journal of Molecular Structure "This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." -Contemporary Physics "A very useful introduction . . . more interesting to read than the often dry equation-based texts." -Journal of the American Chemical Society Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics. Stresses easy-to-use molecules * Provides sample calculations and figures * Includes four complete FORTRAN codes
Book Synopsis Liposomes, Lipid Bilayers and Model Membranes by : Georg Pabst
Download or read book Liposomes, Lipid Bilayers and Model Membranes written by Georg Pabst and published by CRC Press. This book was released on 2014-03-04 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a result of their unique physical properties, biological membrane mimetics, such as liposomes, are used in a broad range of scientific and technological applications. Liposomes, Lipid Bilayers and Model Membranes: From Basic Research to Application describes state-of-the-art research and future directions in the field of membranes, which has evo
Book Synopsis Investigating Molecular Effects on Membrane Structure, Dynamics and Function by : Cari Michelle Anderson
Download or read book Investigating Molecular Effects on Membrane Structure, Dynamics and Function written by Cari Michelle Anderson and published by . This book was released on 2019 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological membranes are heterogeneous structures with complex electrostatic profiles arising from lipids, sterols, membrane proteins, and water molecules. We investigated the effect of cholesterol and its derivative 6-ketocholestanol (6-kc) on membrane electrostatics by directly measuring the dipole electric field (F [arrow above F] [subscript d] ) within lipid bilayers containing cholesterol or 6-kc at concentrations of 0−40 mol% through the vibrational Stark effect (VSE). We found that adding low concentrations of cholesterol, up to ∼10 mol %, increases F [arrow above F] [subscript d], while adding more cholesterol up to 40 mol% lowers F [arrow above F] [subscript d]. In contrast, we measured a monotonic increase in F [arrow above F] [subscript d] as 6-kc concentration increased. We proposed that this membrane electric field is affected by multiple factors: the polarity of the sterol molecules, the reorientation of the phospholipid dipole due to sterol, and the impact of the sterol on hydrogen bonding with surface water. We used molecular dynamics simulations to examine the distribution of phospholipids, sterol, and helix in bilayers containing these sterols. At low concentrations, we observed clustering of sterols near the vibrational probe whereas at high concentrations, we observed spatial correlation between the positions of the sterol molecules. This work demonstrated how a one-atom difference in a sterol changes the physicochemical and electric field properties of the bilayer. Additionally, we set out to understand how a small molecule interacts with the lipid bilayer differently based on its charge. Our laboratory had previously reported that tryptophan permeated through a phosphatidylcholine lipid bilayer membrane at a faster rate when it was positively charged (Trp+) than when negatively charged (Trp−), which corresponded to a lower potential of mean force (PMF) barrier determined through simulations. In the work described here, we demonstrated that Trp+ partitions into the lipid bilayer membrane to a greater degree than Trp− by interacting with the ester linkage of a phosphatidylcholine lipid, where it is stabilized by the electron withdrawing glycerol functional group. These results are in agreement with tryptophan's known role as an anchor for transmembrane proteins, though the tendency for binding of a positively charged tryptophan is surprising. We discussed the implications of our results on the mechanisms of unassisted permeation and penetration of small molecules within and across lipid bilayer membranes based on molecular charge, shape, and molecular interactions within the bilayer structure
Book Synopsis Free Energy Calculations by : Christophe Chipot
Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Book Synopsis Drug Delivery Systems by : Pieter Stroeve
Download or read book Drug Delivery Systems written by Pieter Stroeve and published by World Scientific. This book was released on 2017-11-27 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the alarming increase in cancer diagnoses and genetic illnesses, traditional drug agents and their delivery media need to be re-evaluated to address a quickly evolving field. With newer smart materials for the controlled release of macromolecules, peptides, genetic material, etc. further complications arise, such as material performance, synthesis, functionalization and targeting, biological identity, and biocompatibility.The book provides a comprehensive overview of the recent developments on 'smart' targeting and drug delivery systems with a variety of carriers like nanoparticles, membranes, and hydrogels. It contains detailed descriptions on the recent trends in this field in the ongoing battle with catastrophic diseases like cancer. This field of research has been in its infancy and continues to face growth, and with it, further challenges and difficulties along the way toward maturity, which are accurately introduced in this book.
Book Synopsis Understanding Lipid Membranes' Interactions with Small Molecules and Cholesterol Using Molecular Dynamics Computer Simulations by : Nihit Pokhrel
Download or read book Understanding Lipid Membranes' Interactions with Small Molecules and Cholesterol Using Molecular Dynamics Computer Simulations written by Nihit Pokhrel and published by . This book was released on 2019 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cellular membranes are made up of phospholipids, proteins and cholesterol. The packing of components within the membrane gives rise to important biological phenomena. Understanding these interactions is the most critical step towards predicting membrane behavior. In this dissertation, I focus on lipid bilayer interactions with various molecules. At biologically relevant scale, we investigate how phospholipids interact with small molecules like amino acid residues and cholesterol. At field scale, we study the structure and dynamics of lipid molecules as they bind with clay minerals. I utilize molecular dynamics simulation, both equilibrium and biased, at both coarse-grained and atomistic level to study how these interactions impact membrane thermodynamic properties. I first study membrane permeation by evaluating the efficiency of different computational methods to sample the configurational space of various amino acid and lipid membranes. I show that replica exchange umbrella sampling out-performs others because of the algorithm's ability to sample transition state. Using this method, I calculate cholesterol chemical potential in seven binary lipid membranes. These results demonstrate the sensitivity of the cholesterol chemical potential to the lipid tail unsaturation only if the difference in tail saturation is big, and show that cholesterol has the greatest affinity to saturated PC lipids. These studies provide practical guidance for studying membrane permeation and yield important insight into the thermodynamic properties of lipid bilayer systems. This work will also contribute towards the understanding of cholesterol's effect of membranes, which is a vast and still ongoing field of research. Finally, this research also sheds lights on soil water repellency at the molecular scale. I investigate structural properties of organic matter that are found in soil and find that zwitterionic lipid aggregates bind to the surface of the clay. In this relatively new field, such molecular simulations will have significant scientific impact.
Book Synopsis Probing Lipid Membrane Interactions with Drug Molecules and Cationic Proteins Using Combined Experimental and Computational Analysis by : Lorena Alvarez
Download or read book Probing Lipid Membrane Interactions with Drug Molecules and Cationic Proteins Using Combined Experimental and Computational Analysis written by Lorena Alvarez and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The lipid bilayer's integrity is essential for cell function as it acts as the primary barrier against external molecules like drugs and peptides, which can alter the bilayer's physical properties. This dissertation investigates how amphetamine (AMPH) and methamphetamine (METH), and the charged HIV1-TAT peptide impact the stability of lipid bilayers, using a home-built lipid bilayer apparatus that enables real-time monitoring through electrical and fluorescence measurements. Our findings indicate that AMPH and METH increase the lipid bilayer's ion permeability, with METH having a greater destabilizing effect. High concentrations of these stimulants, akin to levels in blood plasma of individuals with stimulant-related brain injuries, lead to pore formation in the bilayer. The extent of destabilization correlated with the drug concentration. We also studied the translocation dynamics of the charged HIV1-TAT peptide across the lipid bilayer. The analysis of current fluctuations showed that successful translocation of the TAT peptide is concentration-dependent, highlighting the significance of charge in inducing membrane deformation or pore formation. Additionally, molecular dynamic simulations were used to explore AMPH interactions with the lipid bilayer in greater detail. The results revealed AMPH's preferred orientation during interaction and its hydrophobic nature, as evidenced by the larger energy barrier encountered in the hydrophilic head group regions of the lipid bilayer. To complement these findings, we utilized surface-enhanced Raman spectroscopy (SERS) to estimate the concentrations of AMPH within lipid bilayers. The data showed a positive correlation between characteristic peak heights and AMPH concentrations. Moreover, whole-cell patch clamp measurements on neuronal cells were employed to examine AMPH's effects in a more intricate lipid environment. This research contributes to the understanding of how stimulants and charged peptides interact with lipid bilayers, which is vital for insights into their biological impacts and in developing therapeutic interventions.
Book Synopsis Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations by : Vladimir A. Durov
Download or read book Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations written by Vladimir A. Durov and published by Springer Science & Business Media. This book was released on 2004 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Pharmaceutics by : Defang Ouyang
Download or read book Computational Pharmaceutics written by Defang Ouyang and published by John Wiley & Sons. This book was released on 2015-07-20 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular modeling techniques have been widely used in drug discovery fields for rational drug design and compound screening. Now these techniques are used to model or mimic the behavior of molecules, and help us study formulation at the molecular level. Computational pharmaceutics enables us to understand the mechanism of drug delivery, and to develop new drug delivery systems. The book discusses the modeling of different drug delivery systems, including cyclodextrins, solid dispersions, polymorphism prediction, dendrimer-based delivery systems, surfactant-based micelle, polymeric drug delivery systems, liposome, protein/peptide formulations, non-viral gene delivery systems, drug-protein binding, silica nanoparticles, carbon nanotube-based drug delivery systems, diamond nanoparticles and layered double hydroxides (LDHs) drug delivery systems. Although there are a number of existing books about rational drug design with molecular modeling techniques, these techniques still look mysterious and daunting for pharmaceutical scientists. This book fills the gap between pharmaceutics and molecular modeling, and presents a systematic and overall introduction to computational pharmaceutics. It covers all introductory, advanced and specialist levels. It provides a totally different perspective to pharmaceutical scientists, and will greatly facilitate the development of pharmaceutics. It also helps computational chemists to look for the important questions in the drug delivery field. This book is included in the Advances in Pharmaceutical Technology book series.
Book Synopsis Current Frontiers in Cryobiology by : Igor Katkov
Download or read book Current Frontiers in Cryobiology written by Igor Katkov and published by BoD – Books on Demand. This book was released on 2012-03-09 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: Almost a decade has passed since the last textbook on the science of cryobiology, Life in the Frozen State, was published. Recently, there have been some serious tectonic shifts in cryobiology which were perhaps not seen on the surface but will have a profound effect on both the future of cryobiology and the development of new cryopreservation methods. We feel that it is time to revise the previous paradigms and dogmas, discuss the conceptually new cryobiological ideas, and introduce the recently emerged practical protocols for cryopreservation. The present books, "Current Frontiers in Cryobiology" and "Current Frontiers in Cryopreservation" will serve the purpose. This is a global effort by scientists from 27 countries from all continents and we hope it will be interesting to a wide audience.
Book Synopsis Molecular Simulations of Lipid Bilayers and Membrane Helices Interactions by : Ayelet Benjamini
Download or read book Molecular Simulations of Lipid Bilayers and Membrane Helices Interactions written by Ayelet Benjamini and published by . This book was released on 2013 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this work we use mesoscopic simulation to investigate the short and medium range interaction of transmembrane helices. First, we develop a coarse-grained model of a generic transmembrane [alpha]-helix. We use the geometry constraints of an [alpha]-helix, along with a set of homogeneous hydrophobic beads. We discuss the reasoning behind this modeling and why various other plausible models have failed in describing the short-range interactions of transmembrane helices. We then show the effect of hydrophobic mismatch on these model helices. The tilt angle of a single helix is affected by its hydrophobic mismatch with the surrounding bilayer. We show that the hydrophobic mismatch, via its effect on the tilt angle, has a crucial effect on the cross angle of two packed transmembrane helices as well. We further show the effect of hydrophobic mismatch on the potential of mean force between the helices as well as on the thickness and tilt angle of the lipids surrounding the helices. We introduce a class of especially long helices, termed super-positive mismatched helices, to which the response of the lipids differs and discuss the origin of this behavior. These coarse-grained simulations are performed using the Dissipative Particle Dynamics (DPD) scheme Performing large time and length scale simulations using this scheme is highly CPU-time consuming. To enhance our simulation capabilities we develop a novel, massively parallel simulation algorithm. We introduce this algorithm and the original concepts we developed for parallelizing the DPD scheme. We show that this novel approach provides up to 30 times speed up on a Graphical Processing Unit (GPU) over the non-parallel CPU version. Finally, we use our parallel algorithm to perform simulation on a large time and length scale system. We investigate the effect of Cholesterol on the bending rigidity of lipid bilayers and show the effect of a phase transition on the bending modulus. Extracting the bending modulus from simulation requires a large system that enables long-range height fluctuations. Using a fast, parallel simulation algorithm for such a task is therefore crucial.
