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Molecular Dynamics Simulation

ISBN: 9783906980652 9783906980669 Year: Pages: 628 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2015-01-12 11:36:09
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Condensed matter systems, ranging from simple fluids and solids to complex multicomponent materials and even biological matter, are governed by well understood laws of physics, within the formal theoretical framework of quantum theory and statistical mechanics. On the relevant scales of length and time, the appropriate ‘first-principles’ description needs only the Schroedinger equation together with Gibbs averaging over the relevant statistical ensemble. However, this program cannot be carried out straightforwardly—dealing with electron correlations is still a challenge for the methods of quantum chemistry. Similarly, standard statistical mechanics makes precise explicit statements only on the properties of systems for which the many-body problem can be effectively reduced to one of independent particles or quasi-particles. [...]

Transport of Fluids in Nanoporous Materials

Authors: --- --- ---
ISBN: 9783038975298 / 9783038975304 Year: Pages: 260 DOI: 10.3390/books978-3-03897-530-4 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Chemistry (General) --- General and Civil Engineering --- Materials --- Chemical Engineering
Added to DOAB on : 2019-01-25 10:53:11
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Fluid transport in narrow pores is central to the design and optimization of nanoporous materials in industrial applications, such as catalysis, nanofluids, electrochemical batteries, and membrane separation. However, due to the strong potential field in nanopores, conventional models and methods have become inadequate for predicting the transport behavior of molecules confined in the pore space. In addition, the inherent complexity of the pore structure in nanomaterials requires consideration of local or nanoscale transport at the single pore level, and averaging over the macroscale, which further impedes the application and validation of the formulated mechanical models. To solve the problem of fluid transport in narrow nanopores beyond Knudsen limits, experimental characterizations should be combined to molecular simulations in order to probe the fluid movement under realistic conditions. This book provides comprehensive perspectives on the current research in the investigation of fluid transport processes in nanomaterials. The articles from leading scholars in this field are conveniently arranged according to three categories based on the approaches used in the papers: modeling and simulation, nanomaterial manipulation and characterization, and practical application. The 14 contributions not only demonstrate the importance of fluid behavior in different applications but also address the main theories and simulations to model the fluid transport behavior in nanoporous materials. This collection shows that “fluid transport in nanomaterials” remains a versatile and vibrant topic in terms of both theories and applications.

Charge Transport in DNA - Insights from Simulations

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ISBN: 9783731500827 Year: Pages: VI, 139 p. DOI: 10.5445/KSP/1000036065 Language: ENGLISH
Publisher: KIT Scientific Publishing
Subject: Chemistry (General)
Added to DOAB on : 2019-07-30 20:02:00
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Charge transport and charge transfer (CT) capabilities of deoxyribonucleic acid (DNA) are investigated. A QM/MM multi-scale framework is applied to calculate the CT capabilities of DNA under conditions resembling the experimental setup. The simulations are able to explain and predict the outcome of experiments and therefore make suggestions in advance. Based on the findings, suitable DNA sequences can be opted for the design of DNA-based devices as nano-scale electronic elements.

Molecular Modeling in Drug Design

Authors: ---
ISBN: 9783038976141 Year: Pages: 220 DOI: 10.3390/books978-3-03897-615-8 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Chemistry (General) --- Science (General)
Added to DOAB on : 2019-04-05 10:34:31
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This book is a printed edition of the Special Issue Molecular Modeling in Drug Design that was published in Molecules

Keywords

hyperlipidemia --- squalene synthase (SQS) --- molecular modeling --- drug discovery --- Traditional Chinese Medicine --- molecular dynamics simulation --- biophenols --- natural compounds --- amyloid fibrils --- Alzheimer’s disease --- ligand–protofiber interactions --- adhesion --- FimH --- rational drug design --- molecular dynamics --- molecular docking --- ligand binding --- EphA2-ephrin A1 --- PPI inhibition --- interaction energy --- in silico screening --- adenosine --- boron cluster --- adenosine receptors --- AR ligands --- aggregation --- promiscuous mechanism --- human ecto-5?-nucleotidase --- virtual screening --- enzymatic assays --- turbidimetry --- dynamic light scattering --- docking --- solvent effect --- binding affinity --- scoring function --- molecular dynamics --- target-focused pharmacophore modeling --- density-based clustering --- structure-based drug design --- AutoGrid --- grid maps --- probe energies --- method development --- steered molecular dynamics --- all-atom molecular dynamics simulation --- resultant dipole moment --- mechanical stability --- protein-peptide interactions --- molecular dynamics --- proteins --- molecular recognition --- protein protein interactions --- artificial intelligence --- deep learning --- neural networks --- property prediction --- quantitative structure-activity relationship (QSAR) --- quantitative structure-property prediction (QSPR) --- de novo design --- adenosine receptor --- metadynamics --- extracellular loops --- allosterism --- molecular dynamics --- cosolvent molecular dynamics --- drug design --- fragment screening --- docking

Engineering Synthetic Metabolons: From Metabolic Modelling to Rational Design of Biosynthetic Devices

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199211 Year: Pages: 130 DOI: 10.3389/978-2-88919-921-1 Language: English
Publisher: Frontiers Media SA
Subject: General and Civil Engineering --- Biotechnology
Added to DOAB on : 2016-01-19 14:05:46
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The discipline of Synthetic Biology has recently emerged at the interface of biology and engineering. The definition of Synthetic Biology has been dynamic over time ever since, which exemplifies that the field is rapidly moving and comprises a broad range of research areas. In the frame of this Research Topic, we focus on Synthetic Biology approaches that aim at rearranging biological parts/ entities in order to generate novel biochemical functions with inherent metabolic activity. This Research Topic encompasses Pathway Engineering in living systems as well as the in vitro assembly of biomolecules into nano- and microscale bioreactors. Both, the engineering of metabolic pathways in vivo, as well as the conceptualization of bioreactors in vitro, require rational design of assembled synthetic pathways and depend on careful selection of individual biological functions and their optimization. Mathematical modelling has proven to be a powerful tool in predicting metabolic flux in living and artificial systems, although modelling approaches have to cope with a limitation in experimentally verified, reliable input variables. This Research Topic puts special emphasis on the vital role of modelling approaches for Synthetic Biology, i.e. the predictive power of mathematical simulations for (i) the manipulation of existing pathways and (ii) the establishment of novel pathways in vivo as well as (iii) the translation of model predictions into the design of synthetic assemblies.

Advances in Computer Simulation Studies on Crystal Growth

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ISBN: 9783038973560 9783038973577 Year: Pages: 206 DOI: 10.3390/books978-3-03897-357-7 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Chemistry (General)
Added to DOAB on : 2018-11-16 11:51:21
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Crystals are indispensable in technology, nature, and our daily lives. For example, cooking uses many kinds of crystallized products, such as salt, sugar, and fat crystals; electronic devices contain semiconductor crystals; living organisms produce mineral crystals to maintain biological processes; and snow and ice crystals play a crucial role in climate change. For these and other topics related to crystals, an especially important area of research is crystal growth. Computer simulations of crystal growth have become increasingly important as a result of rapid increases in available computing power. Computer simulations can analyze and predict various aspects of crystal growth, including molecular-scale growth and nucleation mechanisms, the structure and dynamics of surfaces and interfaces, and pattern formation. This book presents state-of-the-art research and reviews of computer simulation studies on crystal growth for hard-sphere particles, organic molecules, ice, and functional materials. The studies use a variety of simulation methodologies, including molecular simulations, first-principles simulations, continuum simulations, and multiscale simulations. This book will interest graduate students and researchers in crystal growth science and technology and will provide a helpful reference for scientists who want to familiarize themselves with computer simulations of crystal growth.

New Frontiers in Multiscale Modelling of Advanced Materials

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197552 Year: Pages: 91 DOI: 10.3389/978-2-88919-755-2 Language: English
Publisher: Frontiers Media SA
Subject: General and Civil Engineering --- Materials
Added to DOAB on : 2016-04-07 11:22:02
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Atomistic simulations, based on ab-initio and semi-empirical approaches, are nowadays widespread in many areas of physics, chemistry and, more recently, biology. Improved algorithms and increased computational power widened the areas of application of these computational methods to extended materials of technological interest, in particular allowing unprecedented access to the first-principles investigation of their electronic, optical, thermodynamical and mechanical properties, even where experiments are not available. However, for a big impact on the society, this rapidly growing field of computational approaches to materials science has to face the unfavourable scaling with the system size, and to beat the time-scale bottleneck. Indeed, many phenomena, such as crystal growth or protein folding for example, occur in a space/time scale which is normally out of reach of present simulations. Multi-scale approaches try to combine different scale algorithms along with matching procedures in order to bridge the gap between first-principles and continuum-level simulations. This Research Topic aims at the description of recent advances and applications in these two emerging fields of ab-inito and multi-scale materials modelling for both ground and excited states. A variety of theoretical and computational techniques are included along with the application of these methods to systems at increasing level of complexity, from nano to micro. Crossing the borders between several computational, theoretical and experimental techniques, this Research Topic aims to be of interest to a broad community, including experimental and theoretical physicists, chemists and engineers interested in materials research in a broad sense.

Ice Crystals

Author:
ISBN: 9783039218905 / 9783039218912 Year: Pages: 104 DOI: 10.3390/books978-3-03921-891-2 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Physics (General)
Added to DOAB on : 2019-12-09 11:49:16
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Ice crystals are the most ubiquitous material found in the cryosphere environment of the Earth, in the planetary system, and also in our daily lives. In recent years, ice crystals have increased in importance as one of the key materials for finding solutions to settle various environmental concerns at a global scale. Furthermore, ice crystals are unique materials which are potentially extremely useful in various applications, for example, within the food sciences, medical sciences, and other fields. In dealing with these interesting subjects, research on ice crystals has been more actively pursued in recent years. The Special Issue “Ice Crystals” presents a wide varieties of topics related to ice crystals. It can be considered as a status report reviewing the recent research on ice crystals and serves to provide readers with information on the latest developments concerning ice crystals.

Computational Methods of Multi-Physics Problems

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ISBN: 9783039214174 / 9783039214181 Year: Pages: 128 DOI: 10.3390/books978-3-03921-418-1 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Technology (General) --- General and Civil Engineering
Added to DOAB on : 2019-12-09 11:49:15
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This book offers a collection of six papers addressing problems associated with the computational modeling of multi-field problems. Some of the proposed contributions present novel computational techniques, while other topics focus on applying state-of-the-art techniques in order to solve coupled problems in various areas including the prediction of material failure during the lithiation process, which is of major importance in batteries; efficient models for flexoelectricity, which require higher-order continuity; the prediction of composite pipes under thermomechanical conditions; material failure in rock; and computational materials design. The latter exploits nano-scale modeling in order to predict various material properties for two-dimensional materials with applications in, for example, semiconductors. In summary, this book provides a good overview of the computational modeling of different multi-field problems.

Ionic Liquid Crystals

Author:
ISBN: 9783039210862 / 9783039210879 Year: Pages: 108 DOI: 10.3390/books978-3-03921-087-9 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Technology (General) --- Chemical Engineering
Added to DOAB on : 2019-06-26 08:44:06
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In this book we have collected a series of state-of-the art papers written by specialists in the field of ionic liquid crystals (ILCs) to address key questions concerning the synthesis, properties, and applications of ILCs. New compounds exhibiting ionic liquid crystalline phases are presented, both of calamitic as well as discotic type. Their dynamic and structural properties have been investigated with a series of experimental techniques including differential scanning calorimetry, polarized optical spectroscopy, X-ray scattering, and nuclear magnetic resonance, impedance spectroscopy to mention but a few. Moreover, computer simulations using both fully atomistic and highly coarse-grained force fields have been presented, offering an invaluable microscopic view of the structure and dynamics of these fascinating materials.

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