Modeling the Biomolecular Self-assembly and Interaction - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Modeling the Biomolecular Self-assembly and Interaction write by Xiaojia Mu. This book was released on 2014. Modeling the Biomolecular Self-assembly and Interaction available in PDF, EPUB and Kindle. What materials designers most envy is nature's building design. It has long been a dream for scientists to mimic and further engineer the behaviors, interactions, and reactions of biomolecules beyond experimental limits. To interpret and facilitate novel materials' design, a hierarchical approach is presented in this dissertation. With the advent of molecular modeling, many biomolecular interactions can be studied. Using both computational and experimental approaches, we investigated the self-assembly of fluorenylmethoxycarbonyl-conjugated dipeptides (which are called "biomimetic materials") including Fmoc-dialanine (Fmoc-AA) and Fmoc-Alanine-Lactic acid (Fmoc-ALac) molecules. We simulated the assembly of Fmoc-dipeptides and compared with experiments. We illustrated not only the angstrom-scale self-assembled structures, but also a prevalent polyproline II conformation with [Beta]-sheet-like hydrogen bonding pattern among short peptides. Further, simulations to calculate the potential of mean force (PMF) and melting temperatures were performed to gain deeper insights into the inter-fibril interaction. An energetic preference for fibril-fibril surface contact was demonstrated for the first time, which arises from a fibril-level amphiphilicity. From our study, a hierarchical self-assembly process mediated by the balance between hydrophobicity and hydrophilicity of fibril structures was unveiled. The next major topic in this dissertation involves the development of a chemically accurate polarizable multipole-based molecular mechanics model with the investigation of a series of chloromethanes. The ability of molecular modeling to make prediction is determined by the accuracy of underlying physical model. The traditional fixed-charge based force field is severely limited when applied to highly charged systems, halogen, phosphate and sulfate compounds. Via a sophisticated electrostatic model, an accurate description of electrostatics in organochlorine compounds and halogen bonds were achieved. Our model demonstrated its advantages by reproducing the experimental density and heat of vaporization; besides, the calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes were all in good agreement with experimental and ab initio data.
Mesoscale Chemistry
Mesoscale Chemistry - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Mesoscale Chemistry write by National Research Council. This book was released on 2015-08-06. Mesoscale Chemistry available in PDF, EPUB and Kindle. In the last few decades great strides have been made in chemistry at the nanoscale, where the atomic granularity of matter and the exact positions of individual atoms are key determinants of structure and dynamics. Less attention, however, has been paid to the mesoscale-it is at this scale, in the range extending from large molecules (10 nm) through viruses to eukaryotic cells (10 microns), where interesting ensemble effects and the functionality that is critical to macroscopic phenomenon begins to manifest itself and cannot be described by laws on the scale of atoms and molecules alone. To further explore how knowledge about mesoscale phenomena can impact chemical research and development activities and vice versa, the Chemical Sciences Roundtable of the National Research Council convened a workshop on mesoscale chemistry in November 2014. With a focus on the research on chemical phenomena at the mesoscale, participants examined the opportunities that utilizing those behaviors can have for developing new catalysts, adding new functionality to materials, and increasing our understanding of biological and interfacial systems. The workshop also highlighted some of the challenges for analysis and description of mesoscale structures. This report summarizes the presentations and discussion of the workshop.
Ion-mobility and Computational Modeling of Biomolecular Self-assembly and Aggregation
Ion-mobility and Computational Modeling of Biomolecular Self-assembly and Aggregation - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Ion-mobility and Computational Modeling of Biomolecular Self-assembly and Aggregation write by Thanh D. Do. This book was released on 2015. Ion-mobility and Computational Modeling of Biomolecular Self-assembly and Aggregation available in PDF, EPUB and Kindle. Protein self-assembly leading to fibril formation is an intriguing phenomenon that has been linked to pathological agents in devastating neurodegenerative diseases and has been found to have promising applications in the development of new functional materials. In this dissertation, a combination of ion-mobility mass spectrometry, high level molecular dynamics simulation and microscopy imaging has been employed to investigate the distributions of early oligomers, their conformational transitions in the presence of small-molecule modulators and the structures of toxic and non-toxic oligomers. A variety of biomolecule models was examined to elucidate the driving forces behind amyloid and non-amyloid self-assemblies, and to provide a new approach to aggregation propensity prediction.
Molecular Level Studies of Water-mediated Interactions and Their Role in Biomolecular Self-assembly
Molecular Level Studies of Water-mediated Interactions and Their Role in Biomolecular Self-assembly - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Molecular Level Studies of Water-mediated Interactions and Their Role in Biomolecular Self-assembly write by Tuhin Ghosh. This book was released on 2004. Molecular Level Studies of Water-mediated Interactions and Their Role in Biomolecular Self-assembly available in PDF, EPUB and Kindle.
Biomolecular Decision-making Process for Self Assembly
Biomolecular Decision-making Process for Self Assembly - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Biomolecular Decision-making Process for Self Assembly write by Gordon Cecil Osbourn. This book was released on 2005. Biomolecular Decision-making Process for Self Assembly available in PDF, EPUB and Kindle. The brain is often identified with decision-making processes in the biological world. In fact, single cells, single macromolecules (proteins) and populations of molecules also make simple decisions. These decision processes are essential to survival and to the biological self-assembly and self-repair processes that we seek to emulate. How do these tiny systems make effective decisions? How do they make decisions in concert with a cooperative network of other molecules or cells? How can we emulate the decision-making behaviors of small-scale biological systems to program and self-assemble microsystems? This LDRD supported research to answer these questions. Our work included modeling and simulation of protein populations to help us understand, mimic, and categorize molecular decision-making mechanisms that nonequilibrium systems can exhibit. This work is an early step towards mimicking such nanoscale and microscale biomolecular decision-making processes in inorganic systems.
