Top PDF Backbone flexibility in protein design theory and experiment

Backbone flexibility in protein design theory and experiment

Backbone flexibility in protein design theory and experiment

x Table of Contents Chapter 1: Introduction Chapter 2: Coupling Backbone Flexibility and Amino Acid Sequence Selection in Protein Design Chapter 3: Chapter 6: III-I Assembling De Novo Ba[r]

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Accelerating the Interplay Between Theory and Experiment in Protein Design

Accelerating the Interplay Between Theory and Experiment in Protein Design

Three popular prediction algorithms, Popmusic2, FoldX3, and Rosetta, were used to calculate the stability change of the 935 mutations in our domain mutagenesis dataset. Popmusic2 is a reduced-representation statistical energy function trained to recapitulate a large experimental dataset from the Protherm database. FoldX3 is similarly trained, but uses an empirically derived energy function mixed with weighted statistical terms. Rosetta mixes statistical potentials with an all-atom physical potential, and was trained to recover native sequence composition for protein design. Three versions of Rosetta are used, each with increasing amounts of backbone flexibility. The specific details and parameters used for each algorithm are described in the methods. Unfolded mutations for which only approximate data is available were filtered, leaving 825 mutations. Unrealistic predicted energies from the FoldX3 and Rosetta calculations prompted further filtering by removing mutations with abnormally high van der Waals clash or repulsive energies, respectively. Algorithm performance was evaluated by correlation coefficients (Table 4-4) and fraction correct % (Table 4-5). In addition, these metrics are reported for the datasets broken down by volume change, RESCLASS, and polarity change to assess performance by mutation type.
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Palladium based ferroelectrics and multiferroics : theory and experiment

Palladium based ferroelectrics and multiferroics : theory and experiment

An alternate option is ferroelectric and ferromagnetic composites/heterostructures which have greater design flexibility for ME devices by combining ferroelectric (FE) and ferromagnetic (FM) phases together; among them a heterostructure with FE/FM phases is the most popular design, due to immense potential for high density logic states. 34 Single-phase magnetoelectric materials with large ME coupling coefficients in ultrathin hetero-structured films are important for tunnel junction-based devices, which can provide a higher degree of logic states under combined electric and magnetic control. These factors drive the endeavors for discovering new room temperature single-phase multiferroics with giant ME coupling, beyond BiFeO 3 . Several materials have recently been discovered, such as Pb(Zr 0.53 Ti 0.47 ) 0.60
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OPTIMAL COMMUNICATION BACKBONE DESIGN FOR A TYPICAL LRT URBAN TRANSPORTATION CASE

OPTIMAL COMMUNICATION BACKBONE DESIGN FOR A TYPICAL LRT URBAN TRANSPORTATION CASE

In conjunction with the construction of a LRT line, a new communication infrastructure becomes essential to support safe, reliable and continuous operations. In addition to remote monitoring and control of LRT operations, such an infrastructure facilitates interactions and exchanges between various City services. Typical communication infrastructure covers the entire alignment including operational control center and offices close or remote to the alignment itself. In any case, communication backbone infrastructure is an integrated solution that brings together various aspects of communication services and the entire user’s scope of requirements. Therefore, industry best practices include the following:
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Aspectual Flexibility Increases with Agentivity and ConcretenessA Computational Classification Experiment on Polysemous Verbs

Aspectual Flexibility Increases with Agentivity and ConcretenessA Computational Classification Experiment on Polysemous Verbs

In this work, we focused on the way the aspectual value of French verbs varies across their different readings, as listed and described in a syntactic-semantic lexical resource. We used a machine learning approach based on features ex- tracted from the lexicon. We showed that the extracted in- formation enabled a fairly accurate prediction of the aspec- tual class. In addition, our results based on feature selection suggest that agentivity and abstractness also contribute to the selection of the correct aspectual value. Our results can also be analyzed as confirming the additional hypothesis that aspectual flexibility is higher when verbs are used un- der their agentive and/or concrete (literal) readings than un- der their nonagentive and/or abstract (figurative) readings.
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High Capacity Optical Fiber Link Design For Telecommunication Backbone Network

High Capacity Optical Fiber Link Design For Telecommunication Backbone Network

Now a day’s high speed and high capacity are the two preconditions for telecommunication networks to provide good quality and huge support to the subscribers. Today’s telecommunication network is mainly based on the optical fiber (OF). In many developing countries they have the optical fiber telecommunication network. But the speed and capacity both are low. The users of these telecommunication networks are increasing day by day. So it is necessary to upgrade the existing OF network to a high speedy and high capacity network. To do so we have designed and simulated a 40 Gbps single OF link which is easy and cost effective. For capacity increasing we also designed a WDM system with 8 channels which corresponds the total capacity of 320 Gbps data rate. We analyzed the design from the result of the simulation based on the BER and Eye Diagram. BER is defined as [1]-
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Design and design dogmas : an exploration and thought experiment

Design and design dogmas : an exploration and thought experiment

The framework of ‘Biomimicry’, “the conscious emulation of life’s genius” (Benyus, 1997, p.2), is one of the circa hundred ecological views (Esbjörn-Hargens, 2005) on the natural environment, and it provides a possible methodology to learn from nature by unravelling and copying biological systems, that have evolved over a time-span of 3.8 billion years. Importantly, there are plenty of analogies to draw between nature and technology. On all levels, from nano-sized systems to biomes, and from a low level of imitation to a high level, nature’s functioning can serve as an inspiration for design. One of the key reasons covers that the amount of energy used within technological and natural systems is highly contrasting. “Whereas technology solves 70 per cent of problems in the general area of material processing (taken to be in the micrometre size range) using energy as a control parameter, in biology energy is the least significant control parameter over the entire size range” (Vincent, 2009). “To make a material like e.g. metals, ceramics, polymers and composites, ingredients are put together, and undergo at least one – if not all – of the processes of heat, beat and treat” (Benyus, 1997). Vincent and Benyus indicate that production (and use) of human made systems rely on energy, and nature’s systems rely on information, presented in DNA. The emulation of natural materials in particular will open up a new world for exploration, since its components and structures require a new way of looking at composing new materials, production techniques and the final design’s purposes. Biomimicry can provide a possible answer to our urge for direct resource accessibility, however, it does also rely on a scientific approach towards nature that uses algorithms and systematics. Through the notion of ‘Econs’ and ‘Humans’ 19 ,
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Protein flexibility is key to cisplatin crosslinking in calmodulin

Protein flexibility is key to cisplatin crosslinking in calmodulin

Deletion of the calcium ions from the 1CLL structure [Fig. 2(B)] removes constraints from the network as protein–metal bonds are no longer pres- ent. The effects on the rigidity analysis are greatest at small values of the energy cutoff and are particu- larly visible in the N-terminal region. With calcium bound, residues 5–35 form as a solid robust helix structure [Fig. 2(A)]; upon removal of the calcium, the same region splits into two helices connected by a flexible linker region (residues, 19–30) [Fig. 2(B)]. The flexibility simulations were carried out using three different cutoffs (1, 2, and 3 kcal/mol) for both the native- and the calcium-deleted structures. This allowed us to explore the flexible motion of the structure both when it is largely rigid and when it is largely flexible. 25
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The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone

The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone

largely by the geometric constraints placed upon residues when a folded protein is in its native state. In a peptide chain or unfolded or partly folded protein, there is the possibility that this energy could be larger because the geometric constraints are not so severe and the molecules can approach one another in a more favourable way. Additionally, there is the possibility that several separate interactions can be present. With this in mind, we find that a simple kinetic model does describe the variation of k inst (t)

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The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone

The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone

Although protein folding is often described by motion on a funnel-shaped overall topology of the energy landscape, the many local interactions that can occur result in considerable landscape roughness which slows folding by increasing internal friction. Recent experimental results have brought to light that this roughness also causes unusual diffusional behaviour of the backbone of an unfolded protein, i.e. the relative motion of protein sections cannot be described by the normal diffusion equation, but shows

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Design and status of the Mu2e experiment

Design and status of the Mu2e experiment

A model independent description of the CLFV transi- tions for physics beyond the Standard Model is provided by an effective lagrangian [6] where the different pro- cesses are divided in dipole amplitudes and four-fermion, or contact term, operators. The μ → e γ decay is mainly sensitive to the dipole amplitude, while μ → e conver- sion and μ → 3e receive contributions also from the four- fermion interactions. It is customary to parametrize the interplay between the two amplitudes by means of two pa- rameters [6]: Λ , which sets the mass scale and κ , which governs the ratio of the four-fermion to the dipole ampli- tude. For κ << 1( >> 1) the dipole-type (four-fermion) operator dominates. Figure 1 summarizes the power of different searches to explore this parameter space. A scale Λ < 700 TeV is already excluded by present lim- its and poses serious constraints on Standard Model exten- sions, primarily, supersymmetry. Nevertheless, Λ is only an effective scale and is not immediately proportional to the mass of new particles accessible by direct TeV scale searches at LHC. The interpretation of an eventual di- rect observation of new physics at LHC will have to take into account precise measurements from MEG and Mu2e where the comparison between these determinations will provide the constraints necessary in pinning down the un- derlying theory.
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Investigation of Spin Injection in Semiconductors: Theory and Experiment

Investigation of Spin Injection in Semiconductors: Theory and Experiment

tion techniques has never ceased to amaze me. Bob, thanks for sharing your insight and knowledge of device physics with me. Much of what I have included in the chapter on device characterization I owe to discussions with you. Rob, thank you for your help with the electrical characterization of my devices and with that darn MMR probe station. You could always be counted on to bring a sense of levity to any situation. Thank you, Paul, for your encouragement and dry wit. Talking with you always motivated me to work harder to finish. Thanks, Neal, for helping me to gain a slightly better appreciation for materials science and for helping me from afar with the metalization chamber. I could not have asked for a better o ffi cemate. I hope your desk at Intel is a step up from that big cardboard box you were using! Ed, thanks for showing me that it’s possible to jury-rig just about any- thing in the lab. I bet you could make a new hemispherical analyzer for our XPS system from a handful of peanuts and two Coke cans. Xavier, thank you for sharing your insane understanding of solid state theory with us. The Monte Carlo simulation would have been impossible aside from your contributions to the photon generation code. And Justin, thanks for showing me the ropes on the cryostats. And thanks also for showing me that it is pos- sible to successfully make the transition from high-energy physics to solid state. To all of the guys, thanks for the hours of “network testing.” The stress relief from that has certainly helped me to push through and finish this thesis.
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Investigation of electronic structure of Nd2O3: Experiment and theory

Investigation of electronic structure of Nd2O3: Experiment and theory

alised gradient approximation made simple. Physical Re- view Letters, 77, 3865. doi:10.1103/PhysRevLett.77.3865 [18] Hammer, B., Hansen, L.B. and Norskov, J.K. (1999) Im- proved adsorption energetics within density-functional theory using revised Perdew-Burke-Ernzerhof functionals. Physical Review Letters, 59, 7413.

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Reference dependent ambiguity aversion: theory and experiment

Reference dependent ambiguity aversion: theory and experiment

Constructing the ambiguous gamble properly is critical to the experiment. Although the construction procedure must be perfectly clear, the gamble itself should be regarded by students as ambiguous. We constructed the ambiguous gamble according to the following procedure, which was announced publicly before we implemented it. At the start of the experiment we asked ten randomly selected subjects, who did not participate in rest of the experiment, to pick an integer number between 0 to 10. We did not tell them how are we going to use those numbers. Each of them left the experimental room, secretely wrote the number on a small piece of paper, which they then folded, to hide the number. They then brought the folded pieces of paper into the experimental room and we asked another randomly chosen subject, who did not participate in rest of the experiment, to help us with the construction of the ambiguous gamble. This helper randomly picked one of the ten folded papers. We then gave the helper two bags: one with 10 black chips and one with 10 white chips. We asked the helper to leave the experimental room and use the two bags to produce an ambiguous bag of 10 chips, in which the number of black chips should be the number on the paper she has drawn. When finished, the helper returned with two closed bags, placed the ambiguous bag on the desk in the front and stashed the other away. Neither the experimenters nor the subjects knew the contents of any of the two bags throughout the experiment.
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Diversity and flexibility in sustainable supply chain design

Diversity and flexibility in sustainable supply chain design

flexibility. Process flexibility has been defined as, “The ability to produce a given set of part types, each possibly using different materials in several ways” (Beach et al., 2000; Browne et al., 1984). Consider first then as a beginning illustration the industries described above that draw their feedstock straight from the soil (agriculture, textiles and biorenewables) to be, in some cases, product flexible. Food, as a source of nutrients and energy certainly is so. Some textiles can be made from blends of different plant types by mixing standard cotton-twill denim, as one example, with also hemp and recycled fibers. In bioenergy, conversion technologies like fast pyrolysis have shown the ability to output energy and liquid fuels with a huge variety of different plant-based feedstock (Correll, 2009).
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Developments in plane and concave gratings: theory and experiment

Developments in plane and concave gratings: theory and experiment

Tables 7'.8 and 7.9 compare the behaviour of T ijk 's in the final spectral image as a function of the wavelength for holographic concave gratings generated according to both the general[r]

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The electronic structure of silver orthophosphate: Experiment and theory

The electronic structure of silver orthophosphate: Experiment and theory

We would like to thank Professor Russell Egdell and Professor Louis Piper for very helpful discussions. D. J. P. acknowledges support from the Royal Society (UF100105). J. M. K. acknowl- edges support from EPSRC for a Doctoral Prize Studentship. D. J. P. and D. O. S. acknowledge the support of the Materials Design Network. The work in TCD was supported by SFI through the PI programme (PI Grant numbers 06/IN.1/I92 and 06/IN.1/I92/EC07). Calculations were performed on the Kelvin and Lonsdale supercomputers as maintained by TCHPC. B. J. M. acknowledges support from EPSRC grant ref. EP/ H003819/1. The NCESS XPS Facility was supported by EPSRC Grant no. EP/E025722/1.
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A pseudospark cathode Cherenkov maser : theory and experiment

A pseudospark cathode Cherenkov maser : theory and experiment

For values of the beam and waveguide para- meters relevant to the experiment, the force exerted on the electrons by the waveguide mode is domin- ated by the space-charge force, so the maser will operate in a Raman-type regime, with strongest amplification of the waveguide mode expected when it is resonant with the slow space-charge wave of the beam i.e. when the angular frequency, u , and the axial wavenumber, k, of the waveguide mode satisfy the relation

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The proton size puzzle: experiment vs theory.

The proton size puzzle: experiment vs theory.

more accurate construction of the particle interaction operator in quantum field theory, the calculation of new corrections whose value for muonic atoms can increase substantially in comparison with electronic atoms. The expected results will allow to get also a new very important information about the forces which are responsible for the structure of atoms.

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Software engineering : theory, experiment, practice or performance

Software engineering : theory, experiment, practice or performance

In software engineering, a method for constructing programs is as much a subject of study as a method used in a program to solve a particular problem; one is part of what is called progr[r]

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