scholarly journals A collection of programs for one-dimensional Ising analysis of linear repeat proteins with point substitutions

2020 ◽  
Author(s):  
Jacob D. Marold ◽  
Kevin Sforza ◽  
Kathryn Geiger-Schuller ◽  
Tural Aksel ◽  
Sean Klein ◽  
...  
Keyword(s):  
Parameter Uncertainty ◽  
Free Energies ◽  
Interfacial Coupling ◽  
Bootstrap Analysis ◽  
One Dimensional ◽  
Repeat Proteins ◽  
Rigorous Statistical Analysis ◽  
Estimate Parameter ◽  
Rigorous Framework ◽  
Complex Models

AbstractA collection of programs is presented to analyze the thermodynamics of folding of linear repeat proteins using a 1D Ising model to determine intrinsic folding and interfacial coupling free energies. Expressions for folding transitions are generated for a series of constructs with different repeat numbers and are globally fitted to transitions for these constructs. These programs are designed to analyze Ising parameters for capped homopolymeric consensus repeat constructs as well as heteropolymeric constructs that contain point substitutions, providing a rigorous framework for analysis of the effects of mutation on intrinsic and directional (i.e., N- versus C-terminal) interfacial coupling free-energies. A bootstrap analysis is provided to estimate parameter uncertainty as well as correlations among fitted parameters. Rigorous statistical analysis is essential for interpreting fits using the complex models required for Ising analysis of repeat proteins, especially heteropolymeric repeat proteins. Programs described here are available at https://github.com/barricklab-at-jhu/Ising_programs.

Application of a Generalized Frobenius-Perron Operator Scheme to Multivariate Nonlinear Dynamical Systems

1995 ◽  
Vol 50 (12) ◽  
pp. 1123-1127
Author(s):  
R. Stoop ◽  
W.-H. Steeb
Keyword(s):  
Dynamical Systems ◽  
Nonlinear Dynamical Systems ◽  
Free Energies ◽  
Nonlinear Dynamical ◽  
One Dimensional ◽  
One Dimensional Maps ◽  
Operator Scheme

Abstract The concept of generalized Frobenius-Perron operators is applied to multivariante nonlinear dynamical systems, and the associated generalized free energies are investigated. As important applications, diffusion-related free energies obtained from normally and superlinearly diffusive one-dimensional maps are discussed.

Optimal Design of Sandwich Beam With Frequency Constraints

2007 ◽  
Author(s):  
Vladimir B. Gantovnik ◽  
Alexander V. Lopatin ◽  
Lubov V. Shumkova
Keyword(s):  
Equations Of Motion ◽  
Sandwich Beam ◽  
Vibrational Analysis ◽  
Optimal Parameters ◽  
One Dimensional ◽  
Sandwich Plates And Shells ◽  
Complex Models ◽  
Plates And Shells ◽  
Transversal Vibrations ◽  
Selection Of

In this paper, we analyze selection of optimal parameters of sandwich beam in the presence of constraints on the frequencies of the transversal vibrations. The employed equations of motion take into account the transverse shear deformations in the core and rotatory inertia of the beam cross-section. The expressions for the transversal vibrations are obtained. The results show that one-dimensional model of the sandwich beam can be used for preliminary vibrational analysis of more complex models of sandwich plates and shells.

scholarly journals EFFECTS OF THE DEVIATION ANGLE OF THE BOREHOLE IN THE INDUCTION ANISOTROPY LOGS

2018 ◽  
Vol 36 (4) ◽  
pp. 1
Author(s):  
Paulo Roberto de Carvalho ◽  
Cícero Régis ◽  
Valdelírio da Silva e Silva
Keyword(s):  
Well Logging ◽  
Deviation Angle ◽  
Vertical Wells ◽  
One Dimensional ◽  
Anisotropic Models ◽  
Coil Arrays ◽  
Complex Models ◽  
Dip Angle ◽  
Basic Insight ◽  
Vertical Case

ABSTRACT. This paper performs an analysis of the effects of the well’s deviated angle on the tensor triaxial induction tool signals within a thinly sand-shale laminated reservoirs and their equivalent intrinsic anisotropic models. The responses from coaxial and coplanar coil arrays in inclined wells are studied in detail, including the analysis of their apparent anisotropy logs, as well as their estimation of sand conductivity in the environments with a structural anisotropy.The dip angle effects are modeled in simple geometries as one-dimensional (1D) models, neglecting the presence of the borehole and the invasion zones, since they provide basic insight for understanding tool responses in more complex models. The results show a strong sensitivity of both the coaxial and coplanar signals to the deviated angle. It is verified that the anisotropy values are significantly reduced when the well is inclined as compared to what is found for the true vertical case, even for inclinations small enough for the wells to be classified as technically vertical (30 degrees or less). Therefore, the angle effects must be carefully considered, even for technically vertical wells. Otherwise, potential finely laminated reservoirs can be underestimated or even ignored.Keywords: deviated well logging, tensor induction tool, laminated reservoirs, electrical anisotropy.RESUMO. Neste trabalho é apresentado como as incertezas na interpretação sísmica impactam na cons-trução do modelo de velocidades e na conversão tempo-profundidade resultante. A área de estudo de estudo está localizada na Bacia de Campos, Brasil. O principal objetivo deste trabalho é mostrar como os dados de entrada e parâmetros afetam na modelagem de velocidade e conversão tempo x profundidade. A metodologia é comparar três diferentes cenários para calibração da velocidade de processamento e imageamento com as interpretações sísmicas e de poços: o cenário 1 utiliza ajuste por horizonte com marcador geológico e raio de influência 5 km; no cenário 2 é utilizada as tabelas tempo-profundidade, raio de influência 5 km por krigagem com derivada externa; e o cenário 3 utilizou-se tabelas tempo-profundidade, raio de influência 2 km por krigagem com deriva externa. O controle de qualidade dos três modelos de velocidade são avaliados pela conversão dos horizontes, seções sísmicas e perfis de pseudo-impedância. No cenário 1, os horizontes convertidos apresentam menores diferenças de profundidade em relação aos marcadores comparados aos demais cenários. Por outro lado, os cenários 2 e 3 apresentam maiores correlações entre o sismograma sintético e a seção sísmica convertida para o cenário 1. Palavras-chave: poços desviados, ferramentas triaxiais, reservatórios laminados, anisotropia elétrica.

scholarly journals Getting started with controlled-source electromagnetic 1D modeling

2017 ◽  
Vol 36 (4) ◽  
pp. 352-355 ◽  
Author(s):  
Dieter Werthmüller
Keyword(s):  
Forward Modeling ◽  
Higher Dimensions ◽  
Hydrocarbon Exploration ◽  
Fine Scale ◽  
One Dimensional ◽  
Controlled Source ◽  
1D Modeling ◽  
Resistivity Anisotropy ◽  
Complex Models ◽  
Diffusive Term

Forward modeling is an important part of understanding controlled-source electromagnetic (CSEM) responses. The diffusive term in the electromagnetic wave equation is dominant over the displacement term at these frequencies. It is the diffusive behavior that makes it difficult to imagine the actual propagation of the signal. An important tool in gaining experience therefore is forward modeling, and lots of it. The advantage of one-dimensional (1D) forward modeling, besides its speed, is to study isolated effects (see for instance Key, 2009): What is the influence of resistivity anisotropy, or of fine-scale resistivity variations? What is the influence of the airwave? With 1D modeling you can quickly study these effects in isolation before you go on to more complex models in higher dimensions. For an introduction to CSEM for hydrocarbon exploration see, for instance, Constable (2010).

scholarly journals Stochastic Hydrology: Is Scientific Understanding Growing?

2020 ◽  
Vol 163 ◽  
pp. 06001
Author(s):  
Mikhail Bolgov
Keyword(s):  
Climate Changes ◽  
Probability Distributions ◽  
Random Processes ◽  
Stochastic Hydrology ◽  
One Dimensional ◽  
Probabilistic Forecasts ◽  
Markovian Property ◽  
New Models ◽  
Complex Models ◽  
With Memory

Among many problems of stochastic hydrology, several major problems may be singled out. (1) The methodology problem – may fluctuation of hydro-meteorological values be considered within the framework of probabilities and random processes? Was this topic discussed after 1953? (2) One-dimensional probability distributions – is there progress? Are there new models? (3) Random Processes: Is Markovian property sufficient or more complex models with memory are needed? (4) Lack of stability resulting from climate changes: Is there progress in understanding the approaches to probabilistic forecasts?

scholarly journals Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions

2018 ◽  
Vol 115 (29) ◽  
pp. 7539-7544 ◽  
Author(s):  
Kathryn Geiger-Schuller ◽  
Kevin Sforza ◽  
Max Yuhas ◽  
Fabio Parmeggiani ◽  
David Baker ◽  
...  
Keyword(s):  
Protein Design ◽  
Nearest Neighbor ◽  
De Novo ◽  
Protein Structures ◽  
Free Energies ◽  
Intrinsic Stability ◽  
Repeat Proteins ◽  
Naturally Occurring ◽  
Wide Range ◽  
The Individual

Designed helical repeats (DHRs) are modular helix–loop–helix–loop protein structures that are tandemly repeated to form a superhelical array. Structures combining tandem DHRs demonstrate a wide range of molecular geometries, many of which are not observed in nature. Understanding cooperativity of DHR proteins provides insight into the molecular origins of Rosetta-based protein design hyperstability and facilitates comparison of energy distributions in artificial and naturally occurring protein folds. Here, we use a nearest-neighbor Ising model to quantify the intrinsic and interfacial free energies of four different DHRs. We measure the folding free energies of constructs with varying numbers of internal and terminal capping repeats for four different DHR folds, using guanidine-HCl and glycerol as destabilizing and solubilizing cosolvents. One-dimensional Ising analysis of these series reveals that, although interrepeat coupling energies are within the range seen for naturally occurring repeat proteins, the individual repeats of DHR proteins are intrinsically stable. This favorable intrinsic stability, which has not been observed for naturally occurring repeat proteins, adds to stabilizing interfaces, resulting in extraordinarily high stability. Stable repeats also impart a downhill shape to the energy landscape for DHR folding. These intrinsic stability differences suggest that part of the success of Rosetta-based design results from capturing favorable local interactions.

Osmotic and activity coefficients of triorganophosphates in n-octane

1982 ◽  
Vol 60 (22) ◽  
pp. 2755-2759 ◽  
Author(s):  
Norman H. Sagert ◽  
Danny W. P. Lau
Keyword(s):  
Thermodynamic Properties ◽  
Vapor Pressure ◽  
Activity Coefficients ◽  
Osmotic Coefficients ◽  
Vapor Pressure Osmometry ◽  
Excess Enthalpies ◽  
Free Energies ◽  
Ideal Behavior ◽  
Excess Thermodynamic Properties ◽  
Complex Models

Vapor pressure osmometry was used to measure osmotic coefficients for tributylphosphate (TBP), tricresylphosphate (TCP), and triethylhexylphosphate (TEHP) in n-octane at 30, 40, 50, and 60 °C and at molalities up to 0.3 mol/kg. Activity coefficients and excess thermodynamic properties (unsymmetrical definition) were calculated from these osmotic coefficients. At 30 °C, the excess Gibbs free energies for 0.1 mol of solute in 1.0 kg n-octane were −42 J, −66 J, and −20 J for TBP, TCP, and TEHP, respectively. The more ideal behavior of the TEHP-octane system is attributed to the increasing importance of hydrocarbon–hydrocarbon interactions as the chain length is increased. The excess enthalpies for 0.1 mol of solute in 1.0 kg of solvent were −100 J, −300 J, and −150 J for TBP, TCP, and TEHP, respectively. Thus, association of these solutes arises primarily from entropie effects.Our data could generally be accommodated adequately by postulating association of monomers into dimers. The exception was TCP at lower temperatures, where more complex models were required.

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