THE SCANNING SIMULATION METHOD FOR MACROMOLECULES

1990 ◽  
Vol 01 (01) ◽  
pp. 119-145 ◽  
Author(s):  
HAGAI MEIROVITCH
Keyword(s):  
Critical Exponents ◽  
Simulation Method ◽  
Branched Polymers ◽  
Double Scanning ◽  
Scanning Method ◽  
Collapse Transition ◽  
Wide Range ◽  
The Stability ◽  
Future Work ◽  
Θ Point

We discuss the statistical properties of the scanning simulation method for macromolecules and its variant, the double scanning method. We summarize results (in particular critical exponents and transition temperatures) obtained for a wide range of models, branched polymers, polymers adsorbed on a surface and polymers at their collapse transition (the Flory θ-point). We describe application of the methods for studying the stability of polypeptides and discuss plans for future work.

scholarly journals Large-scale design and refinement of stable proteins using sequence-only models

2021 ◽  
Author(s):  
Jedediah M. Singer ◽  
Scott Novotney ◽  
Devin Strickland ◽  
Hugh K. Haddox ◽  
Nicholas Leiby ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Large Scale ◽  
Amino Acid Sequences ◽  
Novel Proteins ◽  
Wide Range ◽  
The Stability ◽  
Scale Design ◽  
Future Work

AbstractEngineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As a consequence, many designs must be tested computationally and experimentally in order to find stable ones, which is expensive in terms of time and resources. Here we report a neural network model that predicts protein stability based only on sequences of amino acids, and demonstrate its performance by evaluating the stability of almost 200,000 novel proteins. These include a wide range of sequence perturbations, providing a baseline for future work in the field. We also report a second neural network model that is able to generate novel stable proteins. Finally, we show that the predictive model can be used to substantially increase the stability of both expert-designed and model-generated proteins.

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

Insights into Potent Therapeutical Antileukemic Agent L-glutaminase Enzyme Under Solid-state Fermentation: A Review

2020 ◽  
Vol 21 (3) ◽  
pp. 211-220 ◽  
Author(s):  
Chandrasai Potla Durthi ◽  
Madhuri Pola ◽  
Satish Babu Rajulapati ◽  
Anand Kishore Kola
Keyword(s):  
Solid State ◽  
Solid State Fermentation ◽  
Food Industry ◽  
Energy Requirement ◽  
Production Studies ◽  
Wide Range ◽  
Hybridoma Technology ◽  
Bacteria And Fungi ◽  
The Stability ◽  
Glutaminase Activity

Aim & objective: To review the applications and production studies of reported antileukemic drug L-glutaminase under Solid-state Fermentation (SSF). Overview: An amidohydrolase that gained economic importance because of its wide range of applications in the pharmaceutical industry, as well as the food industry, is L-glutaminase. The medical applications utilized it as an anti-tumor agent as well as an antiretroviral agent. L-glutaminase is employed in the food industry as an acrylamide degradation agent, as a flavor enhancer and for the synthesis of theanine. Another application includes its use in hybridoma technology as a biosensing agent. Because of its diverse applications, scientists are now focusing on enhancing the production and optimization of L-glutaminase from various sources by both Solid-state Fermentation (SSF) and submerged fermentation studies. Of both types of fermentation processes, SSF has gained importance because of its minimal cost and energy requirement. L-glutaminase can be produced by SSF from both bacteria and fungi. Single-factor studies, as well as multi-level optimization studies, were employed to enhance L-glutaminase production. It was concluded that L-glutaminase activity achieved by SSF was 1690 U/g using wheat bran and Bengal gram husk by applying feed-forward artificial neural network and genetic algorithm. The highest L-glutaminase activity achieved under SSF was 3300 U/gds from Bacillus sp., by mixture design. Purification and kinetics studies were also reported to find the molecular weight as well as the stability of L-glutaminase. Conclusion: The current review is focused on the production of L-glutaminase by SSF from both bacteria and fungi. It was concluded from reported literature that optimization studies enhanced L-glutaminase production. Researchers have also confirmed antileukemic and anti-tumor properties of the purified L-glutaminase on various cell lines.

Positive Emotion in Generalized Anxiety Disorder

2019 ◽  
pp. 297-311
Author(s):  
Ilana Seager ◽  
Douglas S. Mennin ◽  
Amelia Aldao
Keyword(s):  
Anxiety Disorder ◽  
Positive Affect ◽  
Generalized Anxiety Disorder ◽  
Positive Emotion ◽  
Behavioral Therapy ◽  
Generalized Anxiety ◽  
Emotional Dysfunction ◽  
Wide Range ◽  
Future Work

Generalized anxiety disorder (GAD) is a debilitating condition characterized by excessive, pervasive, uncontrollable, and paralyzing worries about a wide range of future situations. Individuals with this condition frequently find themselves stuck in worry and tension cycles in futile attempts at reducing uncertainty and increasing control. GAD has been associated with substantial impairments in functioning and reduced quality of life. GAD remains poorly understood, and the long-term efficacy and end-state functioning resulting from treatment are weaker compared to other anxiety disorders. Some treatments (e.g., emotion regulation therapy, acceptance-based behavioral therapy) have improved efficacy, partly by targeting emotional dysfunction. Basic psychopathology research has focused on identifying the role of negative affect in GAD, so little is known about how positive affect is experienced and regulated in this disorder. This is particularly important in light of the overlap of this condition with major depressive disorder, which is characterized by low or suppressed positive emotion. Developing such an understanding is essential to further improve the efficacy of emotion-based treatments. This chapter reviews current and future directions in the study of positive affect in GAD. The chapter reviews the nascent research on positive affect and GAD, then illustrates dimensions of future work.

scholarly journals Polymer-Drug Conjugates as Nanotheranostic Agents

2021 ◽  
Vol 2 (1) ◽  
pp. 63-81
Author(s):  
Sajana Manandhar ◽  
Erica Sjöholm ◽  
Johan Bobacka ◽  
Jessica M. Rosenholm ◽  
Kuldeep K. Bansal
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Treatment Options ◽  
The Body ◽  
Drug Conjugates ◽  
Imaging Characteristics ◽  
Wide Range ◽  
Systemic Side Effects ◽  
Theranostic Agents ◽  
The Stability

Since the last decade, the polymer-drug conjugate (PDC) approach has emerged as one of the most promising drug-delivery technologies owing to several benefits like circumventing premature drug release, offering controlled and targeted drug delivery, improving the stability, safety, and kinetics of conjugated drugs, and so forth. In recent years, PDC technology has advanced with the objective to further enhance the treatment outcomes by integrating nanotechnology and multifunctional characteristics into these systems. One such development is the ability of PDCs to act as theranostic agents, permitting simultaneous diagnosis and treatment options. Theranostic nanocarriers offer the opportunity to track the distribution of PDCs within the body and help to localize the diseased site. This characteristic is of particular interest, especially among those therapeutic approaches where external stimuli are supposed to be applied for abrupt drug release at the target site for localized delivery to avoid systemic side effects (e.g., Visudyne®). Thus, with the help of this review article, we are presenting the most recent updates in the domain of PDCs as nanotheranostic agents. Different methodologies utilized to design PDCs along with imaging characteristics and their applicability in a wide range of diseases, have been summarized in this article.

scholarly journals No-z Model for Magnetic Fields of Different Astrophysical Objects and Stability of the Solutions

Data ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 4
Author(s):  
Evgeny Mikhailov ◽  
Daniela Boneva ◽  
Maria Pashentseva
Keyword(s):  
Magnetic Field ◽  
Magnetic Fields ◽  
Large Scale ◽  
Point Of View ◽  
Accretion Discs ◽  
Wide Range ◽  
Astrophysical Objects ◽  
Alpha Effect ◽  
The Stability ◽  
The Magnetic Field

A wide range of astrophysical objects, such as the Sun, galaxies, stars, planets, accretion discs etc., have large-scale magnetic fields. Their generation is often based on the dynamo mechanism, which is connected with joint action of the alpha-effect and differential rotation. They compete with the turbulent diffusion. If the dynamo is intensive enough, the magnetic field grows, else it decays. The magnetic field evolution is described by Steenbeck—Krause—Raedler equations, which are quite difficult to be solved. So, for different objects, specific two-dimensional models are used. As for thin discs (this shape corresponds to galaxies and accretion discs), usually, no-z approximation is used. Some of the partial derivatives are changed by the algebraic expressions, and the solenoidality condition is taken into account as well. The field generation is restricted by the equipartition value and saturates if the field becomes comparable with it. From the point of view of mathematical physics, they can be characterized as stable points of the equations. The field can come to these values monotonously or have oscillations. It depends on the type of the stability of these points, whether it is a node or focus. Here, we study the stability of such points and give examples for astrophysical applications.

scholarly journals Study on Friction in Automotive Shock Absorbers Part 1: Friction Simulation Using a Dynamic Friction Model in the Contact Zone of an FEM Model

Vehicles ◽  
2021 ◽  
Vol 3 (2) ◽  
pp. 212-232
Author(s):  
Ludwig Herzog ◽  
Klaus Augsburg
Keyword(s):  
Ride Comfort ◽  
Viscous Friction ◽  
Simulation Method ◽  
Friction Model ◽  
Model Parameters ◽  
Dynamic Friction ◽  
Friction Modeling ◽  
Shock Absorbers ◽  
Operation Conditions ◽  
Wide Range

The important change in the transition from partial to high automation is that a vehicle can drive autonomously, without active human involvement. This fact increases the current requirements regarding ride comfort and dictates new challenges for automotive shock absorbers. There exist two common types of automotive shock absorber with two friction types: The intended viscous friction dissipates the chassis vibrations, while the unwanted solid body friction is generated by the rubbing of the damper’s seals and guides during actuation. The latter so-called static friction impairs ride comfort and demands appropriate friction modeling for the control of adaptive or active suspension systems. In this article, a simulation approach is introduced to model damper friction based on the most friction-relevant parameters. Since damper friction is highly dependent on geometry, which can vary widely, three-dimensional (3D) structural FEM is used to determine the deformations of the damper parts resulting from mounting and varying operation conditions. In the respective contact zones, a dynamic friction model is applied and parameterized based on the single friction point measurements. Subsequent to the parameterization of the overall friction model with geometry data, operation conditions, material properties and friction model parameters, single friction point simulations are performed, analyzed and validated against single friction point measurements. It is shown that this simulation method allows for friction prediction with high accuracy. Consequently, its application enables a wide range of parameters relevant to damper friction to be investigated with significantly increased development efficiency.

Stability Prediction of Surrounding Rocks and Optimum Design of Roof-Bolt Parameters in Deep Roadway

2013 ◽  
Vol 353-356 ◽  
pp. 436-439
Author(s):  
De Sen Kong ◽  
Yong Po Chen
Keyword(s):  
Prediction Method ◽  
Simulation Method ◽  
Complex Stress ◽  
Roof Bolt ◽  
Deformation And Failure ◽  
Long Run ◽  
Research Findings ◽  
Stress Environment ◽  
Classification Prediction ◽  
The Stability

In order to forecast the stability of deep roadway and optimize the parameters of bolts, the complex stress environment and the multivariate surrounding rocks characteristics of deep roadway were analyzed. Then the classification prediction method and the numerical simulation method were simultaneously used to analysis the stability of surrounding rocks. Furthermore, the supporting parameters of bolts were also designed optimally. It was shown that the characteristics of stress distribution, deformation and failure zone of surrounding rocks are not ideal. So it is necessary to optimize the supporting parameters of deep roadway. All these research findings will provide the theory basis for bolts of deep roadway and will ensure the optimization of bolts and the stability of deep roadway in the long run.

Mechanism Analysis of Anchor Bolt and Cable Synergistic Action in Coal Roadway Support

2014 ◽  
Vol 716-717 ◽  
pp. 735-738 ◽  
Author(s):  
Peng Cheng ◽  
Jian Zhang ◽  
Ai Qing Liu
Keyword(s):  
Simulation Method ◽  
Paper Analysis ◽  
Synergistic Action ◽  
Mechanism Analysis ◽  
Anchor Bolt ◽  
Tension Distribution ◽  
Coal Roadway ◽  
Cable Force ◽  
Roadway Support ◽  
The Stability

Aiming at the current situation of anchor bolt and cable arrangement in mine roadway support, the paper analysis the mechanical characteristics and mechanism of bolts and cables, and numerical simulation method is used to comparison and analysis of pre-tension distribution characteristics under different anchor bolt-cable arrangement. The research indicated that separate anchor bolt-cable layout in different sections, anchor bolt and cable force stable equilibrium, coordinate with each other, at this time roadway surrounding rock of shallow and deep pretension distribution more reasonable, can play a role of bolt anchor cable synergistic action, and form the best pre-tension load-bearing structure, which is helpful to keep the stability of coal roadway.

Periodic Solutions in Rotor Dynamic Systems With Nonlinear Supports: A General Approach

1989 ◽  
Vol 111 (2) ◽  
pp. 187-193 ◽  
Author(s):  
C. Nataraj ◽  
H. D. Nelson
Keyword(s):  
Dynamic Systems ◽  
Original Problem ◽  
Squeeze Film ◽  
Algebraic Equations ◽  
Trigonometric Collocation ◽  
Nonlinear Algebraic Equations ◽  
The Stability ◽  
Future Work ◽  
Rotor Dynamic ◽  
Large Rotor

A new quantitative method of estimating steady state periodic behavior in nonlinear systems, based on the trigonometric collocation method, is outlined. A procedure is developed to analyze large rotor dynamic systems with nonlinear supports by the use of the above method in conjunction with Component Mode Synthesis. The algorithm discussed is seen to reduce the original problem to solving nonlinear algebraic equations in terms of only the coordinates associated with the nonlinear supports and is a big improvement over commonly used integration methods. The feasibility and advantages of the procedure so developed are illustrated with the help of an example of a typical rotor dynamic system with an uncentered squeeze film damper. Future work on the investigation of the stability of the periodic response so obtained is outlined.

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