Effective Computational Techniques for Generating Electroencephalogram Data

Dynamic stochastic general equilibrium (DSGE) models have become one of the workhorses of modern macroeconomics and are extensively used for academic research as well as forecasting and policy analysis at central banks. This book introduces readers to state-of-the-art computational techniques used in the Bayesian analysis of DSGE models. The book covers Markov chain Monte Carlo techniques for linearized DSGE models, novel sequential Monte Carlo methods that can be used for parameter inference, and the estimation of nonlinear DSGE models based on particle filter approximations of the likelihood function. The theoretical foundations of the algorithms are discussed in depth, and detailed empirical applications and numerical illustrations are provided. The book also gives invaluable advice on how to tailor these algorithms to specific applications and assess the accuracy and reliability of the computations. The book is essential reading for graduate students, academic researchers, and practitioners at policy institutions.

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From Atoms to Large Chemical Systems with Computational Chemistry. Synthesis on Theoretical Methods and Computational Techniques

Revue de l Institut Français du Pétrole ◽

10.2516/ogst:1996001 ◽

1996 ◽

Vol 51 (1) ◽

pp. 19-35 ◽

Cited By ~ 2

Author(s):

E. Clementi ◽

G. Corongiu

Keyword(s):

Computational Chemistry ◽

Computational Techniques ◽

Theoretical Methods ◽

Chemical Systems

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Nanosecond Photodynamics Simulations of a Cis-Trans Isomerization Are Enabled by Machine Learning

10.26434/chemrxiv.13047863 ◽

2020 ◽

Author(s):

Jingbai Li ◽

Patrick Reiser ◽

André Eberhard ◽

Pascal Friederich ◽

Steven Lopez

Keyword(s):

Machine Learning ◽

Neural Networks ◽

Excited State ◽

Adaptive Sampling ◽

Computational Cost ◽

Ground Truth ◽

Absolute Error ◽

Photochemical Reactions ◽

Computational Techniques ◽

Full Potential

Photochemical reactions are being increasingly used to construct complex molecular architectures with mild and straightforward reaction conditions. Computational techniques are increasingly important to understand the reactivities and chemoselectivities of photochemical isomerization reactions because they offer molecular bonding information along the excited-state(s) of photodynamics. These photodynamics simulations are resource-intensive and are typically limited to 1–10 picoseconds and 1,000 trajectories due to high computational cost. Most organic photochemical reactions have excited-state lifetimes exceeding 1 picosecond, which places them outside possible computational studies. Westermeyr et al. demonstrated that a machine learning approach could significantly lengthen photodynamics simulation times for a model system, methylenimmonium cation (CH2NH2+).We have developed a Python-based code, Python Rapid Artificial Intelligence Ab Initio Molecular Dynamics (PyRAI2MD), to accomplish the unprecedented 10 ns cis-trans photodynamics of trans-hexafluoro-2-butene (CF3–CH=CH–CF3) in 3.5 days. The same simulation would take approximately 58 years with ground-truth multiconfigurational dynamics. We proposed an innovative scheme combining Wigner sampling, geometrical interpolations, and short-time quantum chemical trajectories to effectively sample the initial data, facilitating the adaptive sampling to generate an informative and data-efficient training set with 6,232 data points. Our neural networks achieved chemical accuracy (mean absolute error of 0.032 eV). Our 4,814 trajectories reproduced the S1 half-life (60.5 fs), the photochemical product ratio (trans: cis = 2.3: 1), and autonomously discovered a pathway towards a carbene. The neural networks have also shown the capability of generalizing the full potential energy surface with chemically incomplete data (trans → cis but not cis → trans pathways) that may offer future automated photochemical reaction discoveries.

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A Study of Computational Techniques Related to Prediction of Centroids of Dosage Beyond Measured Time Tn Where n is Known.

10.21236/ada157406 ◽

1985 ◽

Author(s):

L. A. Bell-Gray

Keyword(s):

Computational Techniques ◽

Measured Time

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Computational Techniques for Probabilistic Inference

10.21236/ada244814 ◽

1991 ◽

Author(s):

Edward H. Shortliffe ◽

Gregory F. Cooper

Keyword(s):

Probabilistic Inference ◽

Computational Techniques

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Analysis of Protein-Protein Interaction Networks through Computational Approaches

Protein and Peptide Letters ◽

10.2174/0929866526666191105142034 ◽

2020 ◽

Vol 27 (4) ◽

pp. 265-278 ◽

Cited By ~ 1

Author(s):

Ying Han ◽

Liang Cheng ◽

Weiju Sun

Keyword(s):

Protein Interaction ◽

Biological Networks ◽

Interaction Networks ◽

Computational Techniques ◽

Cellular Functions ◽

Protein Protein Interaction ◽

Comprehensive Information ◽

Protein Interaction Prediction ◽

Or Gene ◽

Experimental Findings

The interactions among proteins and genes are extremely important for cellular functions. Molecular interactions at protein or gene levels can be used to construct interaction networks in which the interacting species are categorized based on direct interactions or functional similarities. Compared with the limited experimental techniques, various computational tools make it possible to analyze, filter, and combine the interaction data to get comprehensive information about the biological pathways. By the efficient way of integrating experimental findings in discovering PPIs and computational techniques for prediction, the researchers have been able to gain many valuable data on PPIs, including some advanced databases. Moreover, many useful tools and visualization programs enable the researchers to establish, annotate, and analyze biological networks. We here review and list the computational methods, databases, and tools for protein−protein interaction prediction.

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Rational Drug Design Approach of Receptor Tyrosine Kinase Type III Inhibitors

Current Medicinal Chemistry ◽

10.2174/0929867325666180622143548 ◽

2020 ◽

Vol 26 (42) ◽

pp. 7623-7640 ◽

Cited By ~ 1

Author(s):

Cheolhee Kim ◽

Eunae Kim

Keyword(s):

Drug Design ◽

Tyrosine Kinase ◽

Receptor Tyrosine Kinase ◽

Synergistic Effects ◽

Rational Drug Design ◽

Computational Techniques ◽

Biological Targets ◽

Type Iii ◽

Theoretical Approaches ◽

Rational Drug

: Rational drug design is accomplished through the complementary use of structural biology and computational biology of biological macromolecules involved in disease pathology. Most of the known theoretical approaches for drug design are based on knowledge of the biological targets to which the drug binds. This approach can be used to design drug molecules that restore the balance of the signaling pathway by inhibiting or stimulating biological targets by molecular modeling procedures as well as by molecular dynamics simulations. Type III receptor tyrosine kinase affects most of the fundamental cellular processes including cell cycle, cell migration, cell metabolism, and survival, as well as cell proliferation and differentiation. Many inhibitors of successful rational drug design show that some computational techniques can be combined to achieve synergistic effects.

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Appraisal of the role of In silico Methods in Pyrazole based drug design

Mini-Reviews in Medicinal Chemistry ◽

10.2174/1389557520666200901184146 ◽

2020 ◽

Vol 20 ◽

Author(s):

Smriti Sharma ◽

Vinayak Bhatia

Keyword(s):

Drug Design ◽

In Silico ◽

Md Simulations ◽

Quantitative Structure Activity Relationship ◽

Field Analysis ◽

Computational Techniques ◽

Neuroprotective Drugs ◽

Pharmacological Potential ◽

Available Information ◽

Anti Fungal

: Pyrazole and its derivatives are a pharmacologically significant active scaffold that have innumerable physiological and pharmacological activities. They can be very good targets for the discovery of novel anti-bacterial, anticancer, anti-inflammatory, anti-fungal, anti-tubercular, antiviral, antioxidant, antidepressant, anti-convulsant and neuroprotective drugs. This review focuses on the importance of in silico manipulations of pyrazole and its derivatives for medicinal chemistry. The authors have discussed currently available information on the use of computational techniques like molecular docking, structure-based virtual screening (SBVS), molecular dynamics (MD) simulations, quantitative structure activity relationship (QSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) to drug design using pyrazole moieties. Pyrazole based drug design is mainly dependent on the integration of experimental and computational approaches. The authors feel that more studies need to be done to fully explore the pharmacological potential of the pyrazole moiety and in silico method can be of great help.

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Mathematical and Computational Techniques for Drug Discovery: Promises and Developments

Current Topics in Medicinal Chemistry ◽

10.2174/1568026619666190208164005 ◽

2019 ◽

Vol 18 (32) ◽

pp. 2774-2799 ◽

Cited By ~ 8

Author(s):

Krishnan Balasubramanian

Keyword(s):

Drug Discovery ◽

Protein Interactions ◽

Quantum Chemical ◽

Intrinsically Disordered Proteins ◽

Hepatitis Virus ◽

Disordered Proteins ◽

Computational Techniques ◽

Large Set ◽

Structural Protein ◽

Intrinsically Disordered

We review various mathematical and computational techniques for drug discovery exemplifying some recent works pertinent to group theory of nested structures of relevance to phylogeny, topological, computational and combinatorial methods for drug discovery for multiple viral infections. We have reviewed techniques from topology, combinatorics, graph theory and knot theory that facilitate topological and mathematical characterizations of protein-protein interactions, molecular-target interactions, proteomics, genomics and statistical data reduction procedures for a large set of starting chemicals in drug discovery. We have provided an overview of group theoretical techniques pertinent to phylogeny, protein dynamics especially in intrinsically disordered proteins, DNA base permutations and related algorithms. We consider computational techniques derived from high level quantum chemical computations such as QM/MM ONIOM methods, quantum chemical optimization of geometries complexes, and molecular dynamics methods for providing insights into protein-drug interactions. We have considered complexes pertinent to Hepatitis Virus C non-structural protein 5B polymerase receptor binding of C5-Arylidebne rhodanines, complexes of synthetic potential vaccine molecules with dengue virus (DENV) and HIV-1 virus as examples of various simulation studies that exemplify the utility of computational tools. It is demonstrated that these combinatorial and computational techniques in conjunction with experiments can provide promising new insights into drug discovery. These techniques also demonstrate the need to consider a new multiple site or allosteric binding approach to drug discovery, as these studies reveal the existence of multiple binding sites.

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