Molecular modeling

In this study, we explore the potential of graph neural networks (GNNs), in combination with transfer learning, for the prediction of molecular solubility, a crucial property in drug discovery and materials science. Our approach begins with the development of a GNN-based model to predict the dipole moment of molecules.

8p viling 11-10-2024 1 1   Download

Carbon capture and storage is a critical component of negative emission technologies for achieving economy-wide carbon neutrality to mitigate climate change and limit global temperature increase. Removal of CO2 can be undertaken after the standard pollution controls.

5p vikwong 29-09-2024 1 1   Download

Resveratrol is a naturally occurring compound with anti-inflammatory properties. However, the protective molecular mechanisms of resveratrol against LPS-induced inflammation have not been thoroughly known. In the present study, we examined the antiinflammatory effect of resveratrol in inflammatory model using murine macrophage-like cell RAW264.7 stimulated with LPS. Resveratrol suppressed the production of inflammatory cytokines in LPS-stimulated RAW264.7 cells with the IC50 value as 17.5 ± 0.7 μM for IL-6, 14.2 ± 1.9 μM for IL-10, and 18.9 ± 0.6 μM for TNF-α.

9p xuanphongdacy06 18-09-2024 1 1   Download

This study revealed that the major contributing descriptors of 2D QSAR studies are DeltaEpsilonB and DeltaPsiA and 3D QSAR model proves the steric as well as electrostatic effects determine the binding affinity for the drug development. The results of the current computational studies are useful for further designing novel chemical entities of anti-microbial agent.

19p dianmotminh02 03-05-2024 8 3   Download

In this thesis atomistic level modelling is conducted to investigate the design of an environmentally adaptable self-cleaning polymer paint coating that incorporates biomimetics to remain clean in various environmental setting. This work will be used to aid in the development of stay-clean polymer paint coating.

116p runthenight07 01-03-2023 7 3   Download

The document will be structured as follows: In Chapter 2 outline the methodology, discussing the computational techniques used to evaluate the interaction energies and evaluating the construction of the TT and D3(BJ) correction terms. Chapter 3 attempts to establish a foundational understanding of how these methods model vdW interactions by evaluating the performance of the corrected and uncorrected HF and DFT methods in comparison with CCSD(T) energies for a selection of inert gas dimers, and simple molecule-molecule interactions.

63p runthenight04 02-02-2023 9 2   Download

In this Masters thesis computational modelling techniques were employed to investigate iron-free apo-Lactoferrin (apo-Lf) structural conformation changes in the presence of variant temperature and pH. These conditions represent the environment most milk protein goes through in food processing and the production of food products.

162p runthenight04 02-02-2023 8 3   Download

The thesis is organised as follows: Chapter 1 comprises the literature review of protein structure, amyloid fibrils and of the effect of nanomaterials on protein aggregation. Chapter 2 reviews the computational methods used to perform simulations and analysis. Chapter 3 comprises my published article on benchmarking forcefields and sampling methods for disordered proteins using amylin as a case study. Chapter 4 comprises my published article on the effect of oxidation on the properties of graphene oxide flakes in solution.

56p runthenight04 02-02-2023 12 3   Download

Master's thesis of Science "Investigation into the modulation of circadian clock proteins by dietary compounds and small molecules" is structured as follows: Chapter 1 Introduction; Chapter 2 Identification of novel bioactive compounds from Olea europaea by evaluation of chemical compounds in the OliveNetTM library: in silico bioactivity and molecular modelling, and in vitro validation of hERG activity; Chapter 3 Modulation of circadian core clock proteins by dietary compounds; Chapter 4 Molecular mechanisms of action of selected olive phenolics against epigenetic modifiers and the structur...

235p runthenight04 02-02-2023 5 3   Download

The thesis is structured as follows: In Chapter 1, the scientific literature is summarized within the scope of this study. Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study. Chapter 3 identifies the important residues of the LsIA/α7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. The effects of C-terminal modification of LsIA on interactions with α3β2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4.

234p runthenight04 02-02-2023 11 3   Download

Nghiên cứu đã xây đựng thành công 10 mô hình QSAR nhằm dự đoán khả năng ức chế Tyrosinase từ cấu trúc phân tử. Dựa trên các nguyên tắc của OECD, chất lượng của các mô hình này đã được chứng minh, qua đó phản ánh tính đúng đắn của phương pháp nghiên cứu. Mời các bạn cùng tham khảo nội dung chi tiết.

7p closefriend02 07-10-2021 12 2   Download

The research in this thesis follows two directions: The first, using high performance computing currently available, we studied atomic and molecular emissions in astrophysical environment. The radiative transfer model was applied to explain the characteristics of the recombination line masers Hnα in the envelope of the star MWC 349A.

27p beloveinhouse01 15-08-2021 17 4   Download

A database containing chemical structures of 60 inhibitors and their Ki values was put into molecular operating environment (MOE) 2008.10 software, and the two-dimensional (2D) physicochemical descriptors were numerically calculated. After removing the irrelevant descriptors, a QSAR modeling was developed from the 2D-descriptors and Ki values by using the partial least squares (PLS) regression method.

5p larachdumlanat127 02-01-2021 21 2   Download

This paper looks at the influence of SiO2-doped concentration, temperature and pressure on the microstructure of the Al2O3(SiO2)x (ASx) bulk model using the Molecular Dynamics (MD) method with a Born-Mayer pair interaction potential and periodic boundary conditions.

7p tamynhan5 10-12-2020 12 3   Download

This paper studies the influence of temperature 500 K, 1500 K, 2500 K, 3500 K and 4000 K on the microstructure and phase transition of a CaSiO3 bulk model using the Molecular Dynamics method with the Born-Mayer pair interaction potential and periodic boundary conditions.

10p tamynhan9 02-12-2020 14 2   Download

This paper presents the influence of temperature on microstructure and phase transition when heating 3000 nano-iron and bulk-iron particles at a temperature of 300 K, 500 K, 700 K, 900 K, 1100 K, 1300 K, 1500 K, 1700 K, 1900 K and 2100 K using the molecular dynamics (MD) simulation method.

7p tamynhan8 04-11-2020 19 2   Download

Molecular crystals are characterized by strong intramolecular forces and much weaker intermolecular forces. High-pressure spectroscopic studies provide useful data for refining the various model potentials which are used to predict of the physical properties of such systems as well as for the formation of various crystalline phases.

7p tamynhan8 04-11-2020 16 2   Download

This paper studies the structure of the Mullite system (3Al2O3.2SiO2) by Molecular Dynamics simulation (MDs) using the Born–Mayer–Huggins pair interaction and periodic boundary conditions. The simulation was performed with model of 5250 atoms at different pressure and at 3500 K temperature.

7p tamynhan6 14-09-2020 17 2   Download

We present machine learning models for fast estimating atomic forces and energies. In our method, the total energy of a system is approximated as the summation of atomic energy which is the interaction energy with its surrounding chemical environment within a certain cutoff radius.

7p tamynhan6 14-09-2020 16 1   Download

Hiện nay, trên các website và diễn đàn về hóa học, chủ đề đang được độc giả quan tâm là các chủ đề về chia sẻ hình ảnh các cấu trúc phân tử và các phần mềm vẽ cấu trúc phân tử (molecular modeling software). Đa số các thành viên trong các diễn đàn này là học sinh, sinh viên và giáo viên yêu thích và muốn hiểu biết kỹ về hóa học. Như vậy, có thể thấy, nhu cầu về ứng dụng molecular modeling trong giáo dục là rất lớn. Tuy hiện nay phần mềm molecular modeling rất phong phú và đa dạng nhưng để trở thành một công cụ hỗ trợ đắc lực trong việc dạy và học môn hóa thì vẫn còn tồn tại nhiều vấn đề.

5p nanhankhuoctai7 01-07-2020 44 2   Download