Rational design of novel fluorescent analogues of cholesterol: a “step-by-step” computational study

2019 ◽  
Vol 21 (28) ◽  
pp. 15487-15503 ◽  
Author(s):  
Andrea Bonvicini ◽  
Peter Reinholdt ◽  
Vincent Tognetti ◽  
Laurent Joubert ◽  
Daniel Wüstner ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical ◽  
Rational Design ◽  
State Of The Art ◽  
Computational Study ◽  
Dynamics Simulations ◽  
Fluorescent Analogues

State-of-the-art quantum chemical and molecular dynamics simulations are used as guidelines in design of novel fluorescent analogues of cholesterol.

Liquid dibromomethane under pressure: a computational study

2021 ◽  
Vol 23 (4) ◽  
pp. 2964-2971
Author(s):  
Bernadeta Jasiok ◽  
Mirosław Chorążewski ◽  
Eugene B. Postnikov ◽  
Claude Millot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Computational Study ◽  
Thermal Expansivity ◽  
Dynamics Simulations ◽  
Isobaric Thermal Expansivity

Thermophysical properties of liquid dibromomethane are investigated by molecular dynamics simulations between 268 and 328 K at pressures up to 3000 bar. Notably, the isotherms of the isobaric thermal expansivity cross around 800 bar.

Investigation of the interfacial behavior of organics on sulfide semiconductor surfaces by quantum chemical calculations and molecular dynamics simulations

2021 ◽  
Author(s):  
Haiding Zhu ◽  
Xuefeng Ren ◽  
Shengxiang Yan ◽  
Xingyou Liang ◽  
Liguo Gao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical Calculations ◽  
Organic Pollutants ◽  
Quantum Chemical ◽  
Semiconductor Surfaces ◽  
Interfacial Behavior ◽  
The World ◽  
Dynamics Simulations

The presence of organic pollutants in the world is harmful to our existence and the environment.

The Computational Study of Microchannel Thickness Effects on H2O/CuO Nanofluid Flow with Molecular Dynamics Simulations

2021 ◽  
pp. 118240
Author(s):  
Yanpeng Shang ◽  
Reza Balali Dehkordi ◽  
Supat Chupradit ◽  
Davood Toghraie ◽  
Andrei Sevbitov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computational Study ◽  
Nanofluid Flow ◽  
Dynamics Simulations

scholarly journals Molecular Insights into Cage Occupancy of Hydrogen Hydrate: A Computational Study

Processes ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 699 ◽  
Author(s):  
Ma ◽  
Zhong ◽  
Liu ◽  
Zhong ◽  
Yan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Storage ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Storage Capacity ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
Hydrogen Storage Capacity ◽  
Large Cage ◽  
Dynamics Simulations

Density functional theory calculations and molecular dynamics simulations were performed to investigate the hydrogen storage capacity in the sII hydrate. Calculation results show that the optimum hydrogen storage capacity is ~5.6 wt%, with the double occupancy in the small cage and quintuple occupancy in the large cage. Molecular dynamics simulations indicate that these multiple occupied hydrogen hydrates can occur at mild conditions, and their stability will be further enhanced by increasing the pressure or decreasing the temperature. Our work highlights that the hydrate is a promising material for storing hydrogen.

scholarly journals Recognition of shorter and longer trimethyllysine analogues by epigenetic reader proteins

2018 ◽  
Vol 54 (19) ◽  
pp. 2409-2412 ◽  
Author(s):  
Abbas H. K. Al Temimi ◽  
Roman Belle ◽  
Kiran Kumar ◽  
Jordi Poater ◽  
Peter Betlem ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermodynamic Data ◽  
Quantum Chemical ◽  
Chemical Studies ◽  
Quantum Chemical Studies ◽  
Dynamics Simulations

Combined thermodynamic data, molecular dynamics simulations, and quantum chemical studies reveal that epigenetic reader proteins efficiently bind trimethylornithine and trimethylhomolysine.

scholarly journals Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

2019 ◽  
Vol 21 (1) ◽  
pp. 1-31 ◽  
Author(s):  
Lindong Weng ◽  
Shannon L. Stott ◽  
Mehmet Toner
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Motion ◽  
State Of The Art ◽  
Level Structure ◽  
Cost Effective ◽  
Atomic Level ◽  
Computational Research ◽  
Dynamics Simulations ◽  
Biological Entities

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

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