scholarly journals Naphthalene crystal shape prediction from molecular dynamics simulations

CrystEngComm ◽  
2019 ◽  
Vol 21 (21) ◽  
pp. 3280-3288 ◽  
Author(s):  
Zoran Bjelobrk ◽  
Pablo M. Piaggi ◽  
Thilo Weber ◽  
Tarak Karmakar ◽  
Marco Mazzotti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
State Of The Art ◽  
Ethanol Solution ◽  
Crystal Shape ◽  
Shape Prediction ◽  
Dynamics Simulations ◽  
Naphthalene Crystal

The crystal shape of naphthalene grown from ethanol solution at constant supersaturation was predicted using state-of-the-art molecular dynamics simulations.

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.

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.

Molecular dynamics simulations of longer n-alkanes in silicalite: state-of-the-art models achieving close agreement with experiment

2015 ◽  
Vol 17 (3) ◽  
pp. 1943-1948 ◽  
Author(s):  
A. J. O'Malley ◽  
C. R. A. Catlow
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Diffusion Coefficients ◽  
Close Agreement ◽  
State Of The Art ◽  
Elastic Neutron ◽  
Temperature Range ◽  
Elastic Neutron Scattering ◽  
Dynamics Simulations

The diffusion of longer n-alkanes (n-C8–n-C16) in silicalite was studied using molecular dynamics simulations in the temperature range of 300–400 K. A close agreement is found with previous quasi-elastic neutron scattering studies for both calculated diffusion coefficients and activation energies.

Advances in Molecular Dynamics Simulations of Nanotribology

2008 ◽  
Author(s):  
Michael Chandross
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
State Of The Art ◽  
Simulation Method ◽  
Detailed Understanding ◽  
The Past ◽  
Simulation Techniques ◽  
Dynamics Simulations ◽  
The Individual ◽  
Made In

Molecular dynamics is the simulation method that is most amenable to the length and time scales of nanotribological experiments. The ability to track the individual motion of every atom in simulations has led to a detailed understanding of the underlying physics that is difficult to extract from experiment. While significant progress has been made in simulations over the past two decades, computational issues still limit the types of problems that can be approached, and the detailed understanding that results. Here we discuss recent advances in molecular dynamics simulations that push the bounds of simulation size, velocity, and chemistry. These state of the art simulation techniques have made great strides in allowing detailed comparisons to experimental results. These advances will be placed in context by addressing the barriers that remain and where future progress lies.

scholarly journals The interaction with gold suppresses fiber-like conformations of the amyloid β (16–22) peptide

Nanoscale ◽  
2016 ◽  
Vol 8 (16) ◽  
pp. 8737-8748 ◽  
Author(s):  
Luca Bellucci ◽  
Albert Ardèvol ◽  
Michele Parrinello ◽  
Helmut Lutz ◽  
Hao Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
State Of The Art ◽  
Amyloid Β ◽  
Gold Surface ◽  
Preferential Interaction ◽  
Dynamics Simulations

State-of-the-art classical atomistic molecular dynamics simulations reveal that the interaction of the amyloid β (16–22) peptide with a gold surface is suppressing fiber-like conformations, thanks to the preferential interaction with phenylalanine residues.

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