Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to the pseudorotation dynamics of furanose rings

Biopolymers ◽  
1994 ◽  
Vol 34 (3) ◽  
pp. 383-392 ◽  
Author(s):  
Witold R. Rudnicki ◽  
Bogdan Lesyng ◽  
Stephen C. Harvey
Keyword(s):  
Molecular Dynamics ◽  
Degrees Of Freedom ◽  
Conformational Degrees Of Freedom

All-atomistic molecular dynamics study of the glass transition of amorphous polymers

2021 ◽  
Author(s):  
Zhiye Tang ◽  
Susumu Okazaki
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
Spatial Scale ◽  
Degrees Of Freedom ◽  
Main Chain ◽  
Polymer Materials ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Radius Of Gyration ◽  
Chemical Structures

Glass transition is an important phenomenon of polymer materials and it has been intensively studied over the past a few decades. However, the influencing factors arising from the chemical structures of the polymers are often ignored due to a continuous or coarse-grained description of the polymer. Here, we approached this phenomenon using all-atomistic molecular dynamics (MD) simulations and two conventionally used polymer materials, polycarbonate (PC) and poly-(methyl methacrylate) (PMMA). We reproduced the glass transition temperatures (Tg) of the two materials reasonably well. Then we characterized and investigated the glass transition process by looking at the changes of potential energy, dihedral transition, and thermal fluctuation of the individual degrees of freedom in the systems, over the entire temperature range of glass transition. As previously reported, the dihedral angles stop their conformational changes gradually at the Tg, especially for the main chain dihedrals, and sidechain rotations immediately rooting from the main chain. The volumetric change during the temperature decrease is confirmed to be because of conformational adjustment, probably due to the tendency of chain stretching for the maintenance of the radius of gyration, and the loss of thermal energy. The strength of motions of single degrees of freedom and polymer chains, and overall slow motions obtained by normal mode analysis (NMA) shows that different motions at different spatial scale may gradually stop at distinct temperature in the MD simulation temporal and spatial scales. Presumably, the small spatial scale do not contribute to the glass transition at the experimental scale since the timescale is much longer than their relaxation time.

scholarly journals Computational High-Throughput Screening of Polymeric Photocatalysts: Exploring the Effect of Composition, Sequence Isomerism and Conformational Degrees of Freedom

2018 ◽  
Author(s):  
isabelle Heath-Apostolopoulos ◽  
Liam Wilbraham ◽  
Martijn Zwijnenburg
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Degrees Of Freedom ◽  
Chemical Space ◽  
Low Cost ◽  
Computational Screening ◽  
Computational Workflow ◽  
Conformational Degrees Of Freedom

We discuss a low-cost computational workflow for the high-throughput screening of polymeric photocatalysts and demonstrate its utility by applying it to a number of challenging problems that would be difficult to tackle otherwise. Specifically we show how having access to a low-cost method allows one to screen a vast chemical space, as well as to probe the effects of conformational degrees of freedom and sequence isomerism. Finally, we discuss both the opportunities of computational screening in the search for polymer photocatalysts, as well as the biggest challenges.

Towards a Virtual Laboratory for Grain Boundaries and Dislocations

2009 ◽  
Vol 1224 ◽  
Author(s):  
Sebastián Echeverri Restrepo ◽  
Barend J. Thijsse
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundaries ◽  
Systematic Study ◽  
Degrees Of Freedom ◽  
Minimum Energy ◽  
Local Symmetry ◽  
Virtual Laboratory ◽  
Face Centered Cubic ◽  
Face Centered ◽  
Edge Dislocations

AbstractIn order to perform a systematic study of the interaction between grain boundaries (GBs) and dislocations using molecular dynamics (MD), several tools need to be available. A combination of computational geometry and MD was used to build the foundations of what we call a virtual laboratory. First, an algorithm to generate GBs on face-centered cubic bicrystals was developed. Two crystals with different orientations are placed together. Then, by applying “microscopic” rigid body translations along the GB plane to one of the crystals and removing overlapping atoms, a set of initial configurations is sampled and a minimum energy configuration is found. Second, to classify the geometry of the GBs a local symmetry type (LST) describing the angular environment of each atom is calculated. It is found that for a given relaxed GB the number of atoms with different LSTs is not very large and that it is possible to find unique geometrical patterns in each GB. For instance, the LSTs of two GBs having the same “macroscopic” configuration but different “microscopic” degrees of freedom can be dissimilar: the configurations with higher GB energy tend to have a higher number of atoms with different LSTs. Third, edge dislocations are introduced into the bicrystals. We see that full edge dislocations split into Shockley partials. Finally, by loading the bicrystals with tensile stresses the edge dislocations are put into motion. Various examples of dislocation-GB interactions in Cu are presented.

SUB-keV ATOM INDUCED SPUTTERING OF CONDENSED N2: A MOLECULAR DYNAMICS STUDY

1993 ◽  
Vol 07 (13n14) ◽  
pp. 857-863 ◽  
Author(s):  
HEINO KAFEMANN ◽  
HERBERT M. URBASSEK
Keyword(s):  
Molecular Dynamics ◽  
Energy Distribution ◽  
Time Dependence ◽  
Degrees Of Freedom ◽  
Center Of Mass ◽  
Translational Motion ◽  
Original Position ◽  
Time And Space

By molecular dynamics, the sputtering of a condensed N 2 sample due to 100 eV N atom bombardment is studied. The features observed in general parallel those of previous studies of Ar sputtering. Time- and space-resolved measurements give novel information on the original position of sputtered molecules and the time dependence of their energy distribution. Rotational and vibrational degrees of freedom are underpopulated with respect to center-of-mass translational motion.

scholarly journals Decoupling of crystalline and conformational degrees of freedom in lipid monolayers

1989 ◽  
Vol 91 (3) ◽  
pp. 1855-1865 ◽  
Author(s):  
John Hjort Ipsen ◽  
Ole G. Mouritsen ◽  
Martin J. Zuckermann
Keyword(s):  
Degrees Of Freedom ◽  
Lipid Monolayers ◽  
Conformational Degrees Of Freedom

Solid molecular phases of Hydrogen via constant-pressure first-principles Molecular Dynamics

1997 ◽  
Vol 499 ◽  
Author(s):  
Jorge Kohanoff ◽  
Sandro Scandolo
Keyword(s):  
Molecular Dynamics ◽  
First Principles ◽  
Degrees Of Freedom ◽  
Constant Pressure ◽  
Phase Iii ◽  
Orthorhombic Structure ◽  
Lattice Constants ◽  
Symmetry Phase ◽  
Dynamics Simulations ◽  
Zone Sampling

ABSTRACTBy performing constant pressure ab initio molecular dynamics simulations we analyse the high pressure phases of molecular solid hydrogen. We use a gradient corrected LDA, and a freshly implemented efficient technique for Brillouin zone sampling. An extremely good k-point sampling turns out to be crucial for obtaining the correct ground state. Our constant pressure approach allows us to optimize simultaneously the ori-entational degrees of freedom, the lattice constants, and the space group. This can be done either by a local optimization tehcnique, or by running molecular dynamics (MD) trajectories. The MD allows for the system to undergo structural transformations spontaneously. In the lower pressure, namely for the broken symmetry phase (BSP or phase II), we find a quadrupolar orthorhombic structure, of Pca21 symmetry. By means of an MD investigation, we find, at higher pressures, a slightly distorted orthorhombic structure of Cmc21 symmetry. This structure cannot be straightforwardly identified with the H-A phase (or phase III) because: 1) it is metallic, and 2) the Raman vibron discontinuity would be far too large compared to experiment. In fact, we argue that this phase is the first metallic molecular phase of hydrogen. Metallization would happen then, not via a band-overlap mechanism, but due to a structural transformation. By comparing total enthalpies, we also give suggestions for the structure of phase III.

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