Molecular Dynamics Simulation Of A Cyclic Siloxane Based Liquid Crystalline Material

1993 ◽  
Vol 328 ◽  
Author(s):  
Soumya S. Patnaik ◽  
Ruth Pachter ◽  
Steve Plimpton ◽  
W. WADE ADAMS
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Liquid Crystalline ◽  
Molecular System ◽  
Orientational Order ◽  
System Size ◽  
Dynamics Simulation ◽  
Cyclic Siloxane ◽  
Structural Anisotropy ◽  
Principal Axes

ABSTRACTWe have used molecular dynamics (MD) to study the room temperature bulk phase behavior of a cyclic siloxane with a pentamethylcyclosiloxane core and biphenyl-4-allyloxybenzoate Mesogens (BCS). This Material exhibits thermotropic liquid crystalline behavior above 120 °C. Bonded and non-bonded interactions were considered and a Molecular Mechanics force field was used to model the structural anisotropy of the siloxane Molecules. Molecular clusters with and without periodic boundary conditions (pbc) were studied to investigate the effect of the finite system size on the time evolution of the molecular structure. The precise nature of the boundary conditions was found to be significant and simulations that exclude pbc were better able to model the molecular system. It was found that molecular shapes associated with low energy conformations were not cylindrically symmetric but more splayed like. An approximate measure of the shape of the mesogens was obtained by describing ellipsoids around the Mesogens, and estimating the molecular length, breadth, and width from the principal axes of the ellipsoids. The orientational order was then calculated by defining the molecular axis to be along the major principal axis.

Molecular Dynamics Simulations of a Siloxane-Based Liquid Crystal Using an Improved Fast Multipole Algorithm Implementation

1995 ◽  
Vol 408 ◽  
Author(s):  
Alan McKenney ◽  
Ruth Pachter ◽  
Soumya Patnaik ◽  
Wade Adams
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Liquid Crystalline ◽  
Molecular System ◽  
Dynamics Simulation ◽  
Molecular Cluster ◽  
Fast Multipole ◽  
Dynamics Simulations ◽  
Fast Multipole Algorithm

AbstractIn our continuing efforts towards designing materials with controlled optical properties, largescale molecular dynamics simulations of a molecular cluster of a liquid crystalline cyclic siloxane are still limited by the size of the molecular system. Such simulations enable evaluation of the orientation order parameter of the system, as well as modelling the behavior of the material in bulk. This study summarizes improvements in the implementation of the fast multipole algorithm for computing electrostatic interactions which is included in the molecular dynamics program PMD[7, 8], such as the elimination of computations for empty cells and the use of optimal interaction lists. Moreover, an improved implementation of a 3-D Fast Multipole Method (FMM3D) based on the algorithm previously proposed[1, 2] is described in detail. The structure of the module, details of the expansions, parallelization, and its integration with the molecular dynamics simulation code are explained in detail. Finally, the utility of this approach in the study of liquid crystalline materials is briefly illustrated.

scholarly journals Dynamic Graphical Models of Molecular Kinetics

2018 ◽  
Author(s):  
Simon Olsson ◽  
Frank Noé
Keyword(s):  
Graphical Models ◽  
Molecular System ◽  
System Size ◽  
Ising Models ◽  
Metastable States ◽  
Dynamics Simulation ◽  
Global State ◽  
Stable States ◽  
Markov State ◽  
State Models

AbstractMost current molecular dynamics simulation and analysis methods rely on the idea that the molecular system can be characterized by a single global state, e.g., a Markov State in a Markov State Model (MSM). In this approach, molecules can be extensively sampled and analyzed when they only possess a few metastable states, such as small to medium-sized proteins. However this approach breaks down in frustrated systems and in large protein assemblies, where the number of global meta-stable states may grow exponentially with the system size. Here, we introduce Dynamic Graphical Models (DGMs), which build upon the idea of Ising models, and describe molecules as assemblies of coupled subsystems. The switching of each sub-system state is only governed by the states of itself and its neighbors. DGMs need many fewer parameters than MSMs or other global-state models, in particular we do not need to observe all global system configurations to estimate them. Therefore, DGMs can predict new, previously unobserved, molecular configurations. Here, we demonstrate that DGMs can faithfully describe molecular thermodynamics and kinetics and predict previously unobserved metastable states for Ising models and protein simulations.

scholarly journals Dynamic graphical models of molecular kinetics

2019 ◽  
Vol 116 (30) ◽  
pp. 15001-15006 ◽  
Author(s):  
Simon Olsson ◽  
Frank Noé
Keyword(s):  
Graphical Models ◽  
Molecular System ◽  
System Size ◽  
Metastable States ◽  
Dynamics Simulation ◽  
Global State ◽  
Markov State ◽  
Coupled Subsystems ◽  
State Models ◽  
Frustrated Systems

Most current molecular dynamics simulation and analysis methods rely on the idea that the molecular system can be represented by a single global state (e.g., a Markov state in a Markov state model [MSM]). In this approach, molecules can be extensively sampled and analyzed when they only possess a few metastable states, such as small- to medium-sized proteins. However, this approach breaks down in frustrated systems and in large protein assemblies, where the number of global metastable states may grow exponentially with the system size. To address this problem, we here introduce dynamic graphical models (DGMs) that describe molecules as assemblies of coupled subsystems, akin to how spins interact in the Ising model. The change of each subsystem state is only governed by the states of itself and its neighbors. DGMs require fewer parameters than MSMs or other global state models; in particular, we do not need to observe all global system configurations to characterize them. Therefore, DGMs can predict previously unobserved molecular configurations. As a proof of concept, we demonstrate that DGMs can faithfully describe molecular thermodynamics and kinetics and predict previously unobserved metastable states for Ising models and protein simulations.

scholarly journals Molecular dynamics simulation of α-unsubstituted oligo-thiophenes: dependence of their high-temperature liquid-crystalline phase behaviour on molecular length

2019 ◽  
Vol 7 (32) ◽  
pp. 9984-9995 ◽  
Author(s):  
Flora D. Tsourtou ◽  
Stavros D. Peroukidis ◽  
Vlasis G. Mavrantzas
Keyword(s):  
Molecular Dynamics ◽  
Phase Diagram ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Liquid Crystalline ◽  
Md Simulations ◽  
Phase Behaviour ◽  
Dynamics Simulation ◽  
Molecular Length ◽  
Temperature Liquid

Phase diagram of α-nT oligomers with n = 5–8 from the MD simulations.

Molecular dynamics simulation of a liquid crystalline mixture

1997 ◽  
Vol 106 (17) ◽  
pp. 7438-7447 ◽  
Author(s):  
Dick Sandström ◽  
Andrei V. Komolkin ◽  
Arnold Maliniak
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Liquid Crystalline ◽  
Dynamics Simulation ◽  
Crystalline Mixture
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