scholarly journals Connecting Molecular Energy Landscape Analysis with Markov Model-based Analysis of Equilibrium Structural Dynamics

10.29007/tmgc ◽  
2019 ◽  
Author(s):  
Kazi Lutful Kabir ◽  
Nasrin Akhter ◽  
Amarda Shehu
Keyword(s):  
Structural Dynamics ◽  
Energy Landscape ◽  
Clustering Algorithms ◽  
Simulation Software ◽  
Dynamics Simulation ◽  
Stable States ◽  
Structure Space ◽  
State Identification ◽  
State Models ◽  
Model Based Analysis

Molecular dynamics simulation software now provides us with a view of the structure space accessed by a molecule. Increasingly, Markov state models are proposed to integrate various simulations of a molecule and extract its equilibrium structural dynamics. The approach relies on organizing the structures accessed in simulation into states as an at- tempt to identify thermodynamically-stable and semi-stable (macro)states among which transitions can then be quantified. Typically, off-the-shelf clustering algorithms are used for this purpose. In this paper, we investigate two additional complementary approaches to state identification that rely on graph embeddings of the structures. In particular, we show that doing so allows revealing basins in the energy landscape associated with the accessed structure space. Moreover, we demonstrate that basins, directly tied to stable and semi-stable states, yield to a better model of dynamics on a proof-of-concept application.

From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models

2019 ◽  
Vol 17 (06) ◽  
pp. 1940014 ◽  
Author(s):  
Kazi Lutful Kabir ◽  
Nasrin Akhter ◽  
Amarda Shehu
Keyword(s):  
Transition Probability ◽  
Clustering Algorithms ◽  
Simulation Software ◽  
Energy Landscapes ◽  
Stable States ◽  
Equilibrium Dynamics ◽  
Markov State ◽  
Structure Space ◽  
Markov State Models ◽  
State Models

Molecular dynamics (MD) simulation software allows probing the equilibrium structural dynamics of a molecule of interest, revealing how a molecule navigates its structure space one structure at a time. To obtain a broader view of dynamics, typically one needs to launch many such simulations, obtaining many trajectories. A summarization of the equilibrium dynamics requires integrating the information in the various trajectories, and Markov State Models (MSM) are increasingly being used for this task. At its core, the task involves organizing the structures accessed in simulation into structural states, and then constructing a transition probability matrix revealing the transitions between states. While now considered a mature technology and widely used to summarize equilibrium dynamics, the underlying computational process in the construction of an MSM ignores energetics even though the transition of a molecule between two nearby structures in an MD trajectory is governed by the corresponding energies. In this paper, we connect theory with simulation and analysis of equilibrium dynamics. A molecule navigates the energy landscape underlying the structure space. The structural states that are identified via off-the-shelf clustering algorithms need to be connected to thermodynamically-stable and semi-stable (macro)states among which transitions can then be quantified. Leveraging recent developments in the analysis of energy landscapes that identify basins in the landscape, we evaluate the hypothesis that basins, directly tied to stable and semi-stable states, lead to better models of dynamics. Our analysis indicates that basins lead to MSMs of better quality and thus can be useful to further advance this widely-used technology for summarization of molecular equilibrium dynamics.

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 Using SysML to Support Impact Analysis on Structural Dynamics Simulation Models

Procedia CIRP ◽  
2021 ◽  
Vol 100 ◽  
pp. 91-96
Author(s):  
Patrick Jagla ◽  
Georg Jacobs ◽  
Justus Siebrecht ◽  
Stefan Wischmann ◽  
Jonathan Sprehe
Keyword(s):  
Structural Dynamics ◽  
Impact Analysis ◽  
Simulation Models ◽  
Dynamics Simulation

Case Study on Modeling Fire Action Complexity in Fire Safety Engineering of Structures

2017 ◽  
Vol 21 ◽  
pp. 102-107
Author(s):  
Constantin Sorin Scutarasu ◽  
Dan Diaconu-Şotropa ◽  
Marinela Barbuta
Keyword(s):  
Numerical Simulation ◽  
Fire Safety ◽  
Simulation Software ◽  
Dynamics Simulation ◽  
Structural Safety ◽  
Modular Organization ◽  
Field Of Study ◽  
Safety Design ◽  
Fire Safety Design ◽  
Technical Regulations

Important goals in the fire safety design, such as preventing loss of life and goods damage, are achieved by maintaining the stability of structures exposed to fire for a period of time established by norms and standards. Real fire scenarios confirm that the specific technical regulations which actually have a prescriptive character (both national and international) do not deal with sufficient possibilities regarding the assessment of structural fire safety. The new approach on structural safety, based on engineering notions, gives us additional prospects on it and it is included in the issues of the fire safety design of structures. A relatively new field of study, known by a few professionals focused on fire safety (but well acknowledged in the research area), fire safety design met with lots of changes and restructuring of the governing concepts and procedures and of the information with which they operate, due to the fast accumulation of experience in this area of engineering activity. Consequently, after countries such as Australia, Canada, New Zeeland or USA provided towards professionals specific technical regulations for fire safety design, groups of experts in these aforementioned countries have joined their forces to try to diminish the differences that exists between those regulations and to give a unitary character to them, a better conceptualized engineering approach of the fire safety design. The result: occurrence of the publication International Fire Engineering Guidelines (last edition from 2005). The systematic approach of fire safety design in constructions pointed, once again, the possibility of modular organization of this field of study, the relations between modules being established according to the objective or objectives in the fire safety design for a specified building. This article aims to put forward, from this modularized perspective, the study of the fire safety design of a building exposed to fire; hence, the practical part of the article exhibits the numerical simulation of initialization and development of the fire process for a large scale religious building. The main features of the building represent the amount of space that facilitates the spreading of smoke and warm gases and which increases the risk of damaging the structural reinforced concrete elements. Application calls to specific numerical simulation with a higher degree of credibility, such as those realized by the FDS (Fire Dynamics Simulation) software.

The Application of Second-Developed ADAMS on Simulation of Individual Soldier Automatic Weapon

2012 ◽  
Vol 182-183 ◽  
pp. 1056-1059
Author(s):  
Yan Jun Zhao ◽  
Wen Qing Ge ◽  
Cheng Xu
Keyword(s):  
Simulation Software ◽  
Dynamics Simulation ◽  
Design Efficiency ◽  
Parameter Modification

Based on ADAMS, The dynamics simulation software of individual soldier automatic weapon was developed. Parameter modification, remodeling, dynamics simulation, simulation replay, obtain and save of results of Individual Soldier Automatic weapon model by finely Chinese interface were completed. The software brings convenient for user,and improves design efficiency. The results show that the software is reliable.

Integrated Methodology for Investigation of Wagon Bogie Concepts by Simulation

2014 ◽  
Author(s):  
S. S. N. Ahmad ◽  
C. Cole ◽  
M. Spiryagin ◽  
Y. Q. Sun
Keyword(s):  
Dynamic Behaviour ◽  
Simulation Software ◽  
Dynamics Simulation ◽  
Concept Design ◽  
Multibody Simulation ◽  
Worst Case ◽  
Multibody Model ◽  
Second Stage ◽  
Force Components ◽  
Train Simulation

Implementation of a new bogie concept is an integrated part of the vehicle design which must follow a rigorous testing and validation procedure. Use of multibody simulation helps to reduce the amount of time and effort required in selecting a new concept design by analysing results of simulated dynamic behaviour of the proposed design. However, the multibody simulation software mainly looks at the dynamics of a single vehicle; hence, forces from the train configuration operational dynamics are often absent in such simulations. Effects of longitudinal-lateral and longitudinal-vertical interactions between rail vehicles have been found to affect the stability of long trains [1,2]. The effect of wedge design on the vertical dynamics of a bogie has also been discussed in [3,4]. It is important to apply the lateral and vertical forces from a train simulation into a single multibody model of a wagon to check its behaviour when operating in train configuration. In this paper, a novel methodology for the investigation of new bogie designs has been proposed based on integrating dynamic train simulation and the multibody vehicle modelling concept that will help to efficiently achieve the most suitable design of the bogie. The proposed methodology suggests that simulation of any configuration of bogie needs to be carried out in three stages. As the first stage, the bogie designs along with the wagon configurations need to be presented as a multibody model in multibody simulation software to test the suitability of the concept. The model checking needs to be carried out in accordance with the wagon model acceptance procedure established in [5]. As the second stage, the wagon designs need to be tested in train configurations using a longitudinal train dynamics simulation software such as ‘CRE-LTS’ [2], where a train set consisting of the locomotives and wagons will be simulated to give operational wagon parameters such as lateral and vertical coupler force components. As the third stage, the detailed dynamic analysis of bogies and wagons needs to be performed with a multibody software such as ‘Gensys’ where lateral and vertical coupler force components from the train simulation (second stage) will be applied on the multibody model to replicate the worst case scenario. The proposed methodology enhances the selection procedure of any alternate bogie concept by the application of simulated train and vehicle dynamics. The simulated case studies show that simulation of wagon dynamic behaviour in multibody software combined with data obtained from longitudinal train simulation is not only possible, but it can identify issues with a bogie design that can otherwise be overlooked.

scholarly journals Study on Interface Structure of Cu/Al Clad Plates by Roll Casting

Metals ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 770 ◽  
Author(s):  
Qinghua Chang ◽  
Jingpei Xie ◽  
Aixia Mao ◽  
Wenyan Wang
Keyword(s):  
Molecular Dynamics ◽  
Electron Microscope ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Aluminum Atom ◽  
Simulation Software ◽  
Dynamics Simulation ◽  
Aluminum Composite ◽  
Atom Diffusion ◽  
Heating And Cooling

Large scale Atomic/Molecular dynamic Parallel Simulator (LAMMPS) molecular dynamics simulation software was used to simulate the copper and aluminum atom diffusion and changes of interface during heating and cooling process of copper and aluminum composite panels. The structures of the interface were characterized through scanning electron microscope (SEM), X-ray diffraction (XRD), and transmission electron microscope (TEM), and the mechanical properties were also tested. The simulation results show that the diffusion rate of copper atom is higher than that of aluminum atom, and that the CuAl2 radial distribution function of the interface at 300 K is consistent with that of pure CuAl2 at room temperature. At 930 K, t = 50 ps Cu atoms spread at a distance of approximately four Al lattice constants around the Al layer, and Al atoms spread to about half a lattice constant distance to the Cu layer. The experimental results show that the thickness of the interface in copper–aluminum composite plate is about 1 μm, and only one kind of CuAl2 with tetragonal phase structure is generated in the interface, which corresponds with the result of molecular dynamics simulation.

scholarly journals Critical energy landscape of linear soft spheres

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Silvio Franz ◽  
Antonio Sclocchi ◽  
Pierfrancesco Urbani
Keyword(s):  
Critical Exponents ◽  
Solid Phase ◽  
Energy Landscape ◽  
Amorphous Solid ◽  
Critical Energy ◽  
Contact Network ◽  
Stable States ◽  
Potential Energy Landscape ◽  
Soft Spheres ◽  
Non Linear System

We show that soft spheres interacting with a linear ramp potential when overcompressed beyond the jamming point fall in an amorphous solid phase which is critical, mechanically marginally stable and share many features with the jamming point itself. In the whole phase, the relevant local minima of the potential energy landscape display an isostatic contact network of perfectly touching spheres whose statistics is controlled by an infinite lengthscale. Excitations around such energy minima are non-linear, system spanning, and characterized by a set of non-trivial critical exponents. We perform numerical simulations to measure their values and show that, while they coincide, within numerical precision, with the critical exponents appearing at jamming, the nature of the corresponding excitations is richer. Therefore, linear soft spheres appear as a novel class of finite dimensional systems that self-organize into new, critical, marginally stable, states.

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