Applications of Real-Time Multiresolution Analysis for Molecular Dynamics Simulations of Infrequent Events

2001 ◽  
Vol 677 ◽  
Author(s):  
David A. Richie ◽  
Jeongnim Kim ◽  
John W. Wilkins
Keyword(s):  
Molecular Dynamics ◽  
Real Time ◽  
Data Storage ◽  
Multiresolution Analysis ◽  
Materials Science ◽  
Md Simulations ◽  
Structural Transitions ◽  
Compression Scheme ◽  
Detection Scheme ◽  
Acceleration Techniques

ABSTRACTThe simulation of defect dynamics (e.g., transient enhanced diffusion of boron in the presence of silicon interstitials) is a technologically relevant challenge for computational materials science. The dynamics of defect structures in bulk unfolds as a sequence of thermally induced structural transitions. Identifying and characterizing reaction paths, as well as extracting dynamical quantities (e.g., diffusion constants) is important for modeling the macroscopic properties of real materials. Applying real-time multiresolution analysis (RTMRA) to various dynamical quantities using simple Haar wavelets, we have developed a computationally cheap data compression scheme to handle the massive data sets generated in molecular dynamics (MD) simulations; data storage has been reduced hundredfold with no loss of relevant information. More importantly, the same RTMRA techniques are developed into a sophisticated event detection scheme capable of solving three major challenges to multiscale MD simulations, specifically, (1) identifying meta-stable structures against the background of thermal vibrations, (2) detecting infrequent events, e.g., structural transitions, in the presence of thermal noise, and (3) accurately identifying transition times to further enhance recently emerging MD acceleration techniques.

scholarly journals Hydrogenation Dynamics of Biphenylene Carbon (Graphenylene) Membranes

MRS Advances ◽  
2017 ◽  
Vol 2 (29) ◽  
pp. 1571-1576
Author(s):  
Vinicius Splugues ◽  
Pedro Alves da Silva Autreto ◽  
Douglas S. Galvao
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Md Simulations ◽  
Structural Transformations ◽  
Extensive Study ◽  
Massively Parallel ◽  
Porous Membranes ◽  
Two Dimensional ◽  
Reactive Force

ABSTRACTThe advent of graphene created a revolution in materials science. Because of this there is a renewed interest in other carbon-based structures. Graphene is the ultimate (just one atom thick) membrane. It has been proposed that graphene can work as impermeable membrane to standard gases, such argon and helium. Graphene-like porous membranes, but presenting larger porosity and potential selectivity would have many technological applications. Biphenylene carbon (BPC), sometimes called graphenylene, is one of these structures. BPC is a porous two-dimensional (planar) allotrope carbon, with its pores resembling typical sieve cavities and/or some kind of zeolites. In this work, we have investigated the hydrogenation dynamics of BPC membranes under different conditions (hydrogenation plasma density, temperature, etc.). We have carried out an extensive study through fully atomistic molecular dynamics (MD) simulations using the reactive force field ReaxFF, as implemented in the well-known Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. Our results show that the BPC hydrogenation processes exhibit very complex patterns and the formation of correlated domains (hydrogenated islands) observed in the case of graphene hydrogenation was also observed here. MD results also show that under hydrogenation BPC structure undergoes a change in its topology, the pores undergoing structural transformations and extensive hydrogenation can produce significant structural damages, with the formation of large defective areas and large structural holes, leading to structural collapse.

scholarly journals Maximizing resource usage in multifold molecular dynamics with rCUDA

2019 ◽  
Vol 34 (1) ◽  
pp. 5-19
Author(s):  
Javier Prades ◽  
Baldomero Imbernón ◽  
Carlos Reaño ◽  
Jorge Peña-García ◽  
Jose Pedro Cerón-Carrasco ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Graphics Processing Units ◽  
Materials Science ◽  
Dynamical Behavior ◽  
Md Simulations ◽  
Atomic Scale ◽  
Power Budget ◽  
Single Node ◽  
Time Required

The full-understanding of the dynamics of molecular systems at the atomic scale is of great relevance in the fields of chemistry, physics, materials science, and drug discovery just to name a few. Molecular dynamics (MD) is a widely used computer tool for simulating the dynamical behavior of molecules. However, the computational horsepower required by MD simulations is too high to obtain conclusive results in real-world scenarios. This is mainly motivated by two factors: (1) the long execution time required by each MD simulation (usually in the nanoseconds and microseconds scale, and beyond) and (2) the large number of simulations required in drug discovery to study the interactions between a large library of compounds and a given protein target. To deal with the former, graphics processing units (GPUs) have come up into the scene. The latter has been traditionally approached by launching large amounts of simulations in computing clusters that may contain several GPUs on each node. However, GPUs are targeted as a single node that only runs one MD instance at a time, which translates into low GPU occupancy ratios and therefore low throughput. In this work, we propose a strategy to increase the overall throughput of MD simulations by increasing the GPU occupancy through virtualized GPUs. We use the remote CUDA (rCUDA) middleware as a tool to decouple GPUs from CPUs, and thus enabling multi-tenancy of the virtual GPUs. As a working test in the drug discovery field, we studied the binding process of a novel flavonol to DNA with the GROningen MAchine for Chemical Simulations (GROMACS) MD package. Our results show that the use of rCUDA provides with a 1.21× speed-up factor compared to the CUDA counterpart version while requiring a similar power budget.

Large-Scale Molecular Dynamics Simulations of Interstitial Defect Diffusion in Silicon

2002 ◽  
Vol 731 ◽  
Author(s):  
David A. Richie ◽  
Jeongnim Kim ◽  
Richard Hennig ◽  
Kaden Hazzard ◽  
Steve Barr ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Tight Binding ◽  
Md Simulations ◽  
Binding Potential ◽  
Interstitial Defect ◽  
Long Time ◽  
Computational Materials ◽  
Dynamics Simulations

AbstractThe simulation of defect dynamics and evolution is a technologicaly relevant challenge for computational materials science. The diffusion of small defects in silicon unfolds as a sequence of structural transitions. The relative infrequency of transition events requires simulation over extremely long time scales. We simulate the diffusion of small interstitial clusters (I1, I2, I3) for a range of temperatures using large-scale molecular dynamics (MD) simulations with a realistic tight-binding potential. A total of 0.25 μ sec of simulation time is accumulated for the study. A novel real-time multiresolution analysis (RTMRA) technique extracts stable structures directly from the dynamics without structural relaxation. The discovered structures are relaxed to confirm their stability.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Design of Portable Electrocardiograph Monitoring System

2020 ◽  
Author(s):  
Jia Hua-Ping ◽  
Zhao Jun-Long ◽  
Liu Jun
Keyword(s):  
Real Time ◽  
Monitoring System ◽  
Data Storage ◽  
P Wave ◽  
Ecg Monitoring ◽  
The Public ◽  
Ecg Signals ◽  
Early Warning Mechanism ◽  
Timely Treatment ◽  
Ecg Data

Cardiovascular disease is one of the major diseases that threaten the human health. But the existing electrocardiograph (ECG) monitoring system has many limitations in practical application. In order to monitor ECG in real time, a portable ECG monitoring system based on the Android platform is developed to meet the needs of the public. The system uses BMD101 ECG chip to collect and process ECG signals in the Android system, where data storage and waveform display of ECG data can be realized. The Bluetooth HC-07 module is used for ECG data transmission. The abnormal ECG can be judged by P wave, QRS bandwidth, and RR interval. If abnormal ECG is found, an early warning mechanism will be activated to locate the user’s location in real time and send preset short messages, so that the user can get timely treatment, avoiding dangerous occurrence. The monitoring system is convenient and portable, which brings great convenie to the life of ordinary cardiovascular users.

Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Complete Characterization ◽  
Layer By Layer ◽  
Surface Restructuring ◽  
Metastable Structures ◽  
Mechanistic Investigation ◽  
Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals An efficient approach to study membrane nano-inclusions: from the complex biological world to a simple representation

RSC Advances ◽  
2021 ◽  
Vol 11 (18) ◽  
pp. 10962-10974 ◽  
Author(s):  
M. Lemaalem ◽  
N. Hadrioui ◽  
S. El Fassi ◽  
A. Derouiche ◽  
H. Ridouane
Keyword(s):  
Materials Science ◽  
Md Simulations ◽  
Efficient Approach ◽  
Simple Representation ◽  
Biological World

Membrane nano-inclusions are of great interest in biophysics, materials science, nanotechnology, and medicine. In this work, We combined MD simulations and theories to reveal their physics behavior.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

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