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 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 Mechanical Properties and Fracture Dynamics of Silicene Membranes

2013 ◽  
Vol 1549 ◽  
pp. 99-107 ◽  
Author(s):  
Tiago Botari ◽  
Eric Perim ◽  
P. A. S. Autreto ◽  
Ricardo Paupitz ◽  
Douglas S. Galvao
Keyword(s):  
Mechanical Properties ◽  
Materials Science ◽  
Mechanical Strain ◽  
Single Layer ◽  
Md Simulations ◽  
Reactive Force ◽  
New Era ◽  
Fracture Dynamics ◽  
Fracture Patterns ◽  
Silicon And Germanium

ABSTRACTThe advent of graphene created a new era in materials science. Graphene is a two-dimensional planar honeycomb array of carbon atoms in sp2-hybridized states. A natural question is whether other elements of the IV-group of the periodic table (such as silicon and germanium), could also form graphene-like structures. Structurally, the silicon equivalent to graphene is called silicene. Silicene was theoretically predicted in 1994 and recently experimentally realized by different groups. Similarly to graphene, silicene exhibits electronic and mechanical properties that can be exploited to nanoelectronics applications.In this work we have investigated, through fully atomistic molecular dynamics (MD) simulations, the mechanical properties of single-layer silicene under mechanical strain. These simulations were carried out using a reactive force field (ReaxFF), as implemented in the LAMMPS code. We have calculated the elastic properties and the fracture patterns.Our results show that the dynamics of the whole fracturing processes of silicene present some similarities with that of graphene as well as some unique features.

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.

The Continuing Effort to Enhanced Learning of Mechanical Behavior of Materials via Combined Experiments and nanoHUB Simulations: Learning Modules for Sophomore MSE Students

MRS Advances ◽  
2016 ◽  
Vol 1 (56) ◽  
pp. 3721-3726 ◽  
Author(s):  
Aisling Coughlan ◽  
Heidi A. Diefes-Dux ◽  
Kerrie A. Douglas ◽  
Tanya A. Faltens ◽  
David Johnson
Keyword(s):  
Plastic Deformation ◽  
Materials Science ◽  
Md Simulations ◽  
Tensile Tests ◽  
Metal Nanowires ◽  
Science And Engineering ◽  
Learning Modules ◽  
Physical Laboratory ◽  
Materials Science And Engineering ◽  
Enhanced Learning

AbstractThis paper outlines updates to and evaluation of a learning module that incorporates a molecular dynamics (MD) simulation tool with a physical lab to introduce students to the atomic-level processes that are responsible for plastic deformation. Sophomore materials science and engineering (MSE) students at Purdue University get experience with both a physical laboratory, where they perform and analyze tensile tests of macroscopic samples, and a simulation laboratory, where they run and analyze MD simulations of tensile tests of metal nanowires. By integrating these two activities and discussing reasons for the large difference in yield stress, students may build an intuitive feel for how plastic deformation is linked across length scales

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.

Trends in Electron Energy Loss Spectroscopy

1977 ◽  
Vol 35 ◽  
pp. 228-229
Author(s):  
C. Colliex ◽  
P. Trebbia
Keyword(s):  
Energy Loss ◽  
Electron Energy ◽  
Electron Energy Loss Spectroscopy ◽  
Materials Science ◽  
Analytical Technique ◽  
Recent Developments ◽  
Quantitative Results ◽  
Electron Microscopes ◽  
Electron Energy Loss ◽  
Primary Electrons

The physical foundations for the use of electron energy loss spectroscopy towards analytical purposes, seem now rather well established and have been extensively discussed through recent publications. In this brief review we intend only to mention most recent developments in this field, which became available to our knowledge. We derive also some lines of discussion to define more clearly the limits of this analytical technique in materials science problems.The spectral information carried in both low ( 0<ΔE<100eV ) and high ( >100eV ) energy regions of the loss spectrum, is capable to provide quantitative results. Spectrometers have therefore been designed to work with all kinds of electron microscopes and to cover large energy ranges for the detection of inelastically scattered electrons (for instance the L-edge of molybdenum at 2500eV has been measured by van Zuylen with primary electrons of 80 kV). It is rather easy to fix a post-specimen magnetic optics on a STEM, but Crewe has recently underlined that great care should be devoted to optimize the collecting power and the energy resolution of the whole system.

Electron holography in materials science

1991 ◽  
Vol 49 ◽  
pp. 670-671
Author(s):  
Hannes Lichte ◽  
Edgar Voelkl
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Materials Science ◽  
Fourier Spectrum ◽  
Object Wave ◽  
Electron Holography ◽  
Reconstruction Procedure ◽  
Numerical Reconstruction ◽  
Transmission Electron ◽  
Unique Interpretation

The object wave o(x,y) = a(x,y)exp(iφ(x,y)) at the exit face of the specimen is described by two real functions, i.e. amplitude a(x,y) and phase φ(x,y). In stead of o(x,y), however, in conventional transmission electron microscopy one records only the real intensity I(x,y) of the image wave b(x,y) loosing the image phase. In addition, referred to the object wave, b(x,y) is heavily distorted by the aberrations of the microscope giving rise to loss of resolution. Dealing with strong objects, a unique interpretation of the micrograph in terms of amplitude and phase of the object is not possible. According to Gabor, holography helps in that it records the image wave completely by both amplitude and phase. Subsequently, by means of a numerical reconstruction procedure, b(x,y) is deconvoluted from aberrations to retrieve o(x,y). Likewise, the Fourier spectrum of the object wave is at hand. Without the restrictions sketched above, the investigation of the object can be performed by different reconstruction procedures on one hologram. The holograms were taken by means of a Philips EM420-FEG with an electron biprism at 100 kV.

Zero-loss omega-filtered REM and RHEED on the new Zeiss 912

1991 ◽  
Vol 49 ◽  
pp. 616-617
Author(s):  
J.C.H. Spence ◽  
J. Mayer
Keyword(s):  
Electron Microscopy ◽  
Materials Science ◽  
Surface States ◽  
Ccd Camera ◽  
Dark Field ◽  
Ion Pump ◽  
Magnetic Imaging ◽  
Reflection Electron Microscopy ◽  
Diffraction Patterns ◽  
Large Background

The Zeiss 912 is a new fully digital, side-entry, 120 Kv TEM/STEM instrument for materials science, fitted with an omega magnetic imaging energy filter. Pumping is by turbopump and ion pump. The magnetic imaging filter allows energy-filtered images or diffraction patterns to be recorded without scanning using efficient parallel (area) detection. The energy loss intensity distribution may also be displayed on the screen, and recorded by scanning it over the PMT supplied. If a CCD camera is fitted and suitable new software developed, “parallel ELS” recording results. For large fields of view, filtered images can be recorded much more efficiently than by Scanning Reflection Electron Microscopy, and the large background of inelastic scattering removed. We have therefore evaluated the 912 for REM and RHEED applications. Causes of streaking and resonance in RHEED patterns are being studied, and a more quantitative analysis of CBRED patterns may be possible. Dark field band-gap REM imaging of surface states may also be possible.

Dynamical Scattering in Crystalline Biological Specimens. I. Criteria of Validity for Scattering Approximations

1975 ◽  
Vol 33 ◽  
pp. 192-193
Author(s):  
Robert M. Glaeser ◽  
Bing K. Jap
Keyword(s):  
Biological Sciences ◽  
Electron Microscopy ◽  
Electron Microscope ◽  
Electron Diffraction ◽  
Born Approximation ◽  
Materials Science ◽  
Image Data ◽  
Dynamical Effect ◽  
Crystallographic Structure ◽  
Electron Microscope Image

The dynamical scattering effect, which can be described as the failure of the first Born approximation, is perhaps the most important factor that has prevented the widespread use of electron diffraction intensities for crystallographic structure determination. It would seem to be quite certain that dynamical effects will also interfere with structure analysis based upon electron microscope image data, whenever the dynamical effect seriously perturbs the diffracted wave. While it is normally taken for granted that the dynamical effect must be taken into consideration in materials science applications of electron microscopy, very little attention has been given to this problem in the biological sciences.

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