MD Code Research Articles

Evaluation Performance of Two-Dimensional Multi-Diagonal Code Using Polarization and Wavelength of OCDMA System

In this paper, a new encoder/decoder technique has employed two orthogonal polarization states (vertical and horizontal) of a two-dimensional optical code, which combined polarization and wavelength scheme (p/w). This technique employed in order to increase the number of users in the FTTH network. In addition, Optical Fiber Systems (OFS) and Free Space Optics (FSO) scenarios were utilized with different Spectral Amplitude Coding Optical Code Division Multiple Access (SAC-OCDMA) codes. The FTTH network based on incoherent SAC-OCDMA is tested by using the One and Two Dimensional Multi-Diagonal (1D-MD, 2D-MD) codes and 1D and 2D Zero Cross Correlation (ZCC) codes. The results show that the number of the total supported homes for the 2D codes is doubled as a comparison with 1D codes. As well as, the simulation results show the performance of MD code is better presented than ZCC in both OFS and FSO scenarios

MD Codes\u2122: A Methodological Approach to Facial Aesthetic Treatment with Injectable Hyaluronic Acid Fillers

BackgroundPatients often seek aesthetic correction of facial deficiencies (e.g., lines and folds) that are rarely the underlying cause of dissatisfaction with their appearance. Use of a more holistic approach focused on improving the emotional messages of the face (e.g., looking less sad) may improve patient satisfaction with treatment outcomes. The MD Codes™ system was developed to increase clinician success rates by reducing variability in the technical aspects of hyaluronic acid (HA) filler treatment and focusing on addressing unfavorable emotional attributes of the face.MethodsThe MD Codes, or medical codes, represent specific anatomical subunits for injection of HA fillers. Each MD Code includes information regarding the target depth of injection, the proper delivery tool (needle or cannula) and delivery technique (e.g., aliquot, bolus, fanning), and the minimum product volume recommended to achieve visible, reproducible results (active number). During treatment planning, the appropriate MD Codes are selected using algorithms focused on lessening unfavorable facial attributes (a saggy, tired, sad, or angry look) and enhancing positive attributes (an attractive, younger, more contoured, or feminine [soft] or masculine look).ResultsThree case studies are presented to illustrate how the MD Codes and their algorithms were used to address sagginess, tiredness, and sadness in two women and one man.ConclusionsMD Codes provide a universal symbolic language for reducing variability in injection technique. The platform provides user-friendly algorithms to help clinicians increase patient satisfaction by going beyond treatment of lines and folds and to focus on reducing unfavorable facial attributes.Level of Evidence IVThis journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

A Comparative Study of Asynchronous and Synchronous OCDMA Systems

This article presents a detailed survey on both asynchronous and synchronous Optical Code-Division Multiple-Access (OCDMA) systems based on 1-D, 2-D, and 3-D codes, distinctively. Accordingly, different coding schemes along with their multiplexing capacity, correlation features, advantages and drawbacks are addressed and benchmarked. Additionally, different detection techniques such as direct and coherent detection and their capability to handle Multiple Access-Interference are also discussed. Furthermore, the main OCDMA systems from the last two decades are summarized considering their coding schemes, performance, device components, and applications. Therefore, a new comparative study in terms of spectral efficiency and bit error rate for 1-D, 2-D, and 3-D asynchronous and synchronous OCDMA systems is carried out. Numerical results shown that the 3-D MD code stands out among the codes with superior performance as well as support to higher data rates and number of users.

Investigation on Haze Attenuation Impact on Proposed SCM˗SAC˗OCDMA Based on FSO System by Using MD Code

Investigation on Haze Attenuation Impact on Proposed SCM˗SAC˗OCDMA Based on FSO System by Using MD Code

Improving of Scm-Sac-Ocdma System by Using Optical Amplifier Based on Md Code

Free space optic (FSO) is one of the most effective solution technique to transmit the information due to its advantage such as cost and speed, but it suffers from various disadvantage that affects on the signal performance like weather condition that results loss in optical signal power over the communication path. So, in this paper we study the effect of the rain weather in Iraqi cities [ Baghdad, Basra, Mosul ] during 2017 on the FSO signal with system of hybrid Sub-carrier multiplexing _Spectral amplitude coding _ optical code division multiple access (SCM-SAC-OCDMA) with multi diagonal (MD) code and intermediate stage called ‘optical amplifier’. OCDMA allows multiple users to access the medium without any contention; it provides privacy and security with reducing the interference that may occur due to multiple users. MD code has been use to provide simplicity in design and high data rate. The optical amplifier with controlled gain leads to amplify the power of the signal. Results from simulation analysis for the proposed system can transmit data rate with (1Gbps) for (1 Km) distance and transmit power of (5dB) with bit error rate (BER) 10−12 in Mosul, 3× 10−56 in Baghdad, 1 × 10−62 in Basra.

CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space.

CoCo ("complementary coordinates") is a method for ensemble enrichment based on principal component analysis (PCA) that was developed originally for the investigation of NMR data. Here we investigate the potential of the CoCo method, in combination with molecular dynamics simulations (CoCo-MD), to be used more generally for the enhanced sampling of conformational space. Using the alanine penta-peptide as a model system, we find that an iterative workflow, interleaving short multiple-walker MD simulations with long-range jumps through conformational space informed by CoCo analysis, can increase the rate of sampling of conformational space up to 10 times for the same computational effort (total number of MD timesteps). Combined with the reservoir-REMD method, free energies can be readily calculated. An alternative, approximate but fast and practically useful, alternative approach to unbiasing CoCo-MD generated data is also described. Applied to cyclosporine A, we can achieve far greater conformational sampling than has been reported previously, using a fraction of the computational resource. Simulations of the maltose binding protein, begun from the "open" state, effectively sample the "closed" conformation associated with ligand binding. The PCA-based approach means that optimal collective variables to enhance sampling need not be defined in advance by the user but are identified automatically and are adaptive, responding to the characteristics of the developing ensemble. In addition, the approach does not require any adaptations to the associated MD code and is compatible with any conventional MD package.

Muscular Dystrophy Surveillance, Tracking, and Research Network pilot: Population-based surveillance of major muscular dystrophies at four U.S. sites, 2007-2011.

For 10 years, the Muscular Dystrophy Surveillance, Tracking, and Research Network (MD STARnet) conducted surveillance for Duchenne and Becker muscular dystrophy (DBMD). We piloted expanding surveillance to other MDs that vary in severity, onset, and sources of care. Our retrospective surveillance included individuals diagnosed with one of nine eligible MDs before or during the study period (January 2007-December 2011), one or more health encounters, and residence in one of four U.S. sites (Arizona, Colorado, Iowa, or western New York) at any time within the study period. We developed case definitions, surveillance protocols, and software applications for medical record abstraction, clinical review, and data pooling. Potential cases were identified by International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes 359.0, 359.1, and 359.21 and International Classification of Diseases, Tenth Revision (ICD-10) codes G71.0 and G71.1. Descriptive statistics were compared by MD type. Percentage of MD cases identified by each ICD-9-CM code was calculated. Of 2,862 cases, 32.9% were myotonic, dystrophy 25.8% DBMD, 9.7% facioscapulohumeral MD, and 9.1% limb-girdle MD. Most cases were male (63.6%), non-Hispanic (59.8%), and White (80.2%). About, half of cases were genetically diagnosed in self (39.1%) or family (6.2%). About, half had a family history of MD (48.9%). The hereditary progressive MD code (359.1) was the most common code for identifying eligible cases. The myotonic code (359.21) identified 83.4% of eligible myotonic dystrophy cases (786/943). MD STARnet is the only multisite, population-based active surveillance system available for MD in the United States. Continuing our expanded surveillance will contribute important epidemiologic and health outcome information about several MDs.

Investigation of N behavior during coal pyrolysis and oxidation using ReaxFF molecular dynamics

This paper presents ReaxFF molecular dynamics simulations of pyrolysis and oxidation processes at 500–2500 K and 1000–2800 K performed using the GPU-enabled ReaxFF MD code of GMD-Reax and reaction analysis code of VARxMD. The simulation results of a large-scale coal model with varied types of N-containing groups shows that more than 65% N still remains in C40+ fragments and about 25% N migrates into C5–C40 fragments after pyrolysis stage. The evolution tendencies of light gases (NH3, HCN, HNCO, NO, N2 and NO2) and important radicals (CN, NH2/NH, NCO and HNO) with temperature were observed from the slow heat-up coal oxidation simulation at fuel lean condition. The detailed structures and conversion reactions associated with light nitrogen species were obtained. The NCO-containing intermediates are found playing a significant role for NO emission that more than 50% of the NO formation is through NCO-containing intermediates, some of which comes from the oxidation of CN radicals and HNCO. The hydrogen abstraction of N–H in pyrrole groups by O2 will create an initial unstable environment, followed with O insertion reactions into N-containing heterocyclic ring structures to promote the activation of N-containing groups in coal structure.

Pyrolysis simulations of Fugu coal by large-scale ReaxFF molecular dynamics

This paper presents pyrolysis simulations of a multi-component structure model of Fugu sub-bituminous coal containing 23,898 atoms with ReaxFF MD. The slow heat-up and long-time isothermal simulations were performed using the GPU-enabled ReaxFF MD code of GMD-Reax and reaction analysis code of VARxMD. The simulated pyrolyzate evolution trends and pyrolysis stages proposed based on lumped pyrolyzates agree fairly with literature. Major reaction pathways for early generation of CO2, H2O, CH4 and H2 in the activation and primary pyrolysis stages are found closely associated with carboxyl and methoxyl groups, indicating the significant role of oxygen-containing groups in the initialization of Fugu coal pyrolysis. Compared with reported experiments, the coal tar yield is over-predicted, while the gas yield is slightly under-estimated. To shorten the simulation time from 2 ns to 250 ps, an increase of 400 K in average on the basis of temperature range of 1200–2200 K is needed that will result in the over-prediction for the yields of gas and tar, as well as under-prediction for the non-volatile yield. This work suggests that ReaxFF MD simulation is useful for revealing the overall scenario and detailed reactions in coal pyrolysis but cautions should be taken for proper elevated temperatures.

Molecular dynamics simulation of rotating carbon nanotube in uniform liquid argon flow

In this work, nonequilibrium molecular dynamics (NEMD) simulations are performed to investigate liquid argon flow past rotating carbon nanotube and to estimate flow forces on the nanotube. In molecular dynamics simulation, fluid forces on a floating body are calculated directly from summation of the molecular forces exerted on solid atoms by fluid atoms and this method is used also herein. Based on this method, an in-house, parallel MD code was developed to calculate drag and lift forces exerted on a carbon nanotube and investigate fluid atoms positioning around it, in a uniform flow of liquid argon. The simulation is 3-dimensional and consists of 33,669 liquid argon atoms which represent the fluid and 240 carbon atoms as the nanotube for different domain setups used in this work. The single walled carbon nanotube is simulated as a rigid cylinder of fixed carbon atoms. For simulation of rotating nanotube, carbon atoms are rotated around axis of the nanotube in each time step according to its rotational speed. Both argon-argon and carbon-argon interactions are modeled by the Lennard-Jones potential function. Periodic boundary condition is used for the whole system. Flow is driven by rescaling atoms velocity at inlet region each 50 time steps. Drag coefficient on stationary carbon nanotube in some situations are compared with that of Tang and Advani (2006) and so the in-house code is verified. Results indicate that when the nanotube is stationary, drag force increased with inlet flow velocity and lift force almost fluctuated around zero value. At higher inlet velocities, these fluctuations damped and lift force converged to exact zero value. It was also found that drag coefficient exerted on carbon nanotube always reduced with its rotational speed. This reduction was more significant at lower inlet flow velocities and as flow velocity increased, this phenomenon occurred with a lower rate of reduction. Rotational speed did not have significant effects on lift force in comparison to its effects on drag force and so it is neglected. Rotation of carbon nanotube has changed atoms positioning around the nanotube and so atomic density in the nearby bins.

Performance Analysis of SACOCDMA-FSO System Using MD Codes

Performance of SACOCDMA-FSO system using MD codes at 10 Gbps is evaluated. MD code has become an area of interest in optical communication because of its ability to support many users at higher data rates, flexibility to select weight parameters. The proposed system was compared with SACOCDMA-FSO System employing RD codes in different conditions. The simulative results demonstrated that optical system based on MD codes is better than the system employing RD codes.

Simulation of Acoustic Particle Agglomeration in Poly-dispersed Aerosols

This report presents application of the MD for the simulation of acoustic agglomeration of poly-disperse aerosol particles. The conventional time-driven MD approach was applied and in-house developed MD code was modified for simulation purposes. The aerosol is assumed to be a system of dispersed spherical fluid particles while the agglomeration may occur between initial smaller particles sequentially forming larger particles. The modelled processes include the agglomeration due to the orthokinetic and acoustic wake mechanisms. Orthokinetic agglomeration refers to the agglomeration due to direct collisions between particles that are entrained at different velocities in the oscillatory motion of the sound field. Acoustic wake mechanisms are those that produce particle interactions through the surrounding medium because of hydrodynamic forces and the asymmetry of the flow field around the particle.It is assumed that the particles collide and agglomerate due to the interactions induced by sound waves. The aggregates formed during the agglomeration process were characterised as aggregates with a different radius to estimate the average radius of the primary particles in individual aggregates. The MD model was validated by comparison against the available analytical solutions. Finally, interaction process of two and four particles investigated and presented.

Abstract 15297: A Bundled Approach to Improving Code Team Response for In-hospital Cardiac Arrest to Decrease Overcrowding and Improve Role Clarity and Leadership

Background: Little is known about how non-technical factors such as inadequate role definition and overcrowding may impact in-hospital cardiac arrest (IHCA) outcomes. Using a bundled intervention, we sought to decrease overcrowding while improving provider role ambiguity and leadership at IHCA events. Objective: To examine interventions targeted at decreasing overcrowding, improving role ambiguity and leadership during IHCA. Methods: As part of a performance improvement initiative, a multidisciplinary team implemented four countermeasures to improve IHCA code response: an MD/RN leadership dyad, assigned optimal team composition, scripted role definitions, and visual (stickers)/verbal (role-checks) cues. Between 4/2013-4/2014, the number and discipline of providers responding to ICHA events were recorded at each pulse check, and a 10-point Likert scale survey assessing communication and leadership was performed pre- and post-intervention. The primary outcome was the number of providers present after the role checks. Secondary outcome examined communication and leadership performance. Mann-Whitney test was used for continuous variables and chi-squared or Fischer’s exact test was used to compare categorical variables. Results: 20 pre-intervention and 34 post-intervention IHCA events were captured. During both periods, MDs and RNs comprised the majority of the total providers present (61%, 57%). The median number of MDs present in the post-intervention group was lower than in the pre-intervention group (4 (IQR 4-5) vs. 7 (IQR 5-9), p= 0.004), as was the number of total overall providers (14 (IQR 12-16) vs. 18 (IQR 14-22), p=0.04). The number of RNs did not differ post-intervention (data not shown). Survey results showed no significant differences in perceptions of communications or physician leadership post-intervention. However, the overwhelming majority of both the MD code leaders (90%) and primary nurses (97%) identified that there was a clear RN leader and rated the leadership provided by RN lead consistently high with a median score of 9 out of 10 possible points. Conclusions: Using an innovative bundle can decrease overcrowding and improve role ambiguity and leadership during non-ICU IHCA events.

A new two dimensional spectral/spatial multi-diagonal code for noncoherent optical code division multiple access (OCDMA) systems

A new two dimensional codes family, namely two dimensional multi-diagonal (2D-MD) codes, is proposed for spectral/spatial non-coherent OCDMA systems based on the one dimensional MD code. Since the MD code has the property of zero cross correlation, the proposed 2D-MD code also has this property. So that, the multi-access interference (MAI) is fully eliminated and the phase induced intensity noise (PIIN) is suppressed with the proposed code. Code performance is analyzed in terms of bit error rate (BER) while considering the effect of shot noise, PIIN, and thermal noise. The performance of the proposed code is compared with the related MD, modified quadratic congruence (MQC), two dimensional perfect difference (2D-PD) and two dimensional diluted perfect difference (2D-DPD) codes. The analytical and the simulation results reveal that the proposed 2D-MD code outperforms the other codes. Moreover, a large number of simultaneous users can be accommodated at low BER and high data rate.

2115 大規模な剛体分子集合系のための古典MDコードの開発(OS21-4.固体物理/流体物理のマルチフィジックス/マルチスケール解析(4),OS・一般セッション講演)

2115 大規模な剛体分子集合系のための古典MDコードの開発(OS21-4.固体物理/流体物理のマルチフィジックス/マルチスケール解析(4),OS・一般セッション講演)

Molecular dynamics/order parameter extrapolation for bionanosystem simulations.

A multiscale approach, molecular dynamics/order parameter extrapolation (MD/OPX), to the all-atom simulation of large bionanosystems is presented. The approach starts with the introduction of a set of order parameters (OPs) automatically generated with orthogonal polynomials to characterize the nanoscale features of bionanosystems. The OPs are shown to evolve slowly via Newton's equations, and the all-atom multiscale analysis (AMA) developed earlier (Miao and Ortoleva, J Chem Phys 2006, 125, 44901) demonstrates the existence of their stochastic dynamics, which serve as the justification for our MD/OPX approach. In MD/OPX, a short MD run estimates the rate of change of the OPs, which is then used to extrapolate the state of the system over time that is much longer than the 10(-14) second timescale of fast atomic vibrations and collisions. The approach is implemented in NAMD and demonstrated on cowpea chlorotic mottle virus (CCMV) capsid structural transitions (STs). It greatly accelerates the MD code and its underlying all-atom description of the nanosystems enables the use of a universal interatomic force field, avoiding recalibration with each new application as needed for coarse-grained models. The source code of MD/OPX is distributed free of charge at https://simtk.org/home/mdopx and a web portal will be available via http://sysbio.indiana.edu/virusx.

Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations

FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell-lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256 K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell-list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code.

Speeding up parallel GROMACS on high‐latency networks

We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling even on such clusters with only limited bandwidth and high latency. GROMACS 3.3 scales well on supercomputers like the IBM p690 (Regatta) and on Linux clusters with a special interconnect like Myrinet or Infiniband. Because of the high single-node performance of GROMACS, however, on the widely used Ethernet switched clusters, the scaling typically breaks down when more than two computer nodes are involved, limiting the absolute speedup that can be gained to about 3 relative to a single-CPU run. With the LAM MPI implementation, the main scaling bottleneck is here identified to be the all-to-all communication which is required every time step. During such an all-to-all communication step, a huge amount of messages floods the network, and as a result many TCP packets are lost. We show that Ethernet flow control prevents network congestion and leads to substantial scaling improvements. For 16 CPUs, e.g., a speedup of 11 has been achieved. However, for more nodes this mechanism also fails. Having optimized an all-to-all routine, which sends the data in an ordered fashion, we show that it is possible to completely prevent packet loss for any number of multi-CPU nodes. Thus, the GROMACS scaling dramatically improves, even for switches that lack flow control. In addition, for the common HP ProCurve 2848 switch we find that for optimum all-to-all performance it is essential how the nodes are connected to the switch's ports. This is also demonstrated for the example of the Car-Parinello MD code.

Grid-based steered thermodynamic integration accelerates the calculation of binding free energies

The calculation of binding free energies is important in many condensed matter problems. Although formally exact computational methods have the potential to complement, add to, and even compete with experimental approaches, they are difficult to use and extremely time consuming. We describe a Grid-based approach for the calculation of relative binding free energies, which we call Steered Thermodynamic Integration calculations using Molecular Dynamics (STIMD), and its application to Src homology 2 (SH2) protein cell signalling domains. We show that the time taken to compute free energy differences using thermodynamic integration can be significantly reduced: potentially from weeks or months to days of wall-clock time. To be able to perform such accelerated calculations requires the ability to both run concurrently and control in realtime several parallel simulations on a computational Grid. We describe how the RealityGrid computational steering system, in conjunction with a scalable classical MD code, can be used to dramatically reduce the time to achieve a result. This is necessary to improve the adoption of this technique and further allows more detailed investigations into the accuracy and precision of thermodynamic integration. Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach.

MD simulations of the collision between a copper ion and a polyethylene surface: an application to the plasma?insulating material interaction

To allow a better understanding of the physical phenomena occurred between a plasma and an insulating material, we have developed a specific MD code to study this type of interaction. We report results of MD simulations of the interaction of an incoming copper ion with a polyethylene crystal surface. Three initial incoming velocities and four impact angle values are used to check the influence of both the incident energy and impact direction to the resulting surface damage. When the incoming ion velocity is sufficiently high, MD results show that the impact can cause bond breaking leading to uncoordinated carbon atoms and free hydrogen atoms. The values of local temperatures associated with the structural changes show a possible ablation of the polyethylene surface.