Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

With advances in tissue engineering, the possibility of regenerating injured tissue or failing organs has become a realistic prospect for the first time in medical history. Tissue engineering - the combination of bioactive materials with cells to generate engineered constructs that functionally replace lost and/or damaged tissue - is a major strategy to achieve this goal. One facet of tissue engineering is biofabrication, where three-dimensional tissue-like structures composed of biomaterials and cells in a single manufacturing procedure are generated. Cell-laden hydrogels are commonly used in biofabrication and are termed "bioinks". Hydrogels are particularly attractive for biofabrication as they recapitulate several features of the natural extracellular matrix and allow cell encapsulation in a highly hydrated mechanically supportive three-dimensional environment. Additionally, they allow for efficient and homogeneous cell seeding, can provide biologically-relevant chemical and physical signals, and can be formed in various shapes and biomechanical characteristics. However, despite the progress made in modifying hydrogels for enhanced bioactivation, cell survival and tissue formation, little attention has so far been paid to optimize hydrogels for the physico-chemical demands of the biofabrication process. The resulting lack of hydrogel bioinks have been identified as one major hurdle for a more rapid progress of the field. In this review we summarize and focus on the deposition process, the parameters and demands of hydrogels in biofabrication, with special attention to robotic dispensing as an approach that generates constructs of clinically relevant dimensions. We aim to highlight this current lack of effectual hydrogels within biofabrication and initiate new ideas and developments in the design and tailoring of hydrogels. The successful development of a "printable" hydrogel that supports cell adhesion, migration, and differentiation will significantly advance this exciting and promising approach for tissue engineering.

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25th Anniversary Article: Engineering Hydrogels for Biofabrication

3D Printing promises to produce complex biomedical devices according to computer design using patient-specific anatomical data. Since its initial use as pre-surgical visualization models and tooling molds, 3D Printing has slowly evolved to create one-of-a-kind devices, implants, scaffolds for tissue engineering, diagnostic platforms, and drug delivery systems. Fueled by the recent explosion in public interest and access to affordable printers, there is renewed interest to combine stem cells with custom 3D scaffolds for personalized regenerative medicine. Before 3D Printing can be used routinely for the regeneration of complex tissues (e.g. bone, cartilage, muscles, vessels, nerves in the craniomaxillofacial complex), and complex organs with intricate 3D microarchitecture (e.g. liver, lymphoid organs), several technological limitations must be addressed. In this review, the major materials and technology advances within the last five years for each of the common 3D Printing technologies (Three Dimensional Printing, Fused Deposition Modeling, Selective Laser Sintering, Stereolithography, and 3D Plotting/Direct-Write/Bioprinting) are described. Examples are highlighted to illustrate progress of each technology in tissue engineering, and key limitations are identified to motivate future research and advance this fascinating field of advanced manufacturing.

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Recent advances in 3D printing of biomaterials

Conventional optical tweezers, formed at the diffraction-limited focus of a laser beam, have become a powerful and flexible tool for manipulating micrometre-sized objects. Extending optical trapping down to the nanometre scale would open unprecedented opportunities in many fields of science, where such nano-optical tweezers would allow the ultra-accurate positioning of single nano-objects. Among the possible strategies, the ability of metallic nanostructures to control light at the subwavelength scale can be exploited to engineer such nano-optical traps. This Review summarizes the recent advances in the emerging field of plasmon-based optical trapping and discusses the details of plasmon tweezers along with their potential applications to bioscience and quantum optics.

Plasmon nano-optical tweezers

A review of trends and limitations in hydrogel-rapid prototyping for tissue engineering

Reliable interpretation of seismic surveys and borehole loggings requires that the seismic velocities and anisotropies of the bedrock are taken into account. There will be discrepancies in estimated reflector locations if one assumes isotropic velocity. Moreover, improved accuracy in determining reflector locations reduces drilling efforts in ore exploration. Our custom-built ultrasonic triaxial anvil setup permits measuring longitudinal (Vp) (1 MHz center frequency) and shear wave (Vs) (1.1 MHz center frequency with 0° and 90° polarization options) sound velocities in cubic rock samples (sides ~25 mm) under crustal-pressures up to 300 MPa in three directions (X, Y, and Z) simultaneously. Our results of eleven Precambrian rock samples from the FIRE-reflection profile in Central Finland show 3408-7250 m/s (Vs) and 2460-4140 m/s (Vp). The calculated velocity anisotropy values of these samples vary from 22% to 2% with applied pressure (up to 102 MPa).

Anisotropy of longitudinal and shear wave velocities in rocks under controlled pressure

The primary goal of this study is to localize a defect (cavity) in a curved geometry. Curved topologies exhibit multiple resonances and the presence of hotspots for acoustic waves. Launching acoustic waves along a specific direction e.g. by means of an extended laser source reduces the complexity of the scattering problem. We performed experiments to demonstrate the use of a laser line source and verified the experimental results in FEM simulations. In both cases, we could locate and determine the size of a pit in a steel hemisphere which allowed us to visualize the defect on a 3D model of the sample. Such an approach could benefit patients by enabling contactless inspection of acetabular cups.

/pdf/defect-localization-by-an-extended-laser-source-on-a-14xkrtgilb.pdf

Defect localization by an extended laser source on a hemisphere.

We present a simulation model that can be used to study the movement of an object in an acoustic levitator. The model uses the boundary element method (BEM) to compute the levitator's acoustic field, and the finite element method (FEM) to compute the movement of the levitating object. The model was built to act as a virtual tool for testing how objects move in acoustic pressure fields generated by phased array transducers (PATs). This was demonstrated by comparing object dynamics for different PAT optimization methods. We studied the stability of the levitation in fields created by two optimization methods. The fields were optimized to levitate an ellipsoid in the middle of our PAT geometry. By slightly displacing the levitating object from the intended levitation spot, we were able to show that the levitation became unstable and that the object would drop out from the trap. The results demonstrate that the model can be used to rapidly validate optimizers instead of having to run long experiments.

BEM-FEM Simulation of Acoustic Levitation Dynamics with Phased Arrays

Background: Measurement of the residual effects of sedatives on fitness for ambulation is typically performed with subjective measures, if at all. Previous efforts to objectively measure these effects employed dynamic posturography with expensive equipment that is not easily brought to the bedside and carries a risk of patient injury. A simple test employing consumer off-the-shelf technology that exposes the patient to no more risk than standing still might permit a more reliable assessment of fitness for discharge. We have previously shown that a simple tester, using a Nintendo Wii® Balance board and software that determined fuzzy sample entropy of postural sway can separate outpatients’ postural steadiness before (PRE) and after (POST) endoscopy with midazolam/fentanyl conscious sedation. Propofol/fentanyl monitored anesthesia care also alters balance, but recovery is known to be more rapid. We hypothesized that the ability to detect decrements in postural steadiness with fuzzy sample entropy following monitored anesthesia care would be less than that seen in conscious sedation. Methods: Fuzzy sample entropy of sway was measured in 92 patients undergoing monitored anesthesia care and 103 patients undergoing conscious sedation for minor endoscopic procedures under conditions of eyes open and closed in the PRE and POST states. The ability to discriminate the PRE and POST states was assessed by the area under the receiver operating characteristic curve (AUC). Results: In patients undergoing conscious sedation, fuzzy sample entropy was lower both with eyes open and closed (0.83 and 0.80). Following monitored anesthesia care, the PRE and POST states were less separable, with AUC of 0.56 and 0.60 (eyes open and closed). Conclusions: A simple tester that determines fuzzy sample entropy of postural sway yields a result that is expected when applied to groups receiving different sedation modalities. The utility of this tester in assessing outcomes will require further evaluation. Correspondence to: Mandel JE, Department of Anesthesiology & Critical Care, Perelman School of Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA, E-mail: MandelJ@uphs.upenn.edu/Jeff. Mandel@uphs.upenn.edu Received: March 14, 2017; Accepted: April 14, 2017; Published: April 17, 2017 Introduction Patients undergoing elective endoscopy frequently require sedation. While sedation improves patient acceptance of the procedure, and may improve procedural outcome, sedation is associated with a period of impaired postural steadiness. Accurate assessment of the degree of decreased postural steadiness can be challenging, and measures such as time to recovery room discharge or ambulation without assistance may be subject to bias and inter-observer variability. An objective method of assessment could address these limitations. Posturography measures the trajectory of the ground projection of the center-of-pressure of a subject standing on an instrumented surface. Posturography may be static or dynamic, that is, employ exogenous stimuli to introduce a disturbance into posture, such as a moving platform or a shifting artificial horizon. Previous studies of sedation effects on postural stability focused on computerized dynamic posturography as it has greater sensitivity than static posturography. Fujisawa demonstrated that computerized dynamic posturography was affected by midazolam [1], that these effects persisted longer in the elderly than in young people [2], and that the effects were less persistent with propofol sedation [3]. These authors further demonstrated that the results of the timed up and go test, in which a patient stood up, walked five meters, turned, and returned to their chair, correlated with the computerized dynamic posturography score [3,4]. Although computerized dynamic posturography and the timed up and go test may be sensitive measures of recovery, these tests may not be appropriate for all patients. Patients standing on a moving platform or walking and turning may suffer injuries as severe as those we seek to avoid. Thus, static posturography may be preferable to dynamic posturography when assessing patients recovering from anesthesia or sedation. Posturography typically employs simple measures of postural sway such as velocity and sway radius. Since robust control of posture requires random perturbation of the center of pressure to permit dynamic tuning of the system [5], measures that assess entropy may more efficiently identify a decrement in capacity to maintain upright stance than the simpler measures [6,7]. We previously demonstrated the superiority of fuzzy sample entropy over other linear and nonlinear Mandel JE (2017) A simple posturographic method detects the difference in recovery of patients receiving endoscopic sedation with propofol vs. midazolam Volume 1(2): 2-4 Med Res Innov, 2017 doi: 10.15761/MRI.1000107 measures of postural sway in differentiation of the pre-sedative state from the post-recovery state in patients undergoing midazolamfentanyl based conscious sedation [8]. We have also demonstrated that time to ambulation without assistance was shorter with propofolbased sedation than with midazolam-based sedation [9] indeed, in the propofol group time to ambulation was less than the minimum time that patients are required to stay in the recovery room prior to discharge, while in the midazolam group, it was almost identical to this time. It is therefore likely that patients receiving monitored anesthesia care are more completely recovered at discharge than patients receiving conscious sedation. We hypothesized that this difference in recovery to street readiness between midazolam and propofol-based sedation would be demonstrable with fuzzy sample entropy of postural sway.

/pdf/a-simple-posturographic-method-detects-the-difference-in-517eyoadzb.pdf

A simple posturographic method detects the difference in recovery of patients receiving endoscopic sedation with propofol vs. midazolam

Acoustic and photonic hooks have inspired study of new subwavelength structures to be used as lenses for ultrasound. A new V-shaped plate lens structure exhibits anisotropic focusing behavior in 2D finite element method simulations. The near field is shown in both orientations of the structure, and a frequency sweep was performed to study the response of the lens. Such a lens was built from evenly spaced 200 $\boldsymbol{\mu}\mathbf{m}$ thick brass plates, and the near field was visualized with the schlieren method. The results are compared with the simulation, and anisotropic behavior is confirmed.

Edward Hæggström

Papers

Anisotropy of longitudinal and shear wave velocities in rocks under controlled pressure

Defect localization by an extended laser source on a hemisphere.

BEM-FEM Simulation of Acoustic Levitation Dynamics with Phased Arrays

A simple posturographic method detects the difference in recovery of patients receiving endoscopic sedation with propofol vs. midazolam

Schlieren Visualization of Anisotropic Dual Slanted Plate Mesoscale Lens Action for Ultrasound