Predictive Helmet Optimization Framework Based on Reduced-Order Modeling of the Brain Dynamics.

Sports-related traumatic brain injuries (TBIs) are among the leading causes of head injuries in the world. Use of helmets is the main protective measure against this epidemic. The design criteria for the majority of the helmets often only consider the kinematics of the head. This approach neglects the importance of regional deformations of the brain especially near the deep white matter structures such as the corpus callosum (CC) which have been implicated in mTBI studies. In this work, we develop a dynamical reduced-order model of the skull-brain-helmet system to analyze the effect of various helmet parameters on the dynamics of the head and CC. Here, we show that the optimal head-helmet coupling values that minimize the CC dynamics are different from the ones that minimize the skull and brain dynamics (at some kinematics, up to two times stiffer for the head motion mitigation). By comparing our results with experimental impact tests performed on seven different helmets for five different sports, we found that the football helmets with an absorption of about 65-75% of the impact energy had the best performance in mitigating the head motion. Here, we found that none of the helmets are effective in protecting the CC from harmful impact energies. Our computational results reveal that the origin of the difference between the properties of a helmet mitigating the CC motion vs. the head motion is nonlinear vs. linear dynamics. Unlike the globally linear behavior of the head dynamics, we demonstrate that the CC exhibits nonlinear mechanical response similar to an energy sink. This means that there are scenarios where, at the instant of impact, the CC does not undergo extreme motions, but these may occur with a time delay as it absorbs shock energy from other parts of the brain. These findings hint at the importance of considering tissue level dynamics in designing new helmets.

A Nonlinear Reduced-Order Model of the Corpus Callosum Under Planar Coronal Excitation.

Traumatic brain injury (TBI) is often associated with microstructural tissue damage in the brain, which results from its complex biomechanical behavior. Recent studies have shown that the deep white matter (WM) region of the human brain is susceptible to being damaged due to strain localization in that region. Motivated by these studies, in this paper, we propose a geometrically nonlinear dynamical reduced order model (ROM) to model and study the dynamics of the deep WM region of the human brain under coronal excitation. In this model, the brain hemispheres were modeled as lumped masses connected via viscoelastic links, resembling the geometry of the corpus callosum (CC). Employing system identification techniques, we determined the unknown parameters of the ROM, and ensured the accuracy of the ROM by comparing its response against the response of an advanced finite element (FE) model. Next, utilizing modal analysis techniques, we determined the energy distribution among the governing modes of vibration of the ROM and concluded that the demonstrated nonlinear behavior of the FE model might be predominantly due to the special geometry of the brain deep WM region. Furthermore, we observed that, for sufficiently high input energies, high frequency harmonics at approximately 45 Hz, were generated in the response of the CC, which, in turn, are associated with high-frequency oscillations of the CC. Such harmonics might potentially lead to strain localization in the CC. This work is a step toward understanding the brain dynamics during traumatic injury.

Realization by impedance discontinuity of a unidirectional wave in a duct with harmonically perturbed uniform mean flow.

This paper presents a study of intentionally induced acoustic mode complexity in rigid-walled ducts of separable geometry and with uniform mean flow. An intermediately located perforated plate conceptualized as an impedance discontinuity is employed to maximize the acoustic mode complexity, in turn producing a unidirectional traveling wave from the source to the impedance discontinuity. The impedance of the perforated plate for realization of a unidirectional traveling wave is derived analytically and is found to be a function of the modal wavenumbers, the Mach number of the mean flow, the position of the perforated plate, and the termination impedance. The conditions derived analytically are verified computationally by finite element analysis. A measure of acoustic mode complexity is defined and also evaluated from the finite element analysis. It is found that the realization of a unidirectional traveling wave is robust at low Mach number mean flows, except at the occurrence of resonances. The method presented in this work provides a strategy to control the transmission of acoustic energy in rigid-walled ducts of separable geometry in the presence of uniform mean flow.

Ultimate Decoupling between Surface Topography and Material Functionality in Atomic Force Microscopy Using an Inner-Paddled Cantilever.

Atomic force microscopy (AFM) has been widely utilized to gain insight into various material and structural functionalities on the nanometer scale, leading to numerous discoveries and technologies. Despite the phenomenal success in applying AFM to the simultaneous characterization of topological and functional properties of materials, it has continuously suffered from the crosstalk between the observables, causing undesirable artifacts and complicated interpretations. Here, we introduce a two-field AFM probe, namely an inner-paddled cantilever integrating two discrete pathways such that they respond independently to the variations in surface topography and material functionality. Hence, the proposed design allows reliable and potentially quantitative determination of functional properties. In this paper, the efficacy of the proposed design has been demonstrated via piezoresponse force microscopy of periodically poled lithium niobate and collagen, although it can also be applied to other AFM methods such as AFM-based infrared spectroscopy and electrochemical strain microscopy.

Inducing a nonreflective airborne discontinuity in a circular duct by using a nonresonant side branch to create mode complexity.

A nonreflective airborne discontinuity is created in a one-dimensional rigid-walled duct when the mode complexity introduced by a nonresonant side branch reaches a maximum, so that a sound wave can be spatially separated into physical regions of traveling and standing waves. The nonresonance of the side branch is demonstrated, the mode complexity is quantified, and a computational method to optimize side-branch parameters to maximize mode complexity in the duct in the presence of three-dimensional effects is presented. The optimal side-branch parameters that maximize the mode complexity and thus minimize reflection are found using finite element analysis and a derivative-free optimization routine. Sensitivity of mode complexity near the optimum with respect to side-branch parameters is then examined. The results show reflection from the impedance discontinuity in the duct can be reduced nearly to zero, providing a practical means of achieving a nonreflective discontinuity for a plane wave propagating in a duct of finite length.

Characterization of a Plasmodium falciparum Orthologue of the Yeast Ubiquinone-Binding Protein, Coq10p.

Coenzyme Q (CoQ, ubiquinone) is a central electron carrier in mitochondrial respiration. CoQ is synthesized through multiple steps involving a number of different enzymes. The prevailing view that the CoQ used in respiration exists as a free pool that diffuses throughout the mitochondrial inner membrane bilayer has recently been challenged. In the yeast Saccharomyces cerevisiae, deletion of the gene encoding Coq10p results in respiration deficiency without inhibiting the synthesis of CoQ, suggesting that the Coq10 protein is critical for the delivery of CoQ to the site(s) of respiration. The precise mechanism by which this is achieved remains unknown at present. We have identified a Plasmodium orthologue of Coq10 (PfCoq10), which is predominantly expressed in trophozoite-stage parasites, and localizes to the parasite mitochondrion. Expression of PfCoq10 in the S. cerevisiae coq10 deletion strain restored the capability of the yeast to grow on respiratory substrates, suggesting a remarkable functional conservation of this protein over a vast evolutionary distance, and despite a relatively low level of amino acid sequence identity. As the antimalarial drug atovaquone acts as a competitive inhibitor of CoQ, we assessed whether over-expression of PfCoq10 altered the atovaquone sensitivity in parasites and in yeast mitochondria, but found no alteration of its activity.

Utilizing intentional internal resonance to achieve multi-harmonic atomic force microscopy.

During dynamic atomic force microscopy (AFM), the deflection of a scanning cantilever generates multiple frequency terms due to the nonlinear nature of AFM tip-sample interactions. Even though each frequency term is reasonably expected to encode information about the sample, only the fundamental frequency term is typically decoded to provide topographic mapping of the measured surface. One of main reasons for discarding higher harmonic signals is their low signal-to-noise ratio. Here, we introduce a new design concept for multi-harmonic AFM, exploiting intentional nonlinear internal resonance for the enhancement of higher harmonics. The nonlinear internal resonance, triggered by the non-smooth tip-sample dynamic interactions, results in nonlinear energy transfers from the directly excited fundamental bending mode to the higher-frequency mode and, hence, enhancement of the higher harmonic of the measured response. It is verified through detailed theoretical and experimental study that this AFM design can robustly incorporate the required internal resonance and enable high-frequency AFM measurements. Measurements on an inhomogeneous polymer specimen demonstrate the efficacy of the proposed design, namely that the higher harmonic of the measured response is capable of enhanced simultaneous topography imaging and compositional mapping, exhibiting less crosstalk with an abrupt height change.

Host erythrocyte environment influences the localization of exported protein 2, an essential component of the Plasmodium translocon.

Malaria parasites replicating inside red blood cells (RBCs) export a large subset of proteins into the erythrocyte cytoplasm to facilitate parasite growth and survival. PTEX, the parasite-encoded translocon, mediates protein transport across the parasitophorous vacuolar membrane (PVM) in Plasmodium falciparum-infected erythrocytes. Proteins exported into the erythrocyte cytoplasm have been localized to membranous structures, such as Maurer's clefts, small vesicles, and a tubovesicular network. Comparable studies of protein trafficking in Plasmodium vivax-infected reticulocytes are limited. With Plasmodium yoelii-infected reticulocytes, we identified exported protein 2 (Exp2) in a proteomic screen of proteins putatively transported across the PVM. Immunofluorescence studies showed that P. yoelii Exp2 (PyExp2) was primarily localized to the PVM. Unexpectedly, PyExp2 was also associated with distinct, membrane-bound vesicles in the reticulocyte cytoplasm. This is in contrast to P. falciparum in mature RBCs, where P. falciparum Exp2 (PfExp2) is exclusively localized to the PVM. Two P. yoelii-exported proteins, PY04481 (encoded by a pyst-a gene) and PY06203 (PypAg-1), partially colocalized with these PyExp2-positive vesicles. Further analysis revealed that with P. yoelii, Plasmodium berghei, and P. falciparum, cytoplasmic Exp2-positive vesicles were primarily observed in CD71(+) reticulocytes versus mature RBCs. In transgenic P. yoelii 17X parasites, the association of hemagglutinin-tagged PyExp2 with the PVM and cytoplasmic vesicles was retained, but the pyexp2 gene was refractory to deletion. These data suggest that the localization of Exp2 in mouse and human RBCs can be influenced by the host cell environment. Exp2 may function at multiple points in the pathway by which parasites traffic proteins into and through the reticulocyte cytoplasm.

Complex nonlinear dynamics in the limit of weak coupling of a system of microcantilevers connected by a geometrically nonlinear tunable nanomembrane.

Intentional utilization of geometric nonlinearity in micro/nanomechanical resonators provides a breakthrough to overcome the narrow bandwidth limitation of linear dynamic systems. In past works, implementation of intentional geometric nonlinearity to an otherwise linear nano/micromechanical resonator has been successfully achieved by local modification of the system through nonlinear attachments of nanoscale size, such as nanotubes and nanowires. However, the conventional fabrication method involving manual integration of nanoscale components produced a low yield rate in these systems. In the present work, we employed a transfer-printing assembly technique to reliably integrate a silicon nanomembrane as a nonlinear coupling component onto a linear dynamic system with two discrete microcantilevers. The dynamics of the developed system was modeled analytically and investigated experimentally as the coupling strength was finely tuned via FIB post-processing. The transition from the linear to the nonlinear dynamic regime with gradual change in the coupling strength was experimentally studied. In addition, we observed for the weakly coupled system that oscillation was asynchronous in the vicinity of the resonance, thus exhibiting a nonlinear complex mode. We conjectured that the emergence of this nonlinear complex mode could be attributed to the nonlinear damping arising from the attached nanomembrane.

Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum.

The quest for new antimalarial drugs, especially those with novel modes of action, is essential in the face of emerging drug-resistant parasites. Here we describe a new chemical class of molecules, pyrazoleamides, with potent activity against human malaria parasites and showing remarkably rapid parasite clearance in an in vivo model. Investigations involving pyrazoleamide-resistant parasites, whole-genome sequencing and gene transfers reveal that mutations in two proteins, a calcium-dependent protein kinase (PfCDPK5) and a P-type cation-ATPase (PfATP4), are necessary to impart full resistance to these compounds. A pyrazoleamide compound causes a rapid disruption of Na(+) regulation in blood-stage Plasmodium falciparum parasites. Similar effect on Na(+) homeostasis was recently reported for spiroindolones, which are antimalarials of a chemical class quite distinct from pyrazoleamides. Our results reveal that disruption of Na(+) homeostasis in malaria parasites is a promising mode of antimalarial action mediated by at least two distinct chemical classes.

Improved atomic force microscope infrared spectroscopy for rapid nanometer-scale chemical identification.

Atomic force microscope infrared spectroscopy (AFM-IR) can perform IR spectroscopic chemical identification with sub-100 nm spatial resolution, but is relatively slow due to its low signal-to-noise ratio (SNR). In AFM-IR, tunable IR laser light is incident upon a sample, which results in a rise in temperature and thermomechanical expansion of the sample. An AFM tip in contact with the sample senses this nanometer-scale photothermal expansion. The tip motion induces cantilever vibrations, which are measured either in terms of the peak-to-peak amplitude of time-domain data or the integrated magnitude of frequency-domain data. Using a continuous Morlet wavelet transform to the cantilever dynamic response, we show that the cantilever dynamics during AFM-IR vary as a function of both time and frequency. Based on the observed cantilever response, we tailor a time-frequency-domain filter to identify the region of highest vibrational energy. This approach can increase the SNR of the AFM cantilever signal, such that the throughput is increased 32-fold compared to state-of-the art procedures. We further demonstrate significant increases in AFM-IR imaging speed and chemical identification of nanometer-scale domains in polymer films.

Modeling and measurement of geometrically nonlinear damping in a microcantilever-nanotube system.

Nonlinear mechanical systems promise broadband resonance and instantaneous hysteretic switching that can be used for high sensitivity sensing. However, to introduce nonlinear resonances in widely used microcantilever systems, such as AFM probes, requires driving the cantilever to an amplitude that is too large for any practical applications. We introduce a novel design for a microcantilever with a strong nonlinearity at small cantilever oscillation amplitude arising from the geometrical integration of a single BN nanotube. The dynamics of the system was modeled theoretically and confirmed experimentally. The system, besides providing a practical design of a nonlinear microcantilever-based probe, demonstrates also an effective method of studying the nonlinear damping properties of the attached nanotube. Beyond the typical linear mechanical damping, the nonlinear damping contribution from the attached nanotube was found to be essential for understanding the dynamical behavior of the designed system. Experimental results obtained through laser microvibrometry validated the developed model incorporating the nonlinear damping contribution.

The compact conformation of the Plasmodium knowlesi myosin tail interacting protein MTIP in complex with the C-terminal helix of myosin A.

The myosin motor of the malaria parasite's invasion machinery moves over actin fibers while it is making critical contacts with the myosin-tail interacting protein (MTIP). Previously, in a "compact" Plasmodium falciparum MTIP•MyoA complex, MTIP domains 2 (D2) and 3 (D3) make contacts with the MyoA helix, and the central helix is kinked, but in an "extended" Plasmodium knowlesi MTIP•MyoA complex only D3 interacts with the MyoA helix, and the central helix is fully extended. Here we report the crystal structure of the compact P. knowlesi MTIP•MyoA complex. It appears that, depending on the pH, P. knowlesi MTIP can adopt either the compact or the extended conformation to interact with MyoA. Only at pH values above ~7.0, can key hydrogen bonds can be formed by the imidazole group of MyoA His810 with an aspartate carboxylate from the hinge of MTIP and a lysine amino group of MyoA simultaneously.

The structure of the D3 domain of Plasmodium falciparum myosin tail interacting protein MTIP in complex with a nanobody.

Apicomplexan parasites enter host cells by many sophisticated steps including use of an ATP-powered invasion machinery. The machinery consists of multiple proteins, including a special myosin (MyoA) which moves along an actin fiber and which is connected to the myosin tail interaction protein (MTIP). Here we report a crystal structure of the major MyoA-binding domain (D3) of Plasmodium falciparum MTIP in complex with an anti-MTIP nanobody. In this complex, the MyoA-binding groove in MTIP-D3 is considerably less accessible than when occupied by the MyoA helix, due to a shift of two helices. The nanobody binds to an area slightly overlapping with the MyoA binding groove, covering a hydrophobic region next to the groove entrance. This provides a new avenue for arriving at compounds interfering with the invasion machinery since small molecules binding simultaneously to the nanobody binding site and the adjacent MyoA binding groove would prevent MyoA binding by MTIP.

Atomic force microscope infrared spectroscopy on 15 nm scale polymer nanostructures.

We measure the infrared spectra of polyethylene nanostructures of height 15 nm using atomic force microscope infrared spectroscopy (AFM-IR), which is about an order of magnitude improvement over state of the art. In AFM-IR, infrared light incident upon a sample induces photothermal expansion, which is measured by an AFM tip. The thermomechanical response of the sample-tip-cantilever system results in cantilever vibrations that vary in time and frequency. A time-frequency domain analysis of the cantilever vibration signal reveals how sample thermomechanical response and cantilever dynamics affect the AFM-IR signal. By appropriately filtering the cantilever vibration signal in both the time domain and the frequency domain, it is possible to measure infrared absorption spectra on polyethylene nanostructures as small as 15 nm.

Platelet factor 4 activity against P. falciparum and its translation to nonpeptidic mimics as antimalarials.

Plasmodium falciparum pathogenesis is affected by various cell types in the blood, including platelets, which can kill intraerythrocytic malaria parasites. Platelets could mediate these antimalarial effects through human defense peptides (HDPs), which exert antimicrobial effects by permeabilizing membranes. Therefore, we screened a panel of HDPs and determined that human platelet factor 4 (hPF4) kills malaria parasites inside erythrocytes by selectively lysing the parasite digestive vacuole (DV). PF4 rapidly accumulates only within infected erythrocytes and is required for parasite killing in infected erythrocyte-platelet cocultures. To exploit this antimalarial mechanism, we tested a library of small, nonpeptidic mimics of HDPs (smHDPs) and identified compounds that kill P. falciparum by rapidly lysing the parasite DV while sparing the erythrocyte plasma membrane. Lead smHDPs also reduced parasitemia in a murine malaria model. Thus, identifying host molecules that control parasite growth can further the development of related molecules with therapeutic potential.

Remarkable stability in patterns of blood-stage gene expression during episodes of non-lethal Plasmodium yoelii malaria.

BACKGROUND: Microarray studies using in vitro cultures of synchronized, blood-stage Plasmodium falciparum malaria parasites have revealed a 'just-in-time' cascade of gene expression with some indication that these transcriptional patterns remain stable even in the presence of external stressors. However, direct analysis of transcription in P. falciparum blood-stage parasites obtained from the blood of infected patients suggests that parasite gene expression may be modulated by factors present in the in vivo environment of the host. The aim of this study was to examine changes in gene expression of the rodent malaria parasite, Plasmodium yoelii 17X, while varying the in vivo setting of replication. METHODS: Using P. yoelii 17X parasites replicating in vivo, differential gene expression in parasites isolated from individual mice, from independent infections, during ascending, peak and descending parasitaemia and in the presence and absence of host antibody responses was examined using P. yoelii DNA microarrays. A genome-wide analysis to identify coordinated changes in groups of genes associated with specific biological pathways was a primary focus, although an analysis of the expression patterns of two multi-gene families in P. yoelii, the yir and pyst-a families, was also completed. RESULTS: Across experimental conditions, transcription was surprisingly stable with little evidence for distinct transcriptional states or for consistent changes in specific pathways. Differential gene expression was greatest when comparing differences due to parasite load and/or host cell availability. However, the number of differentially expressed genes was generally low. Of genes that were differentially expressed, many involved biologically diverse pathways. There was little to no differential expression of members of the yir and pyst-a multigene families that encode polymorphic proteins associated with the membrane of infected erythrocytes. However, a relatively large number of these genes were expressed during blood-stage infection regardless of experimental condition. CONCLUSIONS: Taken together, these results indicate that 1) P. yoelii gene expression remains stable in the presence of a changing host environment, and 2) concurrent expression of a large number of the polymorphic yir and pyst-a genes, rather than differential expression in response to specific host factors, may in itself limit the effectiveness of host immune responses.

Crystal structure of GAP50, the anchor of the invasion machinery in the inner membrane complex of Plasmodium falciparum.

The glideosome associated protein GAP50 is an essential protein in apicomplexan parasites such as Plasmodium, Toxoplasma and Cryptosporidium, several species of which are important human pathogens. The 44.6kDa protein is part of a multi-protein complex known as the invasion machinery or glideosome, which is required for cell invasion and substrate gliding motility empowered by an actin-myosin motor. GAP50 is anchored through its C-terminal transmembrane helix into the inner membrane complex and interacts via a short six residue C-terminal tail with other proteins of the invasion machinery in the pellicle of the parasite. In this paper we describe the 1.7Å resolution crystal structure of the soluble GAP50 domain from the malaria parasite Plasmodium falciparum. The structure shows an αßßα fold with overall similarity to purple acid phosphatases with, however, little homology regarding the nature of the residues in the active site region of the latter enzyme. While purple acid phosphatases contain a phosphate bridged binuclear Fe-site coordinated by seven side chains with the Fe-ions 3.2Å apart, GAP50 in our crystals contains two cobalt ions each with one protein ligand and a distance between the Co(2+) ions of 18Å.

Elevated levels of the Plasmodium yoelii homologue of macrophage migration inhibitory factor attenuate blood-stage malaria.

The excessive production of proinflammatory cytokines plays a significant role in the pathogenesis of severe malaria. Mammalian macrophage migration inhibitory factor (MIF) (mMIF) is an immune mediator that promotes a sustained proinflammatory response by inhibiting the glucocorticoid-mediated downregulation of inflammation. In addition, Plasmodium parasites also encode a homologue of mammalian MIF that is expressed in asexual-stage parasites. We used the Plasmodium yoelii murine model to study the potential role of parasite-encoded MIF in the pathogenesis of malaria. Antibodies raised against purified, non-epitope-tagged P. yoelii MIF (PyMIF) were used to localize expression in trophozoite- and schizont-stage parasites and demonstrate extracellular release. In vitro, recombinant PyMIF was shown to actively induce the chemotaxis of macrophages but did not induce or enhance tumor necrosis factor alpha (TNF-α) production from peritoneal macrophages. To examine the role of parasite-derived PyMIF in vivo, two transgenic parasite lines that constitutively overexpress PyMIF were generated, one in a nonlethal P. yoelii 17X background [Py17X-MIF(+)] and the other in a lethal P. yoelii 17XL background [Py17XL-MIF(+)]. Challenge studies with transgenic parasites in mice showed that the increased expression of PyMIF resulted in a reduction in disease severity. Mice infected with Py17X-MIF(+) developed lower peak parasitemia levels than controls, while malaria-associated anemia was unaltered. Infection with Py17XL-MIF(+) resulted in a prolonged course of infection and a reduction in the overall mortality rate. Combined, the data indicate that parasite-derived MIF does not contribute significantly to immunopathology but, through its chemotactic ability toward macrophages, may attenuate disease and prolong infection of highly virulent parasite isolates.

Tunable, broadband nonlinear nanomechanical resonator.

A nanomechanical resonator incorporating intrinsically geometric nonlinearity and operated in a highly nonlinear regime is modeled and developed. The nanoresonator is capable of extreme broadband resonance, with tunable resonance bandwidth up to many times its natural frequency. Its resonance bandwidth and drop frequency (the upper jump-down frequency) are found to be very sensitive to added mass and energy dissipation due to damping. We demonstrate a prototype nonlinear mechanical nanoresonator integrating a doubly clamped carbon nanotube and show its broadband resonance over tens of MHz (over 3 times its natural resonance frequency) and its sensitivity to femtogram added mass at room temperature.