Mechanics and microstructure of blood plasma clots in shear driven rupture.

Intravascular blood clots are subject to hydrodynamic shear and other forces that cause clot deformation and rupture (embolization). A portion of the ruptured clot can block blood flow in downstream vessels. The mechanical stability of blood clots is determined primarily by the 3D polymeric fibrin network that forms a gel. Previous studies have primarily focused on the rupture of blood plasma clots under tensile loading (Mode I), our current study investigates the rupture of fibrin induced by shear loading (Mode II), dominating under physiological conditions induced by blood flow. Using experimental and theoretical approaches, we show that fracture toughness, i.e. the critical energy release rate, is relatively independent of the type of loading and is therefore a fundamental property of the gel. Ultrastructural studies and finite element simulations demonstrate that cracks propagate perpendicular to the direction of maximum stretch at the crack tip. These observations indicate that locally, the mechanism of rupture is predominantly tensile. Knowledge gained from this study will aid in the development of methods for prediction/prevention of thrombotic embolization.

Cracks in tensile-contracting and tensile-dilating poroelastic materials.

Fibrous gels such as cartilage, blood clots, and carbon-nanotube-based sponges with absorbed oils suffer a reduction in volume by the expulsion of liquid under uniaxial tension, and this directly affects crack-tip fields and energy release rates. A continuum model is formulated for isotropic fibrous gels that exhibit a range of behaviors from volume increasing to volume decreasing in uniaxial tension by changing the ratio of two material parameters. The motion of liquid in the pores of such gels is modeled using poroelasticity. The direction of liquid fluxes around cracks is shown to depend on whether the gel locally increases or decreases in volume. The energy release rate for cracks is computed using a surface-independent integral and it is shown to have two contributions - one from the stresses in the solid network, and another from the flow of liquid. The contribution to the integral from liquid permeation tends to be negative when the gel exhibits volume decrease, which effectively is a crack shielding mechanism.

Humidity dependence of fracture toughness of cellulose fibrous networks.

Cellulose-based materials are increasingly finding applications in technology due to their sustainability and biodegradability. The sensitivity of cellulose fiber networks to environmental conditions such as temperature and humidity is well known. Yet, there is an incomplete understanding of the dependence of the fracture toughness of cellulose networks on environmental conditions. In the current study, we assess the effect of moisture content on the out-of-plane (i.e., z-dir.) fracture toughness of a particular cellulose network, specifically Whatman cellulose filter paper. Experimental measurements are performed at 16% RH along the desorption isotherm and 23, 37, 50, 75% RH along the adsorption isotherm using out-of-plane tensile tests and double cantilever beam (DCB) tests. Cohesive zone modeling and finite element simulations are used to extract quantitative properties that describe the crack growth behavior. Overall, the fracture toughness of filter paper decreased with increasing humidity. Additionally, a novel model is developed to capture the high peak and sudden drop in the experimental force measurement caused by the existence of an initiation region. This model is found to be in good agreement with experimental data. The relative effect of each independent cohesive parameter is explored to better understand the cohesive zone-based humidity dependence model. The methods described here may be applied to study rupture of other fiber networks with weak bonds.

Kinetics of self-assembly of inclusions due to lipid membrane thickness interactions.

Self-assembly of proteins on lipid membranes underlies many important processes in cell biology, such as, exo- and endo-cytosis, assembly of viruses, etc. An attractive force that can cause self-assembly is mediated by membrane thickness interactions between proteins. The free energy profile associated with this attractive force is a result of the overlap of thickness deformation fields around the proteins which can be calculated from the solution of a boundary value problem. Yet, the time scales over which two inclusions coalesce has not been explored, even though the evolution of particle concentrations on membranes has been modeled using phase-field approaches. In this paper we compute this time scale as a function of the initial distance between two inclusions by viewing their coalescence as a first passage time problem. The mean first passage time is computed using Langevin dynamics and a partial differential equation, and both methods are found to be in excellent agreement. Inclusions of three different shapes are studied and it is found that for two inclusions separated by about hundred nanometers the time to coalescence is hundreds of milliseconds irrespective of shape. An efficient computation of the interaction energy of inclusions is central to our work. We compute it using a finite difference technique and show that our results are in excellent agreement with those from a previously proposed semi-analytical method based on Fourier-Bessel series. The computational strategies described in this paper could potentially lead to efficient methods to explore the kinetics of self-assembly of proteins on lipid membranes.

Bacterial activity hinders particle sedimentation.

Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E. coli concentration. Results show that the presence of swimming bacteria significantly reduces the speed of the sedimentation front even in the dilute regime, in which the sedimentation speed is expected to be independent of particle concentration. Furthermore, bacteria increase the dispersion of the passive particles, which determines the width of the sedimentation front. For short times, particle sedimentation speed has a linear dependence on bacterial concentration. Mean square displacement data shows, however, that bacterial activity decays over long experimental (sedimentation) times. An advection-diffusion equation coupled to bacteria population dynamics seems to capture concentration profiles relatively well. A single parameter, the ratio of single particle speed to the bacteria flow speed can be used to predict front sedimentation speed.

Harnessing fluctuation theorems to discover free energy and dissipation potentials from non-equilibrium data.

The Jarzynski relation, as an equality form of the second law of thermodynamics, represents an exact thermodynamic statement that is valid arbitrarily far away from equilibrium. This remarkable relation directly links the equilibrium free energy difference between two states and the probability distribution of the work done along a process that drives the system from one state to the other. Here, we leverage the Jarzynski equality and a local equilibrium assumption, to go beyond the calculation of free energy differences and also extract the dissipation potential from additional measurements of kinematic field variables (strain and velocity fields). The proposed strategy is exemplified over pulling experiments of mass-spring models obeying overdamped Langevin dynamics, which is a prototype for nanorods, fibrous macro-molecules and the Rouse model of polymers. Different interaction potentials, fluid viscosities and bath temperatures are studied, so as to intrinsically control how close or far away the system is from equilibrium. The data-inferred continuum models are then validated against processes governed by different pulling protocols, thereby demonstrating their predictive capability. The methods presented here represent a first step toward full material characterization from non-equilibrium data of macroscopic observables, which could potentially be obtained from experimental observations.

A Semi-Analytic Elastic Rod Model of Pediatric Spinal Deformity.

The mechanism of the scoliotic curve development in healthy adolescents remains unknown in the field of orthopedic surgery. Variations in the sagittal curvature of the spine are believed to be a leading cause of scoliosis in this patient population. Here, we formulate the mechanics of S-shaped slender elastic rods as a model for pediatric spine under physiological loading. Second, applying inverse mechanics to clinical data of the subtypes of scoliotic spines, with characteristic 3D deformity, we determine the undeformed geometry of the spine before the induction of scoliosis. Our result successfully reproduces the clinical data of the deformed spine under varying loads, confirming that the prescoliotic sagittal curvature of the spine impacts the 3D loading that leads to scoliosis.

Biodegradable Piezoelectric Force Sensor.

Measuring vital physiological pressures is important for monitoring health status, preventing the buildup of dangerous internal forces in impaired organs, and enabling novel approaches of using mechanical stimulation for tissue regeneration. Pressure sensors are often required to be implanted and directly integrated with native soft biological systems. Therefore, the devices should be flexible and at the same time biodegradable to avoid invasive removal surgery that can damage directly interfaced tissues. Despite recent achievements in degradable electronic devices, there is still a tremendous need to develop a force sensor which only relies on safe medical materials and requires no complex fabrication process to provide accurate information on important biophysiological forces. Here, we present a strategy for material processing, electromechanical analysis, device fabrication, and assessment of a piezoelectric Poly-l-lactide (PLLA) polymer to create a biodegradable, biocompatible piezoelectric force sensor, which only employs medical materials used commonly in Food and Drug Administration-approved implants, for the monitoring of biological forces. We show the sensor can precisely measure pressures in a wide range of 0-18 kPa and sustain a reliable performance for a period of 4 d in an aqueous environment. We also demonstrate this PLLA piezoelectric sensor can be implanted inside the abdominal cavity of a mouse to monitor the pressure of diaphragmatic contraction. This piezoelectric sensor offers an appealing alternative to present biodegradable electronic devices for the monitoring of intraorgan pressures. The sensor can be integrated with tissues and organs, forming self-sensing bionic systems to enable many exciting applications in regenerative medicine, drug delivery, and medical devices.

Statistical mechanics of a double-stranded rod model for DNA melting and elasticity.

The double-helical topology of DNA molecules observed at room temperature in the absence of any external loads can be disrupted by increasing the bath temperature or by applying tensile forces, leading to spontaneous strand separation known as DNA melting. Here, continuum mechanics of a 2D birod is combined with statistical mechanics to formulate a unified framework for studying both thermal melting and tensile force induced melting of double-stranded molecules: it predicts the variation of melting temperature with tensile load, provides a mechanics-based understanding of the cooperativity observed in melting transitions, and reveals an interplay between solution electrostatics and micromechanical deformations of DNA which manifests itself as an increase in the melting temperature with increasing ion concentration. This novel predictive framework sheds light on the micromechanical aspects of DNA melting and predicts trends that were observed experimentally or extracted phenomenologically using the Clayperon equation.

Extensions of the worm-like-chain model to tethered active filaments under tension.

Intracellular elastic filaments such as microtubules are subject to thermal Brownian noise and active noise generated by molecular motors that convert chemical energy into mechanical work. Similarly, polymers in living fluids such as bacterial suspensions and swarms suffer bending deformations as they interact with single bacteria or with cell clusters. Often, these filaments perform mechanical functions and interact with their networked environment through cross-links or have other similar constraints placed on them. Here, we examine the mechanical properties-under tension-of such constrained active filaments under canonical boundary conditions motivated by experiments. Fluctuations in the filament shape are a consequence of two types of random forces-thermal Brownian forces and activity derived forces with specified time and space correlation functions. We derive force-extension relationships and expressions for the mean square deflections for tethered filaments under various boundary conditions including hinged and clamped constraints. The expressions for hinged-hinged boundary conditions are reminiscent of the worm-like-chain model and feature effective bending moduli and mode-dependent non-thermodynamic effective temperatures controlled by the imposed force and by the activity. Our results provide methods to estimate the activity by measurements of the force-extension relation of the filaments or their mean square deflections, which can be routinely performed using optical traps, tethered particle experiments, or other single molecule techniques.

Antimicrobial Disposition During Pediatric Continuous Renal Replacement Therapy Using an Ex Vivo Model.

OBJECTIVES: Little is known on the impact of continuous renal replacement therapy on antimicrobial dose requirements in children. In this study, we evaluated the pharmacokinetics of commonly administered antimicrobials in an ex vivo continuous renal replacement therapy model. DESIGN: An ex vivo continuous renal replacement therapy circuit was used to evaluate drug-circuit interactions and determine the disposition of five commonly used antimicrobials (meropenem, piperacillin, liposomal amphotericin B, caspofungin, and voriconazole). SETTING: University research laboratory. PATIENTS: None. INTERVENTIONS: Antimicrobials were administered into a reservoir containing whole human blood. The reservoir was connected to a pediatric continuous renal replacement therapy circuit programmed for a 10 kg child. Continuous renal replacement therapy was performed in the hemodiafiltration mode and in three phases correlating with three different continuous renal replacement therapy clearance rates: 1) no clearance (0 mL/kg/hr, to measure adsorption), 2) low clearance (20 mL/kg/hr), and 3) high clearance (40 mL/kg/hr). Blood samples were drawn directly from the reservoir at baseline and at 5, 20, 60, and 180 minutes during each phase. Five independent continuous renal replacement therapy runs were performed to assess inter-run variability. Antimicrobial concentrations were measured using validated liquid chromatography-mass spectrometry assays. A closed-loop, flow-through pharmacokinetic model was developed to analyze concentration-time profiles for each drug. MEASUREMENTS AND MAIN RESULTS: Circuit adsorption of antimicrobials ranged between 13% and 27%. Meropenem, piperacillin, and voriconazole were cleared by the continuous renal replacement therapy circuit and clearance increased with increasing continuous renal replacement therapy clearance rates (7.66 mL/min, 4.97 mL/min, and 2.67 mL/min, respectively, for high continuous renal replacement therapy clearance). Amphotericin B and caspofungin had minimal circuit clearance and did not change with increasing continuous renal replacement therapy clearance rates. CONCLUSIONS: Careful consideration of drug-circuit interactions during continuous renal replacement therapy is essential for appropriate drug dosing in critically ill children. Antimicrobials have unique adsorption and clearance profiles during continuous renal replacement therapy, and this knowledge is important to optimize antimicrobial therapy.

Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins.

Coiled-coils are filamentous proteins that form the basic building block of important force-bearing cellular elements, such as intermediate filaments and myosin motors. In addition to their biological importance, coiled-coil proteins are increasingly used in new biomaterials including fibers, nanotubes, or hydrogels. Coiled-coils undergo a structural transition from an α-helical coil to an unfolded state upon extension, which allows them to sustain large strains and is critical for their biological function. By performing equilibrium and out-of-equilibrium all-atom molecular dynamics (MD) simulations of coiled-coils in explicit solvent, we show that two-state models based on Kramers' or Bell's theories fail to predict the rate of unfolding at high pulling rates. We further show that an atomistically informed continuum rod model accounting for phase transformations and for the hydrodynamic interactions with the solvent can reconcile two-state models with our MD results. Our results show that frictional forces, usually neglected in theories of fibrous protein unfolding, reduce the thermodynamic force acting on the interface, and thus control the dynamics of unfolding at different pulling rates. Our results may help interpret MD simulations at high pulling rates, and could be pertinent to cytoskeletal networks or protein-based artificial materials subjected to shocks or blasts.

Stick-slip kinetics in a bistable bar immersed in a heat bath.

Structural transitions in some rod-like biological macromolecules under tension are known to proceed by the propagation through the length of the molecule of an interface separating two phases. A continuum mechanical description of the motion of this interface, or phase boundary, takes the form of a kinetic law which relates the thermodynamic driving force across it with its velocity in the reference configuration. For biological macromolecules immersed in a heat bath, thermally activated kinetics described by the Arrhenius law is often a good choice. Here we show that 'stick-slip' kinetics, characteristic of friction, can also arise in an overdamped bistable bar immersed in a heat bath. To mimic a rod-like biomolecule we model the bar as a chain of masses and bistable springs moving in a viscous fluid. We conduct Langevin dynamics calculations on the chain and extract a temperature dependent kinetic relation by observing that the dissipation at a phase boundary can be estimated by performing an energy balance. Using this kinetic relation we solve boundary value problems for a bistable bar immersed in a constant temperature bath and show that the resultant force-extension relation matches very well with the Langevin dynamics results. We estimate the force fluctuations at the pulled end of the bar due to thermal kicks from the bath by using a partition function. We also show rate dependence of hysteresis in cyclic loading of the bar arising from the stick-slip kinetics. Our kinetic relation could be applied to rod-like biomolecules, such as, DNA and coiled-coil proteins which exhibit structural transitions that depend on both temperature and loading rate.

Discontinuous growth of DNA plectonemes due to atomic scale friction.

We develop a model to explain discontinuities in the increase of the length of a DNA plectoneme when the DNA filament is continuously twisted under tension. We account for DNA elasticity, electrostatic interactions and entropic effects due to thermal fluctuation. We postulate that a corrugated energy landscape that contains energy barriers is the cause of jumps in the length of the plectoneme as the number of turns is increased. Thus, our model is similar to the Prandtl-Tomlinson model of atomic scale friction. The existence of a corrugated energy landscape can be justified due to the close proximity of the neighboring pieces of DNA in a plectoneme. We assume the corrugated energy landscape to be sinusoidal since the plectoneme has a periodic helical structure and rotation of the bead is a form of periodic motion. We perform calculations with different tensile forces and ionic concentrations, and show that rotation-extension curves manifest stair-step shapes under relatively high ionic concentrations and high forces. We show that the jump in the plectonemic growth is caused by the flattening of the energy barrier in the corrugated landscape.

Invasive Candida auris infections in Kuwait hospitals: epidemiology, antifungal treatment and outcome.

PURPOSE: Candida auris is a recently recognized yeast pathogen, which has attracted worldwide attention due to its multidrug-resistant nature and associated high mortality rates. Its persistence in hospital environment and propensity of nosocomial transmission underscores the need of continuous monitoring to prevent outbreaks. Since the first case of C. auris candidemia in May, 2014, we have identified 17 additional invasive cases, which are described here. METHODS: Identity of 17 isolates originating from proven or possible cases of invasive C. auris infection and identified as Candida haemulonii by Vitek 2 yeast identification system was confirmed by PCR-sequencing of rDNA. Information about risk factors, treatment and outcomes were retrospectively retrieved from case files. Antifungal susceptibility testing was performed by Etest. RESULTS: Thirteen cases of candidemia and 4 cases of other invasive infections were detected in 6 hospitals across Kuwait. Major risk factors included adult patients with cancer, diabetes, gastrointestinal/liver diseases and extended (> 25 days) hospital stay. All isolates were resistant to fluconazole. Additionally, 5 and 4 isolates were also resistant to voriconazole and amphotericin B, respectively. Despite antifungal treatment, 9 of 15 patients died. Most patients (n = 12) were hospitalized in 2 hospitals that are in close proximity, whereas 5 other patients were from 3 hospitals that are situated > 10 km apart. CONCLUSIONS: Occurrence of successive cases of invasive C. auris infections with resulting mortality in nine patients suggests persistence of this multidrug-resistant yeast in major hospitals in Kuwait. Early detection by continuous surveillance and enforcement of infection control measures are recommended.

Dynamic Transition from α-Helices to ß-Sheets in Polypeptide Coiled-Coil Motifs.

We carried out dynamic force manipulations in silico on a variety of coiled-coil protein fragments from myosin, chemotaxis receptor, vimentin, fibrin, and phenylalanine zippers that vary in size and topology of their α-helical packing. When stretched along the superhelical axis, all superhelices show elastic, plastic, and inelastic elongation regimes and undergo a dynamic transition from the α-helices to the ß-sheets, which marks the onset of plastic deformation. Using the Abeyaratne-Knowles formulation of phase transitions, we developed a new theoretical methodology to model mechanical and kinetic properties of protein coiled-coils under mechanical nonequilibrium conditions and to map out their energy landscapes. The theory was successfully validated by comparing the simulated and theoretical force-strain spectra. We derived the scaling laws for the elastic force and the force for α-to-ß transition, which can be used to understand natural proteins' properties as well as to rationally design novel biomaterials of required mechanical strength with desired balance between stiffness and plasticity.

Sphingobacterium cellulitidis sp. nov., isolated from clinical and environmental sources.

The taxonomic position of two isolates belonging to the genus Sphingobacterium was determined. The first isolate, R-53603T, was obtained from purulent discharge from the toe of a cellulitis patient in Kuwait. Comparative 16S rRNA gene sequence analysis revealed 99.87 % similarity of R-53603T with environmental isolate P031 (=R-53745) originating from activated sludge in Singapore. The two isolates were phylogenetically positioned on the same sub-branch. Highest 16S rRNA gene sequence similarity was found with the type strains of Sphingobacterium mizutaii (98.23 %), Sphingobacterium lactis (97.78 %) and Sphingobacterium daejeonense (97.14 %). DNA-DNA hybridizations revealed <70 % relatedness between the two isolates and the type strains of the close phylogenetic neighbours S. mizutaii(18.0-24.5 %), S. lactis(20.3-25.9 %) and S. daejeonense(13.2-20.0 %). The high relative contribution of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) in the cellular fatty acid profiles of R-53603T and R-53745, the presence of sphingophospholipids, MK-7 as the dominant menaquinone and phosphatidylethanolamine as the major polar lipid in strain R-53603T are typical chemotaxonomic characteristics for members of the genus Sphingobacterium. Phenotypic features most useful for differentiation of the two novel strains from the most closely related species S. mizutaii include growth on MacConkey agar, and utilization of stachyose, guanidine HCl and lithium chloride in Biolog GEN III tests. Strains R-53603T and R-53745 thus represent a novel species, for which the name Sphingobacterium cellulitidis sp. nov. is proposed. The type strain is R-53603T (=LMG 28764T=DSM 102028T).

Subglottic Stenosis Following Cardiac Surgery With Cardiopulmonary Bypass in Infants and Children.

OBJECTIVES: To determine the 1) incidence of subglottic stenosis in infants and children following cardiac surgery with cardiopulmonary bypass and 2) risk factors associated with its development. DESIGN: Retrospective cohort study. SETTING: Tertiary children's hospital in California. PATIENTS: Infants and children who underwent cardiac surgery with cardiopulmonary bypass. INTERVENTIONS: Diagnosis of subglottic stenosis by tracheoscopy. MEASUREMENTS AND MAIN RESULTS: The incidence of subglottic stenosis at our institution during the study period was 0.7%. Young age (p = 0.014), prolonged cardiopulmonary bypass (p = 0.03), and prolonged mechanical ventilation (p < 0.01) were associated with the development of subglottic stenosis. Gender, chromosomal anomaly, presence of a cuffed endotracheal tube, and lowest core temperature during cardiopulmonary bypass were not associated with the development of subglottic stenosis. CONCLUSIONS: The incidence of subglottic stenosis was less than that previously reported in this population. Although the incidence is relatively low, subglottic stenosis is a serious complication of tracheal intubation and all measures to prevent subglottic stenosis should be undertaken.

Particle diffusion in active fluids is non-monotonic in size.

We experimentally investigate the effect of particle size on the motion of passive polystyrene spheres in suspensions of Escherichia coli. Using particles covering a range of sizes from 0.6 to 39 microns, we probe particle dynamics at both short and long time scales. In all cases, the particles exhibit super-diffusive ballistic behavior at short times before eventually transitioning to diffusive behavior. Surprisingly, we find a regime in which larger particles can diffuse faster than smaller particles: the particle long-time effective diffusivity exhibits a peak in particle size, which is a deviation from classical thermal diffusion. We also find that the active contribution to particle diffusion is controlled by a dimensionless parameter, the Péclet number. A minimal model qualitatively explains the existence of the effective diffusivity peak and its dependence on bacterial concentration. Our results have broad implications on characterizing active fluids using concepts drawn from classical thermodynamics.