Molecular dynamics simulation of free and forced BSA adsorption on a hydrophobic graphite surface

The adsorption of bovine serum albumin (BSA) onto a hydrophobic graphite surface is studied using molecular-dynamics simulation. In addition to the free, that is, unsteered, adsorption, we also investigate forced adsorption, in which the action of an AFM tip pushing the protein with constant force to the surface is modeled. Using an implicit inviscid water model, the adsorption dynamics and energetics are monitored for two different initial protein orientations toward the surface. In all cases, we find that the protein partially unfolds and spreads on the surface. The spreading is in agreement with the well-known high biocompatibility of graphite-based implants. The denaturation is, however, greatly enhanced in the case of forced adsorption. We follow the position of the so-called lipid-binding pocket found in subdomain IIIA (Sudlow site II) during adsorption and find that it is tilted and moved toward the graphite surface in all cases, in agreement with its hydrophobic character. The relevance of our findings for the common measurement procedure of studying protein adhesion using AFM experiments is discussed.

Imaging Local Heating and Thermal Diffusion of Nanomaterials with Plasmonic Thermal Microscopy

Measuring local heat generation and dissipation in nanomaterials is critical for understanding the basic properties and developing applications of nanomaterials, including photothermal therapy and joule heating of nanoelectronics. Several technologies have been developed to probe local temperature distributions in nanomaterials, but a sensitive thermal imaging technology with high temporal and spatial resolution is still lacking. Here, we describe plasmonic thermal microscopy (PTM) to image local heat generation and diffusion from nanostructures in biologically relevant aqueous solutions. We demonstrate that PTM can detect local temperature change as small as 6 mK with temporal resolution of 10 μs and spatial resolution of submicrons (diffraction limit). With PTM, we have successfully imaged photothermal generation from single nanoparticles and graphene pieces, studied spatiotemporal distribution of temperature surrounding a heated nanoparticle, and observed heating at defect sites in graphene. We further show that the PTM images are in quantitative agreement with theoretical simulations based on heat transport theories.

Thermophoresis of biological and biocompatible compounds in aqueous solution

With rising popularity of microscale thermophoresis for the characterisation of protein-ligand binding reactions and possible applications in microfluidic devices, there is a growing interest in considering thermodiffusion in the context of life sciences. But although the understanding of thermodiffusion in non-polar mixtures has grown rapidly in recent years, predictions for associated mixtures like aqueous solutions remain challenging. This review aims to give an overview of the literature on thermodiffusion in aqueous systems, show the difficulties in theoretical description that arise from the non-ideal behaviour of water-mixtures, and highlight the relevance of thermodiffusion in a biological context. We find that the thermodiffusion in aqueous systems is dominated by contributions from heat of transfer, hydrogen bond interactions and charge effects. However, the separation of these effects is often difficult, especially in case of biological systems where a systematic exclusion of contributions may not be feasible.

Imaging the passage of a single hydrocarbon chain through a nanopore

Molecular transport through nanoscale pores in films, membranes and wall structures is of fundamental importance in a number of physical, chemical and biological processes. However, there is a lack of experimental methods that can obtain information on the structure and orientation of the molecules as they pass through the pore, and their interactions with the pore during passage. Imaging with a transmission electron microscope is a powerful method for studying structural changes in single molecules as they move and for imaging molecules confined inside carbon nanotubes. Here, we report that such imaging can be used to observe the structure and orientation of a hydrocarbon chain as it passes through nanoscale defects in the walls of a single-walled carbon nanotube to the vacuum outside, and also to study the interactions between the chain and the nanopore. Based on experiments at 293 K and 4 K we conclude that the major energy source for the molecular motions observed at 4 K is the electron beam used for the imaging.

Role of Hydrogen Bonding of Cyclodextrin-Drug Complexes Probed by Thermodiffusion

Temperature gradient-induced migration of biomolecules, known as thermophoresis or thermodiffusion, changes upon ligand binding. In recent years, this effect has been used to determine protein-ligand binding constants. The mechanism through which thermodiffusive properties change when complexes are formed, however, is not understood. An important contribution to thermodiffusive properties originates from the thermal response of hydrogen bonds. Because there is a considerable difference between the degree of solvation of the protein-ligand complex and its isolated components, ligand-binding is accompanied by a significant change in hydration. The aim of the present work is therefore to investigate the role played by hydrogen bonding on the change in thermodiffusive behavior upon ligand-binding. As a model system, we use cyclodextrins (CDs) and acetylsalicylic acid (ASA), where quite a significant change in hydration is expected and where no conformational changes occur when a CD/ASA complex is formed in aqueous solution. Thermophoresis was investigated in the temperature range of 10-50 °C by infrared thermal diffusion forced Rayleigh scattering. Nuclear magnetic resonance measurements were performed at 25 °C to obtain information about the structure of the complexes. All CD/ASA complexes show a stronger affinity toward regions of lower temperature compared to the free CDs. We found that the temperature sensitivity of thermophoresis correlates with the 1-octanol/water partition coefficient. This observation not only establishes the relation between thermodiffusion and degree of hydrogen bonding but also opens the possibility to relate thermodiffusive properties of complexes to their partition coefficient, which cannot be determined otherwise. This concept is especially interesting for protein-ligand complexes where the protein undergoes a conformational change, different from the CD/ASA complexes, giving rise to additional changes in their hydrophilicity.

Evaluation of a bedside monitor of regional CBF as a measure of CO2 reactivity in neurosurgical intensive care patients

OBJECTIVE

Mild hyperventilation remains a key element in the management of elevated intracranial pressure. However, a harmful effect of hyperventilation on the development or deterioration of ischemic lesions has been shown in patients after severe head trauma. The objective of this study was to investigate the clinical feasibility and reliability of continuous monitoring of regional cerebral blood flow (rCBF) during mild hyperventilation using a thermodiffusion probe. CO2 reactivity was calculated. The measurement of the partial pressure of oxygen (PtiO2) in the cerebral tissue served as a reference parameter.

METHODS

An intraparenchymal intracranial pressure sensor, a multiparameter probe for determining the partial pressure of cerebral gases (pHti, PtiO2, PtiCO2), and a thermodiffusion probe for measuring rCBF were used in 10 intensive care patients. All patients were analgosedated and received pressure-controlled mechanical ventilation. Controlled mild hyperventilation was carried out on 2 consecutive days. CO2 reactivity was determined in relation to both CBF and PtiO2.

RESULTS

Controlled hyperventilation resulted in a rCBF reduction from 30+/-3 mL/100 g/min to 25+/-2.4 mL/100 g/min (-17%; P<0.05) on the first day of examination and 31+/-3.6 mL/100 g/min to 22+/-4.9 mL/100 g/min (-29%; P<0.05) on the second day. Likewise, mild hyperventilation resulted in a reduction of regional cerebral tissue oxygen partial pressure from 20+/-2.9 mm Hg to 15+/-4 (-25%; P<0.05) on the first day and 20+/-3.1 mm Hg to 14+/-1.5 mm Hg (-30%; P<0.05) on the second.

CONCLUSIONS

Continuous monitoring of regional CBF, using an intraparenchymally placed thermodiffusion probe, seems to be a simple and safe bedside technique. The promise of reliably monitoring and interpreting additional parameters such as PtiO2 and PtiCO2 warrants further investigation.

Confinement of semiflexible polymers

A variational framework is developed to examine the equilibrium states of a semiflexible polymer that is constrained to lie on a fixed surface. As an application the confinement of a closed polymer loop of fixed length 2π R within a spherical cavity of smaller radius, R(0), is considered. It is shown that an infinite number of distinct periodic completely attached equilibrium states exist, labeled by two integers: n = 2,3,4,... and p = 1,2,3,..., the number of periods of the polar and azimuthal angles, respectively. Small loops oscillate about a geodesic circle: n = 2, p = 1 is the stable ground state; states with higher n exhibit instabilities. If R ≥ 2R(0) new states appear as oscillations about a doubly covered geodesic circle; the state n = 3,p = 2 replaces the twofold as the ground state in a finite band of values of R. With increasing R, loop states make a transition from oscillatory and orbital behavior on crossing the poles, returning to oscillation upon collapse to a multiple cover of a geodesic circle (signaled, respectively, by an increase in p and an increase in n). The force transmitted to the surface does not increase monotonically with loop size, but does asymptotically. It behaves discontinuously where n changes. The contribution to energy from geodesic curvature is bounded. In large loops, the energy becomes dominated by a state independent contribution proportional to the loop size; the energy gap between the ground state and excited states disappears.

Rapid Bead-Based Antimicrobial Susceptibility Testing by Optical Diffusometry

This study combined optical diffusometry and bead-based immunoassays to develop a novel technique for quantifying the growth of specific microorganisms and achieving rapid AST. Diffusivity rises when live bacteria attach to particles, resulting in additional energy from motile microorganisms. However, when UV-sterilized (dead) bacteria attach to particles, diffusivity declines. The experimental data are consistent with the theoretical model predicted according to the equivalent volume diameter. Using this diffusometric platform, the susceptibility of Pseudomonas aeruginosa to the antibiotic gentamicin was tested. The result suggests that the proliferation of bacteria is effectively controlled by gentamicin. This study demonstrated a sensitive (one bacterium on single particles) and time-saving (within 2 h) platform with a small sample volume (~0.5 μL) and a low initial bacteria count (50 CFU per droplet ~ 10⁵ CFU/mL) for quantifying the growth of microorganisms depending on Brownian motion. The technique can be applied further to other bacterial strains and increase the success of treatments against infectious diseases in the near future.

An efficient method of modeling material properties using a thermal diffusion analogy: an example based on craniofacial bone

The ability to incorporate detailed geometry into finite element models has allowed researchers to investigate the influence of morphology on performance aspects of skeletal components. This advance has also allowed researchers to explore the effect of different material models, ranging from simple (e.g., isotropic) to complex (e.g., orthotropic), on the response of bone. However, bone's complicated geometry makes it difficult to incorporate complex material models into finite element models of bone. This difficulty is due to variation in the spatial orientation of material properties throughout bone. Our analysis addresses this problem by taking full advantage of a finite element program's ability to solve thermal-structural problems. Using a linear relationship between temperature and modulus, we seeded specific nodes of the finite element model with temperatures. We then used thermal diffusion to propagate the modulus throughout the finite element model. Finally, we solved for the mechanical response of the finite element model to the applied loads and constraints. We found that using the thermal diffusion analogy to control the modulus of bone throughout its structure provides a simple and effective method of spatially varying modulus. Results compare favorably against both experimental data and results from an FE model that incorporated a complex (orthotropic) material model. This method presented will allow researchers the ability to easily incorporate more material property data into their finite element models in an effort to improve the model's accuracy.

An in-situ thermally regenerated air purifier for indoor formaldehyde removal

Formaldehyde is a common indoor pollutant that is an irritant and has been classified as carcinogen to humans. Adsorption technology is safe and stable and removes formaldehyde efficiently, but its short life span and low adsorption capacity limit its indoor application. To overcome these limitations, we propose an in-situ thermally regenerated air purifier (TRAP) which self-regenerates as needed. This purifier has four working modes: cleaning mode, regeneration mode, exhaust mode, and outdoor air in-take mode, all of which are operated by valve switching. We developed a real-scale TRAP prototype with activated carbon as adsorbent. The experimental testing showed that the regeneration ratios for formaldehyde of TRAP were greater than 90% during 5 cycles of adsorption-regeneration and that through the 5 cycles, there was no damage to the adsorption material as confirmed by scanning electron microscope (SEM) and Brunauer-Emmett-Teller (BET) tests. The total energy consumption by the prototype for purifying 1000 m³ indoor air was 0.26 kWh. This in-situ thermal-regeneration method can recover the purifier's adsorption ability through at least five cycles.

Time-resolved studies of individual molecular rotors

Thioether molecular rotors show great promise as nanoscale models for exploring the fundamental limits of thermally and electrically driven molecular rotation. By using time-resolved measurements which increase the time resolution of the scanning tunneling microscope we were able to record the dynamics of individual thioether molecular rotors as a function of surface structure, rotor chemistry, thermal energy and electrical excitation. Our results demonstrate that the local surface structure can have a dramatic influence on the energy landscape that the molecular rotors experience. In terms of rotor structure, altering the length of the rotor's alkyl tails allowed the origin of the barrier to rotation to be more fully understood. Finally, time-resolved measurement of electrically excited rotation revealed that vibrational excitation of a C-H bond in the rotor's alkyl tail is an efficient channel with which to excite rotation, and that the excitation is a one-electron process.

Continuous Thermal Diffusion-Based Cerebral Blood Flow Monitoring in Adult Traumatic Brain Injury: A Scoping Systematic Review

Thermal diffusion flowmetry (TDF) is an appealing candidate for monitoring of cerebral blood flow (CBF) in neurocritical-care patients as it provides absolute measurements with a high temporal resolution, potentially allowing for bedside intervention that could mitigate secondary injury. We performed a systematic review of TDF-regional(r)CBF measurements and their association with (1) patient functional outcome, (2) other neurophysiological parameters, and (3) imaging-based tissue outcomes. We searched MEDLINE, EMBASE, SCOPUS, BIOSIS, GlobalHealth, and the Cochrane Databases from inception to October 2018 and relevant conference proceedings published over the last 5 years. Nine articles that explored the relationship between TDF-rCBF, mortality, and Glasgow Outcome Scale (GOS) or GOS-Extended (GOS-E) at various intervals were included. Despite being based on an overall weak body of evidence, our analysis suggests a link between sustained low or high CBF and poor functional outcome. Twenty-five studies reporting associations with neurophysiological parameters were included. The available data also point to an association between low or high TDF-rCBF and intracranial hypertension. TDF-rCBF appears to correlate well with regional brain tissue oxygenation measurements. We found no studies reporting on imaging-based tissue outcome in relation to TDF. In conclusion, despite being based on a relatively weak body of evidence, the available literature suggests a link between consistently abnormal TDF-rCBF values, intracranial hypertension, and poor functional outcome. TDF-rCBF also appears to correlate well with regional measurements of brain tissue oxygenation. Currently, such monitoring should be considered experimental, requiring much further evaluation prior to widespread adoption.

Subdiffraction-limited second harmonic photoacoustic microscopy based on nonlinear thermal diffusion

We have developed a second harmonic photoacoustic microscopy (SH-PAM) for subdiffraction-limited imaging based on nonlinear thermal diffusion. When a sine-modulated Gaussian temperature field is introduced by a laser beam, the temperature dependence of the thermal diffusivity induces a nonlinear photoacoustic (PA) effect and thus results in the production of second harmonic PA signals. We demonstrate through both simulation and experiment that the second harmonic PA images can be reconstructed with a lateral resolution exceeding that of conventional optical resolution PA microscopy. The feasibility of SH-PAM was verified on phantom samples. Amphioxus zygotes and germinated pollens have been studied by SH-PAM to demonstrate its biomedical imaging capability. This method expands the scope of conventional PA imaging and opens up new possibilities for super-resolution imaging, prefiguring great potential for biological imaging and material inspection.

Bayesian Analysis of MicroScale Thermophoresis Data to Quantify Affinity of Protein:Protein Interactions with Human Survivin

A biomolecular ensemble exhibits different responses to a temperature gradient depending on its diffusion properties. MicroScale Thermophoresis technique exploits this effect and is becoming a popular technique for analyzing interactions of biomolecules in solution. When comparing affinities of related compounds, the reliability of the determined thermodynamic parameters often comes into question. The thermophoresis binding curves can be assessed by Bayesian inference, which provides a probability distribution for the dissociation constant of the interacting partners. By applying Bayesian machine learning principles, binding curves can be autonomously analyzed without manual intervention and without introducing subjective bias by outlier rejection. We demonstrate the Bayesian inference protocol on the known survivin:borealin interaction and on the putative protein-protein interactions between human survivin and two members of the human Shugoshin-like family (hSgol1 and hSgol2). These interactions were identified in a protein microarray binding assay against survivin and confirmed by MicroScale Thermophoresis.

Towards understanding specific ion effects in aqueous media using thermodiffusion

Specific ion effects play an important role in scientific and technological processes. According to Hofmeister, the influence on the hydrogen bond network depends on the ion and leads to a specific order of the ions. Also thermodiffusion the mass transport caused by a temperature gradient is very sensitive to changes of the hydrogen bond network leading to a ranking according to hydrophilicity of the salt. Hence, we investigate various salt solutions in order to compare with the Hofmeister concept. We have studied three different sodium salts in water as a function of temperature (25-45[Formula: see text]C) and concentration (0.5-5 mol kg[Formula: see text]) using Thermal Diffusion Forced Rayleigh Scattering (TDFRS). The three anions studied, carbonate, acetate and thiocyanate, span the entire range of the Hofmeister series from hydrophilic to hydrophobic. We compare the results with the recent measurements of the corresponding potassium salts to see to what extent the cation changes the thermodiffusion of the salt.

Characterization at 25 °C of sodium hyaluronate in aqueous solutions obtained by transport techniques

Mutual diffusion coefficients, D, were determined for aqueous solutions of sodium hyaluronate (NaHy) at 25 °C and concentrations ranging from 0.00 to 1.00 g·dm(-3) using the Taylor dispersion technique. From these experimental data, it was possible to estimate some parameters, such as the hydrodynamic radius Rh, and the diffusion coefficient at infinitesimal concentration, D0, of hyaluronate ion, permitting us to have a better understanding of the structure of these systems of sodium hyaluronate in aqueous solutions. The additional viscosity measurements were done and Huggins constant, kH, and limiting viscosity number, [η], were computed for interaction NaHy/water and NaHy/NaHy determination.

Faster diffusion across an irregular boundary

We investigate how the shape of a heat source may enhance global heat transfer at short time. An experiment is described that allows us to obtain a direct visualization of heat propagation from a prefractal radiator. We show, both experimentally and numerically, that irregularly shaped passive coolers rapidly dissipate at short times, but their efficiency decreases with time. The de Gennes scaling argument is shown to be only a large scale approximation, which is not sufficient to describe adequately the temperature distribution close to the irregular frontier. This work shows that radiators with irregular surfaces permit increased cooling of pulsed heat sources.

Steady-State and Kinetics-Based Affinity Determination in Effector-Effector Target Interactions

Dissecting the functional basis of pathogenicity and resistance in the context of plant innate immunity benefits greatly from detailed knowledge about biomolecular interactions, as both resistance and virulence depend on specific interactions between pathogen and host biomolecules. While in vivo systems provide biological context to host-pathogen interactions, these experiments typically cannot provide quantitative biochemical characterization of biomolecular interactions. However, in many cases, the biological function does not only depend on whether an interaction occurs at all, but rather on the "intensity" of the interaction, as quantified by affinity. Specifically, microbial effector proteins may bind more than one host target to exert virulence functions, and looking at these interactions more closely than would be possible in a purely black-and-white qualitative assay (as classically based on plant or yeast systems) can reveal new insights into the evolutionary arms race between host and pathogen. Recent advances in biomolecular interaction assays that can be performed in vitro allow quantification of binding events with ever greater fidelity and application range. Here, we describe assays based on microscale thermophoresis (MST) and surface plasmon resonance (SPR). Using these technologies allows affinity determination both in steady-state and in kinetic configurations, providing two conceptually independent pathways to arrive at quantitative affinity data describing the interactions of pathogen and host biomolecules.

Reconstruction of the thermal environment evolution in urban areas from underground temperature distribution

It is possible to estimate the ground surface temperature (GST) history of the past several hundred years from temperature profiles measured in boreholes because the temporal variation in GST propagates into the subsurface by thermal diffusion. This "geothermal method" of reconstructing GST histories can be applied to studies of thermal environment evolution in urban areas, including the development of "heat islands." Temperatures in boreholes were logged at 102 sites in Bangkok, Jakarta, Taipei, Seoul and their surrounding areas in 2004 to 2007. The effects of recent surface warming can be recognized in the shapes of most of the obtained temperature profiles. The preliminary results of reconstruction of GST histories through inversion analysis show that GST increased significantly in the last century. Existing temperature profile data for the areas in and around Tokyo and Osaka can also be used to reconstruct GST histories. Because most of these cities are located on alluvial plains in relatively humid areas, it is necessary to use a model with groundwater flow and a layered subsurface structure for reconstruction analysis. Long-term records of subsurface temperatures at multiple depths may demonstrate how the GST variation propagates downward through formations. Time series data provide information on the mechanism of heat transfer (conduction or advection) and the thermal diffusivity. Long-term temperature monitoring has been carried out in a borehole located on the coast of Lake Biwa, Japan. Temperatures at 30 and 40 m below the ground surface were measured for 4 years and 2 years, respectively, with a resolution of 1 mK. The obtained records indicate steady increases at both depths with different rates, which is probably the result of some recent thermal event(s) near the surface. Borehole temperatures have also been monitored at selected sites in Bangkok, Jakarta, and Taiwan.

Mass effects for thermodiffusion in dilute aqueous solutions

Thermodiffusion is the phenomenon by which molecules in a mixture present concentration gradients in response to an imposed temperature gradient. Despite decades of investigations, this effect remains poorly understood at a molecular level. A common, phenomenological approach is to individuate the molecular factors that influence the Soret coefficient, the parameter that quantifies the resulting concentration-gradient. Experimental studies, often performed on organic mixtures, as well as simulations of model particle systems have evidenced that the difference in masses between the mixture components has an important effect on the amplitude of the Soret coefficient. Here, we use molecular dynamics simulations of a thermophoretic setting to investigate the mass dependence of the Soret coefficient in dilute aqueous solutions. An advantage of simulation approaches is that they are not limited in the range of explored molecular masses, which is often limited to isotopic substitutions in the experiments. Our simulations reveal that the mass dependence of the Soret coefficient in these solutions is in agreement with previous experimental and simulation work on molecular-size systems. In particular, it is sensitive to the relative mass difference between the solute and the solvent, but not to their absolute mass. Adjusting the mass of the solvent and of the solute can turn a thermophobic solution into a thermophilic one, where solute accumulation is reversed. This demonstrates that the mass effect can indeed compensate for the other contributions to the Soret coefficient. Finally, we find that changing the molecular moments of inertia has a much more limited impact as compared to a change in the total molecular mass.

Photoacoustic thermorelaxation microscopy for thermal diffusivity measurement

Thermal diffusivity is one of the main parameters to characterize the thermo-physical properties of materials, and advances in its measurement technique will have significant impact on materials science and related applications. Here a photoacoustic (PA) thermorelaxation microscopy is proposed as a new noncontact method to measure the thermal diffusivity. By delivering co-focused heating/probing laser pulse pairs with tunable time delays, the sample's in situ thermal relaxation behavior after the heating pulse excitation can be photoacoustically monitored based on the temperature-dependent property of the Grueneisen parameter. We theoretically deduced the dependence of the obtained PA thermorelaxation time on the thermal diffusivity, and the results coincided well with simulations. The feasibility of this method was validated by various industrial and biological samples. This method provides a new strategy for high-resolution thermal diffusivity measurement with flexible measurement conditions, prefiguring great potential for material and biological applications.

Light-induced Soret effect and adsorption of nanocrystals in organic solvents

A light-induced Soret effect accompanied by photoinduced adsorption of pigment nanoparticles is described in organic solvents. We report an unexpected inversion of the nanoparticle flux which is directed along the temperarture gradient at short exposures to the light and switches against the gradient at longer exposures. This change of flux direction is due to light-induced adsorption of the nanocrystals onto the substrates of the cell.