Molecular Length Scales Research Articles

The Microbial Sources of Bioactive Compounds: Potential Anticancer Therapeutic Options

Chemotherapy and other traditional anticancer treatments are losing their efficacy in the battle against cancer. As a result, cancer treatment strategies must be continually adjusted to meet the rising demand for alternative medicines. Several viral and non-viral vectors have been used previously. However, it has been shown that microorganisms are a strong contender for successfully combating cancer. They are a remarkable source of toxins, polysaccharides, tumor-specific anticancer genes, nanodrugs and gene-delivery vectors. One of the emerging key players in cancer therapy is bacteria. It has been demonstrated that traditional methods of altering the microbiome, such as antibiotics, probiotics and microbiota transplants, can sometimes increase the effectiveness of cancer therapies. However, problems with these methods, such as consistency and collateral damage to the commensal microbiota, spur the development of new technologies specifically aimed at the microbiome-cancer interface. In light of nanotechnology’s success in transforming cancer diagnostics and treatment, nanotechnologies with the capacity to control interactions that occur across microscopic and molecular length scales in the microbiome and the tumor microenvironment have the potential to provide innovative methods for cancer treatment. The relationship between nanotechnology, the microbiome and cancer offers tremendous potential. This paper highlights the contributions of significant bacterial groups to several anticancer research fields.

3D distribution of biomineral and chitin matrix in the stomatopod dactyl club by high energy XRD-CT

Stomatopods are ferocious hunters that use weaponized appendages to strike down their pray. The clubs of species such as Odontodactylus scyllarus undergo tremendous forces, and in consequence they have intricate structures, consisting of hydroxyapatite, chitin, amorphous calcium phosphate and carbonate, and occasionally calcite. These materials are distributed differently across the four major zones of the dactyl club: the impact, periodic lateral and medial, and striated regions. While stomatopod clubs and their structure have been studied for a long time, studies have thus far been constrained to 2D mapping experiments with moderate resolution due to difficulties in preparing whole club thin sections, and absorption tomography that gives information on densities but not molecular length scales. To address this problem, and shed light on the structure of entire clubs, we herein used X-ray powder diffraction computed tomography (XRD-CT) using high energy X-rays at the P07 beamline of PETRA-III to allow penetrating the large samples whilst still obtaining high resolution information. This allowed mapping the 3D distribution of diffraction phases including the biomineral apatite and the semi-crystal chitin matrix. This showed that hydroxyapatite forms an envelope around the club, and that chitin forms 2D sheets in the periodic region of the club.

Insights into glass surface dynamics from fast scanning calorimetry studies of softening and vaporization of ultrathin molecular films.

Chemical and physical processes on the surfaces of amorphous solids have been the focus of many studies over the past decades. These studies have established that dynamics in a thin layer near a glass surface are often dramatically faster than those in the glass bulk. Nevertheless, recent advances also emphasize the need for new experimental techniques capable of characterizing the structure and dynamics of the near-surface regions in glassy materials at the molecular length scale. Using a quasi-adiabatic fast scanning calorimetry (FSC) technique, we have investigated softening and vaporization of pure amorphous methylbenzene films of moderately heightened kinetic stability with thicknesses ranging from 1 to 20nm. The analysis of the FSC thermograms reveals the existence of a high fictive temperature (liquid-like) layer on the surface of the solid glass with a thickness of 3.5 ± 0.5nm or seven molecular diameters. Furthermore, the width of the boundary between liquid-like and solid layers in the films is less than 1nm. These preliminary findings compliment and substantiate past determinations of the mobile surface layer thicknesses obtained by introduction of nanoparticles or spectroscopic molecular probes to near-surface regions of amorphous samples. The developed FSC methodology will advance the theoretical and computational research by providing calorimetric data on the enhanced interfacial dynamics phenomenon in a variety of low-molecular-weight amorphous materials.

Exploration of Stokes hydrodynamic law at molecular length scales.

The celebrated generalized Stokes law predicts that the velocity of a particle pulled through a liquid by an external force, Fex, is directly proportional to the force and inversely proportional to the friction ζ acted by the medium on the particle. We investigate the range of validity of the generalized Stokes law at molecular length scales by employing computer simulations to calculate friction by pulling a tagged particle with a constant force. We thus calculate friction for two model interaction potentials, Lennard-Jones and soft sphere, for several particle sizes, ranging from radius (a) smaller than the solvent particles to three times larger. We next obtain friction from diffusion (D) by using Einstein's relation between diffusion and friction ζ in an unperturbed liquid. We find a quantitative agreement between the two at a small-to-intermediate pulling force regime for all the sizes studied. The law does break down at a large pulling force beyond a threshold value. Importantly, the range of validity of Stokes' scheme to obtain friction increases substantially if we turn off the attractive part of the interaction potential. Additionally, we calculate the viscosity (η) of the unperturbed liquid and find a good agreement with the Stokes-Einstein relation ζ = Cηa for the viscosity dependence with a value of C close to 5 π, which is intermediate between the slip and stick boundary condition.

Density and confinement effects on fluid velocity slip

Understanding the velocity slip of fluids in channels of molecular length scales is essential for accurately manipulating their flow in engineering applications, such as in water desalination or, by reversing the process, osmotic power generation. This study addresses two major open questions, namely (a) the range of validity of the Navier-Stokes equations with slip boundary conditions in describing fluid flows within channels of molecular confinement, and (b) the effect of fluid density and confinement as well as surface properties, such as microscopic roughness and curvature, on fluid slippage along walls. Using a hard-sphere fluid model and describing the fluid-wall interactions by the Maxwell scattering kernel, an event-driven molecular dynamics simulation study was performed in planar and cylindrical channels of different sizes and accommodation coefficients with varying fluid densities. The results show that the well-known criterion for the slip solution, which is valid in rarefied conditions, also holds for a dense gas, i.e., the predictive accuracy improves with decreasing Knudsen numbers, as long as the channel size is larger than about ten molecular diameters. We also find that the key quantity influencing the friction coefficient of a fluid is the peak density at the walls, rather than the nominal density, the fluid confinement, or the channel curvature, as found in previous studies. In particular, higher nominal densities lead to higher density peaks, and therefore a decrease in slip, while tighter confinements lead to lower density peaks, and therefore an increase in slip, regardless of channel geometry. Furthermore, the velocity slip depends on the microscopic roughness via the Smoluchowski factor. These findings are a stepping stone towards a deeper understanding of the molecular mechanisms underlying fluid velocity slip in molecular-scale channels. Published by the American Physical Society 2024

Sound waves, diffusive transport, and wall slip in nanoconfined compressible fluids

Although continuum theories have been proven quite robust to describe confined fluid flow at molecular length scales, molecular dynamics (MD) simulations reveal mechanistic insights into the interfacial dissipation processes. Most MD simulations of confined fluids have used setups in which the lateral box size is not much larger than the gap height, thus breaking thin-film assumptions usually employed in continuum simulations. Here we explicitly probe the long-wavelength hydrodynamic correlations in confined simple fluids with MD and compare to gap-averaged continuum theories as typically applied in, e.g., lubrication. Relaxation times obtained from equilibrium fluctuations interpolate between the theoretical limits from bulk hydrodynamics and continuum formulations with increasing wavelength. We show how to exploit this characteristic transition to measure viscosity and slip length in confined systems simultaneously from equilibrium MD simulations. Moreover, the gap-averaged theory describes a geometry-induced dispersion relation that leads to overdamped sound relaxation at large wavelengths, which is confirmed by our MD simulations. Our results add to the understanding of transport processes under strong confinement and might be of technological relevance for the design of nanofluidic devices. Published by the American Physical Society 2024

Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes.

DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA-protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA-protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.

New insights into protein stabilized emulsions captured via neutron and X-ray scattering: An approach with β-lactoglobulin at triacylglyceride-oil/water interfaces

HypothesisTo analyze protein stabilized emulsions, SAXS and SANS are emerging techniques capturing oil droplet radius, interfacial coverage and structure. Protein shape, thus protein structure change during interfacial adsorption with partial protein unfolding is detected via SAXS analysis at and below the monolayer concentration for proteins, known as critical interfacial concentration (CIC). SANS determines the same phenomena below and above the CIC, via contrast variation and coarse-grained modelling. Experimentsβ-lactoglobulin concentration dependent SAXS experiments were performed focusing on molecular length scales to characterize protein shape in water, and interfacial structure in emulsions. Complementary SANS experiments with contrast variation via deuterated triacylglyceride-oil provided insight into oil droplet radius, interfacial coverage and structure via data analysis with scattering models and low-resolution shape reconstruction with the DENFERT model. FindingsSAXS and SANS experiments allowed to determine the interfacial structure below and above the CIC, as well as oil droplet radius and interfacial coverage. These findings were identified via Q-4 Porod scattering at low-Q, protein scattering at high Q, and a Q-2 scattering of the interface. Since SANS with accurate contrast variation highlights the interface in comparison to other techniques like FTIR, the presented results show a high impact to understand interfaces in emulsions.

Droplet slipperiness despite surface heterogeneity at molecular scale

Friction determines whether liquid droplets slide off a solid surface or stick to it. Surface heterogeneity is generally acknowledged as the major cause of increased contact angle hysteresis and contact line friction of droplets. Here we challenge this long-standing premise for chemical heterogeneity at the molecular length scale. By tuning the coverage of self-assembled monolayers (SAMs), water contact angles change gradually from about 10° to 110° yet contact angle hysteresis and contact line friction are low for the low-coverage hydrophilic SAMs as well as high-coverage hydrophobic SAMs. Their slipperiness is not expected based on the substantial chemical heterogeneity of the SAMs featuring uncoated areas of the substrate well beyond the size of a water molecule as probed by metal reactants. According to molecular dynamics simulations, the low friction of both low- and high-coverage SAMs originates from the mobility of interfacial water molecules. These findings reveal a yet unknown and counterintuitive mechanism for slipperiness, opening new avenues for enhancing the mobility of droplets.

Virtual Volumetric Additive Manufacturing (VirtualVAM)

AbstractTomographic volumetric additive manufacturing (VAM) produces arbitrary 3D geometries by exposure of a rotating volume of photopolymer resin to tomographically‐patterned illumination. This enables high speed, layer‐less printing of parts from a wide range of photopolymers not amenable to layer‐by‐layer processes. Since the entire geometry is produced at once over the course of a few seconds to minutes, molecular diffusion length scales become significant to the printing process. Understanding these molecular reaction and diffusion processes is imperative for advancing VAM to a usable technology. These processes are experimentally very difficult to monitor and measure. Herein, VirtualVAM ‐ a simulation framework for modeling the tomographic VAM process, is developed and experimentally validated. VirtualVAM simulates reaction, diffusion, and heat generation processes over the course of a print with single‐voxel resolution. From a few experimentally‐determined input parameters and a set of images for projection, VirtualVAM is able to generate a large spatio‐temporal data set for any given tomographic VAM print. Using VirtualVAM, a number of experimentally‐unattainable aspects of the VAM process are investigated such as single‐voxel conversion profiles, effect of molecular oxygen, and stopping time determination. VirtualVAM also enables the optimization of exposure patterns to further improve contrast between in‐part and out‐of‐part delivered dose.

In Situ Study of Structure Formation under Stress in Stretchable Conducting Nanocomposites.

One of the major limitations of flexible sensors is the loss of conductivity upon multiple stretching and bending cycles. Conducting fillers with two different geometries, carbon black and carbon nanotubes, were introduced in polydimethylsiloxane (PDMS) for physical insights into the structure formation of nanofillers by the application of periodic tensile stress. The loading of the nanofillers was selected beyond the percolation threshold to determine the cyclic stability of the resulting network channels. The surface chemistry of carbon nanotubes has been varied to understand the interfacial interactions at the molecular length scale. The combination of in situ stretching, annealing, and vis-à-vis conductometry of nanocomposite films with synchrotron-based ultra-small angle X-ray scattering experiments enables us to highlight the importance of the fractal dimensions of nanofillers for the molecular level interactions. The irreversible formation of nanofiller network geometries under cyclic stress and annealing was found to be responsible for the electrical properties of a flexible conducting film.

In-plane and out-of-plane excitonic coupling in 2D molecular crystals

Understanding the nature of molecular excitons in low-dimensional molecular solids is of paramount importance in fundamental photophysics and various applications such as energy harvesting, switching electronics and display devices. Despite this, the spatial evolution of molecular excitons and their transition dipoles have not been captured in the precision of molecular length scales. Here we show in-plane and out-of-plane excitonic evolution in quasilayered two-dimensional (2D) perylene-3, 4, 9, 10-tetracarboxylic dianhydride (PTCDA) crystals assembly-grown on hexagonal boron nitride (hBN) crystals. Complete lattice constants with orientations of two herringbone-configured basis molecules are determined with polarization-resolved spectroscopy and electron diffraction methods. In the truly 2D limit of single layers, two Frenkel emissions Davydov-split by Kasha-type intralayer coupling exhibit energy inversion with decreasing temperature, which enhances excitonic coherence. As the thickness increases, the transition dipole moments of newly emerging charge transfer excitons are reoriented because of mixing with the Frenkel states. The current spatial anatomy of 2D molecular excitons will inspire a deeper understanding and groundbreaking applications of low-dimensional molecular systems.

Electron hopping heat transport in molecules.

The realization of single-molecule thermal conductance measurements has driven the need for theoretical tools to describe conduction processes that occur over atomistic length scales. In macroscale systems, the principle that is typically used to understand thermal conductivity is Fourier's law. At molecular length scales, however, deviations from Fourier's law are common in part because microscale thermal transport properties typically depend on the complex interplay between multiple heat conduction mechanisms. Here, the thermal transport properties that arise from electron transfer across a thermal gradient in a molecular conduction junction are examined theoretically. We illustrate how transport in a model junction is affected by varying the electronic structure and length of the molecular bridge in the junction as well as the strength of the coupling between the bridge and its surrounding environment. Three findings are of note: First, the transport properties can vary significantly depending on the characteristics of the molecular bridge and its environment; second, the system's thermal conductance commonly deviates from Fourier's law; and third, in properly engineered systems, the magnitude of electron hopping thermal conductance is similar to what has been measured in single-molecule devices.

A cure kinetics investigation of amine-cured epoxy by Rheo-Raman spectroscopy

In a companion paper, fluorescence lifetime imaging revealed a heterogeneous morphology at macroscopic and molecular length scales in a bis-epoxide blend composed of diglycidyl ether of bisphenol-A (DGEBA) and diglycidyl ether of 1,4-butanediol (DGEBD) cured with meta-phenylenediamine (m-PDA) with a strategically integrated mechanophore. This macroscopic heterogeneity most likely originates during the crosslinking process, which motivates measurements of both the reaction progress and the mechanical properties under controlled cure schedules. Rheo-Raman spectroscopy provides simultaneous measurements of Raman spectra to monitor vibrational modes relevant to the crosslinking process and rheology to track the viscoelastic shear modulus during crosslinking. Here, rheo-Raman measurements confirm that the molecular level heterogeneity is influenced by reaction kinetics differences of the two miscible bis-epoxides with m-PDA. In the companion paper the macroscopic heterogeneity was linked to the self-association of oligomers in DGEBD through interchain hydroxyl-hydroxyl hydrogen bonding. Rheo-Raman studies also revealed that this self-association slows down the overall cure-kinetics of the DGEBD/m-PDA and DGEBA/DGEBD/m-PDA curing reaction, thereby supporting the link between the macroscopic heterogeneity and oligomers in DGEBD.

Structural Heterogeneity Dependence of the Fracture Feature Distribution in the Tensile Elongation of Microinjection Molded Polyethylene

The microscopic structure and tensile statistical fracture behavior of microinjection molded polyethylene samples with and without a weldline were investigated as a function of mold temperature using small-angle X-ray scattering (SAXS), wide-angle X-ray diffraction (WAXD), and stress–strain measurements. Probability density functions were adopted to describe the statistical nature of bulk mechanical parameters. The distributions of the elongation at break and fracture toughness follow a Gaussian function for the samples molded at 27 and 50 °C, whereas the fracture feature distributions deviate evidently from Gaussian statistics in the case of the samples molded at 75 °C. This discrepancy is due to the different extent of structural heterogeneity along the shear flow direction as evidenced by the distributions of crystallinity and degree of molecular orientation. Being composed of a more uniform structural distribution on both the lamellar and molecular length scales across the length, a fraction of the samples molded at 75 °C can surpass the barrier of localized homogeneous deformation as observed in the ones produced at low mold temperatures upon tensile stretching and thus are globally elongated to a large strain before ultimate failure, resulting finally in a broad non-Gaussian distribution of the fracture parameters. The fracture toughness–yield stress relationships revealed that the degree of orientation of the polymeric chains is of more importance than the crystallinity with regard to the fracture toughness.

An artificial synapse based on molecular junctions

Shrinking the size of the electronic synapse to molecular length-scale, for example, an artificial synapse directly fabricated by using individual or monolayer molecules, is important for maximizing the integration density, reducing the energy consumption, and enabling functionalities not easily achieved by other synaptic materials. Here, we show that the conductance of the self-assembled peptide molecule monolayer could be dynamically modulated by placing electrical biases, enabling us to implement basic synaptic functions. Both short-term plasticity (e.g., paired-pulse facilitation) and long-term plasticity (e.g., spike-timing-dependent plasticity) are demonstrated in a single molecular synapse. The dynamic current response is due to a combination of both chemical gating and coordination effects between Ag+ and hosting groups within peptides which adjusts the electron hopping rate through the molecular junction. In the end, based on the nonlinearity and short-term synaptic characteristics, the molecular synapses are utilized as reservoirs for waveform recognition with 100% accuracy at a small mask length.

Brominated lipid probes expose structural asymmetries in constricted membranes

Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.

Structural and dynamic heterogeneity in associative networks formed by artificially engineered protein polymers.

This work investigates static gel structure and cooperative multi-chain motion in associative networks using a well-defined model system composed of artificial coiled-coil proteins. The combination of small-angle and ultra-small-angle neutron scattering provides evidence for three static length scales irrespective of protein gel design which are attributed to correlations arising from the blob length, inter-junction spacing, and multi-chain density fluctuations. Self-diffusion measurements using forced Rayleigh scattering demonstrate an apparent superdiffusive regime in all gels studied, reflecting a transition between distinct "slow" and "fast" diffusive species. The interconversion between the two diffusive modes occurs on a length scale on the order of the largest correlation length observed by neutron scattering, suggesting a possible caging effect. Comparison of the self-diffusive behavior with characteristic molecular length scales and the single-sticker dissociation time inferred from tracer diffusion measurements supports the primarily single-chain mechanisms of self-diffusion as previously conceptualized. The step size of the slow mode is comparable to the root-mean-square length of the midblock strands, consistent with a single-chain walking mode rather than collective motion of multi-chain aggregates. The transition to the fast mode occurs on a timescale 10-1000 times the single-sticker dissociation time, which is consistent with the onset of single-molecule hopping. Finally, the terminal diffusivity depends exponentially on the number of stickers per chain, further suggesting that long-range diffusion occurs by molecular hopping rather than sticky Rouse motion of larger assemblies. Collectively, the results suggest that diffusion of multi-chain clusters is dominated by the single-chain pictures proposed in previous coarse-grained modeling.

Differences in water and vapor transport through angstrom-scale pores in atomically thin membranes

The transport of water through nanoscale capillaries/pores plays a prominent role in biology, ionic/molecular separations, water treatment and protective applications. However, the mechanisms of water and vapor transport through nanoscale confinements remain to be fully understood. Angstrom-scale pores (~2.8–6.6 Å) introduced into the atomically thin graphene lattice represent ideal model systems to probe water transport at the molecular-length scale with short pores (aspect ratio ~1–1.9) i.e., pore diameters approach the pore length (~3.4 Å) at the theoretical limit of material thickness. Here, we report on orders of magnitude differences (~80×) between transport of water vapor (~44.2–52.4 g m−2 day−1 Pa−1) and liquid water (0.6–2 g m−2 day−1 Pa−1) through nanopores (~2.8–6.6 Å in diameter) in monolayer graphene and rationalize this difference via a flow resistance model in which liquid water permeation occurs near the continuum regime whereas water vapor transport occurs in the free molecular flow regime. We demonstrate centimeter-scale atomically thin graphene membranes with up to an order of magnitude higher water vapor transport rate (~5.4–6.1 × 104 g m−2 day−1) than most commercially available ultra-breathable protective materials while effectively blocking even sub-nanometer (>0.66 nm) model ions/molecules.

A mobile setup for simultaneous and in situ neutron reflectivity, infrared spectroscopy, and ellipsometry studies.

Neutron reflectivity at the solid/liquid interface offers unique opportunities for resolving the structure-function relationships of interfacial layers in soft matter science. It is a non-destructive technique for detailed analysis of layered structures on molecular length scales, providing thickness, density, roughness, and composition of individual layers or components of adsorbed films. However, there are also some well-known limitations of this method, such as the lack of chemical information, the difficulties in determining large layer thicknesses, and the limited time resolution. We have addressed these shortcomings by designing and implementing a portable sample environment for in situ characterization at neutron reflectometry beamlines, integrating infrared spectroscopy under attenuated total reflection for determination of molecular entities and their conformation, and spectroscopic ellipsometry for rapid and independent measurement of layer thicknesses and refractive indices. The utility of this combined setup is demonstrated by two projects investigating (a) pH-dependent swelling of polyelectrolyte layers and (b) the impact of nanoparticles on lipid membranes to identify potential mechanisms of nanotoxicity.