Compacted States Research Articles

Effects of Hofmeister Ions on the α-Helical Structure of Proteins

The molecular conformation of proteins is sensitive to the nature of the aqueous environment. In particular, the presence of ions can stabilize or destabilize (denature) protein secondary structure. The underlying mechanisms of these actions are still not fully understood. Here, we combine circular dichroism (CD), single-molecule Förster resonance energy transfer, and atomistic computer simulations to elucidate salt-specific effects on the structure of three peptides with large α-helical propensity. CD indicates a complex ion-specific destabilization of the α-helix that can be rationalized by using a single salt-free computer simulation in combination with the recently introduced scheme of ion-partitioning between nonpolar and polar peptide surfaces. Simulations including salt provide a molecular underpinning of this partitioning concept. Furthermore, our single-molecule Förster resonance energy transfer measurements reveal highly compressed peptide conformations in molar concentrations of NaClO4 in contrast to strong swelling in the presence of GdmCl. The compacted states observed in the presence of NaClO4 originate from a tight ion-backbone network that leads to a highly heterogeneous secondary structure distribution and an overall lower α-helical content that would be estimated from CD. Thus, NaClO4 denatures by inducing a molten globule-like structure that seems completely off-pathway between a fully folded helix and a coil state.

How environmental solution conditions determine the compaction velocity of single DNA molecules

Understanding the mechanisms of DNA compaction is becoming increasingly important for gene therapy and nanotechnology DNA applications. The kinetics of the compaction velocity of single DNA molecules was studied using two non-protein condensation systems, poly(ethylene glycol) (PEG) with Mg2+ for the polymer-salt-induced condensation system and spermine for the polyamine condensation system. The compaction velocities of single tandem λ-DNA molecules were measured at various PEG and spermine concentrations by video fluorescent microscopy. Single DNA molecules were observed using a molecular stretching technique in the microfluidic flow. The results show that the compaction velocity of a single DNA molecule was proportional to the PEG or spermine concentration to the power of a half. Theoretical considerations indicate that the compaction velocity is related to differences in the free energy of a single DNA molecule between the random coil and compacted states. In the compaction kinetics with PEG, acceleration of the compaction velocity occurred above the overlap concentration while considerable deceleration occurred during the coexistence state of the random coil and the compacted conformation. This study demonstrates the control factors of DNA compaction kinetics and contributes toward the understanding of the compaction mechanisms of non-protein DNA interactions as well as DNA–protein interactions in vivo.

Consolidation Properties of Compacted Lateritic Soil Treated with Rice Husk Ash

One dimensional laboratory consolidation test was conducted on compacted lateritic soils treated with up to 16% rice husk ash (RHA), to assess its consolidation properties. Specimens were prepared at three different moulding water contents (2% dry of optimum, optimum moisture content and 2% wet of optimum) and compacted using the British Standard Light compactive effort. Preliminary tests on soils showed improved index properties with an increase in liquid limit (LL), an increase in plastic limits (PL) with a resulting decrease in plasticity index (PI). Preconsolidation pressure increased with RHA content, it also decreased before increasing with increased moulding water content. Reductions in compression index (Cc) and Swell Index (Cs) with increased RHA content were recorded. Cc and Cs generally decreased before increasing with increased moulding water content. The coefficient of volume compressibility (Mv) decreased and increased with higher RHA content; they were also affected by the soil particle state with increasing pressure. The coefficient of consolidation (Cv) showed no observable trend with increased RHA content but generally increased with higher consolidation pressure on the dry and wet side of optimum compacted states.

Physical and geotechnical properties of clay phyllites

An experimental programme is presented with the aim of characterising – from physical, microstructural and geotechnical perspectives – the main properties of compacted clay phyllites. These clay phyllites are widely used as waterproofing material for roofs in the Alpujarra (Andalusia, Spain), as sealing liners in irrigation ponds, and as core material of small earthen zoned dams. An exhaustive physical-characterisation programme on the powder fraction has been followed using X-ray fluorescence (XRF), X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), chemical analysis by energy dispersive X-ray spectroscopy (EDX), thermal analysis, particle-size distribution analysis, consistency limits, and density of solid particles. From a microstructural standpoint, mercury intrusion porosimetry (MIP) tests, as well as nitrogen-adsorption tests, were carried out to characterise the pore network and surface area of the material in both natural and compacted states. The geotechnical characterisation programme on the compacted material was focused on the water-permeability and water-retention properties, the volume change on soaking (swelling or collapse), the compressibility on loading, the shear-strength properties, and the mechanical-penetration properties. In this way, an important physical and hydro-mechanical data base is provided, which could help in evaluating the suitability for using this material in a wide range of earthen constructions (liners, road subgrades, embankments, core material in zoned dams). It has been found that the material contains illite, chlorite and quartz as the main components, and feldspar, iron oxide and interstratified illite–smectite as minor ones. Despite the presence of active clay minerals, the compacted material did not display an important swelling on soaking at low stresses, as a consequence of its low specific surface and low water-retention ability. The material exhibited good compaction properties and, consequently, low water permeability plus a stiff response on loading. Nevertheless, despite the low porosity attained on the dry-side compaction, the material underwent some collapse on soaking at stresses greater than 100 kPa.

Thermo‐Switchable Charge Transport and Electrocatalysis Using Metal‐Ion‐Modified pNIPAM‐Functionalized Electrodes

AbstractMetal ions (Ag+, Cu2+, Hg2+) are incorporated into an electropolymerized, poly(N‐isopropyl acrylamide), pNIPAM, thermosensitive polymer associated with an electrode using the “breathing‐in” method. The ion‐functionalized pNIPAM matrices reveal ion‐dependent gel‐to‐solid phase‐transition temperatures (28 ± 1 °C, 25 ± 1 °C, 40 ± 1 °C for the Ag+, Cu2+, and Hg2+‐modified pNIPAM, respectively). Furthermore, the ion‐functionalized polymers exhibit quasi‐reversible redox properties, and the ions are reduced to the respective Ag0, Cu0, and Hg0 nanocluster‐modified polymers. The metal‐nanocluster‐functionalized pNIPAM matrices enhance the electron transfer (they exhibit lower electron‐transfer resistances) in the compacted states. The electron‐transfer resistances of the metal‐nanocluster‐modified pNIPAM can be cycled between low and high values by temperature‐induced switching of the polymer between its contracted solid and expanded gel states, respectively. The enhanced electron‐transfer properties of the metal nanocluster‐functionalized polymer are attributed to the contacting of the metal nanoclusters in the contracted state of the polymers. This temperature‐switchable electron transfer across a Ag0‐modified pNIPAM was implemented to design a thermo‐switchable electrocatalytic process (the temperature‐switchable electrocatalyzed reduction of H2O2 by Ag0‐pNIPAM).

Interaction of selenite with MX-80 bentonite: Effect of minor phases, pH, selenite loading, solution composition and compaction

We propose a simple model describing the retention of selenite, Se(IV), by the MX-80 bentonite in a synthetic groundwater (SGW) in dispersed and compacted states. The model was calibrated on a pure montmorillonite from data obtained for 4 < pH < 10 and total selenite concentrations between 10 −7 and 5 × 10 −3 mol/L. Furthermore, the matrix solution covers a wide range of conditions regarding the ionic strength and the nature of the background electrolyte. Three selenite surface species had to be considered. Below pH 5, sorption is governed by a ligand exchange reaction with H 2SeO 3. Between pH 5 and 7, the experimental data are well described considering the formation of a surface complex implying HSeO 3 −. Finally, at pH above 7, we propose ternary surface complexes involving Ca 2+ and Mg 2+. The model, which we consider as operational, appears in agreement with spectroscopic data available in the literature and predicts surprisingly well selenite sorption on MX-80 bentonite even in the compacted state at a dry density of 1100 kg/m 3. Based on the model, the solid phase montmorillonite is responsible for selenite retention. Minor solid phases containing iron (pyrite, hematite) had not to be considered in the modelling. Interestingly, calcite (an important phase in MX-80 bentonite) has an indirect effect via the release of calcium into solution and its subsequent contribution to Se(IV) sorption through a ternary surface complex.

Study of the Interaction of Ni2+and Cs+ on MX-80 Bentonite; Effect of Compaction Using the “Capillary Method”

The goal of the paper is to assess the applicability of sorption models to describe the retention of contaminants on clay materials, both in dispersed and compacted states. A batch method is used to characterize the sorption equilibria between Cs, Ni, and MX-80 bentonite for solid-to-liquid ratios varying from 0.5 to 4200 kg/m3. For compacted bentonite (dry density of 1100 kg/m3), a new method is presented where the material compaction is performed in PEEK capillaries. Sorption edges and isotherms were measured in the presence of a synthetic groundwater. A model considering cation exchange reactions with interlayer cations and surface complexation reactions with edge sites was used for the dispersed state. Montmorillonite was shown to be the dominant interacting phase in MX-80 bentonite. The applicability of the model to compacted bentonite was tested. The results indicate that under conditions where the cation exchange mechanism is dominant, there is no difference between the dispersed and compacted states. For the degree of compaction studied, all exchange sites are available for sorption. For Ni, when surface complexation is the dominant sorption mechanism, a decrease of the Kd values by a factor of about 3 was observed (pH 7-8, trace concentrations). This could be explained quantitatively by a diminution of the conditional interaction constant between Ni and the edge surface site in the compacted state. One consequence of this decrease is that the contribution of the organic matter content of MX-80 bentonite to the total sorption becomes significant.

Shear strength characteristics of sand-mixed with granular rubber

Waste materials such as waste tires, rubbers, and plastic materials are normally produced in every society, entering the environment and causing serious problems. These problems may be somehow reduced by finding applications for them in engineering, for example, as lightweight materials for backfill in geotechnical projects. To this aim, this paper demonstrates how shear strength characteristics of sand mixed with various percentages of waste garden hose grains are altered. A relatively, uniform sand has been mixed with waste hose grains in loose and slightly compacted states. Waste hose grains were prepared with special popular machinery in a local area. Various sand-rubber mixtures having 0%, 10%, 15%, 20%, 50%, 70%, and 100% waste hose particles by weight were chosen. The rubber grains were distributed in the sand such that uniform mixtures are obtained. In order to compare the shear strength of different sand-rubber samples, two compaction states were considered. The results show that the influencing parameters on shear strength characteristics of sand-rubber mixtures are normal stress, mixture unit weight, and rubber content. With the selected waste hose particles, compaction states, and rubber contents, the initial friction angle φ1 does not change significantly. However, an apparent cohesion appears in the mixtures. From environmental point of view and due to lightweight material for the sand-waste hose particles, it may be useful to use such materials in corresponding geotechnical projects.

Discussion: Suction in compacted states

Discussion: Suction in compacted states

Suction in compacted states

Suction in compacted states

Comparison of the energy histograms and conformations between different lattice models of copolymers

Based on large-scale Monte Carlo simulations the energy probability distribution functions are investigated for a large set of primary sequences in distinct lattice models of copolymers at low temperatures below transitions to compacted states. Amphiphilic copolymers with hydrophobic and hydrophilic units are found to produce single or double peak energy distributions corresponding to mono- or multi-meric micellar conformations. However, copolymers with short-ranged random ‘charge’ interactions in some cases are found to produce energy distribution functions with a well pronounced lowest energy state and a gap separating it from the rest of the spectrum. These, however have rather peculiar conformations corresponding to effectively immiscible domains comprised from monomers of likewise species. The relevance of these observations for coarse-grained models for protein folding is discussed.

Mechanical behaviour of the upper layers of a sandy loam soil under shear loading

The mechanical behaviour of the upper layers of a sandy loam soil was studied under standard triaxial compression and direct shear box tests. Variations of soil material properties were investigated at four different initial dry bulk densities of 1410, 1520, 1610 and 1670 kg/m 3. Soil deformation and volume change under the triaxial compression loading were also studied at these bulk densities. Results from the two tests showed increases in the soil mechanical properties with the initial dry bulk density. The internal friction angle values measured with the triaxial compression apparatus exceeded those measured with the direct shear box. In contrast, the soil cohesion values measured with the direct shear box exceeded those measured with the triaxial compression apparatus. Under the triaxial compression test, the loose soil samples underwent contraction and volume reduction, whereas the dense samples swelled and failure cracks appeared clearly at various planes. The soil contraction for the former case characterizes the occurrence of soil compaction, whereas the cracks propagation and volume increase in the latter case characterizes the breaking up and loosening of soil during tillage operations. For the loose and moderately compacted states, the engineering Poisson's ratio increased with the axial strain until loading was completed. It also increased at the compacted and very compacted states until reaching given loading stages, after which its value started to decrease. This shifting in the engineering Poisson's ratio during loading may provide another identification of the moment of soil failure occurrence, in addition to that of the maximum shear stress.

Suction in compacted states

Examines the possible magnitude of suction in compacted states of clayey soils. From the test results, it is concluded that suction is zero in monotonically loaded unsaturated states. This implies that suction in compacted states should be equal to the compaction stress itself. However, as data previously reported in literature have often shown - suction is strongly related to the water content and not much affected by the compaction stress.

Suction in compacted states

Suction in compacted states

Microstructural and magnetic observations of compacted FeCoV nanoparticles

One attempt to improve core loss of electromagnetic machines is to utilize nanocrystalline alloys, which are predicted to have extremely soft magnetic properties. High magnetic saturation values and high Curie temperatures make iron-cobalt alloys attractive for such applications. In this work iron-cobalt-vanadium nanopowders were synthesized and compacted. The coated particles were characterized and examined in both the powder and compacted states. Higher than expected coercivities are reported and may be due to the inhomogeneous microstructure resulting from interactions with the vanadium.

Discrete Coil−Globule Transition of Single Duplex DNAs Induced by Polyamines

Recently, it has become clear that single, long duplex DNAs exhibit a large discrete transition between elongated coil and compacted globule states. To obtain further insight into this phenomenon, in the present study we observed individual DNA chains in an aqueous environment by fluorescence microscopy. The long-axis lengths of individual T4DNA (166 kbp) were calibrated to obtain a size distribution. The main purpose of the present study was to determine the effect of the valence of cations on the coil−globule transition. We used the following multivalent cations to induce the compaction of long DNA chains: 1,3-diaminopropane (bivalent), spermidine (trivalent), and spermine (tetravalent). Our results showed that the collapse of isolated DNA chains induced by either bivalent or multivalent cations is discrete. The critical concentration of cation for inducing the transition was lowest for the tetravalent cation and highest for the bivalent cation. We also compare the properties of the transition observed...

Highly Effective Compaction of Long Duplex DNA Induced by Polyethylene Glycol with Pendant Amino Groups

By observing isolated long DNA chains with fluorescence microscopy, the collapsing transition of individual single DNAs induced by polyethylene glycol with pendant amino groups (PEG-A) was compared to that induced by neutral polyethylene glycol (PEG). The main results are as follows: (1) DNA is collapsed by PEG-A at concentrations 105 times lower than those required for PEG. (2) In PEG-A, the concentration which induces collapse decreases with an increase in the salt concentration. This trend is similar to that in the collapse induced by PEG. (3) The transition induced by PEG is all-or-none; individual DNA chains exhibit either elongated coil or compacted globule states. On the other hand, segregation of a collapsed region along a single DNA chain occurs as an intermediate state in the collapsing transition induced by PEG-A.

Crystal structures of A-DNA duplexes.

All crystal structures of A-DNA duplexes exhibit a typical crystal packing, with the termini of one molecule abutting the shallow grooves of symmetry related neighbors, while all other forms (B, Z, and RNA) tend to form infinitely stacked helices. The A-DNA arrangement leads to the formation of shallow groove base multiples that have implications for the structure of DNA in compacted states. The characteristic packing leaves big solvent channels, which can be sometimes occupied by B-DNA duplexes. Comparisons of the structures of the same oligomer crystallizing in two different space groups and of different sequences crystallizing in the same space group show that the lattice forces dominate the A-DNA conformation in the crystals, complicating the effort to elucidate the influence of the base sequence on the structures. Nevertheless, in both alternating and nonalternating fragments some sequence effects can still be uncovered. Furthermore, several studies have started to define the minimal sequence changes or chemical modifications that can interconvert the oligomers between different double-helical conformers (A-, B-, and Z-form). Overall, it is seen that the rigid nucleotide principle applies to the oligomeric fragments. Besides the structures of the naked DNAs, their interactions with water, polyamines, and metal ions have attracted considerable attention. There are conserved patterns in the hydration, involving both the grooves and the backbone, which are different from those of B-DNA or Z-DNA. Overall, A-DNA seems to be more economically hydrated than B-DNA, particularly around the sugar-phosphate backbone. Spermine was found to be able to bind exclusively to either of the grooves or to the phosphate groups of the backbone, or exhibit a mixed binding mode. The located metal cations prefer binding to guanine bases and phosphate groups. The only mispairs investigated in A-DNA are the wobble pairs, yielding structural insight into their effects on helix stabilities and hydration. G.T wobble pairs have been determined in various sequence contexts, where they differentially affect the conformations and stableness of the duplexes. The structure of a G.m5C base pair, which surprisingly also adopted the wobble conformation, suggests that a similar geometry may transiently exist for G.C pairs. These results from the crystalline state will be compared to the solution state and discussed in relation to their relevance in biology.

Low-temperature specific heat of compacted vitreous silica

We present low-temperature specific-heat measurements of two types of irreversibly compacted vitreous silica (Suprasil W and Suprasil I, differing in their OH− content). In the whole temperature range investigated (0.1 K<T<35 K), the specific heatC is reduced by up to 50% compared to that of uncompacted samples but exhibits a similar temperature dependence, with the characteristic maximum inC/T3 shifted to higher temperatures. This coherent change ofC, which is roughly the same for both types of vitreous silica, gives strong evidence that the low-energy excitations characteristic of amorphous materials have a common structural origin. Possible relations to the microscopic changes upon compaction are discussed, giving support to the coupled-rotation model of SiO4 tetrahedra. Phenomenologically, the change ofC upon compaction can be understood by the soft-potential model. The relationship between height and position of theC/T3 maximum observed in normal and compacted states for both types of vitreous silica and, surprisingly, also for α-quartz hints at a correlation between the mechanisms leading to theC/T3 maximum for amorphous and crystalline materials with similar short-range order.

The occurrence of copper, iron, zinc and other elements and the nature of some copper and iron complexes in humic substances from municipal refuse disposed of in a landfill

Municipal refuse was allowed to decompose in a simulated landfill for 20 months. Three different models were studied in which the refuse, in 40 m 3 lots, was either compacted or mixed 2:1 with sewage sludge, the latter being studied in both uncompacted and compacted states. At 2, 6, 12 and 20 months, humic substances were extracted from samples with 0.1 M Na 2P 4O 7 and 0.1 M NaOH, and humic acids isolated by precipitation after acidification with HCl. The humic substances were examined by electron paramagnetic resonance (EPR) to determine the free radical content and the nature of some of the metal complexes present. The principal form of copper was present in either a square planar or a tetragonally-distorted octahedral environment, probably coordinated to two nitrogen and two oxygen atoms. Fe 3+ was present in at least three different environments. In one, it was probably in a complex with rhombic symmetry; another showed Fe 3+ in an axially-symmetric environment, most likely as a ferric porphyrin. No distinctions could be made between the concentrations or forms of metals present in the refuse humic substances as a result of adding sewage sludge, but the additions increased the yield of humic substances, particularly in the uncompacted landfill. Humic substances in the refuse retain metal elements in complexed forms which will restrict their release from the landfill.