Quantum sensing of microRNAs with nitrogen-vacancy centers in diamond.

Label-free detection of nucleic acids such as microRNAs holds great potential for early diagnostics of various types of cancers. Measuring intrinsic biomolecular charge using methods based on field effect has been a promising way to accomplish label-free detection. However, the charges of biomolecules are screened by counter ions in solutions over a short distance (Debye length), thereby limiting the sensitivity of these methods. Here, we measure the intrinsic magnetic noise of paramagnetic counter ions, such as Mn2+, interacting with microRNAs using nitrogen-vacancy (NV) centers in diamond. All-atom molecular dynamics simulations show that microRNA interacts with the diamond surface resulting in excess accumulation of Mn ions and stronger magnetic noise. We confirm this prediction by observing an increase in spin relaxation contrast of the NV centers, indicating higher Mn2+ local concentration. This opens new possibilities for next-generation quantum sensing of charged biomolecules, overcoming limitations due to the Debye screening.

Aluminium 8-Hydroxyquinolinate N-Oxide as a Precursor to Heterometallic Aluminium-Lanthanide Complexes.

A reaction in anhydrous toluene between the formally unsaturated fragment [Ln(hfac)3] (Ln3+ = Eu3+, Gd3+ and Er3+; Hhfac = hexafluoroacetylacetone) and [Al(qNO)3] (HqNO = 8-hydroxyquinoline N-oxide), here prepared for the first time from [Al(OtBu)3] and HqNO, affords the dinuclear heterometallic compounds [Ln(hfac)3Al(qNO)3] (Ln3+ = Eu3+, Gd3+ and Er3+) in high yields. The molecular structures of these new compounds revealed a dinuclear species with three phenolic oxygen atoms bridging the two metal atoms. While the europium and gadolinium complexes show the coordination number (CN) 9 for the lanthanide centre, in the complex featuring the smaller erbium ion, only two oxygens bridge the two metal atoms for a resulting CN of 8. The reaction of [Eu(hfac)3] with [Alq3] (Hq = 8-hydroxyquinoline) in the same conditions yields a heterometallic product of composition [Eu(hfac)3Alq3]. A recrystallization attempt from hot heptane in air produced single crystals of two different morphologies and compositions: [Eu2(hfac)6Al2q4(OH)2] and [Eu2(hfac)6(µ-Hq)2]. The latter compound can be directly prepared from [Eu(hfac)3] and Hq at room temperature. Quantum mechanical calculations confirm (i) the higher stability of [Eu(hfac)3Al(qNO)3] vs. the corresponding [Eu(hfac)3Alq3] and (ii) the preference of the Er complexes for the CN 8, justifying the different behaviour in terms of the Lewis acidity of the metal centre.

Pure and Sc-doped diopside (CaMgSi2O6) vibrational spectra: modelling and experiments.

We investigated the structure of pure and Sc-doped synthetic diopside (a monoclinic single-chain silicate nominally CaMgSi2O6); in Sc-doped diopside, Sc3+ substitutes Mg2+ in the structure and, to achieve charge balance, vacancies form at the expense of Ca2+. We compared the structure obtained from ab initio modelling techniques at the density functional theory (DFT) level with the structure solved by employing single crystal X-ray diffraction. Furthermore, we compared IR and Raman spectroscopy experiments with vibrational density of states (VDOS) calculated from the Fourier transform of the velocity autocorrelation function obtained using ab initio (DFT) molecular dynamics simulations. In this framework, we developed a computational tool to assign the vibrational mode associated with a specific frequency. This method consists of projecting velocities along a specific set of internal coordinates such as stretching or bending, in cases involving defects or vacancies, to calculate a partial VDOS (pVDOS) that takes into account only the vibrations associated with selected internal modes, aiding the interpretation of the total VDOS and the experimental spectra in a relevant way. The computed data were validated with the experiments and we observed that doping the diopside structure with Sc produces peak broadening and the occurrence of new peaks in the Raman spectra and that site vacancies are associated with the nearby Sc site. The present work constitutes an interesting starting point to exploit the calculated VDOS/pVDOS to characterize experimental vibrational spectra of complex systems containing local vacancies, substitutions or defects as the Sc-doped diopside.

Aptamer-based gold nanoparticle aggregates for ultrasensitive amplification-free detection of PSMA.

Early diagnosis is one of the most important factors in determining the prognosis in cancer. Sensitive detection and quantification of tumour-specific biomarkers have the potential to improve significantly our diagnostic capability. Here, we introduce a triggerable aptamer-based nanostructure based on an oligonucleotide/gold nanoparticle architecture that selectively disassembles in the presence of the biomarker of interest; its optimization is based also on in-silico determination of the aptamer nucleotides interactions with the protein of interest. We demonstrate this scheme for the case of Prostate Specific Membrane Antigen (PSMA) and PSMA derived from PSMA-positive exosomes. We tested the disassembly of the system by diameter and count rate measurements in dynamic light scattering, and by inspection of its plasmon resonance shift, upon addition of PSMA, finding appreciable differences down to the sub-picomolar range; this points towards the possibility that this approach may lead to sensors competitive with diagnostic biochemical assays that require enzymatic amplification. More generally, this scheme has the potential to be applied to a broad range of pathologies with specific identified biomarkers.

Competing excitation paths in luminescent heterobimetallic Ln-Al complexes: Unraveling interactions via experimental and theoretical investigations.

The interest for heterometallic lanthanide-d or-p metal (Ln-M) complexes is growing because of a potential cooperative or synergistic effect related to the proximity of two different metals in the same molecular architecture affording special tunable physical properties. To exploit the potentiality of Ln-M complexes, suitable synthetic approaches, and the in-depth understanding of the effect of each building block on their properties are mandatory. Here, we report the study on a family of heterometallic luminescent complexes [Ln(hfac)3Al(L)3], Ln= Eu3+ and Tb3+. Using different L ligands, we investigated the effect of the steric and electronic properties of the Al(L)3 fragment, highlighting the general validity of the employed synthetic route. A marked difference in the light emission of [Eu(hfac)3Al(L)3] and [Tb(hfac)3Al(L)3] complexes has been observed. Thanks to photoluminescence experiments and Density Functional Theory calculations, Ln3+ emissions are explained with a model involving two non-interacting excitation paths through hfac or Al(L)3 ligands.

Eutrophication history and organic carbon burial rate recorded in sediment cores from the Mar Piccolo of Taranto (Italy).

During the second half of the twentieth century, coastal lagoons in densely populated regions experienced eutrophication due to excessive nutrient inputs. Detrimental effects, including hypoxia/anoxia and harmful algae blooms, have occurred in many Mediterranean lagoons, but their trophic evolution is poorly documented. The lack of adequate monitoring data can partly be offset by examining sedimentary records. In the Mar Piccolo, a lagoon comprising two basins near Taranto (Italy), eutrophication has followed population growth and pollution resulting from naval activities and massive industrialisation. Based on 210Pb-dated sediment cores, continuous in situ density profiles obtained with computed tomography, organic carbon (OC) and total nitrogen (TN) content and OC and TN isotopic signatures, this paper reconstructs the history of eutrophication, discusses the sources of organic matter and provides an estimate of the OC burial rate before and during the eutrophic period. OC burial increased in the period 1928-1935 and peaked in the decade 1960-1970. OC and TN content were still high in the surface sediments collected in 2013, despite partial diversion of sewage outfalls in the period 2000-2005. The divergent δ13C and δ15N signatures of the two basins during the eutrophic period suggest they were affected by different nutrient sources. The OC burial rate during the eutrophic phase (≈ 46 g m-2 y-1) was close to the world median value for lagoon sediments, and was about twice the burial rate recorded in the preceding oligotrophic phase.

Heat-Driven Iontronic Nanotransistors.

Thermoelectric polyelectrolytes are emerging as ideal material platform for self-powered bio-compatible electronic devices and sensors. However, despite the nanoscale nature of the ionic thermodiffusion processes underlying thermoelectric efficiency boost in polyelectrolytes, to date no evidence for direct probing of ionic diffusion on its relevant length and time scale has been reported. This gap is bridged by developing heat-driven hybrid nanotransistors based on InAs nanowires embedded in thermally biased Na+ -functionalized (poly)ethyleneoxide, where the semiconducting nanostructure acts as a nanoscale probe sensitive to the local arrangement of the ionic species. The impact of ionic thermoelectric gating on the nanodevice electrical response is addressed, investigating the effect of device architecture, bias configuration and frequency of the heat stimulus, and inferring optimal conditions for the heat-driven nanotransistor operation. Microscopic quantities of the polyelectrolyte such as the ionic diffusion coefficient are extracted from the analysis of hysteretic behaviors rising in the nanodevices. The reported experimental platform enables simultaneously the ionic thermodiffusion and nanoscale resolution, providing a framework for direct estimation of polyelectrolytes microscopic parameters. This may open new routes for heat-driven nanoelectronic applications and boost the rational design of next-generation polymer-based thermoelectric materials.

Size Selectivity in Heterolanthanide Molecular Complexes with a Ditopic Ligand.

The similar reactivity of lanthanides generally leads to statistically populated polynuclear complexes, making the rational design of ordered hetero-lanthanide compounds extremely challenging. Here we report on the site selectivity in hetero-lanthanide tetranuclear complexes afforded by the relatively simple ditopic pyterpyNO ligand (4'-(4-pyridil)-2,2':6',2"-terpyridine N-oxide). The sequential room temperature reaction of RE2 (tta)6 (pyterpyNO)2 (where RE=Y, (1); Eu, (2), Dy, (3) Htta=2-thenoyltrifluoroacetone) with La(tta)3 dme (dme=dimethoxyethane) yielded Y2 La2 (tta)12 (pyterpyNO)2 (4), Dy2 La2 (tta)12 (pyterpyNO)2 (5) and Eu2 La2 (tta)12 (pyterpyNO)2 (6). Single crystals X-ray diffraction studies showed that 4, 5 and 6 are isostructural, featuring a tetranuclear structure with two different metal coordination sites with coordination numbers 8 (CN8) and 9 (CN9). The two smaller cations are mainly bridged by the O-donor atoms of the NO groups of two pyterpyNO ligands (CN8), while the larger lanthanum centres are bound by a terpyridine unit (CN9). Size selectivity has been studied with structural and magnetic studies in the solid state and through 19 F NMR and photoluminescence studies in solution, showing a direct dependence on the difference of ionic radii of the ions and yielding a 91 % selectivity for 4. Furthermore, 19 F NMR, X-ray and PL studies pointed out that the nature of the product is independent from the synthetic route for compound Eu2 Y2 (tta)12 (pyterpyNO)2 (7), keeping the ion selectivity also for a self-assembly reaction. Unexpectedly, these studies have evidenced that selectivity is not exclusively governed by electrostatic interactions related to size dimensions.

Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study.

A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin-streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor's gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.

Dataset of analyzes performed to determine the level and timing of selected organic pollutants' inputs in sediments of the Lake of Cavazzo (Italy).

This data article presents the dataset collected for selected organic pollutants in the framework of a larger research project aimed at assessing the effects of different environmental stressors (natural and anthropogenic) in sediments of the Lake of Cavazzo, a basin of glacial origin located in a seismically active region of the Italian Eastern Alps. Information relative to sampling strategy and operations, location of sampling sites, sedimentary chronological benchmarks, and profiles of RGB (Red-Green-Blue) color code determined from high resolution photos taken at cores CAV-04 and CAV-06 are reported, together with analytical data for 15 polycyclic aromatic hydrocarbons, 21 polychlorinated biphenyls' congeners (including the non-Aroclor CB-11), 14 polybrominated diphenyl ethers' congeners, and 22 organochlorine pesticides, whose concentrations were determined by Gas Chromatography coupled both to Low-Resolution and High-Resolution Mass Spectrometry. Interpretation of this dataset is fully discussed in the companion article by Pizzini et al. (2022) and relys on the multi-proxy analysis of sediment samples presented in Polonia et al. (2021) that highlighted lake stratigraphy and major changes occurring at a decadal scale since the 1950s.

Acidic pH Promotes Refolding and Macroscopic Assembly of Amyloid ß (16-22) Peptides at the Air-Water Interface.

Assembly by amyloid-beta (Aß) peptides is vital for various neurodegenerative diseases. The process can be accelerated by hydrophobic interfaces such as the cell membrane interface and the air-water interface. Elucidating the assembly mechanism for Aß peptides at hydrophobic interface requires knowledge of the microscopic structure of interfacial peptides. Here we combine scanning force microscopy, sum-frequency generation spectroscopy, and metadynamics simulations to probe the structure of the central fragment of Aß peptides at the air-water interface. We find that the structure of interfacial peptides depends on pH: at neutral pH, the peptides adopt a less folded, bending motif by forming intra-hydrogen bonds; at acidic pH, the peptides refold into extended ß-strand fibril conformation, which further promotes their macroscopic assembly. The conformational transition of interfacial peptides is driven by the reduced hydrogen bonds, both with water and within peptides, resulting from the protonation of acidic glutamic acid side chains.

PAHs, PCBs, PBDEs, and OCPs trapped and remobilized in the Lake of Cavazzo (NE Italy) sediments: Temporal trends, quality, and sources in an area prone to anthropogenic and natural stressors.

Under the present climatic emergency, the environmental quality of freshwater reservoirs is an increasingly urgent topic as its deterioration threatens humans and ecosystems. It is evident that pollution by natural and anthropogenic contaminants must be avoided or reduced. The Lake of Cavazzo (NE Italy) is a natural perialpine basin which, from the mid-20th century, has sustained several anthropogenic impacts that added to the effects of the intense regional seismicity. Starting from 2015, in response to concerns raised by local authorities, a multidisciplinary investigation of the lake floor and sub-floor was conducted, including a geophysical survey and the collection of sediment cores. Two of them were studied to detect contamination by Polycyclic Aromatic Hydrocarbons (PAHs) and specific Persistent Organic Pollutants (POPs; i.e. PolyChlorinated Biphenyls - PCBs, PolyBrominated Diphenyl Ethers - PBDEs, and OrganoChlorine Pesticides - OCPs), and to verify the link with known anthropogenic stressors. Results were interpreted in light of previous studies suggesting modified conditions after the '50s, and recognized the effects of the 1976-1977 MW 6.5 seismic sequence in resuspending sediments within the basin. Analyzed pollutants defined a potential critical situation only for few OCPs, above all 2,4'- and 4,4'-DDT isomers. In addition, PBDEs were found at concentrations exceeding those of other heavily polluted alpine lakes. Mass movements (either seismic or human induced) have likely resuspended and transferred pollutants from shallower locations to the lake depocenter, showing the potential of re-exposing contaminated layers to biomagnification processes along the lacustrine food chain. Local inputs of pollutants prevail over distributed sources, suggesting a link with local agricultural or industrial activities. Indeed, works connected to the construction of the hydroelectric power plant in the '50s might have reworked local sediments perturbing their natural accretion. Results of this work might inspire similar studies in other problematic lacustrine areas that sustain both natural and anthropogenic stressors.

Stoichiometrically Controlled Assembly of Lanthanide Molecular Complexes of the Heteroditopic Divergent Ligand 4'-(4-Pyridyl)-2,2':6',2″-terpyridine N-Oxide in Hypodentate or Bridging Coordination Modes. Structural, Magnetic, and Photoluminescence Studies.

Mononuclear rare-earth tris-ß-diketonato complexes RE(tta)3dme [RE = Y (1), La (2), Dy (3), or Eu (4); Htta = 2-thenoylacetone; dme = 1,2-dimethoxyethane] react cleanly at room temperature in a 1:1 molar ratio with the heteroditopic divergent ligand 4'-(4-pyridyl)-2,2':6',2″-terpyridine N-oxide (pyterpyNO) to yield RE2(tta)6(pyterpyNO)n, where n = 2 for RE = Y (5), Dy (6), or Eu (7) and n = 3 for RE = La (8). The crystal structure of 5 revealed a dinuclear compound with two pyterpyNO's bridging through the oxygen atom in a hypodentate mode leaving the terpyridine moieties uncoordinated. Using a metal:pyterpyNO molar ratio of 2 for RE = Y (9), Dy (10), or Eu (11), it was possible to isolate the molecular complexes RE4(tta)12(pyterpyNO)2, while using a 5:3 molar ratio, the product La5(tta)12(pyterpyNO)3 (12) can be obtained. 89Y nuclear magnetic resonance spectroscopy revealed two different yttrium centers at room temperature for 9. An X-ray diffraction study of 10 showed a symmetrical tetranuclear structure resulting from the coordination of two Dy(tta)3 fragments to the two hypodentate terpyridines of the dinuclear unit and presenting two different coordination sites for metals with coordination numbers of 8 and 9. Magnetic studies of 6 and 10 revealed the presence of an antiferromagnetic interaction between the two Dy(III) atoms bound by the NO bridges. These compounds displayed a slow relaxing magnetization through Orbach (6) and Raman (10) processes in the absence of an applied magnetic field; the rate increased upon application of a 1 kOe field. 7 and 11 showed a bright red emission typical of Eu3+. The two complexes have similar emission properties mainly determined by the employed ß-diketonato ligands.

1D-Zigzag Eu3+/Tb3+ Coordination Chains as Luminescent Ratiometric Thermometers Endowed with Multicolor Emission.

Two homometallic Coordination Polymers (CPs) with composition [Ln(hfac)3bipy]n (Ln3+ = Eu3+, 1, and Tb3+, 2; hfac = hexafluoroacetylacetonato, bipy = 4,4'-bipyridine) were used to develop a family of ratiometric luminescent thermometers containing Eu3+ and Tb3+ as red and green emitters, respectively. The thermometric properties of pure CPs and of their mixtures having an Eu3+/Tb3+ molar ratio of 1:1, 1:3, 1:5, and 1:10 (samples: Eu1Tb1, Eu1Tb3, Eu1Tb5, and Eu1Tb10) were studied in the 83-383 K temperature range. Irrespective of the chemical composition, we observed similar thermometric responses characterized by broad applicative temperature ranges (from 100 to 165 K wide), and high relative thermal sensitivity values (Sr), up to 2.40% K-1, in the physiological temperature range (298-318 K). All samples showed emissions endowed with peculiar and continuous color variation from green (83 K) to red (383 K) that can be exploited to develop a colorimetric temperature indicator. At fixed temperature, the color of the emitted light can be tuned by varying composition and excitation wavelength.

Multidisciplinary dataset for geological and environmental studies in the lake of Cavazzo (Southern Alps).

The present dataset was collected to evaluate the environmental stressors on a lacustrine basin in the Eastern Alps of glacial origin that has been affected in recent years by natural and anthropogenic events such as the construction of a hydroelectric power plant and a series of strong earthquakes during 1976-1977. We collected sediment cores in different sites from the lake margins to the depocenter and performed a multiproxy analysis of sediment sample to highlight lake stratigraphy and major changes occurring at a decadal scale (Polonia et al., [1]). The integrated analyses of sedimentological, geochemical, isotopic, mineralogical and micropaleontological analyses aimed at reconstructing changes in sediment composition and define the triggering mechanisms of altered environmental conditions. The dataset demonstrates that evaluating ex post the effects of artificial modification in a natural environment during relatively long time spans (decades) can provide important insights for managing and protection strategies in similar environments worldwide.

Screening environmental risk evaluation of As and trace metals in soils and sediments from a developing area (Bac Giang Province, Northern Vietnam).

Despite the key role that areas close to the rivers Cau and Ngu Huyen Khê (Bac Giang Province, Northern Vietnam) play in the socio-economic development of Vietnam, poor information is available on the level of contaminants and their natural backgrounds in local soils and sediments. To partially fill this gap and to take into account for pressures and impacts on different zones and environment types (river sediments, crop fields, family wells, industrial and urban soils), the samples were collected and analyzed for fifteen trace elements at thirty sites distributed over the province. To overcome the lack of information on natural background and to identify the extent of the deviation from natural conditions, we coupled statistical analysis to contamination indices. The multivariate analysis was used to relate sediment chemical composition with a possible alteration from secondary inputs and to highlight those samples that most deviate from the distribution by category and are potentially more problematic. Geoaccumulation indexes and enrichment factors were calculated to discriminate between natural backgrounds and anthropic sources, SQGs were used for a screening evaluation of environmental risk in the study area. Results showed relatively high concentrations, sometimes exceeding international and national guidelines, and local sources could prevail over geogenic origins. Despite its significant natural contribution all over the study area, As evidenced some cases of anthropogenic contamination, similarly to that observed for Cd, Hg, and Zn. Their high concentrations may be a problem for public health, especially when found in family wells.

Covalent organic functionalization of graphene nanosheets and reduced graphene oxide via 1,3-dipolar cycloaddition of azomethine ylide.

Organic functionalization of graphene is successfully performed via 1,3-dipolar cycloaddition of azomethine ylide in the liquid phase. The comparison between 1-methyl-2-pyrrolidinone and N,N-dimethylformamide as dispersant solvents, and between sonication and homogenization as dispersion techniques, proves N,N-dimethylformamide and homogenization as the most effective choice. The functionalization of graphene nanosheets and reduced graphene oxide is confirmed using different techniques. Among them, energy-dispersive X-ray spectroscopy allows to map the pyrrolidine ring of the azomethine ylide on the surface of functionalized graphene, while micro-Raman spectroscopy detects new features arising from the functionalization, which are described in agreement with the power spectrum obtained from ab initio molecular dynamics simulation. Moreover, X-ray photoemission spectroscopy of functionalized graphene allows the quantitative elemental analysis and the estimation of the surface coverage, showing a higher degree of functionalization for reduced graphene oxide. This more reactive behavior originates from the localization of partial charges on its surface due to the presence of oxygen defects, as shown by the simulation of the electrostatic features. Functionalization of graphene using 1,3-dipolar cycloaddition is shown to be a significant step towards the controlled synthesis of graphene-based complex structures and devices at the nanoscale.

Correction: Covalent organic functionalization of graphene nanosheets and reduced graphene oxide via 1,3-dipolar cycloaddition of azomethine ylide.

[This corrects the article DOI: 10.1039/D1NA00335F.].

In silico design, building and gas adsorption of nano-porous graphene scaffolds.

Graphene-based nano-porous materials (GNM) are potentially useful for all those applications needing a large specific surface area (SSA), typical of the bidimensional graphene, yet realized in the bulk dimensionality. Such applications include for instance gas storage and sorting, catalysis and electrochemical energy storage. While a reasonable control of the structure is achieved in micro-porous materials by using nano-micro particles as templates, the controlled production or even characterization of GNMs with porosity strictly at the nano-scale still raises issues. These are usually produced using dispersion of nano-flakes as precursors resulting in little control on the final structure, which in turn reflects in problems in the structural model building for computer simulations. In this work, we describe a strategy to build models for these materials with predetermined structural properties (SSA, density, porosity), which exploits molecular dynamics simulations, Monte Carlo methods and machine learning algorithms. Our strategy is inspired by the real synthesis process: starting from randomly distributed flakes, we include defects, perforation, structure deformation and edge saturation on the fly, and, after structural refinement, we obtain realistic models, with given structural features. We find relationships between the structural characteristics and size distributions of the starting flake suspension and the final structure, which can give indications for more efficient synthesis routes. We subsequently give a full characterization of the models versus H2 adsorption, from which we extract quantitative relationship between the structural parameters and the gravimetric density. Our results quantitatively clarify the role of surfaces and edges relative amount in determining the H2 adsorption, and suggest strategies to overcome the inherent physical limitations of these materials as adsorbers. We implemented the model building and analysis procedures in software tools, freely available upon request.

Atomistic simulations of gold surface functionalization for nanoscale biosensors applications.

A wide class of biosensors can be built via functionalization of gold surface with proper bio conjugation element capable of interacting with the analyte in solution, and the detection can be performed either optically, mechanically or electrically. Any change in physico-chemical environment or any slight variation in mass localization near the surface of the sensor can cause differences in nature of the transduction mechanism. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection of the analyte. Here, we employ molecular modeling techniques to assist the optimization of a gold-surface biosensor. The gold surface of a quartz-crystal-microbalance sensor is functionalized using polymeric chains of poly(ethylene glycol) (PEG) of 2 KDa molecular weight, which is an inert long chain amphiphilic molecule, supporting biotin molecules (bPEG) as the ligand molecules for streptavidin analyte. The PEG linkers are immobilized onto the gold surface through sulphur chemistry. Four gold surfaces with different PEG linker density and different biotinylation ratio between bPEG and PEG, are investigated by means of state-of-the art atomistic simulations and compared with available experimental data. Results suggest that the amount of biotin molecules accessible for the binding with the protein increases upon increasing the linkers density. At the high density a 1:1 ratio of bPEG/PEG can further improve the accessibility of the biotin ligand due to a strong repulsion between linker chains and different degree of hydrophobicity between bPEG and PEG linkers. The study provides a computaional protocol to model sensors at the level of single molecular interactions, and for optimizing the physical properties of surface conjugated ligand which is crucial to enhance output of the sensor.