| 1. |
- Calard, Francois, et al.
(author)
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Designing sterically demanding thiolate coated AuNPs for electrical characterization of BPDT in a NP-molecule-nanoelectrode platform
- 2017
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In: Molecular Systems Design & Engineering. - : ROYAL SOC CHEMISTRY. - 2058-9689. ; 2:2, s. 133-139
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Journal article (peer-reviewed)abstract
- Molecular electronics with single or few molecules requires a stable metal-molecule nanojunction platform. Herein, we report the design and synthesis of gold nanoparticles coated with sterically demanding thiol ligands that are essential to fabricate a versatile and stable nanoelectrode-molecule-nanoparticle platform suitable for electrical characterization of small organic molecules. By combining.-tetraphenylmethane ether functionalized alkyl thioacetate and alkyl thiols, we prepared highly stable gold nanoparticles in a one-phase reaction providing simple and efficient purification. This robust preparation gives highly pure nanoparticles in very high yields (up to 90%) with long-time shelf stability. The synthesis in this work has superior reproducibility compared to previous synthesis processes that are currently being used for such molecular electronics platforms. Electron microscopy confirms the formation of uniform and small nanoparticles in the range of 5 to 7 nm. These nanoparticles with different ligand surface coverages were placed in a 20 nm nanoelectrode setup using dielectrophoretic forces. This setup was utilized to characterize the conductivity of the molecular wire 4,4'-biphenyldithiol introduced via ligand placeexchange under ambient conditions.
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| 2. |
- Falciani, Gabriele, et al.
(author)
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A multi-scale perspective of gas transport through soap-film membranes
- 2020
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In: Molecular Systems Design & Engineering. - : ROYAL SOC CHEMISTRY. - 2058-9689. ; 5:5, s. 911-921
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Journal article (peer-reviewed)abstract
- Soap films represent unique aqueous systems, whose physical properties can be tuned by acting on their nanoscale structure. Here, we specifically focus on transport properties through membranes realized in the form of soap films. While diffusion phenomena in the water core and surfactant monolayers are described using a continuum model, molecular dynamics is used to compute the static and dynamical properties of water, gases and the surfactant in the monolayers which is hexaethylene glycol monododecyl ether (C12E6). The obtained atomistic details are then incorporated into a drift-diffusion model for consistently extracting a boundary condition for the above continuum model describing transport phenomena at a larger scale. Numerical predictions are validated against experimental data from both properly designed experiments and the literature. Finally, the developed model is used to estimate the characteristic time for disparate gas mixing when initially separated by soap film membranes.
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| 3. |
- Leino, Mattias, et al.
(author)
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Optimization of proximity-dependent initiation of hybridization chain reaction for improved performance
- 2019
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In: Molecular Systems Design & Engineering. - : Royal Society of Chemistry (RSC). - 2058-9689. ; 4:5, s. 1058-1065
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Journal article (peer-reviewed)abstract
- Proximity based detection methods are invaluable tools in the field of molecular biology, increasing selectivity and allowing for analysis of protein interactions. ProxHCR utilizes pairs of antibodies labelled with oligonucleotides to probe for proximal binding and to initiate a hybridization chain reaction (HCR) to generate an amplified detection signal. As HCR is based upon hybridization of DNA hairpins, the performance is dependent on salt concentrations and temperature. Herein we have redesigned the proxHCR system to increase the performance and to reduce dependency on temperature and salt concentrations. The new oligonucleotides provide an increased signal when performed at physiological salt concentrations and in room temperature.
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| 4. |
- Papadopoulos, Athanasios I., et al.
(author)
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Computer-aided molecular design and selection of CO2 capture solvents based on thermodynamics, reactivity and sustainability
- 2016
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In: Molecular Systems Design and Engineering. - : Royal Society of Chemistry (RSC). - 2058-9689. ; 1:3, s. 313-334
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Journal article (peer-reviewed)abstract
- The identification of improved carbon dioxide (CO2) capture solvents remains a challenge due to the vast number of potentially-suitable molecules. We propose an optimization-based computer-aided molecular design (CAMD) method to identify and select, from hundreds of thousands of possibilities, a few solvents of optimum performance for CO2 chemisorption processes, as measured by a comprehensive set of criteria. The first stage of the approach involves a fast screening stage where solvent structures are evaluated based on the simultaneous consideration of important pure component properties reflecting thermodynamic, kinetic, and sustainability behaviour. The impact of model uncertainty is considered through a systematic method that employs multiple models for the prediction of performance indices. In the second stage, high-performance solvents are further selected and evaluated using a more detailed thermodynamic model, i.e. the group-contribution statistical associating fluid theory for square well potentials (SAFT-gamma SW), to predict accurately the highly non-ideal chemical and phase equilibrium of the solvent-water-CO2 mixtures. The proposed CAMD method is applied to the design of novel molecular structures and to the screening of a data set of commercially available amines. New molecular structures and commercially-available compounds that have received little attention as CO2 capture solvents are successfully identified and assessed using the proposed approach. We recommend that these solvents should be given priority in experimental studies to identify new compounds.
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| 5. |
- Schritt, D, et al.
(author)
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Repertoire Builder: high-throughput structural modeling of B and T cell receptors
- 2019
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In: MOLECULAR SYSTEMS DESIGN & ENGINEERING. - : Royal Society of Chemistry (RSC). - 2058-9689. ; 4:4, s. 761-768
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Journal article (other academic/artistic)abstract
- Repertoire Builder (https://sysimm.org/rep_builder/) is a method for generating atomic-resolution, three-dimensional models of B cell receptors (BCRs) or T cell receptors (TCRs) from their amino acid sequences.
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