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.
View Article and Find Full Text PDFGold nanoparticles (NPs) with different surface functionalizations can selectively interact with specific proteins, allowing a wide range of possible applications in biotechnology and biomedicine. To prevent their tendency to aggregate and to modulate their interaction with charged biomolecules or substrates (e.g.
View Article and Find Full Text PDFThermoelectric 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.
View Article and Find Full Text PDFFront Mol Biosci
September 2022
Surface functionalization of metal nanoparticles (NPs), e.g., using peptides and proteins, has recently attracted a considerable attention in the field of design of therapeutics and diagnostics.
View Article and Find Full Text PDFOrganic functionalization of graphene is successfully performed 1,3-dipolar cycloaddition of azomethine ylide in the liquid phase. The comparison between 1-methyl-2-pyrrolidinone and ,-dimethylformamide as dispersant solvents, and between sonication and homogenization as dispersion techniques, proves ,-dimethylformamide and homogenization as the most effective choice. The functionalization of graphene nanosheets and reduced graphene oxide is confirmed using different techniques.
View Article and Find Full Text PDFWe study the performance of eleven reactive force fields (ReaxFF), which can be used to study sp carbon systems. Among them a new hybrid ReaxFF is proposed combining two others and introducing two different types of C atoms. The advantages of that potential are discussed.
View Article and Find Full Text PDFGraphene-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.
View Article and Find Full Text PDFGraphene is the prototype of two-dimensional (2D) materials, whose main feature is the extremely large surface-to-mass ratio. This property is interesting for a series of applications that involve interactions between particles and surfaces, such as, for instance, gas, fluid or charge storage, catalysis, and filtering. However, for most of these, a volumetric extension is needed, while preserving the large exposed surface.
View Article and Find Full Text PDFTransitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis, and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of efficiently exploring a vast conformational space in order to seek for the actual transition path for systems whose complexity is already high in the stable states. Here we report a strategy that simplifies this task attacking the complexity on several sides.
View Article and Find Full Text PDFA large number of low-resolution models have been proposed in the last decades to reduce the computational cost of molecular dynamics simulations for bio-nano systems, such as those involving the interactions of proteins with functionalized nanoparticles (NPs). For the proteins, "minimalist" models at the one-bead-per residue (Cα-based) level and with implicit solvent are well established. For the gold NPs, widely explored for biotechnological applications, mesoscale (MS) models treating the NP core with a single spheroidal object are commonly proposed.
View Article and Find Full Text PDFThe buffer carbon layer obtained in the first instance by evaporation of Si from the Si-rich surfaces of silicon carbide (SiC) is often studied only as the intermediate to the synthesis of SiC supported graphene. In this work, we explore its intrinsic potentialities, addressing its structural and electronic properties by means of Density Functional Theory. While the system of corrugation crests organized in a honeycomb super-lattice of nano-metric side returned by calculations is compatible with atomic microscopy observations, our work reveals some possible alternative symmetries, which might coexist in the same sample.
View Article and Find Full Text PDFThis work reports an electronic and micro-structural study of an appealing system for optoelectronics: tungsten disulfide (WS) on epitaxial graphene (EG) on SiC(0001). The WS is grown via chemical vapor deposition (CVD) onto the EG. Low-energy electron diffraction (LEED) measurements assign the zero-degree orientation as the preferential azimuthal alignment for WS/EG.
View Article and Find Full Text PDFThe increasing trend in the recent literature on coarse grained (CG) models testifies their impact in the study of complex systems. However, the CG model landscape is variegated: even considering a given resolution level, the force fields are very heterogeneous and optimized with very different parametrization procedures. Along the road for standardization of CG models for biopolymers, here we describe a strategy to aid building and optimization of statistics based analytical force fields and its implementation in the software package AsParaGS (Assisted Parameterization platform for coarse Grained modelS).
View Article and Find Full Text PDFGraphene and related two-dimensional crystals and hybrid systems showcase several key properties that can address emerging energy needs, in particular for the ever growing market of portable and wearable energy conversion and storage devices. Graphene's flexibility, large surface area, and chemical stability, combined with its excellent electrical and thermal conductivity, make it promising as a catalyst in fuel and dye-sensitized solar cells. Chemically functionalized graphene can also improve storage and diffusion of ionic species and electric charge in batteries and supercapacitors.
View Article and Find Full Text PDFRecent experiments carried out in the dense cytoplasm of living cells have highlighted the importance of proteome composition and nonspecific intermolecular interactions in regulating macromolecule diffusion and organization. Despite this, the dependence of diffusion-interaction on physicochemical properties such as the degree of poly-dispersity and the balance between steric repulsion and nonspecific attraction among macromolecules was not systematically addressed. In this work, we study the problem of diffusion-interaction in the bacterial cytoplasm, combining theory and experimental data to build a minimal coarse-grained representation of the cytoplasm, which also includes, for the first time to our knowledge, the nucleoid.
View Article and Find Full Text PDFWe report a multi-scale simulation study of the photocycle of the rhodopsins. The quasi-atomistic representation ("united atoms" UA) of retinal is combined with a minimalist coarse grained (CG, one-bead-per amino acid) representation of the protein, in a hybrid UA/CG approach, which is the homolog of QM/MM, but at lower resolution. An accurate multi-stable parameterization of the model allows simulating each state and transition among them, and the combination of different scale representation allows addressing the entire photocycle.
View Article and Find Full Text PDFLow-resolution models are often used to address macroscopic time and size scales in molecular dynamics simulations of biomolecular systems. Coarse graining is often coupled to knowledge-based parametrization to obtain empirical potentials able to reproduce the system thermodynamic behavior. Here, a minimalist coarse grained (GC) model for the helical structures of proteins is reported.
View Article and Find Full Text PDFJ Chem Theory Comput
November 2013
Simulations using residue-scale coarse-grained models of biomolecules are less computationally demanding than simulations employing full-atomistic force fields. However, the coarse-grained models are often difficult and tedious to parametrize for certain applications. Therefore, a systematic and objective method to help develop or adapt the coarse-grained models is needed.
View Article and Find Full Text PDFMotivation: Atomistic or coarse grained (CG) potentials derived from statistical distributions of internal variables have recently become popular due to the need of simplified interactions for reaching larger scales in simulations or more efficient conformational space sampling. However, the process of parameterization of accurate and predictive statistics-based force fields requires a huge amount of work and is prone to the introduction of bias and errors.
Results: This article introduces SecStAnT, a software for the creation and analysis of protein structural datasets with user-defined primary/secondary structure composition, with a particular focus on the CG representation.
Hydrogen-based fuel cells are promising solutions for the efficient and clean delivery of electricity. Since hydrogen is an energy carrier, a key step for the development of a reliable hydrogen-based technology requires solving the issue of storage and transport of hydrogen. Several proposals based on the design of advanced materials such as metal hydrides and carbon structures have been made to overcome the limitations of the conventional solution of compressing or liquefying hydrogen in tanks.
View Article and Find Full Text PDFThe last decade has witnessed a renewed interest in the coarse-grained (CG) models for biopolymers, also stimulated by the needs of modern molecular biology, dealing with nano- to micro-sized bio-molecular systems and larger than microsecond timescale. This combination of size and timescale is, in fact, hard to access by atomic-based simulations. Coarse graining the system is a route to be followed to overcome these limits, but the ways of practically implementing it are many and different, making the landscape of CG models very vast and complex.
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