Bioelectronics moves toward designing nanoscale electronic platforms that allow in vivo determinations. Such devices require interfacing complex biomolecular moieties as the sensing units to an platform for signal transduction. Inevitably, a systematic design goes through bottom-up understanding of structurally related electrical signatures circuit, which will ultimately lead us tailor its properties. Toward this aim, we show here first example bioengineered charge transport single-protein...

The sliding of a sharp nanotip on graphene completely immersed in water is investigated by molecular dynamics (MD) and atomic force microscopy. MD simulations predict that the atomic-scale stick–slip almost identical to found ultrahigh vacuum. Furthermore, they show plays purely stochastic role (solid-to-solid) friction. These observations are substantiated friction measurements grown Cu Ni, where, oppositely operation air, lattice resolution readily achieved. Our results promote microscopy...

Significance The mechanical properties of nucleic acids regulate multiple biological processes ranging from complex chromosome packing to replication a plasmid. Single-molecule experiments have reported puzzling differences between the double-stranded DNA (dsDNA) and RNA (dsRNA) subjected force torque. This study investigates these using constant-force, all-atom, microsecond-long molecular dynamics. We provide physical mechanism that explains nonintuitive opposite twist-stretch response...

Large-scale molecular dynamics (MD) simulations and atomic force microscopy (AFM) in liquid are combined to characterize the adsorption of Immunoglobulin G (IgG) antibodies over a hydrophobic surface modeled with three-layer graphene slab. We consider explicitly water solvent, simulating systems massive sizes (up 770 000 atoms), for four different orientations. Protocols based on steered MD speed up protein diffusion stage enhance dehydration process long simulation times (>150 ns) order...

We report 150 ns explicit solvent MD simulations of the adsorption on graphene albumin (BSA) in two orientations and using different protocols, i.e., free forced adsorption. Our results show that occurs with little structural rearrangements. Even taking to an extreme, by forcing it a 5 nN downward force applied during initial 20 ns, we along particular orientation BSA is able preserve properties majority its binding sites. Furthermore, all cases considered this work, ibuprofen site has shown...

Sequence-dependent DNA conformation and flexibility play a fundamental role in the specificity of DNA-protein interactions. Here we quantify crookedness: sequence-dependent deformation that consists periodic bends base pair centers chain. Using extensive $100\text{ }\text{ }\ensuremath{\mu}\mathrm{s}$-long, all-atom molecular dynamics simulations, found crookedness its associated are bijective, which unveils one-to-one relation between structure dynamics. This allowed us to build predictive...

Multiple experiments on the electron transport through solid-state junctions based different proteins have suggested that dominant mechanism is quantum tunneling (or coherent transport). This extremely surprising given length of these molecules (2–7 nm) and their electronic structure (mainly comprising very localized molecular orbitals). Overall, this probably single most important puzzle in field biomolecular electronics calls for rigorous calculations probability protein-based junctions....

While the intrinsically multi-scale nature of most advanced materials necessitates use cost-effective computational models based on classical physics, a reliable description structure and dynamics their components often requires quantum-mechanical treatment. In this work, we present JOYCE3.0, software package for parameterization accurate, quantum-mechanically derived force-fields (QMD-FFs). Since its original release, code has been extensively automated expanded, with all novel...

While the intrinsically multiscale nature of most advanced materials necessitates use cost-effective computational models based on classical physics, a reliable description structure and dynamics their components often requires quantum-mechanical treatment. In this work, we present JOYCE3.0, software package for parametrization accurate, quantum-mechanically derived force fields (QMD-FFs). Since its original release, code has been extensively automated expanded, with all novel...

On-surface synthesis provides exceptional control over nanostructure and material composition, enabling the creation of molecular compounds that are difficult or impossible to obtain with other methods. In this work, we demonstrate possibility synthesizing atropisomeric molecules made chains polyaromatic hydrocarbon units via on-surface synthesis. Scanning probe microscopy reveals adsorbed on Au(111) surfaces adopt a planar structure, adjacent monomeric aligning either in parallel...

Abstract Cryo-electron microscopy can determine the structure of biological matter in vitrified liquids. However, alone is insufficient to understand function native and engineered biomolecules. So far, their mechanical properties have mainly been probed at room temperature using tens pico-newton forces with a resolution limited by thermal fluctuations. Here we combine force spectroscopy computer simulations cryogenic conditions quantify adhesion intra-molecular spray-deposited single-strand...

Abstract A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of has been well characterized. However, the these is controversial their response to force remains unexplored. Here, we rationalize in-phase present Caenorhabditis elegans genome over a wide range external forces, using single-molecule experiments theoretical polymer models. Atomic Force Microscopy imaging shows...

Friction control and technological advancement are intimately intertwined. Concomitantly, two-dimensional materials occupy a unique position for realizing quasi-frictionless contacts. However, the question arises of how to tune superlubric sliding. Drawing inspiration from twistronics, we propose superlubricity via moiré patterning. force microscopy molecular dynamics simulations unequivocally demonstrate transition dissipative sliding regime different twist angles graphene moirés on Pt(111)...

Abstract Thermal expansion, the response in shape, area or volume of a solid with heat, is usually large molecular materials compared to their inorganic counterparts. Resulting from intrinsic molecule flexibility, conformational changes variable intermolecular interactions, exact interplay between these mechanisms however poorly understood down level. Here, we investigate structural variations two-dimensional supramolecular network on Au(111) consisting shape persistent polyphenylene...

We derive the semiclassical Kirzhnits expansion of $D$-dimensional one-particle density matrix up to second order in $\ensuremath{\hbar}$. focus on two-dimensional (2D) case and show that all gradient corrections both 2D kinetic energy vanish. However, satisfies consistency criterion Gross Proetto [J. Chem. Theory Comput. 5, 844 (2009)] for functional derivatives noninteracting with respect Kohn-Sham potential. Finally, we correction exchange diverges agreement previous linear-response study.

We demonstrate how an exponentially saturating increase of the contact area between a nanoasperity and crystal surface, occurring on time scales governed by Arrhenius equation, is consistent with measurements static friction lateral stiffness model alkali-halide surface at different temperatures in ultrahigh vacuum. The ``contact ageing'' effect attributed to atomic attrition eventually broken thermally activated slip surface. combination two effects also leads regions strengthening...

The reliability of molecular dynamics (MD) simulations in predicting macroscopic properties complex fluids and soft materials, such as liquid crystals, colloidal suspensions, or polymers, relies on the accuracy adopted force field (FF). We present an automated protocol to derive specific accurate FFs, fully based ab initio quantum mechanical (QM) data. integration Joyce Picky procedures, recently proposed by our group provide description simple liquids, is here extended larger molecules,...

We derive a generalized gradient approximation to the exchange energy be used in density functional theory calculations of two-dimensional systems. This class approximations has long and successful history, but it not yet been fully investigated for electrons two dimensions. follow approach originally proposed by Becke three-dimensional systems [Int. J. Quantum Chem. 23, 1915 (1983); Phys. 85, 7184 (1986)]. The resulting depends on parameters that are adjusted test set parabolically confined...

We present a theoretical study of the blue-copper azurin extracted from Pseudomonas aeruginosa and several its single amino acid mutants. For first time, we consider whole structure this kind protein rather than limiting our analysis to copper complex only. This is accomplished by combining fully ab initio calculations based on density functional theory with atomic-scale molecular dynamics simulations. Beyond main features arising complex, reveals role played peripheral parts proteins. In...

The mechanical properties of double-stranded RNA (dsRNA) are involved in many its biological functions and relevant for future nanotechnology applications. DsRNA must tightly bend to fit inside viral capsids or deform upon the interaction with proteins that regulate gene silencing immune response against attacks. However, question how nucleotide sequence affects global dsRNA has so far remained largely unexplored. Here, we have employed state-of-the-art atomistic molecular dynamics...

Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of formation and electronic structure metal-protein-metal junction based on blue-copper azurin from pseudomonas aeruginosa. We focus case in protein adsorbed gold surface contacted, at opposite side, to STM (Scanning Tunneling Microscopy) tip by spontaneous attachment. This been simulated through combination molecular dynamics density functional...

In the growing field of biomolecular electronics, blue-copper Azurin stands out as one most widely studied protein in single-molecule contacts. Interestingly, despite paramount importance structure/dynamics molecular contacts their transport properties, these factors remain largely unexplored from theoretical point view context single junctions. Here we address this issue using all-atom Molecular Dynamics (MD) Pseudomonas Aeruginosa adsorbed to a Au(111) substrate. particular, focus on...