Deconstructing the governing dissipative phenomena in the nanoscale

An expression describing the controlling parameters involved in short range nanoscale dissipation is proposed and supported by simulations and experimental findings. The expression is deconstructed into the geometrical, dynamic, chemical and mechanical properties of the system. In atomic force microscopy these are translated into 1) tip radius and tip-sample deformation, 2) resonant frequency and oscillation amplitude and 3) hysteretic and viscous dissipation. The latter are characteristic parameters defining the chemical and mechanical properties of the tip-sample system. Long range processes are also discussed and footprints are identified in experiments conducted on mica and silicon samples. The present methodology can be exploited to validate or invalidate nanoscale dissipative models by comparing predictions with experimental observables

Reconstructing force profiles with an amplitude-modulation AFM in tapping mode

Here we demonstrate how to reconstruct force profiles with an amplitude-modulation AFM operated in in standard tapping mode. Our example is based on the Cypher scanning probe microscope from Asylum Research. The method is based on Sader and Katan’s algorithm, but we have implemented an experimental set-up that allows for robust reconstruction. We discuss the details here

The Mendeleev-Meyer force project

Here we present the Mendeleev–Meyer Force Project which aims at tabulating all materials and substances in a fashion similar to the periodic table. The goal is to group and tabulate substances using nanoscale force footprints rather than atomic number or electronic configuration as in the periodic table. The process is divided into: (1) acquiring nanoscale force data from materials, (2) parameterizing the raw data into standardized input features to generate a library, (3) feeding the standardized library into an algorithm to generate, enhance or exploit a model to identify a material or property. We propose producing databases mimicking the Materials Genome Initiative, the Medical Literature Analysis and Retrieval System Online (MEDLARS) or the PRoteomics IDEntifications database (PRIDE) and making these searchable online via search engines mimicking Pubmed or the PRIDE web interface. A prototype exploiting deep learning algorithms, i.e. multilayer neural networks, is presented.Award-winningPostprint (author's final draft

Common peroneal nerve injuries at the knee: outcomes of nerve repair

Background. Common peroneal nerve (CPn) lesion at the knee is one of the most frequent neurologic injury of the lower limb. Among the etiologies there are also open and closed trauma. If direct nerve repair is not possible, nerve grafting is indicated as a primary or delayed procedure. Nerve and tendon transfer are other possible therapeutic options. Material and methods. In this retrospective double center study, 35 patients with post-traumatic CPn lesion at the knee, that underwent surgical repair, were analyzed. Exclusion criteria were severe concomitant neurological pathologies, complex injury of the lower leg including major vessels lesion and or tibial nerve injury. The objective of the study is to demonstrate the degree of foot dorsiflexion recovery based on the type of trauma and the corresponding performed surgery: the Medical Research Council classification (M0-M5) was used as rating scale. Results. There were 23 closed and 12 open injuries. Time of surgery varied from 6 to 11 months after closed trauma, whereas 2 open traumas were explored at emergency and the remaining 10 patients were explored 3 to 9 months after injury. Neurolysis was performed in 12 cases. Neurorraphy was performed in 2 cases. Sural nerve grafting was performed in 21 patients, with a length range of 6-10,5 cm and 4-9 cm for closed and open trauma respectively. Conclusions. Our series confirms that repairs of traumatic CPn injuries have an unfavorable outcome. Motor recovery score ≥ M3 was obtained in only 10 cases (28,57%). Neurolysis and nerve suture show better results than nerve graft alone, although no statistically significant differences emerged; CPn reconstructions with grafts show unsatisfactory results, particularly if the length of the grafts exceeds 6 cm and when patients are treated over 6 months after the trauma. Patients with closed trauma achieve less satisfactory results than those with open injury (13 vs 58%) and this was statistically significant (p < 0.05), so palliative surgery may be indicated as the first surgical approach for these patients to achieve good foot dorsiflexion

Técnicas de ultrasonido : Una herramienta potencial para la ingeniería de tejidos

El objetivo de este trabajo es desarrollar dos montajes experimentales para la evaluación de las propiedades acústicas de hidrogeles de colágeno y para estudiar su correlación con las propiedades mecánicas. El primero permite estimar la velocidad del sonido, atenuación e impedancia acústica de las muestras manejando la temperatura. En el segundo, la configuración anterior se combina con un ensayo mecánico de compresión, lo que permite interrogar al mismo tiempo, tanto propiedades acústicas como mecánicas de la muestra. Se observan las propiedades acústicas y mecánicas de los geles de colágeno preparados de acuerdo a diferentes condiciones experimentales: pH y la concentración de colágeno. La variación de estos parámetros permite modificar las condiciones mecánicas de la matriz.Facultad de Ingenierí

Elucidation of the wettability of graphene through a multi-length-scale investigation approach

Univocal conclusions around the wettability of graphene exposed to environmental conditions remain elusive despite the recent efforts of several research groups. The main discrepancy rests on the question of whether a graphene monolayer (GML) is transparent or not to water and more generally what the role is that the substrate plays in determining the degree of wetting of the GML. In this work, we investigate the water transparency of GML by means of a multi-length-scale approach. We complement traditional static contact angle measurements and environmental scanning electron microscopy experiments with atomic force microscopy based force spectroscopy to assess the role that intermolecular interactions play in determining the wetting of GML. To gain deeper insight into the wetting transparency issue, we perform experiments on inert metals, such as gold and platinum, covered or not covered by GML. The comparison of the results obtained for different systems (i.e. GML covered and uncovered inert metals), provides unambiguous evidence that supports the non-wetting transparency theory of GML. This work aims to assist the development of technologies based on graphene-water interaction, such as graphitic membranes for water separation processes

Ion exchange and DNA molecular dip sticks: studying the nanoscale surface wetting of muscovite mica

Mica is an abundant crystal mineral that has important and interesting bulk and surface properties for a variety of applications. These properties arise from its anisotropic structure, in which layers of aluminum silicate, 1 nm thick, are ionically bonded together, typically with K+ ions. The surface properties of mica can be varied through ion exchange with the exposed lattice sites. In this study, the effect of kinetics on ion exchange with nickel ions (Ni2+) and its influence on surface water accumulation as a function of time has been investigated. Mica was ion-exchanged for 30 s or 5 min for a range of Ni2+ concentrations (i.e., 1.0-20.0 mM), and its surface properties were measured for up to 96 h after incubation in a controlled environment. The nanoscale physicochemical properties of nickel-functionalized muscovite mica (Ni-mica) were investigated by reconstructing the conservative force profile between an atomic force microscopy (AFM) tip and the surface. This information provides a hint of the surface water accumulation and enables details of the spatial and temporal variations in surface properties due to the ion-mediated adsorption of water to be elucidated. Variations in the water-layer accumulation were confirmed using noncontact AFM imaging under ambient conditions and DNA molecules as "molecular dip sticks". It was found that the surface properties were largely independent of the incubating concentration but did depend on the incubation time during ion exchange and the aging time. For the longer incubation time of 5 min, the water-layer accumulation remained constant at around ∼1.5 nm deep, whereas for the short incubation time of 30 s, the accumulation was initially subnanometer but grew with aging time and converged to a similar final value after 96 h. The extracted force of adhesion (FAD) also showed the same trends, where reduced values of FAD indicated increased screening of the van der Waals interaction through thicker water layers

Molecular Dynamics of Mesophilic-Like Mutants of a Cold-Adapted Enzyme: Insights into Distal Effects Induced by the Mutations

Networks and clusters of intramolecular interactions, as well as their “communication” across the three-dimensional architecture have a prominent role in determining protein stability and function. Special attention has been dedicated to their role in thermal adaptation. In the present contribution, seven previously experimentally characterized mutants of a cold-adapted α-amylase, featuring mesophilic-like behavior, have been investigated by multiple molecular dynamics simulations, essential dynamics and analyses of correlated motions and electrostatic interactions. Our data elucidate the molecular mechanisms underlying the ability of single and multiple mutations to globally modulate dynamic properties of the cold-adapted α-amylase, including both local and complex unpredictable distal effects. Our investigation also shows, in agreement with the experimental data, that the conversion of the cold-adapted enzyme in a warm-adapted variant cannot be completely achieved by the introduction of few mutations, also providing the rationale behind these effects. Moreover, pivotal residues, which are likely to mediate the effects induced by the mutations, have been identified from our analyses, as well as a group of suitable candidates for protein engineering. In fact, a subset of residues here identified (as an isoleucine, or networks of mesophilic-like salt bridges in the proximity of the catalytic site) should be considered, in experimental studies, to get a more efficient modification of the features of the cold-adapted enzyme

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

Protein dynamics and the underlying networks of intramolecular interactions and communicating residues within the three-dimensional (3D) structure are known to influence protein function and stability, as well as to modulate conformational changes and allostery. Acylaminoacyl peptidase (AAP) subfamily of enzymes belongs to a unique class of serine proteases, the prolyl oligopeptidase (POP) family, which has not been thoroughly investigated yet. POPs have a characteristic multidomain three-dimensional architecture with the active site at the interface of the C-terminal catalytic domain and a β-propeller domain, whose N-terminal region acts as a bridge to the hydrolase domain. In the present contribution, protein dynamics signatures of a hyperthermophilic acylaminoacyl peptidase (AAP) of the prolyl oligopeptidase (POP) family, as well as of a deletion variant and alanine mutants (I12A, V13A, V16A, L19A, I20A) are reported. In particular, we aimed at identifying crucial residues for long range communications to the catalytic site or promoting the conformational changes to switch from closed to open ApAAP conformations. Our investigation shows that the N-terminal α1-helix mediates structural intramolecular communication to the catalytic site, concurring to the maintenance of a proper functional architecture of the catalytic triad. Main determinants of the effects induced by α1-helix are a subset of hydrophobic residues (V16, L19 and I20). Moreover, a subset of residues characterized by relevant interaction networks or coupled motions have been identified, which are likely to modulate the conformational properties at the interdomain interface

Machine Learning Techniques for Personality-Based Multimedia Recommender Systems

An individual’s personality can be defined as the set of attributes, feelings, and ways of thinking that, in combination, make her unique [2]. The most widely used model to represent it is the five-factor model [3], a multifactorial approach so named for considering the people’s personality consisting of five traits: Openness (to experience), Conscientiousness, Extraversion, Agreeableness, and Neuroticism (the acronym OCEAN is often adopted). The reason why such a model is so widespread also lies in its suitability for being quantitatively measured (i.e., numerical values for each of the factors). Recommender systems help online users find relevant content by suggesting items (i.e., products and services) of potential interest to them [5]. Numerous studies (see, for instance, [1,4,7]) have shown that taking into account the target user’s personality in the recommendation process can provide significant benefits in terms of performance. Our research activities focused on the study of the correlation between (a) visual features of high and low level extracted from images [6] and video [8] and (b) users’ psychometric traits, in order to produce personalized suggestions for mitigating the multimedia information overload. In this talk, we will present our experience and learned lessons in harnessing machine learning techniques (support vector machines, convolutional neural networks, regression techniques, etc.) for this task