Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data

Electrostatic Screening Modulates Analyte Binding and Emission of Carbon Nanotubes

Many nanomaterials are promising biosensor elements due to capabilities for transduction of biomolecular interactions into an electrical or optical signal. Certain nanomaterials have intrinsic charges and are thus susceptible to electrostatic forces that may enhance or attenuate their response. Here, using a combination of experimental and computational approaches, we found and characterized a critical role of the solvent salt conditions in determining the extent of optical changes due to anionic analyte interaction with an intrinsically responsive nanomaterial, single-walled carbon nanotubes. Using a well-characterized model anionic analyte, we found that monovalent salts enabled greater optical changes of a polyanion-bound carbon nanotube in a highly dose-dependent manner but not with a neutrally charged analyte. Molecular dynamics simulations were used to derive a quantitative understanding of this mechanism from a free-energy perspective. We also show that salt can be used to enhance the sensitivity of detection for a polyanionic analyte. These results suggest that electrostatic screening is an important parameter for intrinsically charged nanoparticle sensors and it may be tuned to control the response to analytes

Observation of Conductance Quantization in InSb Nanowire Networks

Majorana zero modes (MZMs) are prime candidates for robust topological quantum bits, holding a great promise for quantum computing. Semiconducting nanowires with strong spin orbit coupling offer a promising platform to harness one-dimensional electron transport for Majorana physics. Demonstrating the topological nature of MZMs relies on braiding, accomplished by moving MZMs around each other in a certain sequence. Most of the proposed Majorana braiding circuits require nanowire networks with minimal disorder. Here, the electronic transport across a junction between two merged InSb nanowires is studied to investigate how disordered these nanowire networks are. Conductance quantization plateaus are observed in most of the contact pairs of the epitaxial InSb nanowire networks: the hallmark of ballistic transport behavior

Effect of the Substitution Pattern (Peripheral vs Non-Peripheral) on the Spectroscopic, Electrochemical, and Magnetic Properties of Octahexylsulfanyl Copper Phthalocyanines

In order to investigate the substitution position effect on the spectroscopic, electrochemical, and magnetic properties of copper phthalocyanines, a detailed structure–property analysis has been performed by examining two copper phthalocyanines that are octasubstituted by hexylsulfanyl chains respectively in the peripheral (<b>Cu-P</b>) and non-peripheral (<b>Cu-NP</b>) positions. <b>Cu-NP</b> showed a marked near-IR maximum absorption compared to <b>Cu-P</b> and, accordingly, a smaller HOMO–LUMO energy gap, calculated via the electrochemical results and simulations in the gas phase, as well as for <b>Cu-NP</b> from its crystallographic data. An electron-spin resonance (ESR) technique is used to extract the <i>g</i> values from the powder spectra that are taken at room temperature. The <i>g</i> values were determined to be <i>g</i>_∥ = 2.160 and <i>g</i>_⊥ = 2.045 for <b>Cu-P</b> and <i>g</i>_∥ = 2.150 and <i>g</i>_⊥ = 2.050 for <b>Cu-NP</b>. These values indicate that the paramagnetic copper center in both phthalocyanines has axial symmetry with a planar anisotropy (<i>g</i>_∥ > <i>g</i>_⊥). The ESR spectra in solution could be obtained only for <b>Cu-P</b>. Curie law is used to fit the experimental data of the magnetic susceptibility versus temperature graphs, and the Curie constant (<i>C</i>) and diamagnetic/temperature-independent paramagnetic (α) contributions are deduced as 0.37598 (0.39576) cm³·K/mol and −23 × 10^–5 (25 × 10^–5) cm³/mol respectively for <b>Cu-P</b> and <b>Cu-NP</b>. The room temperature magnetic moment value (1.70 μ_B) is close to the spin-only value (1.73 μ_B) for the peripheral complex, showing that there is no orbital contribution to μ_eff. In contrast, at room temperature, the value of the magnetic moment (1.77 μ_B) is above the spin-only value, showing an orbital contribution to the magnetic moment. <b>Cu-NP</b>’s room temperature magnetic moment value is larger than the value for <b>Cu-P</b>, demonstrating that the orbital contribution to the magnetic moment depends upon the substituent position. The magnitudes of the effective magnetic moment values also support that both <b>Cu-P</b> and <b>Cu-NP</b> complexes have square-planar coordination. This result is consistent with the determined <i>g</i> values. The spin densities were determined experimentally, and the results suggest that the positions of the substituents affect these values (0.469 for <b>Cu-P</b> and 0.490 for <b>Cu-NP</b>)

InSb Nanowires with Built-In Ga_<i>x</i>In_1–<i>x</i>Sb Tunnel Barriers for Majorana Devices

Majorana zero modes (MZMs), prime candidates for topological quantum bits, are detected as zero bias conductance peaks (ZBPs) in tunneling spectroscopy measurements. Implementation of a narrow and high tunnel barrier in the next generation of Majorana devices can help to achieve the theoretically predicted quantized height of the ZBP. We propose a material-oriented approach to engineer a sharp and narrow tunnel barrier by synthesizing a thin axial segment of Ga_<i>x</i>In_1–<i>x</i>Sb within an InSb nanowire. By varying the precursor molar fraction and the growth time, we accurately control the composition and the length of the barriers. The height and the width of the Ga_<i>x</i>In_1–<i>x</i>Sb tunnel barrier are extracted from the Wentzel–Kramers-Brillouin (WKB) fits to the experimental <i>I</i>–<i>V</i> traces

New records of rare species in the Mediterranean Sea 2020

This Collective Article presents information about 17 taxa belonging to four Phyla (one Cnidaria, two Arthropo da, four Mollusca, and ten Chordata) and extending from the Western Mediterranean to the Levantine Sea. The new records were reported from nine countries as follows: Algeria: first published records of the clingfishes Apletodon dentatus and Lepadogaster lepadogaster after 1955; France: first record of the tripletail Lobotes surinamensis in French Mediterranean waters; Italy: new records of the rare bonito Orcynopsis unicolor and the recently described nudibranch Elysia rubeni from Sicily; first records of the parasitic cirriped Sacculina eriphiae and the nudibranch Dondice trainitoi in the Ionian Sea; first record of the nudibranch Taringa tritorquis in the Mediterranean Sea; first record of the tripletail Lobotes surinamensis in the North Ionian Sea; first documented record of the cephalopod Macrotritopus defilippi in the Adriatic Sea; Slovenia: first record of the Mediterranean endemic cryptobenthic goby Odondebuenia balearica; Montenegro: several recent occurrences of the critically endangered bull ray Aetomylaeus bovinus in the South-eastern Adriatic Sea; Greece: records of the nudibranch Dondice trainitoi in the Eastern Medi terranean Sea; new record of the occurrence of the Mediterranean spearfish Tetrapturus belone from Greece (Rhodes Island); Turkey: recent captures of the vulnerable ocean sunfish Mola mola, caught by purse-seine, in the Aegean Sea and the Dardanelles; new record of the luvar Luvarus imperialis along the Aegean coast of Turke

Technical Aspects and Clinical Limitations of Sperm DNA Fragmentation Testing in Male Infertility: A Global Survey, Current Guidelines, and Expert Recommendations

Purpose: Sperm DNA fragmentation (SDF) is a functional sperm abnormality that can impact reproductive potential, for which four assays have been described in the recently published sixth edition of the WHO laboratory manual for the examination and processing of human semen. The purpose of this study was to examine the global practices related to the use of SDF assays and investigate the barriers and limitations that clinicians face in incorporating these tests into their practice. Materials and methods: Clinicians managing male infertility were invited to complete an online survey on practices related to SDF diagnostic and treatment approaches. Their responses related to the technical aspects of SDF testing, current professional society guidelines, and the literature were used to generate expert recommendations via the Delphi method. Finally, challenges related to SDF that the clinicians encounter in their daily practice were captured. Results: The survey was completed by 436 reproductive clinicians. Overall, terminal deoxynucleotidyl transferase deoxyuridine triphosphate Nick-End Labeling (TUNEL) is the most commonly used assay chosen by 28.6%, followed by the sperm chromatin structure assay (24.1%), and the sperm chromatin dispersion (19.1%). The choice of the assay was largely influenced by availability (70% of respondents). A threshold of 30% was the most selected cut-off value for elevated SDF by 33.7% of clinicians. Of respondents, 53.6% recommend SDF testing after 3 to 5 days of abstinence. Although 75.3% believe SDF testing can provide an explanation for many unknown causes of infertility, the main limiting factors selected by respondents are a lack of professional society guideline recommendations (62.7%) and an absence of globally accepted references for SDF interpretation (50.3%). Conclusions: This study represents the largest global survey on the technical aspects of SDF testing as well as the barriers encountered by clinicians. Unified global recommendations regarding clinician implementation and standard laboratory interpretation of SDF testing are crucial