Nanoscale Interplay of Membrane Composition and Amyloid Self-Assembly.

Cell membranes are complex assemblies of lipids and proteins exhibiting lipid compositional heterogeneity between the inner and outer leaflets of the bilayer. Aberrant protein aggregation, implicated in a number of neurodegenerative diseases including Alzheimer's, is known to result in both extracellular and intracellular deposits with divergent pathophysiological effects. Mounting evidence substantiates membrane-mediated amyloid effects and indicates membrane composition, particularly gangliosides, as a plausible factor influencing the fibrillation process.

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units.

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g.

Structural Basis of the Potential Binding Mechanism of Remdesivir to SARS-CoV-2 RNA-Dependent RNA Polymerase.

Starting from late 2019, the coronavirus disease 2019 (COVID-19) has emerged as a once-in-a-century pandemic with deadly consequences, which urgently calls for new treatments, cures, and supporting apparatuses. Recently, because of its positive results in clinical trials, remdesivir was approved by the Food and Drug Administration to treat COVID-19 through Emergency Use Authorization. Here, we used molecular dynamics simulations and free energy perturbation methods to study the inhibition mechanism of remdesivir to its target SARS-CoV-2 virus RNA-dependent RNA polymerase (RdRp).

HIV-1 induced changes in HLA-C*03 : 04-presented peptide repertoires lead to reduced engagement of inhibitory natural killer cell receptors.

Objective: Viral infections influence intracellular peptide repertoires available for presentation by HLA-I. Alterations in HLA-I/peptide complexes can modulate binding of killer immunoglobuline-like receptors (KIRs) and thereby the function of natural killer (NK) cells. Although multiple studies have provided evidence that HLA-I/KIR interactions play a role in HIV-1 disease progression, the consequence of HIV-1 infection for HLA-I/KIR interactions remain largely unknown.

Tungsten Oxide Nanodots Exhibit Mild Interactions with WW and SH3 Modular Protein Domains.

Tungsten oxide nanodot (WO ) is an active photothermal nanomaterial that has recently been discovered as a promising candidate for tumor theranostics and treatments. However, its potential cytotoxicity remains elusive and needs to be evaluated to assess its biosafety risks. Herein, we investigate the interactions between WO and two ubiquitous protein domains involved in protein-protein interactions, namely, WW and SH3 domains, using atomistic molecular dynamics simulations.

Precise pitch-scaling of carbon nanotube arrays within three-dimensional DNA nanotrenches.

Precise fabrication of semiconducting carbon nanotubes (CNTs) into densely aligned evenly spaced arrays is required for ultrascaled technology nodes. We report the precise scaling of inter-CNT pitch using a supramolecular assembly method called spatially hindered integration of nanotube electronics. Specifically, by using DNA brick crystal-based nanotrenches to align DNA-wrapped CNTs through DNA hybridization, we constructed parallel CNT arrays with a uniform pitch as small as 10.

Fermionic neural-network states for ab-initio electronic structure.

Neural-network quantum states have been successfully used to study a variety of lattice and continuous-space problems. Despite a great deal of general methodological developments, representing fermionic matter is however still early research activity. Here we present an extension of neural-network quantum states to model interacting fermionic problems.

Length-Dependent Structural Transformations of Huntingtin PolyQ Domain Upon Binding to 2D-Nanomaterials.

There is a strong negative correlation between the polyglutamine (polyQ) domain length (Q-length) in the intrinsically disordered Huntingtin protein (Htt) exon-1 and the age of onset of Huntington's disease (HD). PolyQ of Q-length longer than 40 has the propensity of forming very compact aggregate structures, leading to HD at full penetrance. Recent advances in nanobiotechnology provided a new platform for the development of novel diagnosis and therapeutics.

Combining Social Media and FDA Adverse Event Reporting System to Detect Adverse Drug Reactions.

Introduction: Adverse drug reactions (ADRs) are unintended reactions caused by a drug or combination of drugs taken by a patient. The current safety surveillance system relies on spontaneous reporting systems (SRSs) and more recently on observational health data; however, ADR detection may be delayed and lack geographic diversity. The broad scope of social media conversations, such as those on Twitter, can include health-related topics.

Commensal bacteria stimulate antitumor responses via T cell cross-reactivity.

Recent studies show gut microbiota modulate antitumor immune responses; one proposed mechanism is cross-reactivity between antigens expressed in commensal bacteria and neoepitopes. We found that T cells targeting an epitope called SVYRYYGL (SVY), expressed in the commensal bacterium Bifidobacterium breve (B. breve), cross-react with a model neoantigen, SIYRYYGL (SIY).

Binding patterns and dynamics of double-stranded DNA on the phosphorene surface.

Phosphorene, a monolayer of black phosphorus, has emerged as one of the most promising two-dimensional (2D) nanomaterials for various applications in the post-graphene-discovery period due to its highly anisotropic structure and novel properties. In order to apply phosphorene in biomedical fields, it is crucial to understand how it interacts with biomolecules. Herein, we use both molecular dynamics (MD) simulations and experimental techniques to investigate the interactions of phosphorene with a dsDNA segment.

Loss of nucleus accumbens low-frequency fluctuations is a signature of chronic pain.

Chronic pain is a highly prevalent disease with poorly understood pathophysiology. In particular, the brain mechanisms mediating the transition from acute to chronic pain remain largely unknown. Here, we identify a subcortical signature of back pain.

Quantum orbital-optimized unitary coupled cluster methods in the strongly correlated regime: Can quantum algorithms outperform their classical equivalents?

The Coupled Cluster (CC) method is used to compute the electronic correlation energy in atoms and molecules and often leads to highly accurate results. However, due to its single-reference nature, standard CC in its projected form fails to describe quantum states characterized by strong electronic correlations and multi-reference projective methods become necessary. On the other hand, quantum algorithms for the solution of many-electron problems have also emerged recently.

In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers.

Nucleic acid aptamers hold great promise for therapeutic applications due to their favorable intrinsic properties, as well as high-throughput experimental selection techniques. Despite the utility of the systematic evolution of ligands by the exponential enrichment (SELEX) method for aptamer determination, complementary in silico aptamer design is highly sought after to facilitate virtual screening and increased understanding of important nucleic acid-protein interactions. Here, with a combined experimental and theoretical approach, we have developed two optimal epithelial cellular adhesion molecule (EpCAM) aptamers.

Graphene-extracted membrane lipids facilitate the activation of integrin αβ.

Despite the remarkable electrochemical properties of graphene, strong van der Waals attraction between graphene and biomolecules often causes cytotoxicity, which hinders its applications in the biomedical field. Unfortunately, surface passivation of graphene might stimulate undesired immune response as the nanomaterial triggers cytokine production through membrane receptor activation. Herein, we use all-atom Molecular Dynamics (MD) simulations to unravel the underlying mechanism of graphene-induced inside-out activation of integrin αβ, a prominent membrane receptor expressed in immune cells.

A future for neuronal oscillation research.

Neuronal oscillations represent the most obvious feature of electrical activity in the brain. They are linked in general with global brain state (awake, asleep, etc.) and specifically with organisation of neuronal outputs during sensory perception and cognitive processing.

A Porous Aromatic Framework Functionalized with Luminescent Iridium(III) Organometallic Complexes for Turn-On Sensing of TcO.

Contamination of TcO, a problematic radioactive anion in the nuclear fuel cycle, in groundwater has been observed in a series of legacy nuclear sites, representing a notable radiation hazard and environmental concern. The development of convenient, rapid, and sensitive detection methods is therefore critical for radioactivity control and remediation tasks. Traditional detection methods suffer from clear demerits of either the presence of large interference from coexisting radioactive species (e.

Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms.

Importance: Mammography screening currently relies on subjective human interpretation. Artificial intelligence (AI) advances could be used to increase mammography screening accuracy by reducing missed cancers and false positives.

Objective: To evaluate whether AI can overcome human mammography interpretation limitations with a rigorous, unbiased evaluation of machine learning algorithms.

Stabilization of Open-Shell Single Bonds within Endohedral Metallofullerene.

The open-shell single covalent bond composed of two electrons is unstable under normal conditions, because the closed-shell electronic configuration is generally beneficial to minimize the energy of the system. This classical rule always governs the chemical bonding of s- and p-block homonuclear diatomic molecules, such as the stable σ electron-pair bonds in hydrogen. In this work, surprisingly, we found that the diversified open-shell single bonds between two f-block atoms (e.

Universal approximation with quadratic deep networks.

Recently, deep learning has achieved huge successes in many important applications. In our previous studies, we proposed quadratic/second-order neurons and deep quadratic neural networks. In a quadratic neuron, the inner product of a vector of data and the corresponding weights in a conventional neuron is replaced with a quadratic function.

Directional extraction and penetration of phosphorene nanosheets to cell membranes.

Recently, phosphorene, a novel two-dimensional nanomaterial with a puckered surface morphology, was shown to exhibit cytotoxicity, but its underlying molecular mechanisms remain unknown. Herein, using large scale molecular dynamics simulations, we show that phosphorene nanosheets can penetrate into and extract large amounts of phospholipids from the cell membranes due to the strong dispersion interaction between phosphorene and lipid molecules, which would reduce cell viability. The extracted phospholipid molecules are aligned along the wrinkle direction of the phosphorene nanosheet because of its unique puckered structure.

Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg Ion Bound at the Double Mg-Clamp Structure.

It has been known that the binding of two Mg ions to the phosphate groups of RNA is essential for enhancing the stability of a three-way junction oligomeric prohead RNA (3WJ-pRNA). Here, we investigate the coupling between binding of two Mg ions and the stability of the complex structure by calculating the rupture force of 3WJ-pRNA using steered molecular dynamics simulations. Our simulations showed that the mechanical stability of the pRNA structure is largely retained with a single Mg ion bound.

Author Correction: Single-trial classification of awareness state during anesthesia by measuring critical dynamics of global brain activity.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Different platinum crystal surfaces show very distinct protein denaturation capabilities.

Different platinum (Pt) surfaces of nanocrystals usually exhibit significant distinctions with regard to various biological, physical, and chemical characteristics, such as bio-recognition, surface wetting, and catalytic activities. In this study, we report for the first time that two shape-controlled Pt nanocrystals with the most common low-index surfaces, Pt(100) and Pt(111), show very dissimilar protein denaturation capabilities based on all-atom molecular dynamics simulations employing the widely used model protein, villin headpiece (HP35). We demonstrate that HP35 is well preserved on the Pt(100) crystal surface, whereas it is severely disrupted on the Pt(111) crystal surface.

Surface Inhomogeneity of Graphene Oxide Influences Dissociation of Aβ Peptide Assembly.

Abnormal peptide assembly and aggregation is associated with an array of neurodegenerative diseases including Alzheimer's disease (AD). A detailed understanding of how nanostructured materials such as oxidized graphene perturb the peptide assembly and subsequently induce fibril dissociation may open new directions for the development of potential AD treatments. Here, we investigate the impact of surface inhomogeneity of graphene oxide (GO) on the assembly of amyloid-beta Aβ peptides on GO surfaces with different degrees of oxidation using molecular dynamics simulations.