Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein.

One of the entry mechanisms of the SARS-CoV-2 coronavirus into host cells involves endosomal acidification. It has been proposed that under acidic conditions, the fusion peptide proximal region (FPPR) of the SARS-CoV-2 spike glycoprotein acts as a pH-dependent switch, modulating immune response accessibility by influencing the positioning of the receptor binding domain (RBD). This would provide indirect coupling of RBD opening to the environmental pH.

[Effectiveness of physical rehabilitation methods based on the impact of eccentric load in upper limb injuries].

Unlabelled: The rehabilitation of patients after upper limb injuries is becoming increasingly relevant in current medical practice considering that this pathology is often occurred in professional athletes, elderly people, people with active lifestyle.

Objective: To study the effectiveness of isolated therapeutic exercises (TE) with eccentric muscle loads when using rubber cable compared to traditional TE to restore functional capabilities of patients after upper limb injuries.

Material And Methods: The study included 38 patients with upper limb injuries diagnosed by orthopedic surgeon.

MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction.

The precise prediction of major histocompatibility complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold's capabilities by fine-tuning it with a specialized dataset consisting of exclusively high-resolution class I MHC-peptide crystal structures. This tailored approach aimed to address the generalist nature of AlphaFold's original training, which, while broad-ranging, lacked the granularity necessary for the high-precision demands of class I MHC-peptide interaction prediction.

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.

The precise prediction of Major Histocompatibility Complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold's capabilities by fine-tuning it with a specialized dataset comprised by exclusively high-resolution MHC-peptide crystal structures. This tailored approach aimed to address the generalist nature of AlphaFold's original training, which, while broad-ranging, lacked the granularity necessary for the high-precision demands of MHC-peptide interaction prediction.

SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein.

In this application note, we describe a tool which we developed to help structural biologists who study the SARS-CoV-2 spike glycoprotein. There are more than 500 structures of this protein available in the Protein Data Bank. These structures are available in different flavors: wild type spike, different variants, 2P substitutions, structures with bound antibodies, structures with Receptor Binding Domains (RBD) in closed or open conformation, etc.

Search and Localization Dynamics of the CRISPR-Cas9 System.

The CRISPR-Cas9 system acts as the prokaryotic immune system and has important applications in gene editing. The protein Cas9 is one of its crucial components. The role of Cas9 is to search for specific target sequences on the DNA and cleave them.

Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket.

The SARS-CoV-2 coronavirus is an enveloped, positive-sense single-stranded RNA virus that is responsible for the COVID-19 pandemic. The spike is a class I viral fusion glycoprotein that extends from the viral surface and is responsible for viral entry into the host cell and is the primary target of neutralizing antibodies. The receptor binding domain (RBD) of the spike samples multiple conformations in a compromise between evading immune recognition and searching for the host-cell surface receptor.

Naturally safe: Cellular noise for document security.

Modern document protection relies on the simultaneous combination of many optical features with micron and submicron structures, whose complexity is the main obstacle for unauthorized copying. In that sense, documents are best protected by the diffractive optical elements generated lithographically and mass-produced by embossing. The problem is that the resulting security elements are identical, facilitating mass-production of both original and counterfeited documents.

Effective spin Hamiltonian of a gated triple quantum dot in the presence of spin-orbit interaction.

We derive and study the effective spin Hamiltonian of a gated triple quantum dot that includes the effects of spin-orbit interaction and an external magnetic field. In the analysis of the resulting spin interaction in linear and in general triangular geometry of the dots, we show that the pairwise spin interaction does depend on the position of the third dot. The spin-orbit induced anisotropy, in addition to changing its strength, also changes its symmetry with the motion of the third quantum dot outside the linear arrangement.

Development and study of novel non-contact ultrasonic motor based on principle of structural asymmetry.

The article presents novel design of non-contact rotary ultrasonic motor consisting of ring-shaped stator vibrating in in-plane flexural mode and rotor provided with blades. In contrast to other motors with similar design proposed motor relies on the use of standing ultrasonic waves. This simplifies design and electronic control of motor and becomes possible due to introduction of artificial asymmetry, for example by tilting one or several blades of the rotor relative to the surface normal.

Modeling of flexible waveguides for ultrasonic vibrations transmission: longitudinal and flexural vibrations of non-deformed waveguide.

The article presents the mathematical model allowing to investigate longitudinal and flexural vibrations of stepped flexible waveguides with transitional section without regard to various vibration modes interaction. The model uses original numerical-analytic calculations based on analytical solutions of the equation of waveguide steps vibrations and their continuous matching with numerical solution of the equation of transitional section vibrations. The proposed model can be considered as an initial approximation to the solution of the problem of flexible waveguides design, which makes it possible to determine and validate effective methods of its addressing.

Spin-electric coupling in molecular magnets.

We study the triangular antiferromagnet Cu3 in external electric fields, using symmetry group arguments and a Hubbard model approach. We identify a spin-electric coupling caused by an interplay between spin exchange, spin-orbit interaction, and the chirality of the underlying spin texture of the molecular magnet. This coupling allows for the electric control of the spin (qubit) states, e.

Enhancement of electron spin coherence by optical preparation of nuclear spins.

We study a large ensemble of nuclear spins interacting with a single electron spin in a quantum dot under optical excitation and photon detection. At the two-photon resonance between the two electron-spin states, the detection of light scattering from the intermediate exciton state acts as a weak quantum measurement of the effective magnetic (Overhauser) field due to the nuclear spins. In a coherent population trapping state without light scattering, the nuclear state is projected into an eigenstate of the Overhauser field operator, and electron decoherence due to nuclear spins is suppressed: We show that this limit can be approached by adapting the driving frequencies when a photon is detected.

Universal quantum computation through control of spin-orbit coupling.

We propose a method for quantum computation which uses control of spin-orbit coupling in a linear array of single electron quantum dots. Quantum gates are carried out by pulsing the exchange interaction between neighboring electron spins, including the anisotropic corrections due to spin-orbit coupling. Control over these corrections, even if limited, is sufficient for universal quantum computation over qubits encoded into pairs of electron spins.

Anisotropic spin exchange in pulsed quantum gates.

We show how to eliminate the first-order effects of the spin-orbit interaction in the performance of a two-qubit quantum gate. Our procedure involves tailoring the time dependence of the coupling between neighboring spins. We derive an effective Hamiltonian which permits a systematic analysis of this tailoring.