The DNA molecule consists of chains of nucleotides that, under physiological conditions, are bound by hydrogen bonds and form a double helix. The nitrogenous bases are located inside the helix, whereas the phosphate groups are exposed to the surrounding aqueous environment. This structural organization arises from the hydrophobic nature of the bases and the hydrophilic character of the...
Guanine-rich nucleic acid sequences can fold into G-quadruplexes (GQs), noncanonical DNA structures stabilized by stacked G-tetrads and monovalent cations, which play important roles in genome regulation and are widely investigated as drug targets. Despite extensive experimental and computational work, predicting G-quadruplex stability and ligand-induced stabilization remains difficult....
Measures to combat SARS-CoV-2 infection include the development of antiviral agents as well as the repurposing of existing drugs targeting key stages of the viral life cycle. Viral entry occurs through the interaction of the spike protein with host cell receptors and its subsequent proteolytic activation by host proteases. Identification of host cellular factors exploited during viral entry,...
Cell sorting is a fundamental process in biology and biotechnology that enables the separation of heterogeneous cell populations based on their intrinsic properties. Among the various sorting strategies, affinity-based approaches exploit differences in cell-surface interactions to achieve selective cell attachment and detachment. Micropatterned adhesive surfaces provide a means to tune these...
Protein aggregation refers to the process by which fully or partially unfolded proteins self-associate to make large and insoluble aggregates. Amyloid fibrils - a prominent example of the aggregates, is implicated in various neurodegenertive diseases and also has found multiple uses in technology. In this talk we will focus on what can be learned about amyloid formation using theoretical...
The human civilization runs on rotary motors, from cars to planes, from conveyer belts to power generators, from pumps to ice cream mixers. Surprisingly, very few examples of rotary motors exist at the nanoscale. This lecture will highlight our recent efforts to develop such nanoscale electro-motors using DNA as a building material. First, I will show that a single DNA duplex can itself acts...
Biopolymers demonstrate unique physical properties and are widely used in modern nanotechnologies long molecular bridges in Donor – Acceptor systems. There are numerous experimental evidences of the long-range electron transport in such systems.
Here we show that the mechanism of the long-range transport can be based on the soliton formation in biopolymers. It is shown that there exists a...
arious spectral methods-optical and vibrational spectroscopy, mass spectroscopy, luminescence, NMR, Х-ray etc.- play a key role in analytical and prognostic research in various fields of science, industry, and medicine.In this report, we will focus on vibrational spectroscopy, its linear (IR, Raman) and nonlinear (CARS, SFG) methods, and a new method - surface-enhanced spectroscopy...
In this work, we have successfully dispersed MoS2 in aqueous solutions of canonical nucleotides (dAMP, or dGMP, or dCMP, or UMP) by ultrasound-assisted exfoliation. We report the first observation of visible-range photoluminescence (PL) registered from all suspensions, which we attribute to the presence of MoS2 quantum dots (QDs) in the suspensions. The comparison of PL band intensity, peak...
Quantum programming fundamentally differs from classical programming, as it is based on using the properties of quantum systems in computing. Nowadays, quantum algorithms have been developed to solve a variety of fundamental and applied problems. It is expected that, with the advancement of quantum computing, quantum algorithms will outperform classical ones for a wide range of tasks.
Quantum...
After a brief introduction about the quantum 20 th century, and about the year of 2025 as the international year of quantum theory and quantum technology, according to the United Nations resolution, we begin to discuss the impact of the former and its two key narratives – the observer and the measurement - on quantum chemistry and its core concepts: the bond, localization and delocalization....
Affinity-based cell sorting on microstructured substrates offers a label-free route for separating heterogeneous cell populations based on differences in cell-surface interactions. In such systems, the efficiency of separation is controlled by the spatial distribution of adhesive regions together with the possibility of externally induced switching between adsorbing and desorbing surface...
Protein aggregation refers to the process by which fully or partially unfolded proteins self-associate to make large and insoluble aggregates. Amyloid fibrils - a prominent example of the aggregates, is implicated in various neurodegenertive diseases and also has found multiple uses in technology. In this talk we will focus on what can be learned about amyloid formation using theoretical...
Guanine-rich nucleic acid sequences can fold into G-quadruplexes (GQs), noncanonical DNA structures stabilized by stacked G-tetrads and monovalent cations, which play important roles in genome regulation and are widely investigated as drug targets. Despite extensive experimental and computational work, predicting G-quadruplex stability and ligand-induced stabilization remains difficult....
Modeling of formation of primary organic molecules in the course of prebiological biochemical evolution usually deals with assembling of H, C, O, N, S chemical elements. However, biomolecules of such importance as enzymes incorporate metal atoms. These could get into the structure of evolving organic molecules through direct contact with early Earth’s minerals. This step of biochemical...
Charge transport accompanies redox processes in respiration, and involves electron transport chain in Krebbs cycle. Some stages of this transport occur in polypeptide macromolecules which support the formation of bound nonlinear electron states in the form of solitons formed due to relatively strong electron-lattice interaction in hydrogen-bonded polypeptide chains [1]. As an external magnetic...
Quantum programming fundamentally differs from classical programming, as it is based on using the properties of quantum systems in computing. Nowadays, quantum algorithms have been developed to solve a variety of fundamental and applied problems. It is expected that, with the advancement of quantum computing, quantum algorithms will outperform classical ones for a wide range of tasks.
Quantum...
The development of effective new bionanomaterials for targeted drug delivery is one of the most pressing applied problems of modern nanoscience and nanotechnologies for biomedical applications. The contributions of computational biophysics, as well as combined experimental and theoretical nanobiophysical research, to the study of intermolecular interactions between nanocarriers and therapeutic...
Excessive concentration of the low density lipoproteins (LDLs) in blood increases the risk of cardiovascular diseases. One of the strategies to reduce its contents is the hemoperfusion therapy, when LDLs are selectively retracted by an external adsorber located outside the patient body. Recently, a photo-controllable smart surface was developed characterized by high selectivity and repeated...
We consider a generalized lattice model describing adsorption of dispersed obstacles on a set of branched polymer structures. There is a strong experimental evidence that branched adsorbents could be essentially more efficient than their linear counterparts. We focus on two the simplest
representatives of the core-shell branched architectures: the star-like (with zero-dimensional point-like...
The human civilization runs on rotary motors, from cars to planes, from conveyer belts to power generators, from pumps to ice cream mixers. Surprisingly, very few examples of rotary motors exist at the nanoscale. This lecture will highlight our recent efforts to develop such nanoscale electro-motors using DNA as a building material. First, I will show that a single DNA duplex can itself acts...
Dried films of biofluids and biopolymer solutions are a promising object for querying the state of biomolecules and their interactions with biologically active substances, without requiring complex and expensive equipment. Particularly for express diagnostics, it is important that the resulting textures and patterns can be analyzed with relatively little time and effort. Changes in "zigzag"...
A promising approach that can provide minimally invasive treatment, in particular, of malignant tumours located both in soft tissues and in hard-to-reach areas of the body (e.g., in the cranial cavity), is the implementation of the principles of the latest scientific and practical interdisciplinary direction – X-ray excited photodynamic therapy (XE-PDT), in which X-rays are used to activate...
Now in Ukraine with huge artillery shelling and missile attacks, a large amount of pollution consisting of carbon particles with heavy metals-iron, copper etc. and remains of organic molecules are formed. This is why modeling these particles and collecting them is important for understanding how they affect human health. Here the data on physical, chemical and neuroactive properties of the...
During the transformation of a tumor cell into a metastatic cell, a number of radical transformations occur, in which changes in mechanical properties play a key role, in particular, the loss of epithelial intercellular contacts, cytoskeletal reorganization, cell shape change, and a series of events that include the crossing of barriers. So, the mechanical properties of the cell membrane...
The relevance of studies on π-conjugated molecular systems is determined by their wide application in modern organic electronics, photonics, sensing, and biomedical technologies. Quantum-mechanical calculations make it possible to predict the geometric, electronic, and spectral properties of π-conjugated molecules and their complexes with nanostructures at the stage of material design. This...
The DNA molecule consists of chains of nucleotides that, under physiological conditions, are bound by hydrogen bonds and form a double helix. The nitrogenous bases are located inside the helix, whereas the phosphate groups are exposed to the surrounding aqueous environment. This structural organization arises from the hydrophobic nature of the bases and the hydrophilic character of the...
One of the promising objects for the creation of new functional materials is the metallized DNA molecule. Such a system is a unique combination of the biopolymer matrix of DNA and the properties of metal ions, in particular Ag+. The presence of intercalated Ag+ ions in the DNA structure provides the possibility of forming one-dimensional nanostructures in the form of...
Measures to combat SARS-CoV-2 infection include the development of antiviral agents as well as the repurposing of existing drugs targeting key stages of the viral life cycle. Viral entry occurs through the interaction of the spike protein with host cell receptors and its subsequent proteolytic activation by host proteases. Identification of host cellular factors exploited during viral entry,...
TMPRSS2 (transmembrane serine protease 2) is a key protein involved in SARS-CoV-2 entry into host cells by participating in membrane fusion. Therefore, TMPRSS2 represents a promising therapeutic target with a lower risk of resistance development as a host factor compared to viral proteins.
In this study, the in silico investigation was conducted to evaluate the possibility of interaction...
Computational prediction of small-molecule binding to protein targets has been central to drug discovery for decades, yet conventional physics-based docking methods have largely reached a performance plateau. Machine learning (ML)-based alternatives offer a promising shift, though concerns about prediction quality, chemical plausibility of generated poses, and the lack of rigorous evaluation...
A detailed study of the collective behavior of the lipid bilayer in the presence of peripheral proteins is essential for understanding the molecular signaling processes that occur on membranes. The N75K mutation of the neuronal Ca2+ sensor protein hippocalcin, which is partially embedded in the inner layer of the plasmatic membrane, leads to the development of a severe disease, primary...
The mechanical response of DNA to external forces reveals several anomalous features, including the coupling between twisting and stretching and the unusually large deformation of specific sequence motifs. In this work, I present a theoretical model that incorporates both classical deformation modes of the DNA double helix (stretching, bending and twisting) and an internal conformational...
Tryptophan fluorescence is one of the most widely used intrinsic probes of protein conformational dynamics, as the emission wavelength of a tryptophan residue is sensitive to its local environment. Although a red shift of the emission maximum is conventionally interpreted as an increase in solvent exposure of the indole ring, such interpretation may not always hold, particularly for...
Interactions between nucleotides, biologically active polyphenols, and metal ions play an important role in biochemical processes and molecular recognition in living systems. Adenosine triphosphate (ATP) is a key molecule involved in cellular energy metabolism, while curcumin, a natural polyphenolic compound derived from Curcuma longa, exhibits pronounced antioxidant, anti-inflammatory, and...
The development of efficient drug delivery systems is an important direction in modern biomedical research. Protein carriers are widely investigated as platforms capable of improving the stability, solubility, and targeted delivery of biologically active compounds. One such protein is CRM197, a non-toxic mutant of diphtheria toxin that retains receptor-binding ability while lacking enzymatic...
Protein-based therapeutics represent an important class of modern biopharmaceutical agents due to their high specificity and ability to regulate biological processes. One such molecule is the cytokine Endothelial Monocyte-Activating Polypeptide II (EMAPII), which exhibits antiangiogenic, proapoptotic, and immunomodulatory activity. However, its biomedical application is limited by aggregation...
Quantum programming fundamentally differs from classical programming, as it is based on using the properties of quantum systems in computing. Nowadays, quantum algorithms have been developed to solve a variety of fundamental and applied problems. It is expected that, with the advancement of quantum computing, quantum algorithms will outperform classical ones for a wide range of tasks.
Quantum...
