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Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
Using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complete success in threading tests in a training set of proteins.…
Polymer nanofibers with high thermal conductivities and outstanding thermal stabilities are highly desirable in heat transfer-critical applications such as thermal management, heat exchangers and energy storage. In this work, we unlock the…
Quantum physics emerge and develop as temperature is reduced. Although mesoscopic electrical circuits constitute an outstanding platform to explore quantum behavior, the challenge in cooling the electrons impedes their potential. The strong…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
Magnetic skyrmions are small swirling topological defects in the magnetization texture stabilized by the protection due to their topology. In most cases they are induced by chiral interactions between atomic spins existing in…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
A diathermal wall between two heat baths at different temperatures can be mimicked by a layer of independent spin pairs with some internal energy and where each spin $\sigma_a$ is flipped by thermostat $a$ ($a=1,2$). The transition rates…
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy…
Sub-diffusion in biological systems is conventionally treated as anomalous, requiring fractional derivatives, heavy-tailed waiting times, or fitted memory kernels. We argue that this anomaly is an artifact of an incomplete phase space.…
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e. domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
Biosensors are frequently used nowadays for the sake of their attractive capabilities. Because of their high accuracy and precision, they are more and more used in the medical sector. Natural receptors are mostly used, but their use have…
Molecular junctions comprise small molecules on the order of one or a few nanometers in length, chemically attached to two electrodes of metal or semiconductors. They have recently been identified as promising candidates for…
In this work, we investigate thermodynamic properties of the one-dimensional (1D) spin-crossover molecular chain being a subject of a constant external pressure. Effective compressible degenerate Ising model is used as a theoretical…
Protein identification and profiling is critical for the advancement of cell and molecular biology as well as medical diagnostics. Although mass spectrometry and protein microarrays are commonly used for protein identification, both methods…
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…