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This manuscript addresses a significant research gap in the study by employing a mathematical model of photo thermoelastic wave propagation in a rotator semiconductor medium under the effect of a magnetic field and initial stress, as well as ramp-type heating. The considered model is formulated during the photothermal theory and in two-dimensional (2D) electronic-elastic deformation. The governing equations represent the interaction between the primary physical parameters throughout the process of photothermal transfer. Computational simulations are performed to determine the temperature, carrier density, displacement components, normal stress, and shear stress using the application of Lame's potential and normal mode analysis. Numerical calculations are carried out and graphically displayed for an isotropic semiconductor like silicon (Si) material. Furthermore, comparisons are made with the previous results obtained by the others, as well as in the presence and absence of magnetic field, rotation, and initial stress. The obtained results illustrate that the rotation, initial stress, magnetic field, and ramp-type heating parameter all have significant effects. This investigation provides valuable insights into the synergistic dynamics among a magnetization constituent, semiconducture structures, and wave propagation, enabling advancements in nuclear reactors' construction, operation, electrical circuits, and solar cells., (© 2024. The Author(s).)

Malfunction of the CFTR protein results in cystic fibrosis, one of the most common hereditary diseases. CFTR functions as an anion channel, the gating of which is controlled by long-range allosteric communications. Allostery also has direct bearings on CF treatment: the most effective CFTR drugs modulate its activity allosterically. Herein, we integrated Gaussian network model, transfer entropy, and anisotropic normal mode-Langevin dynamics and investigated the allosteric communications network of CFTR. The results are in remarkable agreement with experimental observations and mutational analysis and provide extensive novel insight. We identified residues that serve as pivotal allosteric sources and transducers, many of which correspond to disease-causing mutations. We find that in the ATP-free form, dynamic fluctuations of the residues that comprise the ATP-binding sites facilitate the initial binding of the nucleotide. Subsequent binding of ATP then brings to the fore and focuses on dynamic fluctuations that were present in a latent and diffuse form in the absence of ATP. We demonstrate that drugs that potentiate CFTR's conductance do so not by directly acting on the gating residues, but rather by mimicking the allosteric signal sent by the ATP-binding sites. We have also uncovered a previously undiscovered allosteric 'hotspot' located proximal to the docking site of the phosphorylated regulatory (R) domain, thereby establishing a molecular foundation for its phosphorylation-dependent excitatory role. This study unveils the molecular underpinnings of allosteric connectivity within CFTR and highlights a novel allosteric 'hotspot' that could serve as a promising target for the development of novel therapeutic interventions., Competing Interests: AE, BA, NL, NB, TH, OL No competing interests declared, (© 2023, Ersoy, Altintel, Livnat Levanon et al.)

Recent experiments have shown that the molecular complex of vault has large conformational changes at its shoulder and cap regions in solution. From the comparison of two configuration structures, it has been found that the shoulder region can twist and move outward, while the cap region will rotate and push upward correspondingly. To further understand these experimental results, in this paper, we study the vault dynamics for the first time. Since vault has an extremely large-sized structure with around 63,336 C α atoms, traditional normal mode method with the C α coarse-grained representation will fall short. We employ a newly invented multiscale virtual particle-based anisotropic network model (MVP-ANM). To reduce the complexity, the 39-folder vault structure is coarse-grained to about 6000 virtual particles, which significantly reduces the computational cost while still maintaining the basic structure information. Among the 14 low frequency eigenmodes from Mode 7 to Mode 20, two eigenmodes, i.e., Mode 9 and Mode 20, are found to be directly associated with the experimental observations. In Mode 9, shoulder region undergoes a significant expansion while the cap part is lifted upward. In Mode 20, a clear rotation of both shoulder and cap regions is well observed. Our results are consistent with the experimental observations. More importantly, these low frequency eigenmodes indicate that the vault waist, shoulder and lower cap regions are the most likely regions for the opening of the vault particle. And the opening mechanism is highly likely to be rotation and expansion at these regions. As far as we know, this is the first work to provide the normal mode analysis for the vault complex., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q-Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.

This paper presents a passive displacement sensor based on a normal mode helical antenna. The sensor consists of an external helical antenna and an inserting dielectric rod. First, the perturbation theory is adopted to demonstrate that both the electric intensity and magnetic intensity have a noticeable gradient change within the in-and-out entrance of the helical antenna, which will cause the sensor to experience a resonant frequency shift. This phenomenon was further verified by numerical simulation using the Ansoft high frequency structure simulator (HFSS), and results show the linear correlation between the retrieved resonant frequency and the displacement. Two sets of proposed sensors were fabricated. The experiments validated that the resonant frequency shifts are linearly proportional to the applied displacement, and the sensing range can be adjusted to accommodate the user's needs., Competing Interests: The authors declare no conflict of interest.

During flight, insect wings bend and twist under the influence of aerodynamic and inertial forces. We tested whether wing resonance of honeybees ( Apis mellifera ) matches the wingbeat frequency, against the 'stiff element' hypothesis that the wing's first longitudinal mode exceeds the wingbeat frequency. Six bees were immobilized with their right wing pair outspread, and stimulated with a shaker while the normal modes were recorded with a scanning Doppler laser vibrometer. The lowest normal mode of the wings was the first longitudinal bending mode and, at 602±145 Hz, was greater than the wingbeat frequency of 234±13.9 Hz. Higher-order normal modes of the wing tended to incorporate nodal lines in the chordwise direction of the trailing edge, suggesting that their mode shape did not strongly resemble wing deformation during flapping flight. These results support the stiff element hypothesis for Apis mellifera ., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2017. Published by The Company of Biologists Ltd.)

We examine the dynamic features of non-trivial allosteric binding sites to elucidate potential drug binding sites. These allosteric sites were previously found to be allosteric after determination of the protein-drug co-crystal structure. After comprehensive search in the Protein Data Bank, we identify 10 complex structures with allosteric ligands whose structures are very similar to their functional forms. Then, possible pockets on the protein surface are searched as potential ligand binding sites. To mimic ligand binding to the pocket, complex models are generated to fill out each pocket with pseudo ligand blocks consisting of spheres. Normal mode analysis of the elastic network model is performed for the complex models and unbound structures to assess the change of protein dynamics induced by ligand binding. We examine nine profiles to describe the dynamic and positional characteristics of the pockets, and identify the change of fluctuation around the ligand, Δ MSF bs , as the best profile for distinguishing the allosteric sites from the other sites in 8 structures. These cases should be considered as examples of dynamics-driven allostery, which accompanies significant changes in protein dynamics. Δ MSF bs is suggested to be used for the search of potential dynamics-driven allosteric sites in proteins for drug discovery.

The room temperature structural (tautomerism, dimerization, conformational preference, geometry parameters) and vibrational spectral (IR and Raman) analyses have been performed on benzothiazoline (benzothiazoline-2-thione, 3-methyl-benzothiazoline-2-thione) and benzothiazole [2-mercaptobenzothiazole, 2-methylthiobenzothiazole, and bis(benzothiazole-2-ylthio)ethane] derivatives at the B3LYP/6-311++G(∗∗) level of theory. Although the keto to enol transition barriers are too high over the most stable benzothiazoline isomers, vibrational spectral analyses reveal some major bands of benzothiazole isomers in the present room temperature experimental FT-IR and FT-Raman specta. Therefore, benzothiazole isomers exist at rare amounts in the powdered samples that are mainly composed of benzothiazoline isomers. The benzothiazole isomers have two stable conformations due to the orientation of their SH and SCH3 moieties. The energetic and vibrational spectral analyses suggest that the benzothiazoline-2-thione molecules can be stabilized further through the NH⋯S intermolecular hydrogen bonds in solid phase. All observed fundamental vibrational bands of the molecules have been assigned based on the calculated mode frequencies and IR/Raman intensities. The mode assignments have been expressed in terms of internal coordinates and their percent potential energy distributions. The effects of substitution at the nitrogen and peripheral sulfur atoms have been analyzed for the geometries and vibrational bands of the molecules., (Copyright © 2015 Elsevier B.V. All rights reserved.)

In this article, we present a Python-based library of high quality semi-global potential energy surfaces for 50 polyatomic molecules with up to six atoms. We anticipate that these surfaces will find widespread application in the testing of new potential energy surface construction algorithms and nuclear ro-vibrational structure theories. To this end, we provide the ability to generate the energy derivatives required for Taylor series expansions to sixth order about any point on the potential energy surface in a range of common coordinate systems, including curvilinear internal, Cartesian, and normal mode coordinates. The PyPES package, along with FORTRAN, C, MATLAB and Mathematica wrappers, is available at http://sourceforge.net/projects/pypes-lib., (© 2015 Wiley Periodicals, Inc.)

The interaction between human Toll-like receptor 4 (hTLR4) and its coreceptor, myeloid differentiation factor 2 (MD-2), is important in Gram-negative bacteria lipopolysaccharide (LPS) recognition. In this process, MD-2 recognizes LPS and promotes the dimerization of the complex hTLR4-MD-2-LPS, triggering an intracellular immune signaling. In this study, we employed distinct computational methods to explore the dynamical properties of the hTLR4-MD-2 complex and investigated the implications of the coreceptor complexation to the structural biology of hTLR4. We characterized both global and local dynamics of free and MD-2 complexed hTLR4, in both (hTLR4-MD-2)1 and (hTLR4-MD-2)2 states. Both molecular dynamics and normal mode analysis reveled a stabilization of the terminal regions of hTLR4 upon complexation to MD-2. We are able to identify conserved important residues involved on the hTLR4-MD-2 interaction dynamics and disclose C-terminal motions that may be associated to the signaling process upon oligomerization., (© 2014 Wiley Periodicals, Inc.)

Fourier transform infrared difference spectroscopy (FTIR DS) has been widely used to study the structural details of electron transfer cofactors (and their binding sites) in many types of photosynthetic protein complexes. This review focuses in particular on work that has been done to investigate the A₁cofactor in photosystem I photosynthetic reaction centers. A review of this subject area last appeared in 2006 [1], so only work undertaken since then will be covered here. Following light excitation of intact photosystem I particles the P700⁺A⁻(1) secondary radical pair state is formed within 100ps. This state decays within 300ns at room temperature, or 300μs at 77K. Given the short-lived nature of this state, it is not easily studied using "static" photo-accumulation FTIR difference techniques at either temperature. Time-resolved techniques are required. This article focuses on the use of time-resolved step-scan FTIR DS for the study of the P700⁺A⁻(1) state in intact photosystem I. Up until now, only our group has undertaken studies in this area. So, in this article, recent work undertaken in our lab is described, where we have used low-temperature (77K), microsecond time-resolved step-scan FTIR DS to study the P700⁺A⁻(1) state in photosystem I. In photosystem I a phylloquinone molecule occupies the A₁binding site. However, different quinones can be incorporated into the A1 binding site, and here work is described for photosystem I particles with plastoquinone-9, 2-phytyl naphthoquinone and 2-methyl naphthoquinone incorporated into the A₁binding site. Studies in which ¹⁸O isotope labeled phylloquinone has been incorporated into the A1 binding site are also discussed. To fully characterize PSI particles with different quinones incorporated into the A1 binding site nanosecond to millisecond visible absorption spectroscopy has been shown to be of considerable value, especially so when undertaken using identical samples under identical conditions to that used in time-resolved step-scan FTIR measurements. In this article the latest work that has been undertaken using both visible and infrared time resolved spectroscopies on the same sample will be described. Finally, vibrational spectroscopic data that has been obtained for phylloquinone in the A1 binding site in photosystem I is compared to corresponding data for ubiquinone in the QA binding site in purple bacterial reaction centers. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Introduction: Molecular docking has become a popular method for virtual screening. Docking small molecules to a rigid biological receptor is fast but could produce many false negatives and identify less diverse compounds. Flexible receptor docking has alleviated this problem., Areas Covered: This article focuses on reviewing ensemble docking as an approximate but inexpensive method to incorporate receptor flexibility in molecular docking. It outlines key features and recent advances of this method and points out problem areas that need to be addressed to make it even more useful in drug discovery., Expert Opinion: Among the different methods introduced for flexible receptor docking, ensemble docking represents one of the most popular approaches, especially for high-throughput virtual screening. One can generate structural ensembles by using experimental structures, by structural modeling and by various types of molecular simulations. In building a structural ensemble, a judicious choice of the structures to be included can improve performance. Furthermore, reducing the size of the structural ensemble can cut computational costs, and removing the structures that can bind few ligands well could enrich the number of true actives identified by ensemble docking. The ability of ensemble docking to identify more true positives at the top of a rank-ordered list also depends on the choice of the methods to score and rank compounds, an area that needs further research.

To circumvent the difficulty of directly solving high-resolution biomolecular structures, low-resolution structural data from Cryo-electron microscopy (EM) and small angle solution X-ray scattering (SAXS) are increasingly used to explore multiple conformational states of biomolecular assemblies. One promising venue to obtain high-resolution structural models from low-resolution data is via data-constrained flexible fitting. To this end, we have developed a new method based on a coarse-grained Cα-only protein representation, and a modified form of the elastic network model (ENM) that allows large-scale conformational changes while maintaining the integrity of local structures including pseudo-bonds and secondary structures. Our method minimizes a pseudo-energy which linearly combines various terms of the modified ENM energy with an EM/SAXS-fitting score and a collision energy that penalizes steric collisions. Unlike some previous flexible fitting efforts using the lowest few normal modes, our method effectively utilizes all normal modes so that both global and local structural changes can be fully modeled with accuracy. This method is also highly efficient in computing time. We have demonstrated our method using adenylate kinase as a test case which undergoes a large open-to-close conformational change. The EM-fitting method is available at a web server (http://enm.lobos.nih.gov), and the SAXS-fitting method is available as a pre-compiled executable upon request., (© 2014 Elsevier Inc. All rights reserved.)

The FT-IR (4000-50 cm(-1)), FT-Raman (4000-50 cm(-1)) and Dispersive-Raman (3500-50 cm(-1)) spectra of solid sample of quinoline-4-carbaldehyde (Q4C) have been recorded. The molecule structure, vibrational frequencies, IR intensities, Raman intensities and thermodynamic properties of the two possible aldehyde rotamers of Q4C have been obtained with the Hartree-Fock (HF) and density functional B3LYP calculations employing the 6-311++G(d,p) basis set. Q4C has two stable conformers, in one of which the O atom of the aldehyde is oriented to form a H-bond with one of the hydrogens of quinoline, while in the other there is no such a H bond. The conformer with an extra H-bond is more stable and, thus it is the ground state. The computed vibrational frequencies of the lowest energy conformer agree also slightly better than those of the higher energy rotamer with the experimental frequencies after the computed frequencies are scaled. The temperature dependence of the standard heat capacities (C), standard entropies (S) and standard enthalpy (H) changes of Q4C has been discussed., (Copyright © 2013 Elsevier B.V. All rights reserved.)

In field-flow fractionation (FFF), there is the 'steric transition' phenomenon where the sample elution mode changes from the normal to steric/hyperlayer mode. Accurate analysis by FFF requires understanding of the steric transition phenomenon, particularly when the sample has a broad size distribution, for which the effect by combination of different modes may become complicated to interpret. In this study, the steric transition phenomenon in asymmetrical flow FFF (AF4) was studied using polystyrene (PS) latex beads. The retention ratio (R) gradually decreases as the particle size increases (normal mode) and reaches a minimum (Ri) at diameter around 0.5μm, after which R increases with increasing diameter (steric/hyperlayer mode). It was found that the size-based selectivity (Sd) tends to increase as the channel thickness (w) increases. The retention behavior of cyclo-1,3,5-trimethylene-2,4,6-trinitramine (commonly called 'research department explosive' (RDX)) particles in AF4 was investigated by varying experimental parameters including w and flow rates. AF4 showed a good reproducibility in size determination of RDX particles with the relative standard deviation of 4.1%. The reliability of separation obtained by AF4 was evaluated by transmission electron microscopy (TEM)., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Fourier transform infrared spectroscopy (FT-IR) was used to study the photochemistry of CO-inhibited Azotobacter vinelandii nitrogenase using visible light at cryogenic temperatures. The FT-IR difference spectrum of photolyzed hi-CO at 4 K comprises negative bands at 1973 cm -1 and 1679 cm -1 together with positive bands at 1711 cm -1 , 2135 and 2123 cm -1 . The negative bands are assigned to a hi-CO state that comprises 2 metal-bound CO ligands, one terminally bound, and one bridged and/or protonated species. The positive band at 1711 cm -1 is assigned to a lo-CO product with a single bridged and/or protonated metal-CO group. We term these species 'Hi-1' and 'Lo-1' respectively. The high-energy bands are assigned to a liberated CO trapped in the protein pocket. Warming results in CO recombination, and the temperature dependence of the recombination rate yields an activation energy of 4 kJ mol -1 . Two α-H195 variant enzymes yielded additional signals. Asparagine substitution, α-H195N, gives a spectrum containing 2 negative 'Hi-2' bands at 1936 and 1858 cm -1 with a positive 'Lo-2' band at 1780 cm -1 , while glutamine substitution, α-H195Q, produces a complex spectrum that includes a third CO species, with negative 'Hi-3' bands at 1938 and 1911 cm -1 and a positive feature 'Lo-3' band at 1921 cm -1 . These species can be assigned to a combination of terminal, bridged, and possibly protonated CO groups bound to the FeMo-cofactor active site. The proposed structures are discussed in terms of both CO inhibition and the mechanism nitrogenase catalysis. Given the intractability of observing nitrogenase intermediates by crystallographic methods, IR-monitored photolysis appears to be a promising and information-rich probe of nitrogenase structure and chemistry.