MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused directly by the components of the biogenesis pathway or indirectly by other regulators. In this study, we have built a detailed mathematical model of microRNA biogenesis to investigate the regulatory role of biogenesis pathway components. We extended a previous model to incorporate Microprocessor regulation of DGCR8 synthesis, exportin-mediated transport to the cytoplasm, and positive auto-regulation catalysed by mature miRNA translocation into the nucleus. Our simulation results lead to three hypotheses (i) Biogenesis is robust to Dicer protein levels at higher Exportin protein levels; (ii) Higher miRNA transcript formation may lead to lower RISC levels: an optimal level of both precursor miRNA and Dicer is required for optimal miRNA formation at lower levels of Exportin protein; and (iii) The positive auto-regulation by mature miRNA translocation into the nucleus can decrease the net functional cytoplasmic miRNA. Wherever possible, we compare these results to experimental observations not used in the model construction or calibration.

Understanding the connection between thermodynamics and dynamics in glass-forming liquids remains a central challenge in condensed matter physics. In this study, we investigate a novel model system that enables a continuous crossover from a standard three dimensional liquid to a fully connected mean field like system by introducing pseudo neighbours. These pseudo neighbours enhance the effective connectivity of the system without altering its local structure. While their presence slows down the dynamics, they influence thermodynamic properties even more significantly. In particular, the configurational entropy obtained via thermodynamic integration vanishes at a temperature much higher than the temperature where the dynamics begin to slow down, leading to a clear breakdown of the Adam Gibbs relation. To uncover a possible dynamical signature of this thermodynamic transition, we analyse bond breakage dynamics. Unlike real-real bonds, which decay similarly in both the parent Kob Andersen model and its mean field variant, real-pseudo bonds exhibit long lived, persistent behaviour with strong temperature dependence. These bonds do not fully decay over time, leading to a finite saturation value of the bond breakage correlation function. Remarkably, we show that the number of surviving pseudo bonds can be analytically estimated and correlates directly with the thermodynamic transition temperature T_K. We propose a phenomenological relation between T_K and the number of surviving pseudo-bonds, establishing a novel link between thermodynamic and dynamic observables. Our results suggest that these persistent pseudo bonds serve as a robust dynamical signature of the thermodynamic transition, and the system might have properties analogous to those of randomly bonded ultrastable glasses.

The molecular dipole moment and magnetic hyperfine structure constant demand an accurate wavefunction far from the nucleus and in near nuclear region, respectively. We, therefore, employ the so-called Z-vector method in the domain of relativistic coupled cluster theory to calculate the first order property of molecular systems in their open-shell ground state configuration. The implemented method is applied to calculate molecular dipole moment and parallel component of the magnetic hyperfine structure constant of SrF molecule. The results of our calculation are compared with the experimental and other available theoretically calculated values. We are successful in achieving good accordance with the experimental results. The result of our calculation of molecular dipole moment is in the accuracy of ~? 0.5 %, which is clearly an improvement over the previous calculation based on the expectation value method in the four component coupled cluster framework [V. S. Prasannaa et al, Phys. Rev. A 90, 052507 (2014)] and it is the best calculated value till date. Thus, it can be inferred that the Z vector method can provide an accurate wavefunction in both near and far nuclear region, which is evident from our calculated results.

A stochastic configuration interaction method based on evolutionary algorithm is designed as an affordable approximation to full configuration interaction (FCI). The algorithm comprises of initiation, propagation and termination steps, where the propagation step is performed with cloning, mutation and cross-over, taking inspiration from genetic algorithm. We have tested its accuracy in 1D Hubbard problem and a molecular system (symmetric bond breaking of water molecule). We have tested two different fitness functions based on energy of the determinants and the CI coefficients of determinants. We find that the absolute value of CI coefficients is a more suitable fitness function when combined with a fixed selection scheme.

In an attempt to extend the mode coupling theory (MCT) to lower temperatures, an Unified theory was proposed which within the MCT framework incorporated the activated dynamics via the random first order transition theory (RFOT). Here we show that the theory although successful in describing other properties of supercooled liquids is unable to capture the Stokes-Einstein breakdown. We then show using continuous time random work (CTRW) formalism that the Unified theory is equivalent to a CTRW dynamics in presence of two waiting time distributions. It is known from earlier work on CTRW that in such cases the total dynamics is dominated by the fast motion. This explains the failure of the Unified theory in predicting the SE breakdown as both the structural relaxation and the diffusion process are described by the comparatively fast MCT like dynamics. The study also predicts that other forms of extended MCT will face a similar issue. We next modify the Unified theory by applying the concept of renewal theory, usually used in CTRW models where the distribution has a long tail. According to this theory the first jump given by the persistent time is slower than the subsequent jumps given by the exchange time. We first show that for systems with two waiting time distributions even when both the distributions are exponential the persistent time is larger than the exchange time. We also identify the persistent time with the slower activated process. The extended Unified theory can now explain the SE breakdown. In this extended theory at low temperatures the structural relaxation is described by the activated dynamics whereas the diffusion is primarily determined by the MCT like dynamics leading to a decoupling between them. We also calculate a dynamic lengthscale from the wavenumber dependence of the relaxation time. We find that this dynamic length scale grows faster than the static length scale.

Water dissociation is a rate limiting step in many industrially important chemical reactions. In this investigation, climbing image nudged elastic band (CINEB) method, within the framework of density functional theory, is used to report the activation energies (E a ) of water dissociation on Cu(111) surface with a vacancy. Introduction of vacancy results in a reduced coordination of the dissociated products, which facilitates their availability for reactions that involve water dissociation as an intermediate step. Activation energy for dissociation of water reduces by nearly 0.2 eV on Cu(111) surface with vacancy, in comparison with that of pristine Cu(111) surface. We also find that surface modification of the Cu upper surface is one of the possible pathways to dissociate water when the vacancy is introduced. Activation energy, and the minimum energy path (MEP) leading to the transition state remain same for various product configurations. CINEB corresponding to hydrogen gas evolution is also performed which shows that it is a two step process involving water dissociation. We conclude that the introduction of vacancy facilitates the water dissociation reaction, by reducing the activation energy by about 20%.

Amorphous solids relax via slow molecular rearrangement induced by thermal fluctuations or applied stress. Although microscopic structural signatures predicting these structural relaxations have long been sought, a physically motivated structural measure relevant to diverse systems remains elusive. Here, we introduce a structural order parameter derived from the mean-field caging potential experienced by the particles due to their neighbors, which reliably predicts the occurrence of structural relaxations. The parameter, derived from density functional theory, is a measure of susceptibility to particle rearrangements that can effectively identify weak or defect-like regions in disordered systems. Using experiments on dense colloidal suspensions, we demonstrate a causal relationship between this order parameter and the structural relaxations of the amorphous solid. In quiescent suspensions, increasing the density leads to stronger correlations between the structure and dynamics. Under applied shear, the mean structural order parameter increases with increasing strain, signaling shear-induced softening, which is accompanied by the proliferation of plastic events. In both cases, the order parameter reliably identifies weak regions where the plastic rearrangements due to thermal fluctuation or applied shear preferentially occur. Our study paves the way to a structural understanding of the relaxation of a wide range of amorphous solids, from suspensions to metallic glasses.

In a system of N particles, with continuous size polydispersity there exists N(N-1) number of partial structure factors making it analytically less tractable. A common practice is to treat the system as an effective one component system which is known to exhibit an artificial softening of the structure. The aim of this study is to describe the system in terms of M pseudo species such that we can avoid this artificial softening but at the same time have a value of M << N. We use potential energy and pair excess entropy to estimate an optimum number of species, M_{0}. We find that systems with polydispersity width, {\Delta}{\sigma}_{0} can be treated as a monodisperse system. We show that M_{0} depends on the degree and type of polydispersity and also on the nature of the interaction potential, whereas, {\Delta}{\sigma}_{0} weakly depends on the type of the polydispersity, but shows a stronger dependence on the type of interaction potential. Systems with softer interaction potential have a higher tolerance with respect to polydispersity. Interestingly, M_{0} is independent of system size, making this study more relevant for bigger systems. Our study reveals that even 1% polydispersity cannot be treated as an effective monodisperse system. Thus while studying the role of polydispersity by using the structure of an effective one component system care must be taken in decoupling the role of polydispersity from that of the artificial softening of the structure.

The recent discovery of non-saturating giant positive magnetoresistance in Td-WTe2 has aroused great interest in this material. We have studied the structural, electronic and vibrational properties of bulk and few-layer Td-WTe2 experimentally and theoretically. Spin-orbit coupling is found to govern the semi-metallic character of Td-WTe2. Its structural link with the metallic 1T form provides an understanding of its structural stability. We observe a metal to insulator transition and a change in the sign of the Seebeck coefficient around 373 K. Lattice vibrations in Td-WTe2 have been analyzed by first principle calculations. Out of the 33 possible zone-center Raman active modes, five distinct Raman bands are observed around 112, 118, 134, 165 and 212 cm-1 in bulk Td-WTe2. Based on symmetry analysis and the calculated Raman tensors, we assign the intense bands at 165 cm-1 and 212 cm-1 to the A_1^' and A_1^" modes respectively. We have examined the effect of temperature and the number of layers on the Raman spectrum. Most of the bands of Td-WTe2 stiffen, and the ratio of the integrated intensities of the A_1^" to A_1^' bands decreases in the few-layer sample, while all the bands soften in both bulk and few-layer samples with increasing temperature.

We have investigated the rheology and structure of a gel formed from a mixture of non-Brownian particles and two immiscible liquids. The suspension of particles in a liquid undergoes gelation upon the addition of a small content of second, wetting liquid which forms liquid bridges between particles leading to a sample spanning network. The rheology of this gel primarily exhibits a yield stress at low shear rates followed by a linear variation of shear stress at high shear rates. The apparent yield stress extracted from the flow curves increases rapidly with volume fraction of second liquid before saturation, while it exhibits a monotonic increase with increasing particle concentration. Rescaling of the yield stress curves using suitable shift factors results in an empirical expression for the yield stress showing squared dependence on liquid fraction and a rapid increase with particle fraction above a certain value, both combined in a highly nonlinear manner. The microstructural variations with changing secondary liquid content and particle fractions are captured using three dimensional X-ray tomography technique. The microstructure is observed to show increased local compactness with increased liquid content and increased spatial homogeneity with increased particle fractions. The images from X-ray tomography are analysed to obtain the distributions of particle-particle bonds (coordination number) in the system which serve to explain the observed yield stress behavior in a qualitative manner.

We introduce a new measure of the structure of a liquid which is the softness of the mean-field potential developed by us earlier. We find that this softness is sensitive to small changes in the structure. We then study its correlation with the supercooled liquid dynamics. The study involves a wide range of liquids (fragile, strong, attractive, repulsive, and active) and predicts some universal behaviours like the softness is linearly proportional to the temperature and inversely proportional to the activation barrier of the dynamics with system dependent proportionality constants. We write down a master equation between the dynamics and the softness parameter and show that indeed the dynamics when scaled by the temperature and system dependent parameters show a data collapse when plotted against softness. The dynamics of fragile liquids show a strong softness dependence whereas that of strong liquids show a much weaker softness dependence. We also connect the present study with the earlier studies of softness involving machine learning (ML) thus providing a theoretical framework for understanding the ML results.

In a recent study by some of us, we have proposed a new measure of the structure of a liquid, the softness of the mean-field caging potential, and shown that it can describe the temperature dependence of the dynamics. In this work, we put this parameter through a stringent test and study the causal relationship between this softness parameter at the local level and the local dynamics. We first extend the earlier study to describe the local softness. We find a distribution of the softness value where the distribution has reasonably strong temperature dependence. This shows that the parameter can identify the local structural heterogeneity. We then study the lifetime of the softness parameter and show that its lifetime is connected to the well-known cage structure in the supercooled liquids. Finally, our theory predicts that the local softness and the local dynamics is causal below the onset temperature where there is a decoupling between the short and long time dynamics, thus allowing a static description of the cage. We find that at lower temperatures, the structural heterogeneity increases, and also, the structure becomes a better predictor of the dynamics, thus giving rise to dynamic heterogeneity. We also find that the softness of a hard, immobile region evolves with time and becomes soft and eventually mobile due to the rearrangements in the neighbourhood, confirming the well-known facilitation effect.

We study multicomponent liquids by increasing the mass of $15\%$ of the particles in a binary Kob-Andersen model. We find that the heavy particles have dual effects on the lighter particles. At higher temperatures, there is a significant decoupling of the dynamics between heavier and lighter particles, with the former resembling a pinned particle to the latter. The dynamics of the lighter particles slow down due to the excluded volume around the nearly immobile heavier particles. Conversely, at lower temperatures, there is a coupling between the dynamics of the heavier and lighter particles. The heavier particles' mass slows down the dynamics of both types of particles. This makes the soft pinning effect of the heavy particles questionable in this regime. We demonstrate that as the mass of the heavy particles increases, the coupling of the dynamics between the lighter and heavier particles weakens. Consequently, the heavier the mass of the heavy particles, the more effectively they act as soft pinning centres in both high and low-temperature regimes. A key finding is that akin to the pinned system, the self and collective dynamics of the lighter particles decouple from each other as the mass of the heavy particles has a more pronounced impact on the latter. We analyze the structure dynamics correlation by considering the system under the binary and modified quaternary framework, the latter describing the pinned system. Our findings indicate that whenever the heavy mass particles function as soft pinning centres, the modified quaternary framework predicts a higher correlation.

The transition metal selenides (MxSey) have gained attention for their unique physical and chemical properties, especially those associated with the transition metal (M). Despite advancements in synthesis, fabricating these selenides is challenging due to their complex stoichiometry and high asymmetry. One such system is monoclinic iron selenide (Fe3Se4), which can be used in permanent-magnet technologies and serve as a model system for understanding magnetism. This study focuses on fabricating monoclinic M3Se4 (M = Fe, Co, or Ni) compounds via thermal decomposition, examining how solution chemistry influences their morphology and properties. With a Curie temperature of about 322 K, Fe3Se4 is ferrimagnetic, whereas Co3Se4 and Ni3Se4 are paramagnetic between 5 and 300 K. The latter two compounds also show higher catalytic activity for hydrogen evolution in water splitting, with maximum H2-evolution rates of 1.01, 5.16, and 6.83 mmol h-1g-1 for Fe3Se4, Co3Se4, and Ni3Se4, respectively.

The spike protein (SP) of SARS-CoV-2 is the major molecular target for making diagnostic tests, vaccines, and therapeutic development. We used a combination of transmission electron microscopy (TEM) and surface enhanced Raman microscopy (SERS) to study its structure. Using SERS on an aluminum substrate, we were able to detect a characteristic spectrum of SP mostly due to vibration of three aromatic amino acids producing Raman shifts at 466 cm-1, 524 cm-1, 773 cm-1, 831 cm-1, 1048 cm-1, 1308 cm-1, 1457 cm-1, and 1610 cm-1. Transmission Electron Microscopy (TEM) of the SP showed periodic 2D-lattice orientation. The findings from this study have translational values for developing surface-enhanced Raman spectroscopy (SERS) based detectors for screening and testing SARS-CoV-2 signatures in diagnostic settings and contamination tracking.

Stabilizing gold nanoparticles with tunable surface composition via reactive metal support interactions under ambient conditions remains a significant challenge. We discovered that a reactive glass metal interaction (RGMI) under ambient conditions, driven by the intrinsic catalytic activity of gold nanoislands (GNIs) and the unique properties of sodium aluminophosphosilicate glass, including its chemical composition, molar volume, and high Na ion mobility, enables the formation of robustly anchored GNIs with altered surface compositions. Comprehensive characterization reveals that the adsorption of Na and P at the GNI surfaces induces lattice distortions in the Au(111) planes. Additionally, a smooth GNI glass interface significantly influences the hot carrier dynamics of the GNIs. Altogether, RGMI presents a versatile strategy for engineering stable, multi element nanostructures with potential applications in heterogeneous catalysis, sensing, and optoelectronics.

Understanding the connection between structure, dynamics, and fragility (the rate at which relaxation time grow with decreasing temperature) is central to unraveling the glass transition. Fragility is often linked to dynamic heterogeneity, and thus it is commonly assumed that if structure influences dynamics, more fragile systems should exhibit stronger structure dynamics correlations. In this study, we test the generality of this assumption using three model systems: Lennard-Jones (LJ) and Weeks--Chandler--Andersen, where fragility is tuned via density, and a modified LJ (q, p) system, where potential softness is changed to vary fragility. We employ a structural order parameter derived from the mean field caging potential and analyze energy barriers at both macroscopic and microscopic levels. While the macroscopic slope of the energy barrier, suitably defined, correlates with fragility, no consistent correlation is found for the microscopic energy barriers. Instead, the latter shows a strong correlation with an independently computed structure dynamics measure obtained from isoconfigurational ensemble. Surprisingly, the two systems with the highest structure dynamics correlation, LJ at rho = 1.1 and the (8, 5) model, are respectively the least and most fragile within their classes. These systems exhibit broad mobility distributions, bimodal displacement profiles, and high non-Gaussian parameters, all indicative of dynamic heterogeneity. However, their dynamic susceptibilities remain low, suggesting a decoupling between spatial correlation and temporal heterogeneity. Both systems lie in the enthalpy-dominated regime and are near the spinodal, suggesting mechanical instability as a source of heterogeneity. These findings challenge the conventional linkage among fragility, heterogeneity, and structure-dynamics correlation.

A central and extensively debated question in glass physics concerns whether a single, growing lengthscale fundamentally controls glassy dynamics, particularly in systems lacking obvious structural motifs or medium range crystalline order (MRCO). In this work, we investigate structural and dynamical lengthscales in supercooled liquids using the Kob Andersen binary Lennard Jones (KALJ) model in two compositions: 80:20 and 60:40. We compute the dynamical lengthscale from displacement displacement correlation functions and observe a consistent growth as temperature decreases. To explore the static counterpart, we use a structural order parameter (SOP) based on the mean field caging potential. While this SOP is known to predict short time dynamics effectively, its bare correlation function reveals minimal spatial growth. Motivated by recent findings that long time dynamics reflect collective rearrangements, we perform spatial coarse-graining of the SOP and identify an optimal lengthscale $L_{max}$ that maximises structure dynamics correlation. We show that the structural correlation length derived from SOP coarse-grained over $L_{max}$ exhibits clear growth with cooling and closely tracks the dynamical lengthscale, especially for A particles in the 80:20 mixture and for both A and B particles in the 60:40 system. Our results reconcile the previously observed absence of static length growth in MRCO-free models like KALJ by highlighting the necessity of intermediate range structural descriptors. Furthermore, we find that the particles with larger structural length growth also correspond to species with latent crystallisation tendencies, suggesting a possible link between structural order, dynamics, and incipient crystallisation.

Understanding the structural origins of glass formation and mechanical response remains a central challenge in condensed matter physics. Recent studies have identified the local caging potential experienced by a particle due to its nearest neighbors as a robust structural metric that links microscopic structure to dynamics under thermal fluctuations and applied shear. However, its connection to locally favored structural motifs has remained unclear. Here, we analyze structural motifs in colloidal crystals and glasses and correlate them with the local caging potential. We find that icosahedral motifs in glasses are associated with deeper caging potentials than crystalline motifs such as face-centered cubic (FCC) and hexagonal close-packed (HCP) structures. Both crystalline and amorphous systems also contain large number of particles belonging to stable defective motifs, which are distortions of the regular motifs. Under shear, large clusters of defective motifs fragment into smaller ones, driving plastic deformation and the transition from a solid-like to a liquid-like state in amorphous suspensions. Particles that leave clusters of stable motifs are associated with shallower caging potentials and are more prone to plastic rearrangements, ultimately leading to motif disintegration during shear. Our results thus reveal that the loss of mechanical stability in amorphous suspensions is governed by the topological evolution of polytetrahedral motifs, uncovering a structural mechanism underlying plastic deformation and fluidization.