arXiv subjects

Sayan Maity

Publications and source records attributed to Sayan Maity.

11 recordsLinked to original sources

arXiv2026

Excitation of Low-Frequency Modes and the Effects of Protein Dynamics on Spectral Densities of Bacteriochlorophyll Molecules

In the theory of open quantum systems, spectral densities are key quantities for modeling the dynamics and spectroscopic properties of the system under investigation. In the case of light-harvesting complexes, they encode the frequency-dependent coupling of electronic excitations in pigment molecules to their environment, reflecting contributions from both intrinsic vibrational modes and the protein surrounding. In particular, the low-frequency components of the spectral densities are crucial for exciton transfer between pigment molecules. Apparently, slow internal modes of bacteriocholophyll molecules in the gas phase are less well represented by common force fields based on classical molecular dynamics (MD) simulations. Here, we demonstrate that Born-Oppenheimer molecular dynamics (BOMD) based on the numerically efficient density functional-based tight-binding approach can accurately recover these low-frequency features, whereas normal mode analysis captures them only partially. In contrasting approaches for determining spectral densities, the low-frequency region of the spectral densities obtained is only associated with protein fluctuations; the usage of BOMD, however, also captures the low-frequency contributions arising from slow intramolecular vibrations of the pigment molecules themselves. Notably, this behavior is consistently observed for both the flexible B800 and the more rigid B850 rings in light-harvesting 2 (LH2) complexes of purple bacteria, as well as in the Fenna-Matthews-Olson (FMO) complex of green sulfur bacteria. Interestingly, we also find that the spectral densities of the pigments in the B850 ring of LH2 are not influenced by the environment, i.e., the gaps between ground and first excited state are not changed significantly by the fluctuations of the protein environment.

physics.chem-ph↗

arXiv2025

Elucidating the High-Pressure Phases of MAPbBr3 Using a Machine Learning Force Field

High-pressure phases of the hybrid perovskite MAPbBr3 have been investigated in detail using a novel machine learning force field (MLFF). MLFF simulations successfully reproduce the sequence of pressure-induced phase transitions from the $\alpha$ ($Pm\bar{3}m$) to the $\beta$ ($Im\bar{3}$) and finally the $\gamma$ ($Pnma$/$Pmn2_1$) phase. In the $\alpha$ phase, the simulations confirm the triple-well character of the potential energy surface for octahedral tilting shedding light into the local dynamic distortions. In the $\beta$ phase, our simulations reveal MA sublattice doubling yielding both orientationally disordered and ordered MA ions mirroring experimental observation. This mixed-order phase results from locally frustrated host-guest couplings arising from the in-phase octahedral tilt system ($a^+a^+a^+$). In the high-pressure $\gamma$ phase, we confirm the formation of polar and anti-polar domains, with the latter have higher lifetimes and persist for over 50 ps at pressures above 1.5 GPa. By elucidating the behavior of various phases of MAPbBr3, this work provides a fundamental understanding of how host-guest interactions and octahedral tilting govern the material's properties. Further, the importance of time scales and length scales in characterizing these phases is emphasized.

cond-mat.mtrl-sci↗

arXiv2024

Excitation Energy Transfer between Porphyrin Dyes on a Clay Surface: A study employing Multifidelity Machine Learning

Natural light-harvesting antenna complexes efficiently capture solar energy using chlorophyll, i.e., magnesium porphyrin pigments, embedded in a protein matrix. Inspired by this natural configuration, artificial clay-porphyrin antenna structures have been experimentally synthesized and have demonstrated remarkable excitation energy transfer properties. The study presents the computational design and simulation of a synthetic light-harvesting system that emulates natural mechanisms by arranging cationic free-base porphyrin molecules on an anionic clay surface. We investigated the transfer of excitation energy among the porphyrin dyes using a multiscale quantum mechanics/molecular mechanics (QM/MM) approach based on the semi-empirical density functional-based tight-binding (DFTB) theory for the ground state dynamics. To improve the accuracy of our results, we incorporated an innovative multifidelity machine learning (MFML) approach, which allows the prediction of excitation energies at the numerically demanding time-dependent density functional theory level with the Def2-SVP basis set. This approach was applied to an extensive dataset of 640K geometries for the 90-atom porphyrin structures, facilitating a thorough analysis of the excitation energy diffusion among the porphyrin molecules adsorbed to the clay surface. The insights gained from this study, inspired by natural light-harvesting complexes, demonstrate the potential of porphyrin-clay systems as effective energy transfer systems.

physics.chem-ph↗

arXiv2024

Role of host/guest coupling in stabilizing the phases of the over-tolerant hybrid perovskite MHyPbX3

$MHyPbBr_xCl_{3-x}$ exhibits an interesting temperature-induced phase diagram transitioning from monoclinic (Phase-II) to orthorhombic (Phase-I) and eventually to the high-temperature disordered cubic phase. However, experimental observations indicate the absence of either the cubic or orthorhombic phases in compositions with x=0 (chloride) and x=3 (bromide), respectively. We explain the composition dependence of the phase transition sequence in MHyPbX3 (X = Cl, Br) from the perspective of a host/guest framework for the system. We argue that the sequence of phase transitions in MHyPbX3 can be anticipated based on the competition between host distortion and host/guest coupling energies. A dominant coupling in MHyPbCl3 ensures the stabilization of the intermediate Phase-I while pushing the transition to cubic phase beyond its decomposition temperature. On the other hand, a balance of the energy scales in MHyPbBr3 suppresses Phase-I and stabilizes the cubic phase. Our expectations were supported by first-principles based estimates of the transition temperatures in both compounds, which yield trends in agreement with experimental observations. Furthermore, ab initio molecular dynamics simulations revealed that the cubic phase of MHyPbBr3 results from a disorder over locally orthorhombic structures, a clear manifestation of the balance of energy scales. We propose that the same concept can be employed to predict the stable phases in other hybrid perovskites.

cond-mat.mtrl-sci↗

arXiv2024

Onset of slow dynamics in dense suspensions of active colloids

Slow relaxation and heterogeneous dynamics are characteristic features of glasses. The presence of glassy dynamics in nonequilibrium systems, such as active matter, is of significant interest due to its implications for living systems and material science. In this study, we use dense suspensions of self-propelled Janus particles moving on a substrate to investigate the onset of slow dynamics. Our findings show that dense active suspensions exhibit several hallmark features of slow dynamics similar to systems approaching equilibrium. The relaxation time fits well with the Vogel-Fulcher-Tamman (VFT) equation, and the system displays heterogeneous dynamics. Furthermore, increasing the activity leads to faster relaxation of the system, and the glass transition density predicted by the VFT equation shifts to higher densities. The measurement of the cage length and persistence length reveal they are of the same order over the range of activities explored in our study. These results are in agreement with recent particle simulations.

cond-mat.soft↗

arXiv2024

Percolation of nonequilibrium assemblies of colloidal particles in active chiral liquids

The growing interest in the non-equilibrium assembly of colloidal particles in active liquids is driven by the motivation to create novel structures endowed with tunable properties unattainable within the confines of equilibrium systems. Here, we present an experimental investigation of the structural features of colloidal assemblies in active liquids of chiral E. coli. The colloidal particles form dynamic clusters due to the effective interaction mediated by active media. The activity and chirality of the swimmers strongly influence the dynamics and local ordering of colloidal particles, resulting in clusters with persistent rotation, whose structure differs significantly from those in equilibrium systems with attractive interactions, such as colloid-polymer mixtures. The colloid-bacteria mixture displays several hallmark features of a percolation transition at a critical density, where the clusters span the system size. However, a closer examination of the critical exponents associated with cluster size distribution, average cluster size, and correlation length in the vicinity of the critical density suggest strong deviations from the prediction of the standard continuum percolation model. Therefore, our experiments reveal a richer phase behavior of colloidal assemblies in active liquids.

cond-mat.soft↗

arXiv2023

Guest-induced phase transition leads to polarization enhancement in MHyPbCl3

We present a detailed first-principles investigation of the structural and polar properties of 3D hybrid perovskite, methylhydrazinium lead chloride, MHyPbCl3, as it transitions from a highly polar Phase-I (high temperature, HT) to less polar Phase-II (low temperature, LT) from the perspective of host/guest interactions. Structurally, the two phases vary in the orientation of the guest and the two differently distorted host layers. The transition character (TC) across the path of phase transition and a relatively high guest-reorientation barrier tells that the transition is primarily governed by guest-reorientation. This overall guest/host transition is interesting because it leads to enhancement in polarization with temperature which is quite unusual. Maximally localized Wannier functions (MLWFs) have been used to probe into the atomistic origin of this enhancement which establishes the leading role of the host atoms, especially those lying in the more distorted octahedral layer, with only a negligible contribution from the guest, despite the fact that it is the primary effect leading to transition. Furthermore, we also find a significant feedback polarization of ~9% that the host distortion induces on the guest. This has a direct effect on the density of states occupied by the guest, which shifts away from the band edge with the increase in the host distortion (for Phase-II guest orientation). Thus the organic cations in 3D perovskites can also have a non-trivial contribution to the optoelectronic properties and exciton binding energies.

cond-mat.mtrl-sci↗

arXiv2023

Multi-Fidelity Machine Learning for Excited State Energies of Molecules

The accurate but fast calculation of molecular excited states is still a very challenging topic. For many applications, detailed knowledge of the energy funnel in larger molecular aggregates is of key importance requiring highly accurate excited state energies. To this end, machine learning techniques can be an extremely useful tool though the cost of generating highly accurate training datasets still remains a severe challenge. To overcome this hurdle, this work proposes the use of multi-fidelity machine learning where very little training data from high accuracies is combined with cheaper and less accurate data to achieve the accuracy of the costlier level. In the present study, the approach is employed to predict the first excited state energies for three molecules of increasing size, namely, benzene, naphthalene, and anthracene. The energies are trained and tested for conformations stemming from classical molecular dynamics simulations and from real-time density functional tight-binding calculations. It can be shown that the multi-fidelity machine learning model can achieve the same accuracy as a machine learning model built only on high cost training data while having a much lower computational effort to generate the data. The numerical gain observed in these benchmark test calculations was over a factor of 30 but certainly can be much higher for high accuracy data.

physics.chem-ph↗

arXiv2023

Phase separation of passive particles in active liquids

The transport properties of colloidal particles in active liquids have been studied extensively. It has led to a deeper understanding of the interactions between passive and active particles. However, the phase behavior of colloidal particles in active media has received little attention. Here, we present a combined experimental and numerical investigation of passive colloids dispersed in suspensions of active particles. Our study reveals dynamic clustering of colloids in active media due to an interplay of active noise and an attractive effective potential between the colloids. The size-ratio of colloidal particles to the bacteria sets the strength of the interaction. As the relative size of the colloids increases, the effective potential becomes stronger and the average size of the clusters grows. The simulations reveal a macroscopic phase separation of passive colloids at sufficiently large size-ratios. We will present the role of density fluctuations and hydrodynamic interactions in the emergence of effective interactions.

cond-mat.soft↗

arXiv2021

Deciphering the nature of temperature-induced phases of MAPbBr3 by ab initio molecular dynamics

We present an \textit{ab initio} molecular dynamics study of the temperature-induced phases of methylammonium lead bromide (MAPbBr$_3$). We confirm that the low-temperature phase is not ferroelectric, and rule out the existence of any overall polarization arising from the motion of the individual sub-lattices. Our simulations at room temperature resulted in a cubic \textit{Pm-3m} phase with no discernible local orthorhombic distortions. At low temperatures, such distortions are shown to originate from octahedral scissoring modes, but they vanish at room temperature. The predicted timescales of MA motion agree very well with experimental estimates, establishing dynamic disordering of the molecular dipoles over several orientational minima at room temperature. We also identify the key modes of the inorganic and organic sub-lattices that are coupled at all temperatures mainly through the N-H$\cdots$Br hydrogen-bonds. Estimated lifetimes of the H-bonds correlate well with MA dynamics indicating a strong connection between these two aspects of organic inorganic hybrid perovskites. We also confirm that, in addition to disordering of MA orientations, the transition to the cubic phase is also associated with displacive characteristics arising from both MA as well as Br ions in the lattice.

cond-mat.mtrl-sci↗

arXiv2021

Time-Dependent Atomistic Simulations of the CP29 Light-Harvesting Complex

Light harvesting as the first step in photosynthesis is of prime importance for life on earth. For a theoretical description of photochemical processes during light harvesting, spectral densities are key quantities. They serve as input functions for modeling the excitation energy transfer dynamics and spectroscopic properties. Herein, a recently developed procedure is applied to determine the spectral densities of the pigments in the minor antenna complex CP29 of photosystem II which has recently gained attention because of its active role in non-photochemical quenching processes in higher plants. To this end, the density functional based tight binding (DFTB) method has been employed to enable simulation of the ground state dynamics in a quantum-mechanics/molecular mechanics (QM/MM) scheme for each chlorophyll pigment. Subsequently, the time-dependent extension of the long-range corrected DFTB approach has been used to obtain the excitation energy fluctuations along the ground-state trajectories also in a QM/MM setting. From these results the spectral densities have been determined and compared for different force fields and to spectral densities from other light-harvesting complexes. In addition, the excitation energy transfer in the CP29 complex has been studied using ensemble-average wave packet dynamics.

physics.chem-ph↗