arXiv subjects

Debasish Koner

Publications and source records attributed to Debasish Koner.

At least 19 recordsLinked to original sources

arXiv2025

Compositional fluctuations and polymorph selection in crystallization of model soft colloids

Understanding polymorph selection in atomic and molecular systems and its control through thermodynamic conditions and external factors (such as seed characteristics) is fundamental to the design of targeted materials and holds great significance in materials sciences. In this work, using Monte Carlo simulations on the Gaussian Core Model and Hard-Core Yukawa colloidal systems, we investigated the control of polymorph selection and explored the underlying mechanisms by tuning thermodynamic parameters. We demonstrate that by carefully modifying the free energy landscape to render the globally stable face-centered cubic (FCC) phase metastable with respect to the body-centered cubic (BCC) phase, the polymorphic identity of particles transitions from FCC-dominated to BCC-dominated via an intermediate regime where both phases nucleate -- either selectively or competitively -- giving rise to a critical-like composition fluctuation of the growing solid-like cluster during the nucleation process. We further probed the critical solid-like cluster compositions, especially in the vicinity of the triple point where the three phases coexist, and observed an interpenetrating arrangement of FCC- and BCC-like particles rather than a commonly observed non-classical core-shell-like two-step nucleation scenario. In addition, we investigated the polymorph selection signatures encoded in local structural fluctuations of the metastable fluid using a machine learning approach based on structural descriptors derived from persistent homology, a topological data analysis method. We believe that the insights gained from this work have the potential to add to the ongoing efforts to control crystallization pathways to obtain the desired functional material.

cond-mat.soft↗

arXiv2024

The Bigger the Better? Accurate Molecular Potential Energy Surfaces from Minimalist Neural Networks

Atomistic simulations are a powerful tool for studying the dynamics of molecules, proteins, and materials on wide time and length scales. Their reliability and predictiveness, however, depend directly on the accuracy of the underlying potential energy surface (PES). Guided by the principle of parsimony this work introduces KerNN, a combined kernel/neural network-based approach to represent molecular PESs. Compared to state-of-the-art neural network PESs the number of learnable parameters of KerNN is significantly reduced. This speeds up training and evaluation times by several orders of magnitude while retaining high prediction accuracy. Importantly, using kernels as the features also improves the extrapolation capabilities of KerNN far beyond the coverage provided by the training data which solves a general problem of NN-based PESs. KerNN applied to spectroscopy and reaction dynamics shows excellent performance on test set statistics and observables including vibrational bands computed from classical and quantum simulations.

physics.chem-ph↗

arXiv2024

Microscopic pathways of transition from low-density to high-density amorphous phase of water

Much attention has been devoted to understanding the microscopic pathways of phase transition between two equilibrium condensed phases (such as liquids and solids). However, the microscopic pathways between non-equilibrium, non-diffusive amorphous (glassy) phases still remain poorly understood. In this work, we have employed computer simulations, persistence homology (a tool rooted in topological data analysis), and machine learning to probe the microscopic pathway of pressure-induced non-equilibrium transition between the low- and high-density amorphous (LDA and HDA, respectively) ice phases of TIP4P/2005 and ST2 water models. Using persistence homology and machine learning, we introduced a new order parameter that unambiguously identifies the LDA and HDA-like local environments. The system transitions continuously and collectively in the order parameter space via a pre-ordered intermediate phase during the compression of the LDA phase. The local order parameter susceptibilities show a maximum near the transition pressure ($P^*$) -- suggesting maximum structural heterogeneities near $P^*$. The HDA-like clusters are structurally ramified and spatially delocalized inside the LDA phase near the transition pressure. We have further investigated the (geometrical) structures and topologies of the LDA and HDA ices formed via different protocols and also studied the dependence of the microscopic pathway of phase transition in the order parameter space on the protocol followed to prepare the initial LDA phase. Finally, the method adopted here to study the microscopic pathways of transition is not restricted to the system under consideration and provides a robust way of probing phase transition pathways involving any two condensed phases at both equilibrium and out-of-equilibrium conditions.

physics.chem-ph↗

arXiv2023

Low-Temperature Kinetics for the N + NO reaction: Experiment Guides the Way

The reaction N(4S) + NO -> O(3P) + N2 plays a pivotal role in the conversion of atomic to molecular nitrogen in dense interstellar clouds and in the atmosphere. Here we report a joint experimental and computational investigation of the N + NO reaction with the aim of providing improved constraints on its low temperature reactivity. Thermal rates were measured over the 50 to 296 K range in a continuous supersonic flow reactor coupled with pulsed laser photolysis and laser induced fluorescence for the production and detection of N(4S) atoms, respectively. With decreasing temperature, the experimentally measured reaction rate was found to monotonously increase up to a value of (6.6 +- 1.3) x 10-11 cm3 s-1 at 50 K. To confirm this finding, quasi-classical trajectory simulations were carried out on a previously validated, full-dimensional potential energy surface (PES). However, around 50 K the computed rates decreased which required re-evaluation of the reactive PES in the long-range part due to a small spurious barrier with height 40 K in the entrance channel. By exploring different correction schemes the measured thermal rates can be adequately reproduced, displaying a clear negative temperature dependence over the entire temperature range. The possible astrochemical implications of an increased reaction rate at low temperature are also discussed.

astro-ph.GA↗

arXiv2023

Molecular-Level Understanding of the Ro-vibrational Spectra of N$_2$O in Gaseous, Supercritical and Liquid SF$_6$ and Xe

The transition between the gas-, supercritical-, and liquid-phase behaviour is a fascinating topic which still lacks molecular-level understanding. Recent ultrafast two-dimensional infrared spectroscopy experiments suggested that the vibrational spectroscopy of N$_2$O embedded in xenon and SF$_6$ as solvents provides an avenue to characterize the transitions between different phases as the concentration (or density) of the solvent increases. The present work demonstrates that classical molecular dynamics simulations together with accurate interaction potentials allows to (semi-)quantitatively describe the transition in rotational vibrational infrared spectra from the P-/R-branch lineshape for the stretch vibrations of N$_2$O at low solvent densities to the Q-branch-like lineshapes at high densities. The results are interpreted within the classical theory of rigid-body rotation in more/less constraining environments at high/low solvent densities or based on phenomenological models for the orientational relaxation of rotational motion. It is concluded that classical MD simulations provide a powerful approach to characterize and interpret the ultrafast motion of solutes in low to high density solvents at a molecular level.

physics.chem-ph↗

arXiv2022

Photodissociation dynamics of N$_{3}^{+}$

The photodissociation dynamics of N$_3^+$ excited from its $^3 Σ_{\rm g}^{-}$ ground to the first excited singlet and triplet states is investigated. Three dimensional potential energy surfaces for the $^1$A$'$, $^1$A$''$, and $^3$A$'$ electronic states, correlating with the $^1 Δ_{\rm g}$ and $^3 Π_{\rm u}$ states in linear geometry, for N$_3^+$ are constructed using high level electronic structure calculations and represented as reproducing kernels. The reference {\it ab initio} energies are calculated at the MRCI+Q/aug-cc-pVTZ level of theory. For following the photodissociation dynamics in the excited states, rotational and vibrational distributions $P(v')$ and $P(j')$ for the N$_2$ product are determined from vertically excited ground state distributions. Due to the different shapes of the ground state $^3$A$^{''}$ PES and the excited states, appreciable angular momentum $j' \sim 60$ is generated in the diatomic fragments. The lifetimes in the excited states extend to at least 50 ps. Notably, results from sampling initial conditions from a thermal ensemble and from the Wigner distribution of the ground state wavefunction are comparable.

physics.chem-ph↗

arXiv2021

Machine Learning Product State Distributions from Initial Reactant States for a Reactive Atom-Diatom Collision System

A machine learned (ML) model for predicting product state distributions from specific initial states (state-to-distribution or STD) for reactive atom-diatom collisions is presented and quantitatively tested for the N($^4$S)+O$_{2}$(X$^3 \Sigma_{\rm g}^{-}$) $\rightarrow$ NO(X$^2\Pi$) +O($^3$P) reaction. The reference data set for training the neural network (NN) consists of final state distributions determined from explicit quasi-classical trajectory (QCT) simulations for $\sim 2000$ initial conditions. Overall, the prediction accuracy as quantified by the root-mean-squared difference $(\sim 0.003)$ and the $R^2$ $(\sim 0.99)$ between the reference QCT and predictions of the STD model is high for the test set and off-grid state specific initial conditions and for initial conditions drawn from reactant state distributions characterized by translational, rotational and vibrational temperatures. Compared with a more coarse grained distribution-to-distribution (DTD) model evaluated on the same initial state distributions, the STD model shows comparable performance with the additional benefit of the state resolution in the reactant preparation. Starting from specific initial states also leads to a more diverse range of final state distributions which requires a more expressive neural network to be used compared with DTD. Direct comparison between explicit QCT simulations, the STD model, and the widely used Larsen-Borgnakke (LB) model shows that the STD model is quantitative whereas the LB model is qualitative at best for rotational distributions $P(j')$ and fails for vibrational distributions $P(v')$. As such the STD model can be well-suited for simulating nonequilibrium high-speed flows, e.g., using the direct simulation Monte Carlo method.

physics.chem-ph↗

arXiv2021

The C($^3$P) + O$_2$($^3 Σ_g^-$) $\leftrightarrow$ CO$_2$ $\leftrightarrow$ CO($^1 Σ^+$)+ O($^1$D)/O($^3$P) Reaction: Thermal and Vibrational Relaxation Rates from 15 K to 20000 K

Thermal rates for the C($^3$P) + O$_2$($^3 Σ_g^-$) $\leftrightarrow$ CO($^1 Σ^+$)+ O($^1$D)/O($^3$P) reaction are investigated over a wide temperature range based on quasi classical trajectory (QCT) simulations on 3-dimensional, reactive potential energy surfaces (PESs) for the $^1$A$'$, $(2)^1$A$'$, $^1$A$''$, $^3$A$'$ and $^3$A$''$ states. The forward rate matches measurements at 15 K to 295 K whereas the equilibrium constant determined from the forward and reverse rates are consistent with those derived from statistical mechanics at high temperature. Vibrational relaxation, O+CO($ν=1, 2$) $\rightarrow$ O+CO$(ν=0)$, is found to involve both, non-reactive and reactive processes. The contact time required for vibrational relaxation to take place is $τ\geq 150$ fs for non-reacting and $τ\geq 330$ fs for reacting (oxygen atom exchange) trajectories and the two processes are shown to probe different parts of the global potential energy surface. In agreement with experiments, low collision energy reactions for the C($^3$P) + O$_2$($^3 Σ_g^-$, $v=0$) $\rightarrow$ CO($^1 Σ^+$)+ O($^1$D) lead to CO($^{1}Σ^{+}$, $v'=17$) with an onset at $E_{\rm c} \sim 0.15$ eV, dominated by the $^1$A$'$ surface with contributions from the $^3$A$'$ surface. Finally, the barrier for the CO$_{\rm A}$($^1Σ^+$) + O$_{\rm B}$($^3$P) $\rightarrow$ CO$_{\rm B}$($^{1}Σ^{+}$) + O$_{\rm A}$($^3$P) atom exchange reaction on the $^3$A$'$ PES yields a barrier of $\sim 7$ kcal/mol (0.300 eV), consistent with an experimentally reported value of 6.9 kcal/mol (0.299 eV).

physics.chem-ph↗

arXiv2020

The Dynamics and Infrared Spectrocopy of Monomeric and Dimeric Wild Type and Mutant Insulin

The infrared spectroscopy and dynamics of -CO labels in wild type and mutant insulin monomer and dimer are characterized from molecular dynamics simulations using validated force fields. It is found that the spectroscopy of monomeric and dimeric forms in the region of the amide-I vibration differs for residues B24-B26 and D24-D26, which are involved in dimerization of the hormone. Also, the spectroscopic signatures change for mutations at position B24 from phenylalanine - which is conserved in many organisms and known to play a central role in insulin aggregation - to alanine or glycine. Using three different methods to determine the frequency trajectories - solving the nuclear Schrödinger equation on an effective 1-dimensional potential energy curve, instantaneous normal modes, and using parametrized frequency maps - lead to the same overall conclusions. The spectroscopic response of monomeric WT and mutant insulin differs from that of their respective dimers and the spectroscopy of the two monomers in the dimer is also not identical. For the WT and F24A and F24G monomers spectroscopic shifts are found to be $\sim 20$ cm$^{-1}$ for residues (B24 to B26) located at the dimerization interface. Although the crystal structure of the dimer is that of a symmetric homodimer, dynamically the two monomers are not equivalent on the nanosecond time scale. Together with earlier work on the thermodynamic stability of the WT and the same mutants it is concluded that combining computational and experimental infrared spectroscopy provides a potentially powerful way to characterize the aggregation state and dimerization energy of modified insulins.

physics.bio-ph↗

arXiv2020

ML Models of Vibrating H$_2$CO: Comparing Reproducing Kernels, FCHL and PhysNet

Machine Learning (ML) has become a promising tool for improving the quality of atomistic simulations. Using formaldehyde as a benchmark system for intramolecular interactions, a comparative assessment of ML models based on state-of-the-art variants of deep neural networks (NN), reproducing kernel Hilbert space (RKHS+F), and kernel ridge regression (KRR) is presented. Learning curves for energies and atomic forces indicate rapid convergence towards excellent predictions for B3LYP, MP2, and CCSD(T)-F12 reference results for modestly sized (in the hundreds) training sets. Typically, learning curve off-sets decay as one goes from NN (PhysNet) to RKHS+F to KRR (FCHL). Conversely, the predictive power for extrapolation of energies towards new geometries increases in the same order with RKHS+F and FCHL performing almost equally. For harmonic vibrational frequencies, the picture is less clear, with PhysNet and FCHL yielding respectively flat learning at $\sim$ 1 and $\sim$ 0.2 cm$^{-1}$ no matter which reference method, while RKHS+F models level off for B3LYP, and exhibit continued improvements for MP2 and CCSD(T)-F12. Finite-temperature molecular dynamics (MD) simulations with the same initial conditions yield indistinguishable infrared spectra with good performance compared with experiment except for the high-frequency modes involving hydrogen stretch motion which is a known limitation of MD for vibrational spectroscopy. For sufficiently large training set sizes all three models can detect insufficient convergence (``noise'') of the reference electronic structure calculations in that the learning curves level off. Transfer learning (TL) from B3LYP to CCSD(T)-F12 with PhysNet indicates that additional improvements in data efficiency can be achieved.

physics.chem-ph↗

arXiv2020

Machine Learning for Observables: Reactant to Product State Distributions for Atom-Diatom Collisions

Machine learning-based models to predict product state distributions from a distribution of reactant conditions for atom-diatom collisions are presented and quantitatively tested. The models are based on function-, kernel- and grid-based representations of the reactant and product state distributions. While all three methods predict final state distributions from explicit quasi-classical trajectory simulations with R$^2$ > 0.998, the grid-based approach performs best. Although a function-based approach is found to be more than two times better in computational performance, the kernel- and grid-based approaches are preferred in terms of prediction accuracy, practicability and generality. The function-based approach also suffers from lacking a general set of model functions. Applications of the grid-based approach to nonequilibrium, multi-temperature initial state distributions are presented, a situation common to energy distributions in hypersonic flows. The role of such models in Direct Simulation Monte Carlo and computational fluid dynamics simulations is also discussed.

physics.chem-ph↗

arXiv2020

Permutationally Invariant, Reproducing Kernel-Based Potential Energy Surfaces for Polyatomic Molecules: From Formaldehyde to Acetone

Constructing accurate, high dimensional molecular potential energy surfaces (PESs) for polyatomic molecules is challenging. Reproducing Kernel Hilbert space (RKHS) interpolation is an efficient way to construct such PESs. However, the scheme is most effective when the input energies are available on a regular grid. Thus the number of reference energies required can become very large even for penta-atomic systems making such an approach computationally prohibitive when using high-level electronic structure calculations. Here an efficient and robust scheme is presented to overcome these limitations and is applied to constructing high dimensional PESs for systems with up to 10 atoms. Using energies as well as gradients reduces the number of input data required and thus keeps the number of coefficients at a manageable size. Correct implementation of permutational symmetry in the kernel products is tested and explicitly demonstrated for the highly symmetric CH$_4$ molecule.

physics.chem-ph↗

arXiv2020

N$_3^+$: Full-Dimensional Potential Energy Surface, Vibrational Energy Levels and Ground State Dynamics

The fundamentals and higher vibrationally excited states for the N$_3^+$ ion in its electronic ground state have been determined from quantum bound state calculations on 3-dimensional potential energy surfaces (PESs) at the CCSD(T)-F12 and MRCI+Q levels of theory. The vibrational fundamentals are at 1130 cm$^{-1}$ ($ν_1$, symmetric stretch), 807 cm$^{-1}$ ($ν_3$, asymmetric stretch), and 406 cm$^{-1}$ ($ν_2$, bend) on the higher-quality CCSD(T)-F12 surface. For $ν_1$, the calculations are close to the estimated frequency from experiment (1170 cm$^{-1}$) and previous calculations\cite{rosmus.n3:1994} which find it at 1190 cm$^{-1}$. Calculations of the vibrational states on the MRCI+Q PES are in qualitative agreement with those using the CCSD(T)-F12 PES. Analysis of the reference CASSCF wave function for the MRCI+Q calculations provides further insight into the shape of the PES and lends support for the reliability of Hartree-Fock as the reference wave function for the coupled cluster calculations. According to this, N$_3^+$ has mainly single reference character in all low-energy regions of its electronic ground state ($^3$A$''$) 3d PES.

physics.chem-ph↗

arXiv2020

Dynamics on Multiple Potential Energy Surfaces: Quantitative Studies of Elementary Processes Relevant to Hypersonics

The determination of thermal and vibrational relaxation rates of triatomic systems suitable for application in hypersonic model calculations is discussed. For this, potential energy surfaces for ground and electronically excited state species need to be computed and represented with high accuracy and quasiclassical or quantum nuclear dynamics simulations provide the basis for determining the relevant rates. These include thermal reaction rates, state-to-state cross-sections, or vibrational relaxation rates. For exemplary systems - [NNO], [NOO], and [CNO] - all individual steps are described and a literature overview for them is provided. Finally, as some of these quantities involve considerable computational expense, for the example of state-to-state cross sections the construction of an efficient model based on neural networks is discussed. All such data is required and being used in more coarse-grained computational fluid dynamics simulations.

physics.chem-ph↗

arXiv2020

Accurate Reproducing Kernel-Based Potential Energy Surfaces for the Triplet Ground States of N$_2$O and Dynamics for the N+NO$\leftrightarrow$O+N$_2$ and N$_2$+O$\rightarrow$2N+O Reactions

Accurate potential energy surfaces (PESs) have been determined for the $^3$A$'$ and $^3$A$''$ states of N$_2$O using electronic structure calculations at the multireference configuration interaction level with Davidson correction (MRCI+Q) and the augmented Dunning-type correlation consistent polarize triple zeta (aug-cc-pVTZ) basis set. More than 20000 MRCI+Q/aug-cc-pVTZ energies are represented using a reproducing kernel Hilbert space (RKHS) interpolation scheme. The RKHS PESs successfully describe all reactant channels with high accuracy. The analytical PESs are characterized by computing the minima and transition states on it. Quasiclassical dynamics simulations are then used to determine thermal and vibrational relaxation rates for the N+NO and O+N$_2$ collisions. The agreement between results obtained from the simulations and from available experiments is favourable for both types of observables, which provides a test for the accuracy of the PESs. The PESs can be used to calculate more detailed state-to-state observables relevant for applications to hypersonic reentry.

physics.chem-ph↗

arXiv2019

Formation and Stabilization of Ground and Excited State Singlet O$_2$ upon Recombination of $^3$P Oxygen on Amorphous Solid Water

The recombination dynamics of $^3$P oxygen atoms on cold amorphous solid water to form triplet and singlet molecular oxygen (O$_2$) is followed under conditions representative for cold clouds. It is found that both, formation of ground state ($X ^3 Σ_{g}^{-}$) O$_2$ and molecular oxygen in the two lowest singlet states ($a ^1Δ_g$ and $b ^1Σ_g^+$) is possible and that the species can stabilize. The relative proportions of the species is approximately 1:1:1. These results also agree qualitatively with a kinetic model based on simplified wavepacket simulations. As the chemical reactivity of triplet and singlet O$_2$ is different it is likely that substantial amounts of $a ^1Δ_g$ and $b ^1Σ_g^+$ oxygen influences the chemical evolution of cold clouds.

physics.chem-ph↗

arXiv2019

The ${\rm N}(^4S) +{\rm O}_2(X^3Σ^-_g) \leftrightarrow {\rm O}(^3P) + {\rm NO}(X^2Π)$ Reaction: Thermal and Vibrational Relaxation Rates for the $^{2}$A$'$, $^{4}$A$'$ and $^{2}$A$''$ States

The kinetics and vibrational relaxation of the ${\rm N}(^4S) +{\rm O}_2(X^3Σ^-_g) \leftrightarrow {\rm O}(^3P) + {\rm NO}(X^2Π)$ reaction is investigated over a wide temperature range based on quasiclassical trajectory simulations on 3-dimensional potential energy surfaces (PESs) for the lowest three electronic states. Reference energies at the multi reference configuration interaction level are represented as a reproducing kernel and the topology of the PESs is rationalized by analyzing the CASSCF wavefunction of the relevant states. The forward rate matches one measurement at 1575 K and is somewhat lower than the high-temperature measurement at 2880 K whereas for the reverse rate the computations are in good agreement for temperatures between 3000 and 4100 K. The temperature-dependent equilibrium rates are consistent with results from JANAF and CEA results. Vibrational relaxation rates for O + NO($ν=1$) $\rightarrow$ O + NO($ν=0$) are consistent with a wide range of experiments. This process is dominated by the dynamics on the $^2$A$'$ and $^4$A$'$ surfaces which both contribute similarly up to temperatures $T \sim 3000$ K, and it is found that vibrationally relaxing and non-relaxing trajectories probe different parts of the potential energy surface. The total cross section depending on the final vibrational state monotonically decreases which is consistent with early experiments and previous simulations but at variance with other recent experiments which reported an oscillatory cross section.

physics.chem-ph↗

arXiv2019

High-Dimensional Potential Energy Surfaces for Molecular Simulations

An overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods discussed. They include empirical force fields, representations based on reproducing kernels, using permutationally invariant polynomials, and neural network-learned representations and combinations thereof. Future directions and potential improvements are discussed primarily from a practical, application-oriented perspective.

physics.chem-ph↗