BITS Faculty Publications

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Start date: 2020Subject: search.filters.subject.Molecular dynamics

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    High-throughput computational screening of metal organic frameworks (MOFs) for CO2 selective separations: trends, challenges, and future perspectives
    (Elsevier, 2026-01) Kuncharam, Bhanu Vardhan Reddy; Gupta, Suresh
    Efficient separation of CO2 from industrial gas mixtures such as CO2/N2, CO2/CH4, CO2/H2, and CH4/H2 is central to carbon capture, clean fuel production, and hydrogen purification. While metal organic frameworks (MOFs) offer an unparalleled design space for addressing these separations, the vast chemical and structural diversity of MOFs renders experimental evaluation impractical. High-throughput computational screening (HTCS), enabled by molecular simulations, has therefore emerged as a powerful approach to systematically evaluate and rank MOFs across multiple separation targets. This review critically examines HTCS methodologies for both adsorption and membrane-based separations, with a unified analysis of four industrially important gas systems. Further, emerging structure-property relationships to extract general design principles for CO2-selective separations are also highlighted. The review emphasizes that the choice of appropriate simulation inputs such as modelling the framework, force field and charge assignment significantly influence the screening and ranking of MOFs. CO2 typically exhibits strong electrostatic interactions with MOF surfaces, resulting in higher adsorption affinity compared to other gases, whereas the smaller and lighter H2 molecule displays rapid diffusivity. In kinetic separation, mixture diffusivity data is crucial in determining membrane performance. There exists a correlation between MOF structural features and their separation performance. In general, MOFs with narrow pores (3-5 Å) and moderate porosities (0.5-.75) perform better for CO2 separation. This review details the approaches adopted in HTCS of MOFs and the screening outcomes to guide future HTCS-driven MOF discovery.
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    Voltage-dependent transport of neutral solutes through nanopores: a molecular view
    (ACS, 2020-11) Prajapati, Jigneshkumar Dahyabhai
    The permeation of (neutral) molecules through nanopores in the presence of external voltages depends on several factors including pore electrostatics, electrophoretic force, and electro-osmotic drag. In earlier single-channel electrophysiology experiments, voltage-dependent asymmetric transport of neutral α-cyclodextrin (α-CD) molecules through the biological nanopore ΔCymA was observed. The voltage-dependent ion-associated flow of water, the so-called electro-osmotic flow, has been suggested to be the key factor behind the observed asymmetric behavior. The influence of pore electrostatics and electrophoretic force and their interplay with the electro-osmotic drag with varying buffers and voltages has not yet been analyzed at the molecular level. Hence, the detailed physical mechanism behind this intriguing permeation process is in part still unclear. In the present study, we have performed 36 μs all-atom free energy calculations by combining applied-field molecular dynamics simulations with metadynamics techniques. The influence of several ionic conditions as well as external voltages on the permeation of α-CD molecules across the ΔCymA pore has been investigated. To decipher the thermodynamic and kinetic details, the lowest energy paths and the permeation times for α-CD translocation have been estimated. In the presence of KCl or MgCl2 salts, the charge of the cations is found to control the direction and magnitude of the electro-osmotic flow, which in turn strongly affects α-CD permeation. Overall, the present findings significantly improve the fundamental understanding of the voltage-dependent transport of neutral solutes across nanopores.
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    Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements
    (RNA Publications, 2024-03) Prajapati, Jigneshkumar Dahyabhai
    Residing in the 5′ untranslated region of the mRNA, the 2′-deoxyguanosine (2′-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2′-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg2+). We have quantitatively explored the combined effect of ligand (2′-dG) and Mg2+ binding on the energy landscape of the aptamer domain of the 2′-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2′-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg2+ and ligand also facilitate a more compact structure in the three-way junction region.
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    Deformation and boundary motion analysis of a faceted twin grain boundary
    (Elsevier, 2024-05) Mishra, Radha Raman
    In this article, molecular dynamics simulations are used to understand how a nickel bicrystal with faceted incoherent Σ3 grain boundaries responds to uniaxial tensile loading. The deformation response is studied over a wide range of temperatures (100 – 900 K) and strain rates (107 – 1010 s−1). The dislocation extraction algorithm and common neighbor analysis are employed to identify the deformation mechanisms. Our results reveal that the yield stress decreases with temperature and increases with strain rate; whereas the elastic modulus decreases with temperature and is independent of strain rate. Furthermore, incipient plasticity is detected ahead of the yield point at lower temperatures and lower strain rates. Interestingly, the incoherent twin grain boundaries are quite mobile under the uniaxial tensile loading at lower temperatures and lower strain rates. But this mobility decreased at higher temperatures and higher strain rates, thereby, confirming this faceted grain boundary's non-Arrhenius (anti-thermal) migration behavior even under mechanical loading. From a deformation perspective, the incoherent twin facet of the grain boundary served as the major source for stacking fault formation at lower temperatures and higher strain rates. However, with the increase in temperature, the stacking faults became shorter and originated from both the incoherent twin facet and the tips of coherent twin facet. These results are in qualitative agreement with the experimental results documented in the literature.
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    A close-packed sphere model for characterising porous networks in atomistic simulations and its application in energy storage and conversion
    (Elsevier, 2024-05) Belgamwar, Sachin U.; Mishra, Radha Raman; Roy, Tribeni
    Hierarchical (micro, meso & macro) porosity in materials plays a crucial role in influencing the movement of ions which governs the energy and power density during energy storage and conversion. The extant available methods to characterise porosity across scales (nano to meso to macro) lacks rigour and accuracy. Having accurate assessment of the porosity in materials can unlock new designs of electrodes for energy efficient energy storage and conversion devices such as batteries, supercapacitors and fuel cells. Through this work, we report the systematic development of a method to fully characterise the carbon porous networks using a molecular dynamics simulation testbed. Our work entails modelling and simulation of porous carbon structures using quenched molecular dynamics (QMD) simulations using Gaussian Approximation potential (GAP) and benchmarking the results with prior literature. This modelling technique can reliably be used for quantitative characterisation of the interconnectivity in porous structures to study ionic movements and charge transfer mechanisms. A new parameter, namely nearest neighbour search (NNS) coefficient was introduced to quantify homogeneity and networking in the porous structures. NNS coefficient increased from 1.62 to 1.92 with decrease of the annealing temperature from 8000 K to 4000 K in carbon. The procedure outlined was although tested on porous carbon networks, but adaptable to study any other material system at multi-length scales.
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    Synergistic effects of temperature and strain rate on tensile properties of simulated Ni-6Cu alloy with Σ3 non-Arrhenius grain boundary
    (Taylor & Francis, 2023) Mishra, Radha Raman
    Comprehending the mechanical response of materials on an atomic level is pivotal in the optimisation of advanced materials with superior mechanical properties. This research article utilises the atomistic-scale based molecular dynamics simulations to report the uniaxial tensile behaviour of bicrystalline Ni-6Cu (Nickel – 94% and Copper – 6%) alloy incorporated with pre-existing faceted Σ3 [111] 60° {11 8 5} grain boundaries. The primary aim of this investigation is to comprehend the performance of bicrystalline Ni-6Cu alloy under varying thermodynamic conditions and to assess the influence of pre-existing faceted grain boundaries on its tensile behaviour. This work encompasses a range of strain rates (108 to 1010 1/s) and temperatures (spanning from 100 to 900 K) for the uniaxial tensile deformation simulations. The outcomes unveil that the Young’s modulus of Ni-6Cu alloy (with pre-existing faceted grain boundaries embedded in its domain) was inversely proportional to temperature and constant with respect to strain rate. For the same configuration, yield stress was inversely and directly proportional to temperature and strain rate, respectively. Interestingly, incipient plasticity in the tensile stress–strain response was observed at lower temperature and lower strain rate. From the microstructural point of view, at lower temperatures, the incoherent twin boundary served as a source for the nucleation of stacking faults; however, as the temperature increased, both the incoherent twin boundary and the tips of coherent twin boundary function as the source for stacking faults formation. Our simulations also verified the GB’s anti-thermal (or non-Arrhenius) migration behaviour even under tensile load.
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    Exploring deformation mechanisms in a refractory high entropy alloy (MoNbTaW)
    (Elsevier, 2025-02) Mishra, Radha Raman
    Understanding the deformation behaviour of refractory high-entropy alloy (rHEA) at elevated temperatures are crucial due to their potential for high-temperature applications. In this study, molecular dynamics simulations were employed using a highly accurate machine learning- based forcefield to investigate the deformation behaviour of MoNbTaW rHEA under uniaxial tensile and compressive loading. Additionally, the dependency of deformation behaviour on the applied strain rates (5e8, 1e9, 5e9 and 1e10 s−1) and temperatures (300, 800, 1000 and 1200 K) was investigated. The yield strength of MoNbTaW rHEA increased by two-fold during compressive loading when compared to tensile loading. During tensile deformation, the BCC-FCC-other atom transition resulted in the formation of stripe-like twinning along the {112} plane. On the contrary, during compressive loading, BCC directly transitioned into other atoms, forming twinning that later acted as the nucleation sites for dislocations. These findings further demonstrate that the deformation mechanism during tensile loading is governed by the twinning mechanism, whereas during compressive loading, dislocation-induced plasticity plays a vital role.
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    On the equivalence of Eulerian Smoothed Particle Hydrodynamics, Total Lagrangian Smoothed Particle Hydrodynamics and molecular dynamics simulations for solids
    (Elsevier, 2022-03) Islam, Md Rushdie Ibne
    Significant advances in nanoscale research have enabled the continuous miniaturization of devices. With the reduction in the size of the devices, it is important to identify if the continuum scale methods remain applicable to such small-scale systems. Motivated by this, the present work tries to understand the equivalence, or its lack thereof, of the continuum scale Eulerian Smoothed Particle Hydrodynamics (ESPH) and Total Lagrangian Smoothed Particle Hydrodynamics (TLSPH) with the atomistic scale molecular dynamics (MD) simulations. The equivalence is studied using four simple problems — (i) uniaxial tensile testing of a beam, (ii) stress profile in a pre-notched plate under small extension, (iii) head-on collision of two elastic rubber-like rings, and (iv) large deformation of a cantilever beam subjected to an impact at the free end. Using MD simulation data as the pseudo-experimental data, we show that both ESPH and TLSPH provide results that are qualitatively and quantitatively in agreement with the MD simulations if the properties at the continuum scale are obtained directly from the MD simulations, and the same initial conditions are chosen. The comparisons are based on the stress–strain behavior, the distribution of normal and shear stresses, the temporal evolution of the variables such as kinetic energy, etc.
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    Identification of synthetically tractable MERS-CoV main protease inhibitors using structure-based virtual screening and molecular dynamics potential of mean force (PMF) calculations
    (Taylor & Francis, 2023-11) Sundriyal, Sandeep
    The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a potentially lethal infection that presents a substantial threat to health, especially in Middle East nations. Given that no FDA-approved specific therapy for MERS infection exists, designing and discovering a potent antiviral therapy for MERS-CoV is crucial. One pivotal strategy for inhibiting MERS replication is to focus on the viral main protease (Mpro). In this study, we identify potential novel Mpro inhibitors employing structure-based virtual screening of our recently reported Ugi reaction-derived library (URDL) consisting of cherry-picked molecules from the literature. The key features of the URDL library include synthetic tractability (1–2 pot synthesis) of the molecules scaffold and unexplored chemical space. The hits were ranked based on the docking score, MM-GBSA free energy of binding, and the interaction pattern with the active site residues. A molecular dynamics (MD) simulation study was performed for the first two top-ranked compounds to analyze the stability and free binding energy based on the molecular mechanics Poisson-Boltzmann surface area. The potential mean force calculated from the steered molecular dynamics (SMD) simulations of the hits indicates improved H-bond potential, enhanced conformational stability, and binding affinity toward the target, compared to the cocrystallized ligand. The discovered hits represent novel synthetically tractable scaffolds as potential MERS-CoV Mpro inhibitors.
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    A structure-based pharmacophore modelling approach to identify and design new neprilysin (NEP) inhibitors: an in silico-based investigation
    (Elsevier, 2024-06) Gaikwad, Anil Bhanudas; Jadhav, Hemant R.
    Neutral endopeptidase or neprilysin (NEP) cleaves the natriuretic peptides, bradykinin, endothelin, angiotensin II, amyloid β protein, substance P, etc., thus modulating their effects on heart, kidney, and other organs. NEP has a proven role in hypertension, heart disease, renal disease, Alzheimer's, diabetes, and some cancers. NEP inhibitor development has been in focus since the US FDA approved a combination therapy of angiotensin II type 1 receptor inhibitor (valsartan) and NEP inhibitor (sacubitril) for use in heart failure. Considering the importance of NEP inhibitors the present work focuses on the designing of a potential lead for NEP inhibition. A structure-based pharmacophore modelling approach was employed to identify NEP inhibitors from the pool of 1140 chemical entities obtained from the ZINC database. Based on the docking score and pivotal interactions, ten molecules were selected and subjected to binding free energy calculations and ADMET predictions. The top two compounds were studied further by molecular dynamics simulations to determine the stability of the ligand-receptor complex. ZINC0000004684268, a phenylalanine derivative, showed affinity and complex stability comparable to sacubitril. However, in silico studies indicated that it may have poor pharmacokinetic parameters. Therefore, the molecule was optimized using bioisosteric replacements, keeping the phenylalanine moiety intact, to obtain five potential lead molecules with an acceptable pharmacokinetic profile. The works thus open up the scope to further corroborate the present in silico findings with the biological analysis.